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When it is not found, a full rebuild will be done. -config: acc8fdbd02a463ba1382fbabe698b77b -tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_build/html/_sources/changelog.rst.txt b/docs/_build/html/_sources/changelog.rst.txt deleted file mode 100644 index ac0e993c..00000000 --- a/docs/_build/html/_sources/changelog.rst.txt +++ /dev/null @@ -1,75 +0,0 @@ -========== -Changelog -========== - - -0.7.2 (2020-07-18) ------------------- - -- PANDA reads arguments as dataframes in addition to file paths -- changed condor ground truth to match output of `python-igraph 0.8.2 `_. - -0.7.1 (2020-06-27) ------------------- - -- Major fix for OTTER behavior across platforms. - -0.7.0 (2020-01-18) ------------------- - -- new tool: OTTER -- unit test for OTTER -- fix for PANDA `force` field -- tweaks for compatibility of gpuPANDA with cupy - -0.6.2 (Stockholm) (2020-05-15) ------------------------------- - -- Added gpuPANDA, which is a gpu-accelerated implementation of PANDA -- Added gpuLIONESS -- Added a gpuPANDA and gpuLIONESS tutorial -- Fixed condor dependency to python-igraph (still under investigation in #82 ) - -0.6.1 (2020-01-18) ------------------- - -- sambar tutorial -- condor tutorial -- added 3.8 to Ubunutu test server (along with 3.6 and 3.7 ) -- Created three options for data processing in PANDA. - - Union: adds rows for genes/TFs that are missing in at least one prior (expression, ppi, motif) - - Intersection: removes TF/genes that missing in at least one prior - - Legacy: previous data processing behavior -- The default was set to union in netZooM, netZooR, netZooPy as it is the default in netZooC. - -0.5.0 (2019-11-22) ------------------- - -- pysambar - -0.4.0 (2019-11-18) ------------------- - -- pycondor - -0.3.0 (2019-11-14) ------------------- - -- pypuma - -0.2.0 (2019-11-13) ------------------- - -- pylioness - -0.1.1 (2019-9-3) ------------------- - -- fixed call to save_memory=True - -0.1.0 (2019-7-26) ------------------- - -- transition to python 3 -- Changelog added to the doc -- pypanda: original import and NaN values in normalized matrices are replaced with values normalized by the overall z-score. This allows running the Toy Data provided in this repository. diff --git a/docs/_build/html/_sources/functions/index.md.txt b/docs/_build/html/_sources/functions/index.md.txt deleted file mode 100644 index 13d5bcbb..00000000 --- a/docs/_build/html/_sources/functions/index.md.txt +++ /dev/null @@ -1,341 +0,0 @@ -# Functions - -## netZooPy.panda - -### analyze_panda - -#### class AnalyzePanda - - AnalyzePanda(Panda) - Network plot. - -#### top_network_plot - - top_network_plot(self, top = 100, file = 'panda_top_100.png') - Select top genes - -#### shape_plot_network - - __shape_plot_network(self, subset_panda_results, file = 'panda.png') - Create plot - -#### create_plot - - __create_plot(self, unique_genes, links, file = 'panda.png') - Run plot - -### run_panda - - Description: - - Run PANDA algorithm from the command line. - - Usage: - - -h, --help: help - -e, --expression: expression values - -m, --motif: pair file of motif edges, or Pearson correlation matrix when not provided - -p, --ppi: pair file of PPI edges - -o, --out: output file - -r, --rm_missing - -q, --lioness: output for Lioness single sample networks - - Example: - - python run_panda.py -e ./ToyData/ToyExpressionData.txt -m ./ToyData/ToyMotifData.txt -p ./ToyData/ToyPPIData.txt -o test_panda.txt -q output_panda.txt - -### panda - -#### class Panda - - Panda(object) - - Description: - - Using PANDA to infer gene regulatory network. - - Usage: - - 1. Reading in input data (expression data, motif prior, TF PPI data) - 2. Computing coexpression network - 3. Normalizing networks - 4. Running PANDA algorithm - 5. Writing out PANDA network - - Authors: - - cychen, davidvi, alessandromarin - -##### init - init__(self, expression_file, motif_file, ppi_file, save_memory = False, save_tmp=True, remove_missing=False, keep_expression_matrix = False): - # ===================================================================== - # Data loading - # ===================================================================== - -##### remove_missing - remove_missing(self) - Remove genes and tfs not present in all files. - -##### normalize_network - normalize_network(self, x) - -##### panda_loop - panda_loop(self, correlation_matrix, motif_matrix, ppi_matrix) - Panda algorithm. - -###### t_function - t_function(x, y=None) - T function. - -###### update_diagonal - update_diagonal(diagonal_matrix, num, alpha, step) - Update diagonal. - -##### pearson_results_data_frame - pearson_results_data_frame(self) - Results to data frame. - -##### save_panda_results - save_panda_results(self, path='panda.npy') - -##### top_network_plot - top_network_plot(self, top = 100, file = 'panda_top_100.png') - Select top genes. - -##### shape_plot_network - shape_plot_network(self, subset_panda_results, file = 'panda.png') - Create plot. - -##### create_plot - create_plot(self, unique_genes, links, file = 'panda.png') - Run plot. - -###### split_label - split_label(label) - -##### return_panda_indegree - return_panda_indegree(self) - Return Panda indegree. - -##### return_panda_outdegree - return_panda_outdegree(self) - Return Panda outdegree. - -## netZooPy.lioness - -### run_lioness - - Description: - - Run LIONESS algorithm from the command line. - - Usage: - - -h, --help: help - -e, --expression: expression matrix (.npy) - -m, --motif: motif matrix, normalized (.npy) - -p, --ppi: ppi matrix, normalized (.npy) - -n, --npy: PANDA network (.npy) - -o, --out: output folder - -f, --format: output format (txt, npy, or mat) - start: to start from nth sample (optional) - end: to end at nth sample (optional, must with start) - - Example: - - python run_lioness.py -e expression.npy -m motif.npy -p ppi.npy -n panda.npy -o /tmp -f npy 1 100 - -### lioness - -#### class Lioness - - Lioness(Panda) - - Description: - - Using LIONESS to infer single-sample gene regulatory networks. - - Usage: - - 1. Reading in PANDA network and preprocessed middle data - 2. Computing coexpression network - 3. Normalizing coexpression network - 4. Running PANDA algorithm - 5. Writing out LIONESS networks - - Authors: - - cychen, davidvi - -##### init - - init__(self, obj, start=1, end=None, save_dir='lioness_output', save_fmt='npy') - -##### lioness_loop - - lioness_loop(self) - -##### save_lioness_results - - save_lioness_results(self, file='lioness.txt') - -### analyze_lioness - -#### class AnalyzeLioness - - AnalyzeLioness(Lioness) - -##### init - - init__(self, lioness_data) - Load variables from lioness. - -##### top_network_plot - - top_network_plot(self, column = 0, top = 100, file = 'lioness_top_100.png') - Select top genes. - -### lioness_for_puma - -#### class LionessPuma - - LionessPuma(Puma) - - Description: - Using LIONESS to infer single-sample gene regulatory networks. - - Usage: - 1. Reading in PUMA network and preprocessed middle data - 2. Computing coexpression network - 3. Normalizing coexpression network - 4. Running PUMA algorithm - 5. Writing out LIONESS networks - - Authors: - cychen, davidvi - -##### init - - init__(self, obj, start=1, end=None, save_dir='lioness_output', save_fmt='npy') - -##### lioness_loop - - lioness_loop(self) - -##### save_lioness_results - - save_lioness_results(self, file='lioness.txt') - -## netZooPy.puma - -### run_puma - - Description: - Run PUMA algorithm from the command line. - - Usage: - run_puma - -h, --help: help - -e, --expression: expression values - -m, --motif: pair file of motif edges, or Pearson correlation matrix when not provided - -p, --ppi: pair file of PPI edges - -i, --mir (required): miR file - -o, --out: output file - -r, --rm_missing - -q, --lioness: output for Lioness single sample networks - - Example: - python run_puma.py -e ./ToyData/ToyExpressionData.txt -m ./ToyData/ToyMotifData.txt -p ./ToyData/ToyPPIData.txt -i ToyData/ToyMiRList.txt -o test_puma.txt -q output_lioness.txt - -### puma - -#### class Puma - - Puma(object) - - Description: - Using PUMA to infer gene regulatory network. - - Usage: - 1. Reading in input data (expression data, motif prior, TF PPI data, miR) - 2. Computing coexpression network - 3. Normalizing networks - 4. Running PUMA algorithm - 5. Writing out PUMA network - - Authors: - cychen, davidvi, alessandromarin - -##### init - - init__(self, expression_file, motif_file, ppi_file, mir_file, save_memory = False, save_tmp=True, remove_missing=False, keep_expression_matrix = False) - # ===================================================================== - # Data loading - # ===================================================================== - -##### remove_missing - - remove_missing(self) - Remove genes and tfs not present in all files. - -##### normalize_network - - normalize_network(self, x) - -##### puma_loop - - puma_loop(self, correlation_matrix, motif_matrix, ppi_matrix) - Puma algorithm - -###### t_function - - t_function(x, y=None) - T function - -###### update_diagonal - - update_diagonal(diagonal_matrix, num, alpha, step) - Update diagoanl - -##### pearson_results_data_frame - - pearson_results_data_frame(self) - Results to data frame - -##### pearson_results_data_frame - - pearson_results_data_frame(self) - Results to data frame. - -##### save_puma_results - - save_puma_results(self, path='puma.npy') - -##### top_network_plot - - top_network_plot(self, top = 100, file = 'puma_top_100.png') - Select top genes. - -##### shape_plot_network - - shape_plot_network(self, subset_puma_results, file = 'puma.png') - Create plot - -##### create_plot - - create_plot(self, unique_genes, links, file = 'puma.png') - Run plot - -###### split_label - - split_label(label) - -##### return_puma_indegree - - return_puma_indegree(self) - Return Puma indegree - -##### return_puma_outdegree - - return_puma_outdegree(self) - Return Puma outdegree diff --git a/docs/_build/html/_sources/index.rst.txt b/docs/_build/html/_sources/index.rst.txt deleted file mode 100644 index 7e2a2481..00000000 --- a/docs/_build/html/_sources/index.rst.txt +++ /dev/null @@ -1,55 +0,0 @@ -.. netZooPy documentation master file, created by - sphinx-quickstart on Mon Oct 7 21:05:11 2019. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - - -.. toctree:: - :maxdepth: 3 - :caption: Contents: - -Home -=================================== - -netZooPy is a catalog of methods for the reconstruction and analysis of gene regulatory networks. - -netZooPy has started as a merge of the following repositories and forks: - -- `pypanda `_ from David Van Ijzendorn, - -- Alessandro Marin's pypanda and Marieke Kuijjer's pypuma `fork `_, and - -- Cho-Yi Chen's `fork `_. - -- Genis Calderer's `pysambar `_ and `pycondor `_ - -Contents -======== - -.. toctree:: - :hidden: - - self - -.. toctree:: - - install/index - -.. toctree:: - - functions/index - -.. toctree:: - - tutos/index - -.. toctree:: - - changelog - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/_build/html/_sources/install/index.md.txt b/docs/_build/html/_sources/install/index.md.txt deleted file mode 100644 index 45018d41..00000000 --- a/docs/_build/html/_sources/install/index.md.txt +++ /dev/null @@ -1,41 +0,0 @@ -# Installation guide - -To install netZooPy on your computer, please check the following requirements: - -## Requirements - -- Python 3 - -In addition to the following pip packages: - -- networkx - -- numpy - -- pandas - -- matplotlib - -- scipy - -- python-igraph - -## Install - -- `git clone https://github.com/netZoo/netZooPy.git` - -- `cd netZooPy` - -- `pip3 install -e .` - -- Then you can import netZooPy in your code through `import netZooPy` - -## Troubleshooting - -- If you experience installation issues with igraph on MacOs. Please install igraph through `brew install igraph`. - - Please refer to the detailed error fix for MacOs and Ubuntu [here](https://github.com/igraph/python-igraph/issues/159). - - Refer to the igraph instrallation [manual](https://igraph.org/python/#pyinstallosx) - -- To report any installation issue or function bug, please report through opening an [issue](https://github.com/netZoo/netZooPy/issues) on github. diff --git a/docs/_build/html/_sources/tutos/index.md.txt b/docs/_build/html/_sources/tutos/index.md.txt deleted file mode 100644 index 11a54e8d..00000000 --- a/docs/_build/html/_sources/tutos/index.md.txt +++ /dev/null @@ -1,15 +0,0 @@ -# Tutorials - -Tutorials in netZooPy use [Jupter](https://jupyter.org/) notebooks. - -- [Up_and_running_with_PANDA_and_netZooPy](https://github.com/netZoo/netZooPy/tree/master/tutorials/panda) by Daniel C. Morgan. - -- [Building single-sample regulatory networks using LIONESS and netZooPy](https://github.com/netZoo/netZooPy/tree/devel/tutorials/lioness) by Alex Qi Song. - -- [CONDOR usage example](https://github.com/netZoo/netZooPy/tree/devel/tutorials/condor) by Genìs Calderer. - -- [SAMBAR usage example](https://github.com/netZoo/netZooPy/tree/devel/tutorials/sambar) by Genìs Calderer. - -- [Running Panda and Lioness using the Graphical Processing Unit (GPU)](https://github.com/netZoo/netZooPy/blob/master/tutorials/gpupanda/gpuPanda_tutorial.ipynb) by Daniel C. Morgan. - -- [Controlling the variance of PANDA networks](https://github.com/netZoo/netZooPy/tree/master/tutorials/panda) by Kalyan Palepu. diff --git a/docs/_build/html/_static/ajax-loader.gif b/docs/_build/html/_static/ajax-loader.gif deleted file mode 100644 index 61faf8ca..00000000 Binary files a/docs/_build/html/_static/ajax-loader.gif and /dev/null differ diff --git a/docs/_build/html/_static/basic.css b/docs/_build/html/_static/basic.css deleted file mode 100644 index 19ced105..00000000 --- a/docs/_build/html/_static/basic.css +++ /dev/null @@ -1,665 +0,0 @@ -/* - * basic.css - * ~~~~~~~~~ - * - * Sphinx stylesheet -- basic theme. - * - * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * - */ - -/* -- main layout ----------------------------------------------------------- */ - -div.clearer { - clear: both; -} - -/* -- relbar ---------------------------------------------------------------- */ - -div.related { - width: 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All rights reserved. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/docs/_build/html/_static/fonts/fontawesome-webfont.ttf b/docs/_build/html/_static/fonts/fontawesome-webfont.ttf deleted file mode 100644 index 35acda2f..00000000 Binary files a/docs/_build/html/_static/fonts/fontawesome-webfont.ttf and /dev/null differ diff --git a/docs/_build/html/_static/fonts/fontawesome-webfont.woff b/docs/_build/html/_static/fonts/fontawesome-webfont.woff deleted file mode 100644 index 400014a4..00000000 Binary files a/docs/_build/html/_static/fonts/fontawesome-webfont.woff and /dev/null differ diff --git a/docs/_build/html/_static/fonts/fontawesome-webfont.woff2 b/docs/_build/html/_static/fonts/fontawesome-webfont.woff2 deleted file mode 100644 index 4d13fc60..00000000 Binary files a/docs/_build/html/_static/fonts/fontawesome-webfont.woff2 and /dev/null differ diff --git a/docs/_build/html/_static/jquery-3.2.1.js b/docs/_build/html/_static/jquery-3.2.1.js deleted file mode 100644 index d2d8ca47..00000000 --- a/docs/_build/html/_static/jquery-3.2.1.js +++ /dev/null @@ -1,10253 +0,0 @@ -/*! - * jQuery JavaScript Library v3.2.1 - * https://jquery.com/ - * - * Includes Sizzle.js - * https://sizzlejs.com/ - * - * Copyright JS Foundation and other contributors - * Released under the MIT license - * https://jquery.org/license - * - * Date: 2017-03-20T18:59Z - */ -( function( global, factory ) { - - "use strict"; - - if ( typeof module === "object" && typeof module.exports === "object" ) { - - // For CommonJS and CommonJS-like environments where a proper `window` - // is present, execute the factory and get jQuery. - // For environments that do not have a `window` with a `document` - // (such as Node.js), expose a factory as module.exports. - // This accentuates the need for the creation of a real `window`. - // e.g. var jQuery = require("jquery")(window); - // See ticket #14549 for more info. - module.exports = global.document ? - factory( global, true ) : - function( w ) { - if ( !w.document ) { - throw new Error( "jQuery requires a window with a document" ); - } - return factory( w ); - }; - } else { - factory( global ); - } - -// Pass this if window is not defined yet -} )( typeof window !== "undefined" ? window : this, function( window, noGlobal ) { - -// Edge <= 12 - 13+, Firefox <=18 - 45+, IE 10 - 11, Safari 5.1 - 9+, iOS 6 - 9.1 -// throw exceptions when non-strict code (e.g., ASP.NET 4.5) accesses strict mode -// arguments.callee.caller (trac-13335). 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[ this[ j ] ] : [] ); - }, - - end: function() { - return this.prevObject || this.constructor(); - }, - - // For internal use only. - // Behaves like an Array's method, not like a jQuery method. - push: push, - sort: arr.sort, - splice: arr.splice -}; - -jQuery.extend = jQuery.fn.extend = function() { - var options, name, src, copy, copyIsArray, clone, - target = arguments[ 0 ] || {}, - i = 1, - length = arguments.length, - deep = false; - - // Handle a deep copy situation - if ( typeof target === "boolean" ) { - deep = target; - - // Skip the boolean and the target - target = arguments[ i ] || {}; - i++; - } - - // Handle case when target is a string or something (possible in deep copy) - if ( typeof target !== "object" && !jQuery.isFunction( target ) ) { - target = {}; - } - - // Extend jQuery itself if only one argument is passed - if ( i === length ) { - target = this; - i--; - } - - for ( ; i < length; i++ ) { - - // Only deal with non-null/undefined values - if ( ( options = arguments[ i ] ) != null ) { - - // Extend the base object - for ( name in options ) { - src = target[ name ]; - copy = options[ name ]; - - // Prevent never-ending loop - if ( target === copy ) { - continue; - } - - // Recurse if we're merging plain objects or arrays - if ( deep && copy && ( jQuery.isPlainObject( copy ) || - ( copyIsArray = Array.isArray( copy ) ) ) ) { - - if ( copyIsArray ) { - copyIsArray = false; - clone = src && Array.isArray( src ) ? src : []; - - } else { - clone = src && jQuery.isPlainObject( src ) ? src : {}; - } - - // Never move original objects, clone them - target[ name ] = jQuery.extend( deep, clone, copy ); - - // Don't bring in undefined values - } else if ( copy !== undefined ) { - target[ name ] = copy; - } - } - } - } - - // Return the modified object - return target; -}; - -jQuery.extend( { - - // Unique for each copy of jQuery on the page - expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ), - - // Assume jQuery is ready without the ready module - isReady: true, - - error: function( msg ) { - throw new Error( msg ); - }, - - noop: function() {}, - - isFunction: function( obj ) { - return jQuery.type( obj ) === "function"; - }, - - isWindow: function( obj ) { - return obj != null && obj === obj.window; - }, - - isNumeric: function( obj ) { - - // As of jQuery 3.0, isNumeric is limited to - // strings and numbers (primitives or objects) - // that can be coerced to finite numbers (gh-2662) - var type = jQuery.type( obj ); - return ( type === "number" || type === "string" ) && - - // parseFloat NaNs numeric-cast false positives ("") - // ...but misinterprets leading-number strings, particularly hex literals ("0x...") - // subtraction forces infinities to NaN - !isNaN( obj - parseFloat( obj ) ); - }, - - isPlainObject: function( obj ) { - var proto, Ctor; - - // Detect obvious negatives - // Use toString instead of jQuery.type to catch host objects - if ( !obj || toString.call( obj ) !== "[object Object]" ) { - return false; - } - - proto = getProto( obj ); - - // Objects with no prototype (e.g., `Object.create( null )`) are plain - if ( !proto ) { - return true; - } - - // Objects with prototype are plain iff they were constructed by a global Object function - Ctor = hasOwn.call( proto, "constructor" ) && proto.constructor; - return typeof Ctor === "function" && fnToString.call( Ctor ) === ObjectFunctionString; - }, - - isEmptyObject: function( obj ) { - - /* eslint-disable no-unused-vars */ - // See https://github.com/eslint/eslint/issues/6125 - var name; - - for ( name in obj ) { - return false; - } - return true; - }, - - type: function( obj ) { - if ( obj == null ) { - return obj + ""; - } - - // Support: Android <=2.3 only (functionish RegExp) - return typeof obj === "object" || typeof obj === "function" ? - class2type[ toString.call( obj ) ] || "object" : - typeof obj; - }, - - // Evaluates a script in a global context - globalEval: function( code ) { - DOMEval( code ); - }, - - // Convert dashed to camelCase; used by the css and data modules - // Support: IE <=9 - 11, Edge 12 - 13 - // Microsoft forgot to hump their vendor prefix (#9572) - camelCase: function( string ) { - return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase ); - }, - - each: function( obj, callback ) { - var length, i = 0; - - if ( isArrayLike( obj ) ) { - length = obj.length; - for ( ; i < length; i++ ) { - if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { - break; - } - } - } else { - for ( i in obj ) { - if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { - break; - } - } - } - - return obj; - }, - - // Support: Android <=4.0 only - trim: function( text ) { - return text == null ? - "" : - ( text + "" ).replace( rtrim, "" ); - }, - - // results is for internal usage only - makeArray: function( arr, results ) { - var ret = results || []; - - if ( arr != null ) { - if ( isArrayLike( Object( arr ) ) ) { - jQuery.merge( ret, - typeof arr === "string" ? - [ arr ] : arr - ); - } else { - push.call( ret, arr ); - } - } - - return ret; - }, - - inArray: function( elem, arr, i ) { - return arr == null ? -1 : indexOf.call( arr, elem, i ); - }, - - // Support: Android <=4.0 only, PhantomJS 1 only - // push.apply(_, arraylike) throws on ancient WebKit - merge: function( first, second ) { - var len = +second.length, - j = 0, - i = first.length; - - for ( ; j < len; j++ ) { - first[ i++ ] = second[ j ]; - } - - first.length = i; - - return first; - }, - - grep: function( elems, callback, invert ) { - var callbackInverse, - matches = [], - i = 0, - length = elems.length, - callbackExpect = !invert; - - // Go through the array, only saving the items - // that pass the validator function - for ( ; i < length; i++ ) { - callbackInverse = !callback( elems[ i ], i ); - if ( callbackInverse !== callbackExpect ) { - matches.push( elems[ i ] ); - } - } - - return matches; - }, - - // arg is for internal usage only - map: function( elems, callback, arg ) { - var length, value, - i = 0, - ret = []; - - // Go through the array, translating each of the items to their new values - if ( isArrayLike( elems ) ) { - length = elems.length; - for ( ; i < length; i++ ) { - value = callback( elems[ i ], i, arg ); - - if ( value != null ) { - ret.push( value ); - } - } - - // Go through every key on the object, - } else { - for ( i in elems ) { - value = callback( elems[ i ], i, arg ); - - if ( value != null ) { - ret.push( value ); - } - } - } - - // Flatten any nested arrays - return concat.apply( [], ret ); - }, - - // A global GUID counter for objects - guid: 1, - - // Bind a function to a context, optionally partially applying any - // arguments. - proxy: function( fn, context ) { - var tmp, args, proxy; - - if ( typeof context === "string" ) { - tmp = fn[ context ]; - context = fn; - fn = tmp; - } - - // Quick check to determine if target is callable, in the spec - // this throws a TypeError, but we will just return undefined. - if ( !jQuery.isFunction( fn ) ) { - return undefined; - } - - // Simulated bind - args = slice.call( arguments, 2 ); - proxy = function() { - return fn.apply( context || this, args.concat( slice.call( arguments ) ) ); - }; - - // Set the guid of unique handler to the same of original handler, so it can be removed - proxy.guid = fn.guid = fn.guid || jQuery.guid++; - - return proxy; - }, - - now: Date.now, - - // jQuery.support is not used in Core but other projects attach their - // properties to it so it needs to exist. - support: support -} ); - -if ( typeof Symbol === "function" ) { - jQuery.fn[ Symbol.iterator ] = arr[ Symbol.iterator ]; -} - -// Populate the class2type map -jQuery.each( "Boolean Number String Function Array Date RegExp Object Error Symbol".split( " " ), -function( i, name ) { - class2type[ "[object " + name + "]" ] = name.toLowerCase(); -} ); - -function isArrayLike( obj ) { - - // Support: real iOS 8.2 only (not reproducible in simulator) - // `in` check used to prevent JIT error (gh-2145) - // hasOwn isn't used here due to false negatives - // regarding Nodelist length in IE - var length = !!obj && "length" in obj && obj.length, - type = jQuery.type( obj ); - - if ( type === "function" || jQuery.isWindow( obj ) ) { - return false; - } - - return type === "array" || length === 0 || - typeof length === "number" && length > 0 && ( length - 1 ) in obj; -} -var Sizzle = -/*! - * Sizzle CSS Selector Engine v2.3.3 - * https://sizzlejs.com/ - * - * Copyright jQuery Foundation and other contributors - * Released under the MIT license - * http://jquery.org/license - * - * Date: 2016-08-08 - */ -(function( window ) { - -var i, - support, - Expr, - getText, - isXML, - tokenize, - compile, - select, - outermostContext, - sortInput, - hasDuplicate, - - // Local document vars - setDocument, - document, - docElem, - documentIsHTML, - rbuggyQSA, - rbuggyMatches, - matches, - contains, - - // Instance-specific data - expando = "sizzle" + 1 * new Date(), - preferredDoc = window.document, - dirruns = 0, - done = 0, - classCache = createCache(), - tokenCache = createCache(), - compilerCache = createCache(), - sortOrder = function( a, b ) { - if ( a === b ) { - hasDuplicate = true; - } - return 0; - }, - - // Instance methods - hasOwn = ({}).hasOwnProperty, - arr = [], - pop = arr.pop, - push_native = arr.push, - push = arr.push, - slice = arr.slice, - // Use a stripped-down indexOf as it's faster than native - // https://jsperf.com/thor-indexof-vs-for/5 - indexOf = function( list, elem ) { - var i = 0, - len = list.length; - for ( ; i < len; i++ ) { - if ( list[i] === elem ) { - return i; - } - } - return -1; - }, - - booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|ismap|loop|multiple|open|readonly|required|scoped", - - // Regular expressions - - // http://www.w3.org/TR/css3-selectors/#whitespace - whitespace = "[\\x20\\t\\r\\n\\f]", - - // http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier - identifier = "(?:\\\\.|[\\w-]|[^\0-\\xa0])+", - - // Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors - attributes = "\\[" + whitespace + "*(" + identifier + ")(?:" + whitespace + - // Operator (capture 2) - "*([*^$|!~]?=)" + whitespace + - // "Attribute values must be CSS identifiers [capture 5] or strings [capture 3 or capture 4]" - "*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + whitespace + - "*\\]", - - pseudos = ":(" + identifier + ")(?:\\((" + - // To reduce the number of selectors needing tokenize in the preFilter, prefer arguments: - // 1. quoted (capture 3; capture 4 or capture 5) - "('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" + - // 2. simple (capture 6) - "((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" + - // 3. anything else (capture 2) - ".*" + - ")\\)|)", - - // Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter - rwhitespace = new RegExp( whitespace + "+", "g" ), - rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ), - - rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ), - rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + "*" ), - - rattributeQuotes = new RegExp( "=" + whitespace + "*([^\\]'\"]*?)" + whitespace + "*\\]", "g" ), - - rpseudo = new RegExp( pseudos ), - ridentifier = new RegExp( "^" + identifier + "$" ), - - matchExpr = { - "ID": new RegExp( "^#(" + identifier + ")" ), - "CLASS": new RegExp( "^\\.(" + identifier + ")" ), - "TAG": new RegExp( "^(" + identifier + "|[*])" ), - "ATTR": new RegExp( "^" + attributes ), - "PSEUDO": new RegExp( "^" + pseudos ), - "CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + whitespace + - "*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + whitespace + - "*(\\d+)|))" + whitespace + "*\\)|)", "i" ), - "bool": new RegExp( "^(?:" + booleans + ")$", "i" ), - // For use in libraries implementing .is() - // We use this for POS matching in `select` - "needsContext": new RegExp( "^" + whitespace + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" + - whitespace + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" ) - }, - - rinputs = /^(?:input|select|textarea|button)$/i, - rheader = /^h\d$/i, - - rnative = /^[^{]+\{\s*\[native \w/, - - // Easily-parseable/retrievable ID or TAG or CLASS selectors - rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/, - - rsibling = /[+~]/, - - // CSS escapes - // http://www.w3.org/TR/CSS21/syndata.html#escaped-characters - runescape = new RegExp( "\\\\([\\da-f]{1,6}" + whitespace + "?|(" + whitespace + ")|.)", "ig" ), - funescape = function( _, escaped, escapedWhitespace ) { - var high = "0x" + escaped - 0x10000; - // NaN means non-codepoint - // Support: Firefox<24 - // Workaround erroneous numeric interpretation of +"0x" - return high !== high || escapedWhitespace ? - escaped : - high < 0 ? - // BMP codepoint - String.fromCharCode( high + 0x10000 ) : - // Supplemental Plane codepoint (surrogate pair) - String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 ); - }, - - // CSS string/identifier serialization - // https://drafts.csswg.org/cssom/#common-serializing-idioms - rcssescape = /([\0-\x1f\x7f]|^-?\d)|^-$|[^\0-\x1f\x7f-\uFFFF\w-]/g, - fcssescape = function( ch, asCodePoint ) { - if ( asCodePoint ) { - - // U+0000 NULL becomes U+FFFD REPLACEMENT CHARACTER - if ( ch === "\0" ) { - return "\uFFFD"; - } - - // Control characters and (dependent upon position) numbers get escaped as code points - return ch.slice( 0, -1 ) + "\\" + ch.charCodeAt( ch.length - 1 ).toString( 16 ) + " "; - } - - // Other potentially-special ASCII characters get backslash-escaped - return "\\" + ch; - }, - - // Used for iframes - // See setDocument() - // Removing the function wrapper causes a "Permission Denied" - // error in IE - unloadHandler = function() { - setDocument(); - }, - - disabledAncestor = addCombinator( - function( elem ) { - return elem.disabled === true && ("form" in elem || "label" in elem); - }, - { dir: "parentNode", next: "legend" } - ); - -// Optimize for push.apply( _, NodeList ) -try { - push.apply( - (arr = slice.call( preferredDoc.childNodes )), - preferredDoc.childNodes - ); - // Support: Android<4.0 - // Detect silently failing push.apply - arr[ preferredDoc.childNodes.length ].nodeType; -} catch ( e ) { - push = { apply: arr.length ? - - // Leverage slice if possible - function( target, els ) { - push_native.apply( target, slice.call(els) ); - } : - - // Support: IE<9 - // Otherwise append directly - function( target, els ) { - var j = target.length, - i = 0; - // Can't trust NodeList.length - while ( (target[j++] = els[i++]) ) {} - target.length = j - 1; - } - }; -} - -function Sizzle( selector, context, results, seed ) { - var m, i, elem, nid, match, groups, newSelector, - newContext = context && context.ownerDocument, - - // nodeType defaults to 9, since context defaults to document - nodeType = context ? context.nodeType : 9; - - results = results || []; - - // Return early from calls with invalid selector or context - if ( typeof selector !== "string" || !selector || - nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) { - - return results; - } - - // Try to shortcut find operations (as opposed to filters) in HTML documents - if ( !seed ) { - - if ( ( context ? context.ownerDocument || context : preferredDoc ) !== document ) { - setDocument( context ); - } - context = context || document; - - if ( documentIsHTML ) { - - // If the selector is sufficiently simple, try using a "get*By*" DOM method - // (excepting DocumentFragment context, where the methods don't exist) - if ( nodeType !== 11 && (match = rquickExpr.exec( selector )) ) { - - // ID selector - if ( (m = match[1]) ) { - - // Document context - if ( nodeType === 9 ) { - if ( (elem = context.getElementById( m )) ) { - - // Support: IE, Opera, Webkit - // TODO: identify versions - // getElementById can match elements by name instead of ID - if ( elem.id === m ) { - results.push( elem ); - return results; - } - } else { - return results; - } - - // Element context - } else { - - // Support: IE, Opera, Webkit - // TODO: identify versions - // getElementById can match elements by name instead of ID - if ( newContext && (elem = newContext.getElementById( m )) && - contains( context, elem ) && - elem.id === m ) { - - results.push( elem ); - return results; - } - } - - // Type selector - } else if ( match[2] ) { - push.apply( results, context.getElementsByTagName( selector ) ); - return results; - - // Class selector - } else if ( (m = match[3]) && support.getElementsByClassName && - context.getElementsByClassName ) { - - push.apply( results, context.getElementsByClassName( m ) ); - return results; - } - } - - // Take advantage of querySelectorAll - if ( support.qsa && - !compilerCache[ selector + " " ] && - (!rbuggyQSA || !rbuggyQSA.test( selector )) ) { - - if ( nodeType !== 1 ) { - newContext = context; - newSelector = selector; - - // qSA looks outside Element context, which is not what we want - // Thanks to Andrew Dupont for this workaround technique - // Support: IE <=8 - // Exclude object elements - } else if ( context.nodeName.toLowerCase() !== "object" ) { - - // Capture the context ID, setting it first if necessary - if ( (nid = context.getAttribute( "id" )) ) { - nid = nid.replace( rcssescape, fcssescape ); - } else { - context.setAttribute( "id", (nid = expando) ); - } - - // Prefix every selector in the list - groups = tokenize( selector ); - i = groups.length; - while ( i-- ) { - groups[i] = "#" + nid + " " + toSelector( groups[i] ); - } - newSelector = groups.join( "," ); - - // Expand context for sibling selectors - newContext = rsibling.test( selector ) && testContext( context.parentNode ) || - context; - } - - if ( newSelector ) { - try { - push.apply( results, - newContext.querySelectorAll( newSelector ) - ); - return results; - } catch ( qsaError ) { - } finally { - if ( nid === expando ) { - context.removeAttribute( "id" ); - } - } - } - } - } - } - - // All others - return select( selector.replace( rtrim, "$1" ), context, results, seed ); -} - -/** - * Create key-value caches of limited size - * @returns {function(string, object)} Returns the Object data after storing it on itself with - * property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength) - * deleting the oldest entry - */ -function createCache() { - var keys = []; - - function cache( key, value ) { - // Use (key + " ") to avoid collision with native prototype properties (see Issue #157) - if ( keys.push( key + " " ) > Expr.cacheLength ) { - // Only keep the most recent entries - delete cache[ keys.shift() ]; - } - return (cache[ key + " " ] = value); - } - return cache; -} - -/** - * Mark a function for special use by Sizzle - * @param {Function} fn The function to mark - */ -function markFunction( fn ) { - fn[ expando ] = true; - return fn; -} - -/** - * Support testing using an element - * @param {Function} fn Passed the created element and returns a boolean result - */ -function assert( fn ) { - var el = document.createElement("fieldset"); - - try { - return !!fn( el ); - } catch (e) { - return false; - } finally { - // Remove from its parent by default - if ( el.parentNode ) { - el.parentNode.removeChild( el ); - } - // release memory in IE - el = null; - } -} - -/** - * Adds the same handler for all of the specified attrs - * @param {String} attrs Pipe-separated list of attributes - * @param {Function} handler The method that will be applied - */ -function addHandle( attrs, handler ) { - var arr = attrs.split("|"), - i = arr.length; - - while ( i-- ) { - Expr.attrHandle[ arr[i] ] = handler; - } -} - -/** - * Checks document order of two siblings - * @param {Element} a - * @param {Element} b - * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b - */ -function siblingCheck( a, b ) { - var cur = b && a, - diff = cur && a.nodeType === 1 && b.nodeType === 1 && - a.sourceIndex - b.sourceIndex; - - // Use IE sourceIndex if available on both nodes - if ( diff ) { - return diff; - } - - // Check if b follows a - if ( cur ) { - while ( (cur = cur.nextSibling) ) { - if ( cur === b ) { - return -1; - } - } - } - - return a ? 1 : -1; -} - -/** - * Returns a function to use in pseudos for input types - * @param {String} type - */ -function createInputPseudo( type ) { - return function( elem ) { - var name = elem.nodeName.toLowerCase(); - return name === "input" && elem.type === type; - }; -} - -/** - * Returns a function to use in pseudos for buttons - * @param {String} type - */ -function createButtonPseudo( type ) { - return function( elem ) { - var name = elem.nodeName.toLowerCase(); - return (name === "input" || name === "button") && elem.type === type; - }; -} - -/** - * Returns a function to use in pseudos for :enabled/:disabled - * @param {Boolean} disabled true for :disabled; false for :enabled - */ -function createDisabledPseudo( disabled ) { - - // Known :disabled false positives: fieldset[disabled] > legend:nth-of-type(n+2) :can-disable - return function( elem ) { - - // Only certain elements can match :enabled or :disabled - // https://html.spec.whatwg.org/multipage/scripting.html#selector-enabled - // https://html.spec.whatwg.org/multipage/scripting.html#selector-disabled - if ( "form" in elem ) { - - // Check for inherited disabledness on relevant non-disabled elements: - // * listed form-associated elements in a disabled fieldset - // https://html.spec.whatwg.org/multipage/forms.html#category-listed - // https://html.spec.whatwg.org/multipage/forms.html#concept-fe-disabled - // * option elements in a disabled optgroup - // https://html.spec.whatwg.org/multipage/forms.html#concept-option-disabled - // All such elements have a "form" property. - if ( elem.parentNode && elem.disabled === false ) { - - // Option elements defer to a parent optgroup if present - if ( "label" in elem ) { - if ( "label" in elem.parentNode ) { - return elem.parentNode.disabled === disabled; - } else { - return elem.disabled === disabled; - } - } - - // Support: IE 6 - 11 - // Use the isDisabled shortcut property to check for disabled fieldset ancestors - return elem.isDisabled === disabled || - - // Where there is no isDisabled, check manually - /* jshint -W018 */ - elem.isDisabled !== !disabled && - disabledAncestor( elem ) === disabled; - } - - return elem.disabled === disabled; - - // Try to winnow out elements that can't be disabled before trusting the disabled property. - // Some victims get caught in our net (label, legend, menu, track), but it shouldn't - // even exist on them, let alone have a boolean value. - } else if ( "label" in elem ) { - return elem.disabled === disabled; - } - - // Remaining elements are neither :enabled nor :disabled - return false; - }; -} - -/** - * Returns a function to use in pseudos for positionals - * @param {Function} fn - */ -function createPositionalPseudo( fn ) { - return markFunction(function( argument ) { - argument = +argument; - return markFunction(function( seed, matches ) { - var j, - matchIndexes = fn( [], seed.length, argument ), - i = matchIndexes.length; - - // Match elements found at the specified indexes - while ( i-- ) { - if ( seed[ (j = matchIndexes[i]) ] ) { - seed[j] = !(matches[j] = seed[j]); - } - } - }); - }); -} - -/** - * Checks a node for validity as a Sizzle context - * @param {Element|Object=} context - * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value - */ -function testContext( context ) { - return context && typeof context.getElementsByTagName !== "undefined" && context; -} - -// Expose support vars for convenience -support = Sizzle.support = {}; - -/** - * Detects XML nodes - * @param {Element|Object} elem An element or a document - * @returns {Boolean} True iff elem is a non-HTML XML node - */ -isXML = Sizzle.isXML = function( elem ) { - // documentElement is verified for cases where it doesn't yet exist - // (such as loading iframes in IE - #4833) - var documentElement = elem && (elem.ownerDocument || elem).documentElement; - return documentElement ? documentElement.nodeName !== "HTML" : false; -}; - -/** - * Sets document-related variables once based on the current document - * @param {Element|Object} [doc] An element or document object to use to set the document - * @returns {Object} Returns the current document - */ -setDocument = Sizzle.setDocument = function( node ) { - var hasCompare, subWindow, - doc = node ? node.ownerDocument || node : preferredDoc; - - // Return early if doc is invalid or already selected - if ( doc === document || doc.nodeType !== 9 || !doc.documentElement ) { - return document; - } - - // Update global variables - document = doc; - docElem = document.documentElement; - documentIsHTML = !isXML( document ); - - // Support: IE 9-11, Edge - // Accessing iframe documents after unload throws "permission denied" errors (jQuery #13936) - if ( preferredDoc !== document && - (subWindow = document.defaultView) && subWindow.top !== subWindow ) { - - // Support: IE 11, Edge - if ( subWindow.addEventListener ) { - subWindow.addEventListener( "unload", unloadHandler, false ); - - // Support: IE 9 - 10 only - } else if ( subWindow.attachEvent ) { - subWindow.attachEvent( "onunload", unloadHandler ); - } - } - - /* Attributes - ---------------------------------------------------------------------- */ - - // Support: IE<8 - // Verify that getAttribute really returns attributes and not properties - // (excepting IE8 booleans) - support.attributes = assert(function( el ) { - el.className = "i"; - return !el.getAttribute("className"); - }); - - /* getElement(s)By* - ---------------------------------------------------------------------- */ - - // Check if getElementsByTagName("*") returns only elements - support.getElementsByTagName = assert(function( el ) { - el.appendChild( document.createComment("") ); - return !el.getElementsByTagName("*").length; - }); - - // Support: IE<9 - support.getElementsByClassName = rnative.test( document.getElementsByClassName ); - - // Support: IE<10 - // Check if getElementById returns elements by name - // The broken getElementById methods don't pick up programmatically-set names, - // so use a roundabout getElementsByName test - support.getById = assert(function( el ) { - docElem.appendChild( el ).id = expando; - return !document.getElementsByName || !document.getElementsByName( expando ).length; - }); - - // ID filter and find - if ( support.getById ) { - Expr.filter["ID"] = function( id ) { - var attrId = id.replace( runescape, funescape ); - return function( elem ) { - return elem.getAttribute("id") === attrId; - }; - }; - Expr.find["ID"] = function( id, context ) { - if ( typeof context.getElementById !== "undefined" && documentIsHTML ) { - var elem = context.getElementById( id ); - return elem ? [ elem ] : []; - } - }; - } else { - Expr.filter["ID"] = function( id ) { - var attrId = id.replace( runescape, funescape ); - return function( elem ) { - var node = typeof elem.getAttributeNode !== "undefined" && - elem.getAttributeNode("id"); - return node && node.value === attrId; - }; - }; - - // Support: IE 6 - 7 only - // getElementById is not reliable as a find shortcut - Expr.find["ID"] = function( id, context ) { - if ( typeof context.getElementById !== "undefined" && documentIsHTML ) { - var node, i, elems, - elem = context.getElementById( id ); - - if ( elem ) { - - // Verify the id attribute - node = elem.getAttributeNode("id"); - if ( node && node.value === id ) { - return [ elem ]; - } - - // Fall back on getElementsByName - elems = context.getElementsByName( id ); - i = 0; - while ( (elem = elems[i++]) ) { - node = elem.getAttributeNode("id"); - if ( node && node.value === id ) { - return [ elem ]; - } - } - } - - return []; - } - }; - } - - // Tag - Expr.find["TAG"] = support.getElementsByTagName ? - function( tag, context ) { - if ( typeof context.getElementsByTagName !== "undefined" ) { - return context.getElementsByTagName( tag ); - - // DocumentFragment nodes don't have gEBTN - } else if ( support.qsa ) { - return context.querySelectorAll( tag ); - } - } : - - function( tag, context ) { - var elem, - tmp = [], - i = 0, - // By happy coincidence, a (broken) gEBTN appears on DocumentFragment nodes too - results = context.getElementsByTagName( tag ); - - // Filter out possible comments - if ( tag === "*" ) { - while ( (elem = results[i++]) ) { - if ( elem.nodeType === 1 ) { - tmp.push( elem ); - } - } - - return tmp; - } - return results; - }; - - // Class - Expr.find["CLASS"] = support.getElementsByClassName && function( className, context ) { - if ( typeof context.getElementsByClassName !== "undefined" && documentIsHTML ) { - return context.getElementsByClassName( className ); - } - }; - - /* QSA/matchesSelector - ---------------------------------------------------------------------- */ - - // QSA and matchesSelector support - - // matchesSelector(:active) reports false when true (IE9/Opera 11.5) - rbuggyMatches = []; - - // qSa(:focus) reports false when true (Chrome 21) - // We allow this because of a bug in IE8/9 that throws an error - // whenever `document.activeElement` is accessed on an iframe - // So, we allow :focus to pass through QSA all the time to avoid the IE error - // See https://bugs.jquery.com/ticket/13378 - rbuggyQSA = []; - - if ( (support.qsa = rnative.test( document.querySelectorAll )) ) { - // Build QSA regex - // Regex strategy adopted from Diego Perini - assert(function( el ) { - // Select is set to empty string on purpose - // This is to test IE's treatment of not explicitly - // setting a boolean content attribute, - // since its presence should be enough - // https://bugs.jquery.com/ticket/12359 - docElem.appendChild( el ).innerHTML = "" + - ""; - - // Support: IE8, Opera 11-12.16 - // Nothing should be selected when empty strings follow ^= or $= or *= - // The test attribute must be unknown in Opera but "safe" for WinRT - // https://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section - if ( el.querySelectorAll("[msallowcapture^='']").length ) { - rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" ); - } - - // Support: IE8 - // Boolean attributes and "value" are not treated correctly - if ( !el.querySelectorAll("[selected]").length ) { - rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" ); - } - - // Support: Chrome<29, Android<4.4, Safari<7.0+, iOS<7.0+, PhantomJS<1.9.8+ - if ( !el.querySelectorAll( "[id~=" + expando + "-]" ).length ) { - rbuggyQSA.push("~="); - } - - // Webkit/Opera - :checked should return selected option elements - // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked - // IE8 throws error here and will not see later tests - if ( !el.querySelectorAll(":checked").length ) { - rbuggyQSA.push(":checked"); - } - - // Support: Safari 8+, iOS 8+ - // https://bugs.webkit.org/show_bug.cgi?id=136851 - // In-page `selector#id sibling-combinator selector` fails - if ( !el.querySelectorAll( "a#" + expando + "+*" ).length ) { - rbuggyQSA.push(".#.+[+~]"); - } - }); - - assert(function( el ) { - el.innerHTML = "" + - ""; - - // Support: Windows 8 Native Apps - // The type and name attributes are restricted during .innerHTML assignment - var input = document.createElement("input"); - input.setAttribute( "type", "hidden" ); - el.appendChild( input ).setAttribute( "name", "D" ); - - // Support: IE8 - // Enforce case-sensitivity of name attribute - if ( el.querySelectorAll("[name=d]").length ) { - rbuggyQSA.push( "name" + whitespace + "*[*^$|!~]?=" ); - } - - // FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled) - // IE8 throws error here and will not see later tests - if ( el.querySelectorAll(":enabled").length !== 2 ) { - rbuggyQSA.push( ":enabled", ":disabled" ); - } - - // Support: IE9-11+ - // IE's :disabled selector does not pick up the children of disabled fieldsets - docElem.appendChild( el ).disabled = true; - if ( el.querySelectorAll(":disabled").length !== 2 ) { - rbuggyQSA.push( ":enabled", ":disabled" ); - } - - // Opera 10-11 does not throw on post-comma invalid pseudos - el.querySelectorAll("*,:x"); - rbuggyQSA.push(",.*:"); - }); - } - - if ( (support.matchesSelector = rnative.test( (matches = docElem.matches || - docElem.webkitMatchesSelector || - docElem.mozMatchesSelector || - docElem.oMatchesSelector || - docElem.msMatchesSelector) )) ) { - - assert(function( el ) { - // Check to see if it's possible to do matchesSelector - // on a disconnected node (IE 9) - support.disconnectedMatch = matches.call( el, "*" ); - - // This should fail with an exception - // Gecko does not error, returns false instead - matches.call( el, "[s!='']:x" ); - rbuggyMatches.push( "!=", pseudos ); - }); - } - - rbuggyQSA = rbuggyQSA.length && new RegExp( rbuggyQSA.join("|") ); - rbuggyMatches = rbuggyMatches.length && new RegExp( rbuggyMatches.join("|") ); - - /* Contains - ---------------------------------------------------------------------- */ - hasCompare = rnative.test( docElem.compareDocumentPosition ); - - // Element contains another - // Purposefully self-exclusive - // As in, an element does not contain itself - contains = hasCompare || rnative.test( docElem.contains ) ? - function( a, b ) { - var adown = a.nodeType === 9 ? a.documentElement : a, - bup = b && b.parentNode; - return a === bup || !!( bup && bup.nodeType === 1 && ( - adown.contains ? - adown.contains( bup ) : - a.compareDocumentPosition && a.compareDocumentPosition( bup ) & 16 - )); - } : - function( a, b ) { - if ( b ) { - while ( (b = b.parentNode) ) { - if ( b === a ) { - return true; - } - } - } - return false; - }; - - /* Sorting - ---------------------------------------------------------------------- */ - - // Document order sorting - sortOrder = hasCompare ? - function( a, b ) { - - // Flag for duplicate removal - if ( a === b ) { - hasDuplicate = true; - return 0; - } - - // Sort on method existence if only one input has compareDocumentPosition - var compare = !a.compareDocumentPosition - !b.compareDocumentPosition; - if ( compare ) { - return compare; - } - - // Calculate position if both inputs belong to the same document - compare = ( a.ownerDocument || a ) === ( b.ownerDocument || b ) ? - a.compareDocumentPosition( b ) : - - // Otherwise we know they are disconnected - 1; - - // Disconnected nodes - if ( compare & 1 || - (!support.sortDetached && b.compareDocumentPosition( a ) === compare) ) { - - // Choose the first element that is related to our preferred document - if ( a === document || a.ownerDocument === preferredDoc && contains(preferredDoc, a) ) { - return -1; - } - if ( b === document || b.ownerDocument === preferredDoc && contains(preferredDoc, b) ) { - return 1; - } - - // Maintain original order - return sortInput ? - ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) : - 0; - } - - return compare & 4 ? -1 : 1; - } : - function( a, b ) { - // Exit early if the nodes are identical - if ( a === b ) { - hasDuplicate = true; - return 0; - } - - var cur, - i = 0, - aup = a.parentNode, - bup = b.parentNode, - ap = [ a ], - bp = [ b ]; - - // Parentless nodes are either documents or disconnected - if ( !aup || !bup ) { - return a === document ? -1 : - b === document ? 1 : - aup ? -1 : - bup ? 1 : - sortInput ? - ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) : - 0; - - // If the nodes are siblings, we can do a quick check - } else if ( aup === bup ) { - return siblingCheck( a, b ); - } - - // Otherwise we need full lists of their ancestors for comparison - cur = a; - while ( (cur = cur.parentNode) ) { - ap.unshift( cur ); - } - cur = b; - while ( (cur = cur.parentNode) ) { - bp.unshift( cur ); - } - - // Walk down the tree looking for a discrepancy - while ( ap[i] === bp[i] ) { - i++; - } - - return i ? - // Do a sibling check if the nodes have a common ancestor - siblingCheck( ap[i], bp[i] ) : - - // Otherwise nodes in our document sort first - ap[i] === preferredDoc ? -1 : - bp[i] === preferredDoc ? 1 : - 0; - }; - - return document; -}; - -Sizzle.matches = function( expr, elements ) { - return Sizzle( expr, null, null, elements ); -}; - -Sizzle.matchesSelector = function( elem, expr ) { - // Set document vars if needed - if ( ( elem.ownerDocument || elem ) !== document ) { - setDocument( elem ); - } - - // Make sure that attribute selectors are quoted - expr = expr.replace( rattributeQuotes, "='$1']" ); - - if ( support.matchesSelector && documentIsHTML && - !compilerCache[ expr + " " ] && - ( !rbuggyMatches || !rbuggyMatches.test( expr ) ) && - ( !rbuggyQSA || !rbuggyQSA.test( expr ) ) ) { - - try { - var ret = matches.call( elem, expr ); - - // IE 9's matchesSelector returns false on disconnected nodes - if ( ret || support.disconnectedMatch || - // As well, disconnected nodes are said to be in a document - // fragment in IE 9 - elem.document && elem.document.nodeType !== 11 ) { - return ret; - } - } catch (e) {} - } - - return Sizzle( expr, document, null, [ elem ] ).length > 0; -}; - -Sizzle.contains = function( context, elem ) { - // Set document vars if needed - if ( ( context.ownerDocument || context ) !== document ) { - setDocument( context ); - } - return contains( context, elem ); -}; - -Sizzle.attr = function( elem, name ) { - // Set document vars if needed - if ( ( elem.ownerDocument || elem ) !== document ) { - setDocument( elem ); - } - - var fn = Expr.attrHandle[ name.toLowerCase() ], - // Don't get fooled by Object.prototype properties (jQuery #13807) - val = fn && hasOwn.call( Expr.attrHandle, name.toLowerCase() ) ? - fn( elem, name, !documentIsHTML ) : - undefined; - - return val !== undefined ? - val : - support.attributes || !documentIsHTML ? - elem.getAttribute( name ) : - (val = elem.getAttributeNode(name)) && val.specified ? - val.value : - null; -}; - -Sizzle.escape = function( sel ) { - return (sel + "").replace( rcssescape, fcssescape ); -}; - -Sizzle.error = function( msg ) { - throw new Error( "Syntax error, unrecognized expression: " + msg ); -}; - -/** - * Document sorting and removing duplicates - * @param {ArrayLike} results - */ -Sizzle.uniqueSort = function( results ) { - var elem, - duplicates = [], - j = 0, - i = 0; - - // Unless we *know* we can detect duplicates, assume their presence - hasDuplicate = !support.detectDuplicates; - sortInput = !support.sortStable && results.slice( 0 ); - results.sort( sortOrder ); - - if ( hasDuplicate ) { - while ( (elem = results[i++]) ) { - if ( elem === results[ i ] ) { - j = duplicates.push( i ); - } - } - while ( j-- ) { - results.splice( duplicates[ j ], 1 ); - } - } - - // Clear input after sorting to release objects - // See https://github.com/jquery/sizzle/pull/225 - sortInput = null; - - return results; -}; - -/** - * Utility function for retrieving the text value of an array of DOM nodes - * @param {Array|Element} elem - */ -getText = Sizzle.getText = function( elem ) { - var node, - ret = "", - i = 0, - nodeType = elem.nodeType; - - if ( !nodeType ) { - // If no nodeType, this is expected to be an array - while ( (node = elem[i++]) ) { - // Do not traverse comment nodes - ret += getText( node ); - } - } else if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) { - // Use textContent for elements - // innerText usage removed for consistency of new lines (jQuery #11153) - if ( typeof elem.textContent === "string" ) { - return elem.textContent; - } else { - // Traverse its children - for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) { - ret += getText( elem ); - } - } - } else if ( nodeType === 3 || nodeType === 4 ) { - return elem.nodeValue; - } - // Do not include comment or processing instruction nodes - - return ret; -}; - -Expr = Sizzle.selectors = { - - // Can be adjusted by the user - cacheLength: 50, - - createPseudo: markFunction, - - match: matchExpr, - - attrHandle: {}, - - find: {}, - - relative: { - ">": { dir: "parentNode", first: true }, - " ": { dir: "parentNode" }, - "+": { dir: "previousSibling", first: true }, - "~": { dir: "previousSibling" } - }, - - preFilter: { - "ATTR": function( match ) { - match[1] = match[1].replace( runescape, funescape ); - - // Move the given value to match[3] whether quoted or unquoted - match[3] = ( match[3] || match[4] || match[5] || "" ).replace( runescape, funescape ); - - if ( match[2] === "~=" ) { - match[3] = " " + match[3] + " "; - } - - return match.slice( 0, 4 ); - }, - - "CHILD": function( match ) { - /* matches from matchExpr["CHILD"] - 1 type (only|nth|...) - 2 what (child|of-type) - 3 argument (even|odd|\d*|\d*n([+-]\d+)?|...) - 4 xn-component of xn+y argument ([+-]?\d*n|) - 5 sign of xn-component - 6 x of xn-component - 7 sign of y-component - 8 y of y-component - */ - match[1] = match[1].toLowerCase(); - - if ( match[1].slice( 0, 3 ) === "nth" ) { - // nth-* requires argument - if ( !match[3] ) { - Sizzle.error( match[0] ); - } - - // numeric x and y parameters for Expr.filter.CHILD - // remember that false/true cast respectively to 0/1 - match[4] = +( match[4] ? match[5] + (match[6] || 1) : 2 * ( match[3] === "even" || match[3] === "odd" ) ); - match[5] = +( ( match[7] + match[8] ) || match[3] === "odd" ); - - // other types prohibit arguments - } else if ( match[3] ) { - Sizzle.error( match[0] ); - } - - return match; - }, - - "PSEUDO": function( match ) { - var excess, - unquoted = !match[6] && match[2]; - - if ( matchExpr["CHILD"].test( match[0] ) ) { - return null; - } - - // Accept quoted arguments as-is - if ( match[3] ) { - match[2] = match[4] || match[5] || ""; - - // Strip excess characters from unquoted arguments - } else if ( unquoted && rpseudo.test( unquoted ) && - // Get excess from tokenize (recursively) - (excess = tokenize( unquoted, true )) && - // advance to the next closing parenthesis - (excess = unquoted.indexOf( ")", unquoted.length - excess ) - unquoted.length) ) { - - // excess is a negative index - match[0] = match[0].slice( 0, excess ); - match[2] = unquoted.slice( 0, excess ); - } - - // Return only captures needed by the pseudo filter method (type and argument) - return match.slice( 0, 3 ); - } - }, - - filter: { - - "TAG": function( nodeNameSelector ) { - var nodeName = nodeNameSelector.replace( runescape, funescape ).toLowerCase(); - return nodeNameSelector === "*" ? - function() { return true; } : - function( elem ) { - return elem.nodeName && elem.nodeName.toLowerCase() === nodeName; - }; - }, - - "CLASS": function( className ) { - var pattern = classCache[ className + " " ]; - - return pattern || - (pattern = new RegExp( "(^|" + whitespace + ")" + className + "(" + whitespace + "|$)" )) && - classCache( className, function( elem ) { - return pattern.test( typeof elem.className === "string" && elem.className || typeof elem.getAttribute !== "undefined" && elem.getAttribute("class") || "" ); - }); - }, - - "ATTR": function( name, operator, check ) { - return function( elem ) { - var result = Sizzle.attr( elem, name ); - - if ( result == null ) { - return operator === "!="; - } - if ( !operator ) { - return true; - } - - result += ""; - - return operator === "=" ? result === check : - operator === "!=" ? result !== check : - operator === "^=" ? check && result.indexOf( check ) === 0 : - operator === "*=" ? check && result.indexOf( check ) > -1 : - operator === "$=" ? check && result.slice( -check.length ) === check : - operator === "~=" ? ( " " + result.replace( rwhitespace, " " ) + " " ).indexOf( check ) > -1 : - operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" : - false; - }; - }, - - "CHILD": function( type, what, argument, first, last ) { - var simple = type.slice( 0, 3 ) !== "nth", - forward = type.slice( -4 ) !== "last", - ofType = what === "of-type"; - - return first === 1 && last === 0 ? - - // Shortcut for :nth-*(n) - function( elem ) { - return !!elem.parentNode; - } : - - function( elem, context, xml ) { - var cache, uniqueCache, outerCache, node, nodeIndex, start, - dir = simple !== forward ? "nextSibling" : "previousSibling", - parent = elem.parentNode, - name = ofType && elem.nodeName.toLowerCase(), - useCache = !xml && !ofType, - diff = false; - - if ( parent ) { - - // :(first|last|only)-(child|of-type) - if ( simple ) { - while ( dir ) { - node = elem; - while ( (node = node[ dir ]) ) { - if ( ofType ? - node.nodeName.toLowerCase() === name : - node.nodeType === 1 ) { - - return false; - } - } - // Reverse direction for :only-* (if we haven't yet done so) - start = dir = type === "only" && !start && "nextSibling"; - } - return true; - } - - start = [ forward ? parent.firstChild : parent.lastChild ]; - - // non-xml :nth-child(...) stores cache data on `parent` - if ( forward && useCache ) { - - // Seek `elem` from a previously-cached index - - // ...in a gzip-friendly way - node = parent; - outerCache = node[ expando ] || (node[ expando ] = {}); - - // Support: IE <9 only - // Defend against cloned attroperties (jQuery gh-1709) - uniqueCache = outerCache[ node.uniqueID ] || - (outerCache[ node.uniqueID ] = {}); - - cache = uniqueCache[ type ] || []; - nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ]; - diff = nodeIndex && cache[ 2 ]; - node = nodeIndex && parent.childNodes[ nodeIndex ]; - - while ( (node = ++nodeIndex && node && node[ dir ] || - - // Fallback to seeking `elem` from the start - (diff = nodeIndex = 0) || start.pop()) ) { - - // When found, cache indexes on `parent` and break - if ( node.nodeType === 1 && ++diff && node === elem ) { - uniqueCache[ type ] = [ dirruns, nodeIndex, diff ]; - break; - } - } - - } else { - // Use previously-cached element index if available - if ( useCache ) { - // ...in a gzip-friendly way - node = elem; - outerCache = node[ expando ] || (node[ expando ] = {}); - - // Support: IE <9 only - // Defend against cloned attroperties (jQuery gh-1709) - uniqueCache = outerCache[ node.uniqueID ] || - (outerCache[ node.uniqueID ] = {}); - - cache = uniqueCache[ type ] || []; - nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ]; - diff = nodeIndex; - } - - // xml :nth-child(...) - // or :nth-last-child(...) or :nth(-last)?-of-type(...) - if ( diff === false ) { - // Use the same loop as above to seek `elem` from the start - while ( (node = ++nodeIndex && node && node[ dir ] || - (diff = nodeIndex = 0) || start.pop()) ) { - - if ( ( ofType ? - node.nodeName.toLowerCase() === name : - node.nodeType === 1 ) && - ++diff ) { - - // Cache the index of each encountered element - if ( useCache ) { - outerCache = node[ expando ] || (node[ expando ] = {}); - - // Support: IE <9 only - // Defend against cloned attroperties (jQuery gh-1709) - uniqueCache = outerCache[ node.uniqueID ] || - (outerCache[ node.uniqueID ] = {}); - - uniqueCache[ type ] = [ dirruns, diff ]; - } - - if ( node === elem ) { - break; - } - } - } - } - } - - // Incorporate the offset, then check against cycle size - diff -= last; - return diff === first || ( diff % first === 0 && diff / first >= 0 ); - } - }; - }, - - "PSEUDO": function( pseudo, argument ) { - // pseudo-class names are case-insensitive - // http://www.w3.org/TR/selectors/#pseudo-classes - // Prioritize by case sensitivity in case custom pseudos are added with uppercase letters - // Remember that setFilters inherits from pseudos - var args, - fn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] || - Sizzle.error( "unsupported pseudo: " + pseudo ); - - // The user may use createPseudo to indicate that - // arguments are needed to create the filter function - // just as Sizzle does - if ( fn[ expando ] ) { - return fn( argument ); - } - - // But maintain support for old signatures - if ( fn.length > 1 ) { - args = [ pseudo, pseudo, "", argument ]; - return Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ? - markFunction(function( seed, matches ) { - var idx, - matched = fn( seed, argument ), - i = matched.length; - while ( i-- ) { - idx = indexOf( seed, matched[i] ); - seed[ idx ] = !( matches[ idx ] = matched[i] ); - } - }) : - function( elem ) { - return fn( elem, 0, args ); - }; - } - - return fn; - } - }, - - pseudos: { - // Potentially complex pseudos - "not": markFunction(function( selector ) { - // Trim the selector passed to compile - // to avoid treating leading and trailing - // spaces as combinators - var input = [], - results = [], - matcher = compile( selector.replace( rtrim, "$1" ) ); - - return matcher[ expando ] ? - markFunction(function( seed, matches, context, xml ) { - var elem, - unmatched = matcher( seed, null, xml, [] ), - i = seed.length; - - // Match elements unmatched by `matcher` - while ( i-- ) { - if ( (elem = unmatched[i]) ) { - seed[i] = !(matches[i] = elem); - } - } - }) : - function( elem, context, xml ) { - input[0] = elem; - matcher( input, null, xml, results ); - // Don't keep the element (issue #299) - input[0] = null; - return !results.pop(); - }; - }), - - "has": markFunction(function( selector ) { - return function( elem ) { - return Sizzle( selector, elem ).length > 0; - }; - }), - - "contains": markFunction(function( text ) { - text = text.replace( runescape, funescape ); - return function( elem ) { - return ( elem.textContent || elem.innerText || getText( elem ) ).indexOf( text ) > -1; - }; - }), - - // "Whether an element is represented by a :lang() selector - // is based solely on the element's language value - // being equal to the identifier C, - // or beginning with the identifier C immediately followed by "-". - // The matching of C against the element's language value is performed case-insensitively. - // The identifier C does not have to be a valid language name." - // http://www.w3.org/TR/selectors/#lang-pseudo - "lang": markFunction( function( lang ) { - // lang value must be a valid identifier - if ( !ridentifier.test(lang || "") ) { - Sizzle.error( "unsupported lang: " + lang ); - } - lang = lang.replace( runescape, funescape ).toLowerCase(); - return function( elem ) { - var elemLang; - do { - if ( (elemLang = documentIsHTML ? - elem.lang : - elem.getAttribute("xml:lang") || elem.getAttribute("lang")) ) { - - elemLang = elemLang.toLowerCase(); - return elemLang === lang || elemLang.indexOf( lang + "-" ) === 0; - } - } while ( (elem = elem.parentNode) && elem.nodeType === 1 ); - return false; - }; - }), - - // Miscellaneous - "target": function( elem ) { - var hash = window.location && window.location.hash; - return hash && hash.slice( 1 ) === elem.id; - }, - - "root": function( elem ) { - return elem === docElem; - }, - - "focus": function( elem ) { - return elem === document.activeElement && (!document.hasFocus || document.hasFocus()) && !!(elem.type || elem.href || ~elem.tabIndex); - }, - - // Boolean properties - "enabled": createDisabledPseudo( false ), - "disabled": createDisabledPseudo( true ), - - "checked": function( elem ) { - // In CSS3, :checked should return both checked and selected elements - // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked - var nodeName = elem.nodeName.toLowerCase(); - return (nodeName === "input" && !!elem.checked) || (nodeName === "option" && !!elem.selected); - }, - - "selected": function( elem ) { - // Accessing this property makes selected-by-default - // options in Safari work properly - if ( elem.parentNode ) { - elem.parentNode.selectedIndex; - } - - return elem.selected === true; - }, - - // Contents - "empty": function( elem ) { - // http://www.w3.org/TR/selectors/#empty-pseudo - // :empty is negated by element (1) or content nodes (text: 3; cdata: 4; entity ref: 5), - // but not by others (comment: 8; processing instruction: 7; etc.) - // nodeType < 6 works because attributes (2) do not appear as children - for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) { - if ( elem.nodeType < 6 ) { - return false; - } - } - return true; - }, - - "parent": function( elem ) { - return !Expr.pseudos["empty"]( elem ); - }, - - // Element/input types - "header": function( elem ) { - return rheader.test( elem.nodeName ); - }, - - "input": function( elem ) { - return rinputs.test( elem.nodeName ); - }, - - "button": function( elem ) { - var name = elem.nodeName.toLowerCase(); - return name === "input" && elem.type === "button" || name === "button"; - }, - - "text": function( elem ) { - var attr; - return elem.nodeName.toLowerCase() === "input" && - elem.type === "text" && - - // Support: IE<8 - // New HTML5 attribute values (e.g., "search") appear with elem.type === "text" - ( (attr = elem.getAttribute("type")) == null || attr.toLowerCase() === "text" ); - }, - - // Position-in-collection - "first": createPositionalPseudo(function() { - return [ 0 ]; - }), - - "last": createPositionalPseudo(function( matchIndexes, length ) { - return [ length - 1 ]; - }), - - "eq": createPositionalPseudo(function( matchIndexes, length, argument ) { - return [ argument < 0 ? argument + length : argument ]; - }), - - "even": createPositionalPseudo(function( matchIndexes, length ) { - var i = 0; - for ( ; i < length; i += 2 ) { - matchIndexes.push( i ); - } - return matchIndexes; - }), - - "odd": createPositionalPseudo(function( matchIndexes, length ) { - var i = 1; - for ( ; i < length; i += 2 ) { - matchIndexes.push( i ); - } - return matchIndexes; - }), - - "lt": createPositionalPseudo(function( matchIndexes, length, argument ) { - var i = argument < 0 ? argument + length : argument; - for ( ; --i >= 0; ) { - matchIndexes.push( i ); - } - return matchIndexes; - }), - - "gt": createPositionalPseudo(function( matchIndexes, length, argument ) { - var i = argument < 0 ? argument + length : argument; - for ( ; ++i < length; ) { - matchIndexes.push( i ); - } - return matchIndexes; - }) - } -}; - -Expr.pseudos["nth"] = Expr.pseudos["eq"]; - -// Add button/input type pseudos -for ( i in { radio: true, checkbox: true, file: true, password: true, image: true } ) { - Expr.pseudos[ i ] = createInputPseudo( i ); -} -for ( i in { submit: true, reset: true } ) { - Expr.pseudos[ i ] = createButtonPseudo( i ); -} - -// Easy API for creating new setFilters -function setFilters() {} -setFilters.prototype = Expr.filters = Expr.pseudos; -Expr.setFilters = new setFilters(); - -tokenize = Sizzle.tokenize = function( selector, parseOnly ) { - var matched, match, tokens, type, - soFar, groups, preFilters, - cached = tokenCache[ selector + " " ]; - - if ( cached ) { - return parseOnly ? 0 : cached.slice( 0 ); - } - - soFar = selector; - groups = []; - preFilters = Expr.preFilter; - - while ( soFar ) { - - // Comma and first run - if ( !matched || (match = rcomma.exec( soFar )) ) { - if ( match ) { - // Don't consume trailing commas as valid - soFar = soFar.slice( match[0].length ) || soFar; - } - groups.push( (tokens = []) ); - } - - matched = false; - - // Combinators - if ( (match = rcombinators.exec( soFar )) ) { - matched = match.shift(); - tokens.push({ - value: matched, - // Cast descendant combinators to space - type: match[0].replace( rtrim, " " ) - }); - soFar = soFar.slice( matched.length ); - } - - // Filters - for ( type in Expr.filter ) { - if ( (match = matchExpr[ type ].exec( soFar )) && (!preFilters[ type ] || - (match = preFilters[ type ]( match ))) ) { - matched = match.shift(); - tokens.push({ - value: matched, - type: type, - matches: match - }); - soFar = soFar.slice( matched.length ); - } - } - - if ( !matched ) { - break; - } - } - - // Return the length of the invalid excess - // if we're just parsing - // Otherwise, throw an error or return tokens - return parseOnly ? - soFar.length : - soFar ? - Sizzle.error( selector ) : - // Cache the tokens - tokenCache( selector, groups ).slice( 0 ); -}; - -function toSelector( tokens ) { - var i = 0, - len = tokens.length, - selector = ""; - for ( ; i < len; i++ ) { - selector += tokens[i].value; - } - return selector; -} - -function addCombinator( matcher, combinator, base ) { - var dir = combinator.dir, - skip = combinator.next, - key = skip || dir, - checkNonElements = base && key === "parentNode", - doneName = done++; - - return combinator.first ? - // Check against closest ancestor/preceding element - function( elem, context, xml ) { - while ( (elem = elem[ dir ]) ) { - if ( elem.nodeType === 1 || checkNonElements ) { - return matcher( elem, context, xml ); - } - } - return false; - } : - - // Check against all ancestor/preceding elements - function( elem, context, xml ) { - var oldCache, uniqueCache, outerCache, - newCache = [ dirruns, doneName ]; - - // We can't set arbitrary data on XML nodes, so they don't benefit from combinator caching - if ( xml ) { - while ( (elem = elem[ dir ]) ) { - if ( elem.nodeType === 1 || checkNonElements ) { - if ( matcher( elem, context, xml ) ) { - return true; - } - } - } - } else { - while ( (elem = elem[ dir ]) ) { - if ( elem.nodeType === 1 || checkNonElements ) { - outerCache = elem[ expando ] || (elem[ expando ] = {}); - - // Support: IE <9 only - // Defend against cloned attroperties (jQuery gh-1709) - uniqueCache = outerCache[ elem.uniqueID ] || (outerCache[ elem.uniqueID ] = {}); - - if ( skip && skip === elem.nodeName.toLowerCase() ) { - elem = elem[ dir ] || elem; - } else if ( (oldCache = uniqueCache[ key ]) && - oldCache[ 0 ] === dirruns && oldCache[ 1 ] === doneName ) { - - // Assign to newCache so results back-propagate to previous elements - return (newCache[ 2 ] = oldCache[ 2 ]); - } else { - // Reuse newcache so results back-propagate to previous elements - uniqueCache[ key ] = newCache; - - // A match means we're done; a fail means we have to keep checking - if ( (newCache[ 2 ] = matcher( elem, context, xml )) ) { - return true; - } - } - } - } - } - return false; - }; -} - -function elementMatcher( matchers ) { - return matchers.length > 1 ? - function( elem, context, xml ) { - var i = matchers.length; - while ( i-- ) { - if ( !matchers[i]( elem, context, xml ) ) { - return false; - } - } - return true; - } : - matchers[0]; -} - -function multipleContexts( selector, contexts, results ) { - var i = 0, - len = contexts.length; - for ( ; i < len; i++ ) { - Sizzle( selector, contexts[i], results ); - } - return results; -} - -function condense( unmatched, map, filter, context, xml ) { - var elem, - newUnmatched = [], - i = 0, - len = unmatched.length, - mapped = map != null; - - for ( ; i < len; i++ ) { - if ( (elem = unmatched[i]) ) { - if ( !filter || filter( elem, context, xml ) ) { - newUnmatched.push( elem ); - if ( mapped ) { - map.push( i ); - } - } - } - } - - return newUnmatched; -} - -function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) { - if ( postFilter && !postFilter[ expando ] ) { - postFilter = setMatcher( postFilter ); - } - if ( postFinder && !postFinder[ expando ] ) { - postFinder = setMatcher( postFinder, postSelector ); - } - return markFunction(function( seed, results, context, xml ) { - var temp, i, elem, - preMap = [], - postMap = [], - preexisting = results.length, - - // Get initial elements from seed or context - elems = seed || multipleContexts( selector || "*", context.nodeType ? [ context ] : context, [] ), - - // Prefilter to get matcher input, preserving a map for seed-results synchronization - matcherIn = preFilter && ( seed || !selector ) ? - condense( elems, preMap, preFilter, context, xml ) : - elems, - - matcherOut = matcher ? - // If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results, - postFinder || ( seed ? preFilter : preexisting || postFilter ) ? - - // ...intermediate processing is necessary - [] : - - // ...otherwise use results directly - results : - matcherIn; - - // Find primary matches - if ( matcher ) { - matcher( matcherIn, matcherOut, context, xml ); - } - - // Apply postFilter - if ( postFilter ) { - temp = condense( matcherOut, postMap ); - postFilter( temp, [], context, xml ); - - // Un-match failing elements by moving them back to matcherIn - i = temp.length; - while ( i-- ) { - if ( (elem = temp[i]) ) { - matcherOut[ postMap[i] ] = !(matcherIn[ postMap[i] ] = elem); - } - } - } - - if ( seed ) { - if ( postFinder || preFilter ) { - if ( postFinder ) { - // Get the final matcherOut by condensing this intermediate into postFinder contexts - temp = []; - i = matcherOut.length; - while ( i-- ) { - if ( (elem = matcherOut[i]) ) { - // Restore matcherIn since elem is not yet a final match - temp.push( (matcherIn[i] = elem) ); - } - } - postFinder( null, (matcherOut = []), temp, xml ); - } - - // Move matched elements from seed to results to keep them synchronized - i = matcherOut.length; - while ( i-- ) { - if ( (elem = matcherOut[i]) && - (temp = postFinder ? indexOf( seed, elem ) : preMap[i]) > -1 ) { - - seed[temp] = !(results[temp] = elem); - } - } - } - - // Add elements to results, through postFinder if defined - } else { - matcherOut = condense( - matcherOut === results ? - matcherOut.splice( preexisting, matcherOut.length ) : - matcherOut - ); - if ( postFinder ) { - postFinder( null, results, matcherOut, xml ); - } else { - push.apply( results, matcherOut ); - } - } - }); -} - -function matcherFromTokens( tokens ) { - var checkContext, matcher, j, - len = tokens.length, - leadingRelative = Expr.relative[ tokens[0].type ], - implicitRelative = leadingRelative || Expr.relative[" "], - i = leadingRelative ? 1 : 0, - - // The foundational matcher ensures that elements are reachable from top-level context(s) - matchContext = addCombinator( function( elem ) { - return elem === checkContext; - }, implicitRelative, true ), - matchAnyContext = addCombinator( function( elem ) { - return indexOf( checkContext, elem ) > -1; - }, implicitRelative, true ), - matchers = [ function( elem, context, xml ) { - var ret = ( !leadingRelative && ( xml || context !== outermostContext ) ) || ( - (checkContext = context).nodeType ? - matchContext( elem, context, xml ) : - matchAnyContext( elem, context, xml ) ); - // Avoid hanging onto element (issue #299) - checkContext = null; - return ret; - } ]; - - for ( ; i < len; i++ ) { - if ( (matcher = Expr.relative[ tokens[i].type ]) ) { - matchers = [ addCombinator(elementMatcher( matchers ), matcher) ]; - } else { - matcher = Expr.filter[ tokens[i].type ].apply( null, tokens[i].matches ); - - // Return special upon seeing a positional matcher - if ( matcher[ expando ] ) { - // Find the next relative operator (if any) for proper handling - j = ++i; - for ( ; j < len; j++ ) { - if ( Expr.relative[ tokens[j].type ] ) { - break; - } - } - return setMatcher( - i > 1 && elementMatcher( matchers ), - i > 1 && toSelector( - // If the preceding token was a descendant combinator, insert an implicit any-element `*` - tokens.slice( 0, i - 1 ).concat({ value: tokens[ i - 2 ].type === " " ? "*" : "" }) - ).replace( rtrim, "$1" ), - matcher, - i < j && matcherFromTokens( tokens.slice( i, j ) ), - j < len && matcherFromTokens( (tokens = tokens.slice( j )) ), - j < len && toSelector( tokens ) - ); - } - matchers.push( matcher ); - } - } - - return elementMatcher( matchers ); -} - -function matcherFromGroupMatchers( elementMatchers, setMatchers ) { - var bySet = setMatchers.length > 0, - byElement = elementMatchers.length > 0, - superMatcher = function( seed, context, xml, results, outermost ) { - var elem, j, matcher, - matchedCount = 0, - i = "0", - unmatched = seed && [], - setMatched = [], - contextBackup = outermostContext, - // We must always have either seed elements or outermost context - elems = seed || byElement && Expr.find["TAG"]( "*", outermost ), - // Use integer dirruns iff this is the outermost matcher - dirrunsUnique = (dirruns += contextBackup == null ? 1 : Math.random() || 0.1), - len = elems.length; - - if ( outermost ) { - outermostContext = context === document || context || outermost; - } - - // Add elements passing elementMatchers directly to results - // Support: IE<9, Safari - // Tolerate NodeList properties (IE: "length"; Safari: ) matching elements by id - for ( ; i !== len && (elem = elems[i]) != null; i++ ) { - if ( byElement && elem ) { - j = 0; - if ( !context && elem.ownerDocument !== document ) { - setDocument( elem ); - xml = !documentIsHTML; - } - while ( (matcher = elementMatchers[j++]) ) { - if ( matcher( elem, context || document, xml) ) { - results.push( elem ); - break; - } - } - if ( outermost ) { - dirruns = dirrunsUnique; - } - } - - // Track unmatched elements for set filters - if ( bySet ) { - // They will have gone through all possible matchers - if ( (elem = !matcher && elem) ) { - matchedCount--; - } - - // Lengthen the array for every element, matched or not - if ( seed ) { - unmatched.push( elem ); - } - } - } - - // `i` is now the count of elements visited above, and adding it to `matchedCount` - // makes the latter nonnegative. - matchedCount += i; - - // Apply set filters to unmatched elements - // NOTE: This can be skipped if there are no unmatched elements (i.e., `matchedCount` - // equals `i`), unless we didn't visit _any_ elements in the above loop because we have - // no element matchers and no seed. - // Incrementing an initially-string "0" `i` allows `i` to remain a string only in that - // case, which will result in a "00" `matchedCount` that differs from `i` but is also - // numerically zero. - if ( bySet && i !== matchedCount ) { - j = 0; - while ( (matcher = setMatchers[j++]) ) { - matcher( unmatched, setMatched, context, xml ); - } - - if ( seed ) { - // Reintegrate element matches to eliminate the need for sorting - if ( matchedCount > 0 ) { - while ( i-- ) { - if ( !(unmatched[i] || setMatched[i]) ) { - setMatched[i] = pop.call( results ); - } - } - } - - // Discard index placeholder values to get only actual matches - setMatched = condense( setMatched ); - } - - // Add matches to results - push.apply( results, setMatched ); - - // Seedless set matches succeeding multiple successful matchers stipulate sorting - if ( outermost && !seed && setMatched.length > 0 && - ( matchedCount + setMatchers.length ) > 1 ) { - - Sizzle.uniqueSort( results ); - } - } - - // Override manipulation of globals by nested matchers - if ( outermost ) { - dirruns = dirrunsUnique; - outermostContext = contextBackup; - } - - return unmatched; - }; - - return bySet ? - markFunction( superMatcher ) : - superMatcher; -} - -compile = Sizzle.compile = function( selector, match /* Internal Use Only */ ) { - var i, - setMatchers = [], - elementMatchers = [], - cached = compilerCache[ selector + " " ]; - - if ( !cached ) { - // Generate a function of recursive functions that can be used to check each element - if ( !match ) { - match = tokenize( selector ); - } - i = match.length; - while ( i-- ) { - cached = matcherFromTokens( match[i] ); - if ( cached[ expando ] ) { - setMatchers.push( cached ); - } else { - elementMatchers.push( cached ); - } - } - - // Cache the compiled function - cached = compilerCache( selector, matcherFromGroupMatchers( elementMatchers, setMatchers ) ); - - // Save selector and tokenization - cached.selector = selector; - } - return cached; -}; - -/** - * A low-level selection function that works with Sizzle's compiled - * selector functions - * @param {String|Function} selector A selector or a pre-compiled - * selector function built with Sizzle.compile - * @param {Element} context - * @param {Array} [results] - * @param {Array} [seed] A set of elements to match against - */ -select = Sizzle.select = function( selector, context, results, seed ) { - var i, tokens, token, type, find, - compiled = typeof selector === "function" && selector, - match = !seed && tokenize( (selector = compiled.selector || selector) ); - - results = results || []; - - // Try to minimize operations if there is only one selector in the list and no seed - // (the latter of which guarantees us context) - if ( match.length === 1 ) { - - // Reduce context if the leading compound selector is an ID - tokens = match[0] = match[0].slice( 0 ); - if ( tokens.length > 2 && (token = tokens[0]).type === "ID" && - context.nodeType === 9 && documentIsHTML && Expr.relative[ tokens[1].type ] ) { - - context = ( Expr.find["ID"]( token.matches[0].replace(runescape, funescape), context ) || [] )[0]; - if ( !context ) { - return results; - - // Precompiled matchers will still verify ancestry, so step up a level - } else if ( compiled ) { - context = context.parentNode; - } - - selector = selector.slice( tokens.shift().value.length ); - } - - // Fetch a seed set for right-to-left matching - i = matchExpr["needsContext"].test( selector ) ? 0 : tokens.length; - while ( i-- ) { - token = tokens[i]; - - // Abort if we hit a combinator - if ( Expr.relative[ (type = token.type) ] ) { - break; - } - if ( (find = Expr.find[ type ]) ) { - // Search, expanding context for leading sibling combinators - if ( (seed = find( - token.matches[0].replace( runescape, funescape ), - rsibling.test( tokens[0].type ) && testContext( context.parentNode ) || context - )) ) { - - // If seed is empty or no tokens remain, we can return early - tokens.splice( i, 1 ); - selector = seed.length && toSelector( tokens ); - if ( !selector ) { - push.apply( results, seed ); - return results; - } - - break; - } - } - } - } - - // Compile and execute a filtering function if one is not provided - // Provide `match` to avoid retokenization if we modified the selector above - ( compiled || compile( selector, match ) )( - seed, - context, - !documentIsHTML, - results, - !context || rsibling.test( selector ) && testContext( context.parentNode ) || context - ); - return results; -}; - -// One-time assignments - -// Sort stability -support.sortStable = expando.split("").sort( sortOrder ).join("") === expando; - -// Support: Chrome 14-35+ -// Always assume duplicates if they aren't passed to the comparison function -support.detectDuplicates = !!hasDuplicate; - -// Initialize against the default document -setDocument(); - -// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27) -// Detached nodes confoundingly follow *each other* -support.sortDetached = assert(function( el ) { - // Should return 1, but returns 4 (following) - return el.compareDocumentPosition( document.createElement("fieldset") ) & 1; -}); - -// Support: IE<8 -// Prevent attribute/property "interpolation" -// https://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx -if ( !assert(function( el ) { - el.innerHTML = ""; - return el.firstChild.getAttribute("href") === "#" ; -}) ) { - addHandle( "type|href|height|width", function( elem, name, isXML ) { - if ( !isXML ) { - return elem.getAttribute( name, name.toLowerCase() === "type" ? 1 : 2 ); - } - }); -} - -// Support: IE<9 -// Use defaultValue in place of getAttribute("value") -if ( !support.attributes || !assert(function( el ) { - el.innerHTML = ""; - el.firstChild.setAttribute( "value", "" ); - return el.firstChild.getAttribute( "value" ) === ""; -}) ) { - addHandle( "value", function( elem, name, isXML ) { - if ( !isXML && elem.nodeName.toLowerCase() === "input" ) { - return elem.defaultValue; - } - }); -} - -// Support: IE<9 -// Use getAttributeNode to fetch booleans when getAttribute lies -if ( !assert(function( el ) { - return el.getAttribute("disabled") == null; -}) ) { - addHandle( booleans, function( elem, name, isXML ) { - var val; - if ( !isXML ) { - return elem[ name ] === true ? name.toLowerCase() : - (val = elem.getAttributeNode( name )) && val.specified ? - val.value : - null; - } - }); -} - -return Sizzle; - -})( window ); - - - -jQuery.find = Sizzle; -jQuery.expr = Sizzle.selectors; - -// Deprecated -jQuery.expr[ ":" ] = jQuery.expr.pseudos; -jQuery.uniqueSort = jQuery.unique = Sizzle.uniqueSort; -jQuery.text = Sizzle.getText; -jQuery.isXMLDoc = Sizzle.isXML; -jQuery.contains = Sizzle.contains; -jQuery.escapeSelector = Sizzle.escape; - - - - -var dir = function( elem, dir, until ) { - var matched = [], - truncate = until !== undefined; - - while ( ( elem = elem[ dir ] ) && elem.nodeType !== 9 ) { - if ( elem.nodeType === 1 ) { - if ( truncate && jQuery( elem ).is( until ) ) { - break; - } - matched.push( elem ); - } - } - return matched; -}; - - -var siblings = function( n, elem ) { - var matched = []; - - for ( ; n; n = n.nextSibling ) { - if ( n.nodeType === 1 && n !== elem ) { - matched.push( n ); - } - } - - return matched; -}; - - -var rneedsContext = jQuery.expr.match.needsContext; - - - -function nodeName( elem, name ) { - - return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase(); - -}; -var rsingleTag = ( /^<([a-z][^\/\0>:\x20\t\r\n\f]*)[\x20\t\r\n\f]*\/?>(?:<\/\1>|)$/i ); - - - -var risSimple = /^.[^:#\[\.,]*$/; - -// Implement the identical functionality for filter and not -function winnow( elements, qualifier, not ) { - if ( jQuery.isFunction( qualifier ) ) { - return jQuery.grep( elements, function( elem, i ) { - return !!qualifier.call( elem, i, elem ) !== not; - } ); - } - - // Single element - if ( qualifier.nodeType ) { - return jQuery.grep( elements, function( elem ) { - return ( elem === qualifier ) !== not; - } ); - } - - // Arraylike of elements (jQuery, arguments, Array) - if ( typeof qualifier !== "string" ) { - return jQuery.grep( elements, function( elem ) { - return ( indexOf.call( qualifier, elem ) > -1 ) !== not; - } ); - } - - // Simple selector that can be filtered directly, removing non-Elements - if ( risSimple.test( qualifier ) ) { - return jQuery.filter( qualifier, elements, not ); - } - - // Complex selector, compare the two sets, removing non-Elements - qualifier = jQuery.filter( qualifier, elements ); - return jQuery.grep( elements, function( elem ) { - return ( indexOf.call( qualifier, elem ) > -1 ) !== not && elem.nodeType === 1; - } ); -} - -jQuery.filter = function( expr, elems, not ) { - var elem = elems[ 0 ]; - - if ( not ) { - expr = ":not(" + expr + ")"; - } - - if ( elems.length === 1 && elem.nodeType === 1 ) { - return jQuery.find.matchesSelector( elem, expr ) ? [ elem ] : []; - } - - return jQuery.find.matches( expr, jQuery.grep( elems, function( elem ) { - return elem.nodeType === 1; - } ) ); -}; - -jQuery.fn.extend( { - find: function( selector ) { - var i, ret, - len = this.length, - self = this; - - if ( typeof selector !== "string" ) { - return this.pushStack( jQuery( selector ).filter( function() { - for ( i = 0; i < len; i++ ) { - if ( jQuery.contains( self[ i ], this ) ) { - return true; - } - } - } ) ); - } - - ret = this.pushStack( [] ); - - for ( i = 0; i < len; i++ ) { - jQuery.find( selector, self[ i ], ret ); - } - - return len > 1 ? jQuery.uniqueSort( ret ) : ret; - }, - filter: function( selector ) { - return this.pushStack( winnow( this, selector || [], false ) ); - }, - not: function( selector ) { - return this.pushStack( winnow( this, selector || [], true ) ); - }, - is: function( selector ) { - return !!winnow( - this, - - // If this is a positional/relative selector, check membership in the returned set - // so $("p:first").is("p:last") won't return true for a doc with two "p". - typeof selector === "string" && rneedsContext.test( selector ) ? - jQuery( selector ) : - selector || [], - false - ).length; - } -} ); - - -// Initialize a jQuery object - - -// A central reference to the root jQuery(document) -var rootjQuery, - - // A simple way to check for HTML strings - // Prioritize #id over to avoid XSS via location.hash (#9521) - // Strict HTML recognition (#11290: must start with <) - // Shortcut simple #id case for speed - rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]+))$/, - - init = jQuery.fn.init = function( selector, context, root ) { - var match, elem; - - // HANDLE: $(""), $(null), $(undefined), $(false) - if ( !selector ) { - return this; - } - - // Method init() accepts an alternate rootjQuery - // so migrate can support jQuery.sub (gh-2101) - root = root || rootjQuery; - - // Handle HTML strings - if ( typeof selector === "string" ) { - if ( selector[ 0 ] === "<" && - selector[ selector.length - 1 ] === ">" && - selector.length >= 3 ) { - - // Assume that strings that start and end with <> are HTML and skip the regex check - match = [ null, selector, null ]; - - } else { - match = rquickExpr.exec( selector ); - } - - // Match html or make sure no context is specified for #id - if ( match && ( match[ 1 ] || !context ) ) { - - // HANDLE: $(html) -> $(array) - if ( match[ 1 ] ) { - context = context instanceof jQuery ? context[ 0 ] : context; - - // Option to run scripts is true for back-compat - // Intentionally let the error be thrown if parseHTML is not present - jQuery.merge( this, jQuery.parseHTML( - match[ 1 ], - context && context.nodeType ? context.ownerDocument || context : document, - true - ) ); - - // HANDLE: $(html, props) - if ( rsingleTag.test( match[ 1 ] ) && jQuery.isPlainObject( context ) ) { - for ( match in context ) { - - // Properties of context are called as methods if possible - if ( jQuery.isFunction( this[ match ] ) ) { - this[ match ]( context[ match ] ); - - // ...and otherwise set as attributes - } else { - this.attr( match, context[ match ] ); - } - } - } - - return this; - - // HANDLE: $(#id) - } else { - elem = document.getElementById( match[ 2 ] ); - - if ( elem ) { - - // Inject the element directly into the jQuery object - this[ 0 ] = elem; - this.length = 1; - } - return this; - } - - // HANDLE: $(expr, $(...)) - } else if ( !context || context.jquery ) { - return ( context || root ).find( selector ); - - // HANDLE: $(expr, context) - // (which is just equivalent to: $(context).find(expr) - } else { - return this.constructor( context ).find( selector ); - } - - // HANDLE: $(DOMElement) - } else if ( selector.nodeType ) { - this[ 0 ] = selector; - this.length = 1; - return this; - - // HANDLE: $(function) - // Shortcut for document ready - } else if ( jQuery.isFunction( selector ) ) { - return root.ready !== undefined ? - root.ready( selector ) : - - // Execute immediately if ready is not present - selector( jQuery ); - } - - return jQuery.makeArray( selector, this ); - }; - -// Give the init function the jQuery prototype for later instantiation -init.prototype = jQuery.fn; - -// Initialize central reference -rootjQuery = jQuery( document ); - - -var rparentsprev = /^(?:parents|prev(?:Until|All))/, - - // Methods guaranteed to produce a unique set when starting from a unique set - guaranteedUnique = { - children: true, - contents: true, - next: true, - prev: true - }; - -jQuery.fn.extend( { - has: function( target ) { - var targets = jQuery( target, this ), - l = targets.length; - - return this.filter( function() { - var i = 0; - for ( ; i < l; i++ ) { - if ( jQuery.contains( this, targets[ i ] ) ) { - return true; - } - } - } ); - }, - - closest: function( selectors, context ) { - var cur, - i = 0, - l = this.length, - matched = [], - targets = typeof selectors !== "string" && jQuery( selectors ); - - // Positional selectors never match, since there's no _selection_ context - if ( !rneedsContext.test( selectors ) ) { - for ( ; i < l; i++ ) { - for ( cur = this[ i ]; cur && cur !== context; cur = cur.parentNode ) { - - // Always skip document fragments - if ( cur.nodeType < 11 && ( targets ? - targets.index( cur ) > -1 : - - // Don't pass non-elements to Sizzle - cur.nodeType === 1 && - jQuery.find.matchesSelector( cur, selectors ) ) ) { - - matched.push( cur ); - break; - } - } - } - } - - return this.pushStack( matched.length > 1 ? jQuery.uniqueSort( matched ) : matched ); - }, - - // Determine the position of an element within the set - index: function( elem ) { - - // No argument, return index in parent - if ( !elem ) { - return ( this[ 0 ] && this[ 0 ].parentNode ) ? this.first().prevAll().length : -1; - } - - // Index in selector - if ( typeof elem === "string" ) { - return indexOf.call( jQuery( elem ), this[ 0 ] ); - } - - // Locate the position of the desired element - return indexOf.call( this, - - // If it receives a jQuery object, the first element is used - elem.jquery ? elem[ 0 ] : elem - ); - }, - - add: function( selector, context ) { - return this.pushStack( - jQuery.uniqueSort( - jQuery.merge( this.get(), jQuery( selector, context ) ) - ) - ); - }, - - addBack: function( selector ) { - return this.add( selector == null ? - this.prevObject : this.prevObject.filter( selector ) - ); - } -} ); - -function sibling( cur, dir ) { - while ( ( cur = cur[ dir ] ) && cur.nodeType !== 1 ) {} - return cur; -} - -jQuery.each( { - parent: function( elem ) { - var parent = elem.parentNode; - return parent && parent.nodeType !== 11 ? parent : null; - }, - parents: function( elem ) { - return dir( elem, "parentNode" ); - }, - parentsUntil: function( elem, i, until ) { - return dir( elem, "parentNode", until ); - }, - next: function( elem ) { - return sibling( elem, "nextSibling" ); - }, - prev: function( elem ) { - return sibling( elem, "previousSibling" ); - }, - nextAll: function( elem ) { - return dir( elem, "nextSibling" ); - }, - prevAll: function( elem ) { - return dir( elem, "previousSibling" ); - }, - nextUntil: function( elem, i, until ) { - return dir( elem, "nextSibling", until ); - }, - prevUntil: function( elem, i, until ) { - return dir( elem, "previousSibling", until ); - }, - siblings: function( elem ) { - return siblings( ( elem.parentNode || {} ).firstChild, elem ); - }, - children: function( elem ) { - return siblings( elem.firstChild ); - }, - contents: function( elem ) { - if ( nodeName( elem, "iframe" ) ) { - return elem.contentDocument; - } - - // Support: IE 9 - 11 only, iOS 7 only, Android Browser <=4.3 only - // Treat the template element as a regular one in browsers that - // don't support it. - if ( nodeName( elem, "template" ) ) { - elem = elem.content || elem; - } - - return jQuery.merge( [], elem.childNodes ); - } -}, function( name, fn ) { - jQuery.fn[ name ] = function( until, selector ) { - var matched = jQuery.map( this, fn, until ); - - if ( name.slice( -5 ) !== "Until" ) { - selector = until; - } - - if ( selector && typeof selector === "string" ) { - matched = jQuery.filter( selector, matched ); - } - - if ( this.length > 1 ) { - - // Remove duplicates - if ( !guaranteedUnique[ name ] ) { - jQuery.uniqueSort( matched ); - } - - // Reverse order for parents* and prev-derivatives - if ( rparentsprev.test( name ) ) { - matched.reverse(); - } - } - - return this.pushStack( matched ); - }; -} ); -var rnothtmlwhite = ( /[^\x20\t\r\n\f]+/g ); - - - -// Convert String-formatted options into Object-formatted ones -function createOptions( options ) { - var object = {}; - jQuery.each( options.match( rnothtmlwhite ) || [], function( _, flag ) { - object[ flag ] = true; - } ); - return object; -} - -/* - * Create a callback list using the following parameters: - * - * options: an optional list of space-separated options that will change how - * the callback list behaves or a more traditional option object - * - * By default a callback list will act like an event callback list and can be - * "fired" multiple times. - * - * Possible options: - * - * once: will ensure the callback list can only be fired once (like a Deferred) - * - * memory: will keep track of previous values and will call any callback added - * after the list has been fired right away with the latest "memorized" - * values (like a Deferred) - * - * unique: will ensure a callback can only be added once (no duplicate in the list) - * - * stopOnFalse: interrupt callings when a callback returns false - * - */ -jQuery.Callbacks = function( options ) { - - // Convert options from String-formatted to Object-formatted if needed - // (we check in cache first) - options = typeof options === "string" ? - createOptions( options ) : - jQuery.extend( {}, options ); - - var // Flag to know if list is currently firing - firing, - - // Last fire value for non-forgettable lists - memory, - - // Flag to know if list was already fired - fired, - - // Flag to prevent firing - locked, - - // Actual callback list - list = [], - - // Queue of execution data for repeatable lists - queue = [], - - // Index of currently firing callback (modified by add/remove as needed) - firingIndex = -1, - - // Fire callbacks - fire = function() { - - // Enforce single-firing - locked = locked || options.once; - - // Execute callbacks for all pending executions, - // respecting firingIndex overrides and runtime changes - fired = firing = true; - for ( ; queue.length; firingIndex = -1 ) { - memory = queue.shift(); - while ( ++firingIndex < list.length ) { - - // Run callback and check for early termination - if ( list[ firingIndex ].apply( memory[ 0 ], memory[ 1 ] ) === false && - options.stopOnFalse ) { - - // Jump to end and forget the data so .add doesn't re-fire - firingIndex = list.length; - memory = false; - } - } - } - - // Forget the data if we're done with it - if ( !options.memory ) { - memory = false; - } - - firing = false; - - // Clean up if we're done firing for good - if ( locked ) { - - // Keep an empty list if we have data for future add calls - if ( memory ) { - list = []; - - // Otherwise, this object is spent - } else { - list = ""; - } - } - }, - - // Actual Callbacks object - self = { - - // Add a callback or a collection of callbacks to the list - add: function() { - if ( list ) { - - // If we have memory from a past run, we should fire after adding - if ( memory && !firing ) { - firingIndex = list.length - 1; - queue.push( memory ); - } - - ( function add( args ) { - jQuery.each( args, function( _, arg ) { - if ( jQuery.isFunction( arg ) ) { - if ( !options.unique || !self.has( arg ) ) { - list.push( arg ); - } - } else if ( arg && arg.length && jQuery.type( arg ) !== "string" ) { - - // Inspect recursively - add( arg ); - } - } ); - } )( arguments ); - - if ( memory && !firing ) { - fire(); - } - } - return this; - }, - - // Remove a callback from the list - remove: function() { - jQuery.each( arguments, function( _, arg ) { - var index; - while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) { - list.splice( index, 1 ); - - // Handle firing indexes - if ( index <= firingIndex ) { - firingIndex--; - } - } - } ); - return this; - }, - - // Check if a given callback is in the list. - // If no argument is given, return whether or not list has callbacks attached. - has: function( fn ) { - return fn ? - jQuery.inArray( fn, list ) > -1 : - list.length > 0; - }, - - // Remove all callbacks from the list - empty: function() { - if ( list ) { - list = []; - } - return this; - }, - - // Disable .fire and .add - // Abort any current/pending executions - // Clear all callbacks and values - disable: function() { - locked = queue = []; - list = memory = ""; - return this; - }, - disabled: function() { - return !list; - }, - - // Disable .fire - // Also disable .add unless we have memory (since it would have no effect) - // Abort any pending executions - lock: function() { - locked = queue = []; - if ( !memory && !firing ) { - list = memory = ""; - } - return this; - }, - locked: function() { - return !!locked; - }, - - // Call all callbacks with the given context and arguments - fireWith: function( context, args ) { - if ( !locked ) { - args = args || []; - args = [ context, args.slice ? args.slice() : args ]; - queue.push( args ); - if ( !firing ) { - fire(); - } - } - return this; - }, - - // Call all the callbacks with the given arguments - fire: function() { - self.fireWith( this, arguments ); - return this; - }, - - // To know if the callbacks have already been called at least once - fired: function() { - return !!fired; - } - }; - - return self; -}; - - -function Identity( v ) { - return v; -} -function Thrower( ex ) { - throw ex; -} - -function adoptValue( value, resolve, reject, noValue ) { - var method; - - try { - - // Check for promise aspect first to privilege synchronous behavior - if ( value && jQuery.isFunction( ( method = value.promise ) ) ) { - method.call( value ).done( resolve ).fail( reject ); - - // Other thenables - } else if ( value && jQuery.isFunction( ( method = value.then ) ) ) { - method.call( value, resolve, reject ); - - // Other non-thenables - } else { - - // Control `resolve` arguments by letting Array#slice cast boolean `noValue` to integer: - // * false: [ value ].slice( 0 ) => resolve( value ) - // * true: [ value ].slice( 1 ) => resolve() - resolve.apply( undefined, [ value ].slice( noValue ) ); - } - - // For Promises/A+, convert exceptions into rejections - // Since jQuery.when doesn't unwrap thenables, we can skip the extra checks appearing in - // Deferred#then to conditionally suppress rejection. - } catch ( value ) { - - // Support: Android 4.0 only - // Strict mode functions invoked without .call/.apply get global-object context - reject.apply( undefined, [ value ] ); - } -} - -jQuery.extend( { - - Deferred: function( func ) { - var tuples = [ - - // action, add listener, callbacks, - // ... .then handlers, argument index, [final state] - [ "notify", "progress", jQuery.Callbacks( "memory" ), - jQuery.Callbacks( "memory" ), 2 ], - [ "resolve", "done", jQuery.Callbacks( "once memory" ), - jQuery.Callbacks( "once memory" ), 0, "resolved" ], - [ "reject", "fail", jQuery.Callbacks( "once memory" ), - jQuery.Callbacks( "once memory" ), 1, "rejected" ] - ], - state = "pending", - promise = { - state: function() { - return state; - }, - always: function() { - deferred.done( arguments ).fail( arguments ); - return this; - }, - "catch": function( fn ) { - return promise.then( null, fn ); - }, - - // Keep pipe for back-compat - pipe: function( /* fnDone, fnFail, fnProgress */ ) { - var fns = arguments; - - return jQuery.Deferred( function( newDefer ) { - jQuery.each( tuples, function( i, tuple ) { - - // Map tuples (progress, done, fail) to arguments (done, fail, progress) - var fn = jQuery.isFunction( fns[ tuple[ 4 ] ] ) && fns[ tuple[ 4 ] ]; - - // deferred.progress(function() { bind to newDefer or newDefer.notify }) - // deferred.done(function() { bind to newDefer or newDefer.resolve }) - // deferred.fail(function() { bind to newDefer or newDefer.reject }) - deferred[ tuple[ 1 ] ]( function() { - var returned = fn && fn.apply( this, arguments ); - if ( returned && jQuery.isFunction( returned.promise ) ) { - returned.promise() - .progress( newDefer.notify ) - .done( newDefer.resolve ) - .fail( newDefer.reject ); - } else { - newDefer[ tuple[ 0 ] + "With" ]( - this, - fn ? [ returned ] : arguments - ); - } - } ); - } ); - fns = null; - } ).promise(); - }, - then: function( onFulfilled, onRejected, onProgress ) { - var maxDepth = 0; - function resolve( depth, deferred, handler, special ) { - return function() { - var that = this, - args = arguments, - mightThrow = function() { - var returned, then; - - // Support: Promises/A+ section 2.3.3.3.3 - // https://promisesaplus.com/#point-59 - // Ignore double-resolution attempts - if ( depth < maxDepth ) { - return; - } - - returned = handler.apply( that, args ); - - // Support: Promises/A+ section 2.3.1 - // https://promisesaplus.com/#point-48 - if ( returned === deferred.promise() ) { - throw new TypeError( "Thenable self-resolution" ); - } - - // Support: Promises/A+ sections 2.3.3.1, 3.5 - // https://promisesaplus.com/#point-54 - // https://promisesaplus.com/#point-75 - // Retrieve `then` only once - then = returned && - - // Support: Promises/A+ section 2.3.4 - // https://promisesaplus.com/#point-64 - // Only check objects and functions for thenability - ( typeof returned === "object" || - typeof returned === "function" ) && - returned.then; - - // Handle a returned thenable - if ( jQuery.isFunction( then ) ) { - - // Special processors (notify) just wait for resolution - if ( special ) { - then.call( - returned, - resolve( maxDepth, deferred, Identity, special ), - resolve( maxDepth, deferred, Thrower, special ) - ); - - // Normal processors (resolve) also hook into progress - } else { - - // ...and disregard older resolution values - maxDepth++; - - then.call( - returned, - resolve( maxDepth, deferred, Identity, special ), - resolve( maxDepth, deferred, Thrower, special ), - resolve( maxDepth, deferred, Identity, - deferred.notifyWith ) - ); - } - - // Handle all other returned values - } else { - - // Only substitute handlers pass on context - // and multiple values (non-spec behavior) - if ( handler !== Identity ) { - that = undefined; - args = [ returned ]; - } - - // Process the value(s) - // Default process is resolve - ( special || deferred.resolveWith )( that, args ); - } - }, - - // Only normal processors (resolve) catch and reject exceptions - process = special ? - mightThrow : - function() { - try { - mightThrow(); - } catch ( e ) { - - if ( jQuery.Deferred.exceptionHook ) { - jQuery.Deferred.exceptionHook( e, - process.stackTrace ); - } - - // Support: Promises/A+ section 2.3.3.3.4.1 - // https://promisesaplus.com/#point-61 - // Ignore post-resolution exceptions - if ( depth + 1 >= maxDepth ) { - - // Only substitute handlers pass on context - // and multiple values (non-spec behavior) - if ( handler !== Thrower ) { - that = undefined; - args = [ e ]; - } - - deferred.rejectWith( that, args ); - } - } - }; - - // Support: Promises/A+ section 2.3.3.3.1 - // https://promisesaplus.com/#point-57 - // Re-resolve promises immediately to dodge false rejection from - // subsequent errors - if ( depth ) { - process(); - } else { - - // Call an optional hook to record the stack, in case of exception - // since it's otherwise lost when execution goes async - if ( jQuery.Deferred.getStackHook ) { - process.stackTrace = jQuery.Deferred.getStackHook(); - } - window.setTimeout( process ); - } - }; - } - - return jQuery.Deferred( function( newDefer ) { - - // progress_handlers.add( ... ) - tuples[ 0 ][ 3 ].add( - resolve( - 0, - newDefer, - jQuery.isFunction( onProgress ) ? - onProgress : - Identity, - newDefer.notifyWith - ) - ); - - // fulfilled_handlers.add( ... ) - tuples[ 1 ][ 3 ].add( - resolve( - 0, - newDefer, - jQuery.isFunction( onFulfilled ) ? - onFulfilled : - Identity - ) - ); - - // rejected_handlers.add( ... ) - tuples[ 2 ][ 3 ].add( - resolve( - 0, - newDefer, - jQuery.isFunction( onRejected ) ? - onRejected : - Thrower - ) - ); - } ).promise(); - }, - - // Get a promise for this deferred - // If obj is provided, the promise aspect is added to the object - promise: function( obj ) { - return obj != null ? jQuery.extend( obj, promise ) : promise; - } - }, - deferred = {}; - - // Add list-specific methods - jQuery.each( tuples, function( i, tuple ) { - var list = tuple[ 2 ], - stateString = tuple[ 5 ]; - - // promise.progress = list.add - // promise.done = list.add - // promise.fail = list.add - promise[ tuple[ 1 ] ] = list.add; - - // Handle state - if ( stateString ) { - list.add( - function() { - - // state = "resolved" (i.e., fulfilled) - // state = "rejected" - state = stateString; - }, - - // rejected_callbacks.disable - // fulfilled_callbacks.disable - tuples[ 3 - i ][ 2 ].disable, - - // progress_callbacks.lock - tuples[ 0 ][ 2 ].lock - ); - } - - // progress_handlers.fire - // fulfilled_handlers.fire - // rejected_handlers.fire - list.add( tuple[ 3 ].fire ); - - // deferred.notify = function() { deferred.notifyWith(...) } - // deferred.resolve = function() { deferred.resolveWith(...) } - // deferred.reject = function() { deferred.rejectWith(...) } - deferred[ tuple[ 0 ] ] = function() { - deferred[ tuple[ 0 ] + "With" ]( this === deferred ? undefined : this, arguments ); - return this; - }; - - // deferred.notifyWith = list.fireWith - // deferred.resolveWith = list.fireWith - // deferred.rejectWith = list.fireWith - deferred[ tuple[ 0 ] + "With" ] = list.fireWith; - } ); - - // Make the deferred a promise - promise.promise( deferred ); - - // Call given func if any - if ( func ) { - func.call( deferred, deferred ); - } - - // All done! - return deferred; - }, - - // Deferred helper - when: function( singleValue ) { - var - - // count of uncompleted subordinates - remaining = arguments.length, - - // count of unprocessed arguments - i = remaining, - - // subordinate fulfillment data - resolveContexts = Array( i ), - resolveValues = slice.call( arguments ), - - // the master Deferred - master = jQuery.Deferred(), - - // subordinate callback factory - updateFunc = function( i ) { - return function( value ) { - resolveContexts[ i ] = this; - resolveValues[ i ] = arguments.length > 1 ? slice.call( arguments ) : value; - if ( !( --remaining ) ) { - master.resolveWith( resolveContexts, resolveValues ); - } - }; - }; - - // Single- and empty arguments are adopted like Promise.resolve - if ( remaining <= 1 ) { - adoptValue( singleValue, master.done( updateFunc( i ) ).resolve, master.reject, - !remaining ); - - // Use .then() to unwrap secondary thenables (cf. gh-3000) - if ( master.state() === "pending" || - jQuery.isFunction( resolveValues[ i ] && resolveValues[ i ].then ) ) { - - return master.then(); - } - } - - // Multiple arguments are aggregated like Promise.all array elements - while ( i-- ) { - adoptValue( resolveValues[ i ], updateFunc( i ), master.reject ); - } - - return master.promise(); - } -} ); - - -// These usually indicate a programmer mistake during development, -// warn about them ASAP rather than swallowing them by default. -var rerrorNames = /^(Eval|Internal|Range|Reference|Syntax|Type|URI)Error$/; - -jQuery.Deferred.exceptionHook = function( error, stack ) { - - // Support: IE 8 - 9 only - // Console exists when dev tools are open, which can happen at any time - if ( window.console && window.console.warn && error && rerrorNames.test( error.name ) ) { - window.console.warn( "jQuery.Deferred exception: " + error.message, error.stack, stack ); - } -}; - - - - -jQuery.readyException = function( error ) { - window.setTimeout( function() { - throw error; - } ); -}; - - - - -// The deferred used on DOM ready -var readyList = jQuery.Deferred(); - -jQuery.fn.ready = function( fn ) { - - readyList - .then( fn ) - - // Wrap jQuery.readyException in a function so that the lookup - // happens at the time of error handling instead of callback - // registration. - .catch( function( error ) { - jQuery.readyException( error ); - } ); - - return this; -}; - -jQuery.extend( { - - // Is the DOM ready to be used? Set to true once it occurs. - isReady: false, - - // A counter to track how many items to wait for before - // the ready event fires. See #6781 - readyWait: 1, - - // Handle when the DOM is ready - ready: function( wait ) { - - // Abort if there are pending holds or we're already ready - if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) { - return; - } - - // Remember that the DOM is ready - jQuery.isReady = true; - - // If a normal DOM Ready event fired, decrement, and wait if need be - if ( wait !== true && --jQuery.readyWait > 0 ) { - return; - } - - // If there are functions bound, to execute - readyList.resolveWith( document, [ jQuery ] ); - } -} ); - -jQuery.ready.then = readyList.then; - -// The ready event handler and self cleanup method -function completed() { - document.removeEventListener( "DOMContentLoaded", completed ); - window.removeEventListener( "load", completed ); - jQuery.ready(); -} - -// Catch cases where $(document).ready() is called -// after the browser event has already occurred. -// Support: IE <=9 - 10 only -// Older IE sometimes signals "interactive" too soon -if ( document.readyState === "complete" || - ( document.readyState !== "loading" && !document.documentElement.doScroll ) ) { - - // Handle it asynchronously to allow scripts the opportunity to delay ready - window.setTimeout( jQuery.ready ); - -} else { - - // Use the handy event callback - document.addEventListener( "DOMContentLoaded", completed ); - - // A fallback to window.onload, that will always work - window.addEventListener( "load", completed ); -} - - - - -// Multifunctional method to get and set values of a collection -// The value/s can optionally be executed if it's a function -var access = function( elems, fn, key, value, chainable, emptyGet, raw ) { - var i = 0, - len = elems.length, - bulk = key == null; - - // Sets many values - if ( jQuery.type( key ) === "object" ) { - chainable = true; - for ( i in key ) { - access( elems, fn, i, key[ i ], true, emptyGet, raw ); - } - - // Sets one value - } else if ( value !== undefined ) { - chainable = true; - - if ( !jQuery.isFunction( value ) ) { - raw = true; - } - - if ( bulk ) { - - // Bulk operations run against the entire set - if ( raw ) { - fn.call( elems, value ); - fn = null; - - // ...except when executing function values - } else { - bulk = fn; - fn = function( elem, key, value ) { - return bulk.call( jQuery( elem ), value ); - }; - } - } - - if ( fn ) { - for ( ; i < len; i++ ) { - fn( - elems[ i ], key, raw ? - value : - value.call( elems[ i ], i, fn( elems[ i ], key ) ) - ); - } - } - } - - if ( chainable ) { - return elems; - } - - // Gets - if ( bulk ) { - return fn.call( elems ); - } - - return len ? fn( elems[ 0 ], key ) : emptyGet; -}; -var acceptData = function( owner ) { - - // Accepts only: - // - Node - // - Node.ELEMENT_NODE - // - Node.DOCUMENT_NODE - // - Object - // - Any - return owner.nodeType === 1 || owner.nodeType === 9 || !( +owner.nodeType ); -}; - - - - -function Data() { - this.expando = jQuery.expando + Data.uid++; -} - -Data.uid = 1; - -Data.prototype = { - - cache: function( owner ) { - - // Check if the owner object already has a cache - var value = owner[ this.expando ]; - - // If not, create one - if ( !value ) { - value = {}; - - // We can accept data for non-element nodes in modern browsers, - // but we should not, see #8335. - // Always return an empty object. - if ( acceptData( owner ) ) { - - // If it is a node unlikely to be stringify-ed or looped over - // use plain assignment - if ( owner.nodeType ) { - owner[ this.expando ] = value; - - // Otherwise secure it in a non-enumerable property - // configurable must be true to allow the property to be - // deleted when data is removed - } else { - Object.defineProperty( owner, this.expando, { - value: value, - configurable: true - } ); - } - } - } - - return value; - }, - set: function( owner, data, value ) { - var prop, - cache = this.cache( owner ); - - // Handle: [ owner, key, value ] args - // Always use camelCase key (gh-2257) - if ( typeof data === "string" ) { - cache[ jQuery.camelCase( data ) ] = value; - - // Handle: [ owner, { properties } ] args - } else { - - // Copy the properties one-by-one to the cache object - for ( prop in data ) { - cache[ jQuery.camelCase( prop ) ] = data[ prop ]; - } - } - return cache; - }, - get: function( owner, key ) { - return key === undefined ? - this.cache( owner ) : - - // Always use camelCase key (gh-2257) - owner[ this.expando ] && owner[ this.expando ][ jQuery.camelCase( key ) ]; - }, - access: function( owner, key, value ) { - - // In cases where either: - // - // 1. No key was specified - // 2. A string key was specified, but no value provided - // - // Take the "read" path and allow the get method to determine - // which value to return, respectively either: - // - // 1. The entire cache object - // 2. The data stored at the key - // - if ( key === undefined || - ( ( key && typeof key === "string" ) && value === undefined ) ) { - - return this.get( owner, key ); - } - - // When the key is not a string, or both a key and value - // are specified, set or extend (existing objects) with either: - // - // 1. An object of properties - // 2. A key and value - // - this.set( owner, key, value ); - - // Since the "set" path can have two possible entry points - // return the expected data based on which path was taken[*] - return value !== undefined ? value : key; - }, - remove: function( owner, key ) { - var i, - cache = owner[ this.expando ]; - - if ( cache === undefined ) { - return; - } - - if ( key !== undefined ) { - - // Support array or space separated string of keys - if ( Array.isArray( key ) ) { - - // If key is an array of keys... - // We always set camelCase keys, so remove that. - key = key.map( jQuery.camelCase ); - } else { - key = jQuery.camelCase( key ); - - // If a key with the spaces exists, use it. - // Otherwise, create an array by matching non-whitespace - key = key in cache ? - [ key ] : - ( key.match( rnothtmlwhite ) || [] ); - } - - i = key.length; - - while ( i-- ) { - delete cache[ key[ i ] ]; - } - } - - // Remove the expando if there's no more data - if ( key === undefined || jQuery.isEmptyObject( cache ) ) { - - // Support: Chrome <=35 - 45 - // Webkit & Blink performance suffers when deleting properties - // from DOM nodes, so set to undefined instead - // https://bugs.chromium.org/p/chromium/issues/detail?id=378607 (bug restricted) - if ( owner.nodeType ) { - owner[ this.expando ] = undefined; - } else { - delete owner[ this.expando ]; - } - } - }, - hasData: function( owner ) { - var cache = owner[ this.expando ]; - return cache !== undefined && !jQuery.isEmptyObject( cache ); - } -}; -var dataPriv = new Data(); - -var dataUser = new Data(); - - - -// Implementation Summary -// -// 1. Enforce API surface and semantic compatibility with 1.9.x branch -// 2. Improve the module's maintainability by reducing the storage -// paths to a single mechanism. -// 3. Use the same single mechanism to support "private" and "user" data. -// 4. _Never_ expose "private" data to user code (TODO: Drop _data, _removeData) -// 5. Avoid exposing implementation details on user objects (eg. expando properties) -// 6. Provide a clear path for implementation upgrade to WeakMap in 2014 - -var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/, - rmultiDash = /[A-Z]/g; - -function getData( data ) { - if ( data === "true" ) { - return true; - } - - if ( data === "false" ) { - return false; - } - - if ( data === "null" ) { - return null; - } - - // Only convert to a number if it doesn't change the string - if ( data === +data + "" ) { - return +data; - } - - if ( rbrace.test( data ) ) { - return JSON.parse( data ); - } - - return data; -} - -function dataAttr( elem, key, data ) { - var name; - - // If nothing was found internally, try to fetch any - // data from the HTML5 data-* attribute - if ( data === undefined && elem.nodeType === 1 ) { - name = "data-" + key.replace( rmultiDash, "-$&" ).toLowerCase(); - data = elem.getAttribute( name ); - - if ( typeof data === "string" ) { - try { - data = getData( data ); - } catch ( e ) {} - - // Make sure we set the data so it isn't changed later - dataUser.set( elem, key, data ); - } else { - data = undefined; - } - } - return data; -} - -jQuery.extend( { - hasData: function( elem ) { - return dataUser.hasData( elem ) || dataPriv.hasData( elem ); - }, - - data: function( elem, name, data ) { - return dataUser.access( elem, name, data ); - }, - - removeData: function( elem, name ) { - dataUser.remove( elem, name ); - }, - - // TODO: Now that all calls to _data and _removeData have been replaced - // with direct calls to dataPriv methods, these can be deprecated. - _data: function( elem, name, data ) { - return dataPriv.access( elem, name, data ); - }, - - _removeData: function( elem, name ) { - dataPriv.remove( elem, name ); - } -} ); - -jQuery.fn.extend( { - data: function( key, value ) { - var i, name, data, - elem = this[ 0 ], - attrs = elem && elem.attributes; - - // Gets all values - if ( key === undefined ) { - if ( this.length ) { - data = dataUser.get( elem ); - - if ( elem.nodeType === 1 && !dataPriv.get( elem, "hasDataAttrs" ) ) { - i = attrs.length; - while ( i-- ) { - - // Support: IE 11 only - // The attrs elements can be null (#14894) - if ( attrs[ i ] ) { - name = attrs[ i ].name; - if ( name.indexOf( "data-" ) === 0 ) { - name = jQuery.camelCase( name.slice( 5 ) ); - dataAttr( elem, name, data[ name ] ); - } - } - } - dataPriv.set( elem, "hasDataAttrs", true ); - } - } - - return data; - } - - // Sets multiple values - if ( typeof key === "object" ) { - return this.each( function() { - dataUser.set( this, key ); - } ); - } - - return access( this, function( value ) { - var data; - - // The calling jQuery object (element matches) is not empty - // (and therefore has an element appears at this[ 0 ]) and the - // `value` parameter was not undefined. An empty jQuery object - // will result in `undefined` for elem = this[ 0 ] which will - // throw an exception if an attempt to read a data cache is made. - if ( elem && value === undefined ) { - - // Attempt to get data from the cache - // The key will always be camelCased in Data - data = dataUser.get( elem, key ); - if ( data !== undefined ) { - return data; - } - - // Attempt to "discover" the data in - // HTML5 custom data-* attrs - data = dataAttr( elem, key ); - if ( data !== undefined ) { - return data; - } - - // We tried really hard, but the data doesn't exist. - return; - } - - // Set the data... - this.each( function() { - - // We always store the camelCased key - dataUser.set( this, key, value ); - } ); - }, null, value, arguments.length > 1, null, true ); - }, - - removeData: function( key ) { - return this.each( function() { - dataUser.remove( this, key ); - } ); - } -} ); - - -jQuery.extend( { - queue: function( elem, type, data ) { - var queue; - - if ( elem ) { - type = ( type || "fx" ) + "queue"; - queue = dataPriv.get( elem, type ); - - // Speed up dequeue by getting out quickly if this is just a lookup - if ( data ) { - if ( !queue || Array.isArray( data ) ) { - queue = dataPriv.access( elem, type, jQuery.makeArray( data ) ); - } else { - queue.push( data ); - } - } - return queue || []; - } - }, - - dequeue: function( elem, type ) { - type = type || "fx"; - - var queue = jQuery.queue( elem, type ), - startLength = queue.length, - fn = queue.shift(), - hooks = jQuery._queueHooks( elem, type ), - next = function() { - jQuery.dequeue( elem, type ); - }; - - // If the fx queue is dequeued, always remove the progress sentinel - if ( fn === "inprogress" ) { - fn = queue.shift(); - startLength--; - } - - if ( fn ) { - - // Add a progress sentinel to prevent the fx queue from being - // automatically dequeued - if ( type === "fx" ) { - queue.unshift( "inprogress" ); - } - - // Clear up the last queue stop function - delete hooks.stop; - fn.call( elem, next, hooks ); - } - - if ( !startLength && hooks ) { - hooks.empty.fire(); - } - }, - - // Not public - generate a queueHooks object, or return the current one - _queueHooks: function( elem, type ) { - var key = type + "queueHooks"; - return dataPriv.get( elem, key ) || dataPriv.access( elem, key, { - empty: jQuery.Callbacks( "once memory" ).add( function() { - dataPriv.remove( elem, [ type + "queue", key ] ); - } ) - } ); - } -} ); - -jQuery.fn.extend( { - queue: function( type, data ) { - var setter = 2; - - if ( typeof type !== "string" ) { - data = type; - type = "fx"; - setter--; - } - - if ( arguments.length < setter ) { - return jQuery.queue( this[ 0 ], type ); - } - - return data === undefined ? - this : - this.each( function() { - var queue = jQuery.queue( this, type, data ); - - // Ensure a hooks for this queue - jQuery._queueHooks( this, type ); - - if ( type === "fx" && queue[ 0 ] !== "inprogress" ) { - jQuery.dequeue( this, type ); - } - } ); - }, - dequeue: function( type ) { - return this.each( function() { - jQuery.dequeue( this, type ); - } ); - }, - clearQueue: function( type ) { - return this.queue( type || "fx", [] ); - }, - - // Get a promise resolved when queues of a certain type - // are emptied (fx is the type by default) - promise: function( type, obj ) { - var tmp, - count = 1, - defer = jQuery.Deferred(), - elements = this, - i = this.length, - resolve = function() { - if ( !( --count ) ) { - defer.resolveWith( elements, [ elements ] ); - } - }; - - if ( typeof type !== "string" ) { - obj = type; - type = undefined; - } - type = type || "fx"; - - while ( i-- ) { - tmp = dataPriv.get( elements[ i ], type + "queueHooks" ); - if ( tmp && tmp.empty ) { - count++; - tmp.empty.add( resolve ); - } - } - resolve(); - return defer.promise( obj ); - } -} ); -var pnum = ( /[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/ ).source; - -var rcssNum = new RegExp( "^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i" ); - - -var cssExpand = [ "Top", "Right", "Bottom", "Left" ]; - -var isHiddenWithinTree = function( elem, el ) { - - // isHiddenWithinTree might be called from jQuery#filter function; - // in that case, element will be second argument - elem = el || elem; - - // Inline style trumps all - return elem.style.display === "none" || - elem.style.display === "" && - - // Otherwise, check computed style - // Support: Firefox <=43 - 45 - // Disconnected elements can have computed display: none, so first confirm that elem is - // in the document. - jQuery.contains( elem.ownerDocument, elem ) && - - jQuery.css( elem, "display" ) === "none"; - }; - -var swap = function( elem, options, callback, args ) { - var ret, name, - old = {}; - - // Remember the old values, and insert the new ones - for ( name in options ) { - old[ name ] = elem.style[ name ]; - elem.style[ name ] = options[ name ]; - } - - ret = callback.apply( elem, args || [] ); - - // Revert the old values - for ( name in options ) { - elem.style[ name ] = old[ name ]; - } - - return ret; -}; - - - - -function adjustCSS( elem, prop, valueParts, tween ) { - var adjusted, - scale = 1, - maxIterations = 20, - currentValue = tween ? - function() { - return tween.cur(); - } : - function() { - return jQuery.css( elem, prop, "" ); - }, - initial = currentValue(), - unit = valueParts && valueParts[ 3 ] || ( jQuery.cssNumber[ prop ] ? "" : "px" ), - - // Starting value computation is required for potential unit mismatches - initialInUnit = ( jQuery.cssNumber[ prop ] || unit !== "px" && +initial ) && - rcssNum.exec( jQuery.css( elem, prop ) ); - - if ( initialInUnit && initialInUnit[ 3 ] !== unit ) { - - // Trust units reported by jQuery.css - unit = unit || initialInUnit[ 3 ]; - - // Make sure we update the tween properties later on - valueParts = valueParts || []; - - // Iteratively approximate from a nonzero starting point - initialInUnit = +initial || 1; - - do { - - // If previous iteration zeroed out, double until we get *something*. - // Use string for doubling so we don't accidentally see scale as unchanged below - scale = scale || ".5"; - - // Adjust and apply - initialInUnit = initialInUnit / scale; - jQuery.style( elem, prop, initialInUnit + unit ); - - // Update scale, tolerating zero or NaN from tween.cur() - // Break the loop if scale is unchanged or perfect, or if we've just had enough. - } while ( - scale !== ( scale = currentValue() / initial ) && scale !== 1 && --maxIterations - ); - } - - if ( valueParts ) { - initialInUnit = +initialInUnit || +initial || 0; - - // Apply relative offset (+=/-=) if specified - adjusted = valueParts[ 1 ] ? - initialInUnit + ( valueParts[ 1 ] + 1 ) * valueParts[ 2 ] : - +valueParts[ 2 ]; - if ( tween ) { - tween.unit = unit; - tween.start = initialInUnit; - tween.end = adjusted; - } - } - return adjusted; -} - - -var defaultDisplayMap = {}; - -function getDefaultDisplay( elem ) { - var temp, - doc = elem.ownerDocument, - nodeName = elem.nodeName, - display = defaultDisplayMap[ nodeName ]; - - if ( display ) { - return display; - } - - temp = doc.body.appendChild( doc.createElement( nodeName ) ); - display = jQuery.css( temp, "display" ); - - temp.parentNode.removeChild( temp ); - - if ( display === "none" ) { - display = "block"; - } - defaultDisplayMap[ nodeName ] = display; - - return display; -} - -function showHide( elements, show ) { - var display, elem, - values = [], - index = 0, - length = elements.length; - - // Determine new display value for elements that need to change - for ( ; index < length; index++ ) { - elem = elements[ index ]; - if ( !elem.style ) { - continue; - } - - display = elem.style.display; - if ( show ) { - - // Since we force visibility upon cascade-hidden elements, an immediate (and slow) - // check is required in this first loop unless we have a nonempty display value (either - // inline or about-to-be-restored) - if ( display === "none" ) { - values[ index ] = dataPriv.get( elem, "display" ) || null; - if ( !values[ index ] ) { - elem.style.display = ""; - } - } - if ( elem.style.display === "" && isHiddenWithinTree( elem ) ) { - values[ index ] = getDefaultDisplay( elem ); - } - } else { - if ( display !== "none" ) { - values[ index ] = "none"; - - // Remember what we're overwriting - dataPriv.set( elem, "display", display ); - } - } - } - - // Set the display of the elements in a second loop to avoid constant reflow - for ( index = 0; index < length; index++ ) { - if ( values[ index ] != null ) { - elements[ index ].style.display = values[ index ]; - } - } - - return elements; -} - -jQuery.fn.extend( { - show: function() { - return showHide( this, true ); - }, - hide: function() { - return showHide( this ); - }, - toggle: function( state ) { - if ( typeof state === "boolean" ) { - return state ? this.show() : this.hide(); - } - - return this.each( function() { - if ( isHiddenWithinTree( this ) ) { - jQuery( this ).show(); - } else { - jQuery( this ).hide(); - } - } ); - } -} ); -var rcheckableType = ( /^(?:checkbox|radio)$/i ); - -var rtagName = ( /<([a-z][^\/\0>\x20\t\r\n\f]+)/i ); - -var rscriptType = ( /^$|\/(?:java|ecma)script/i ); - - - -// We have to close these tags to support XHTML (#13200) -var wrapMap = { - - // Support: IE <=9 only - option: [ 1, "" ], - - // XHTML parsers do not magically insert elements in the - // same way that tag soup parsers do. So we cannot shorten - // this by omitting or other required elements. - thead: [ 1, "", "
" ], - col: [ 2, "", "
" ], - tr: [ 2, "", "
" ], - td: [ 3, "", "
" ], - - _default: [ 0, "", "" ] -}; - -// Support: IE <=9 only -wrapMap.optgroup = wrapMap.option; - -wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead; -wrapMap.th = wrapMap.td; - - -function getAll( context, tag ) { - - // Support: IE <=9 - 11 only - // Use typeof to avoid zero-argument method invocation on host objects (#15151) - var ret; - - if ( typeof context.getElementsByTagName !== "undefined" ) { - ret = context.getElementsByTagName( tag || "*" ); - - } else if ( typeof context.querySelectorAll !== "undefined" ) { - ret = context.querySelectorAll( tag || "*" ); - - } else { - ret = []; - } - - if ( tag === undefined || tag && nodeName( context, tag ) ) { - return jQuery.merge( [ context ], ret ); - } - - return ret; -} - - -// Mark scripts as having already been evaluated -function setGlobalEval( elems, refElements ) { - var i = 0, - l = elems.length; - - for ( ; i < l; i++ ) { - dataPriv.set( - elems[ i ], - "globalEval", - !refElements || dataPriv.get( refElements[ i ], "globalEval" ) - ); - } -} - - -var rhtml = /<|&#?\w+;/; - -function buildFragment( elems, context, scripts, selection, ignored ) { - var elem, tmp, tag, wrap, contains, j, - fragment = context.createDocumentFragment(), - nodes = [], - i = 0, - l = elems.length; - - for ( ; i < l; i++ ) { - elem = elems[ i ]; - - if ( elem || elem === 0 ) { - - // Add nodes directly - if ( jQuery.type( elem ) === "object" ) { - - // Support: Android <=4.0 only, PhantomJS 1 only - // push.apply(_, arraylike) throws on ancient WebKit - jQuery.merge( nodes, elem.nodeType ? [ elem ] : elem ); - - // Convert non-html into a text node - } else if ( !rhtml.test( elem ) ) { - nodes.push( context.createTextNode( elem ) ); - - // Convert html into DOM nodes - } else { - tmp = tmp || fragment.appendChild( context.createElement( "div" ) ); - - // Deserialize a standard representation - tag = ( rtagName.exec( elem ) || [ "", "" ] )[ 1 ].toLowerCase(); - wrap = wrapMap[ tag ] || wrapMap._default; - tmp.innerHTML = wrap[ 1 ] + jQuery.htmlPrefilter( elem ) + wrap[ 2 ]; - - // Descend through wrappers to the right content - j = wrap[ 0 ]; - while ( j-- ) { - tmp = tmp.lastChild; - } - - // Support: Android <=4.0 only, PhantomJS 1 only - // push.apply(_, arraylike) throws on ancient WebKit - jQuery.merge( nodes, tmp.childNodes ); - - // Remember the top-level container - tmp = fragment.firstChild; - - // Ensure the created nodes are orphaned (#12392) - tmp.textContent = ""; - } - } - } - - // Remove wrapper from fragment - fragment.textContent = ""; - - i = 0; - while ( ( elem = nodes[ i++ ] ) ) { - - // Skip elements already in the context collection (trac-4087) - if ( selection && jQuery.inArray( elem, selection ) > -1 ) { - if ( ignored ) { - ignored.push( elem ); - } - continue; - } - - contains = jQuery.contains( elem.ownerDocument, elem ); - - // Append to fragment - tmp = getAll( fragment.appendChild( elem ), "script" ); - - // Preserve script evaluation history - if ( contains ) { - setGlobalEval( tmp ); - } - - // Capture executables - if ( scripts ) { - j = 0; - while ( ( elem = tmp[ j++ ] ) ) { - if ( rscriptType.test( elem.type || "" ) ) { - scripts.push( elem ); - } - } - } - } - - return fragment; -} - - -( function() { - var fragment = document.createDocumentFragment(), - div = fragment.appendChild( document.createElement( "div" ) ), - input = document.createElement( "input" ); - - // Support: Android 4.0 - 4.3 only - // Check state lost if the name is set (#11217) - // Support: Windows Web Apps (WWA) - // `name` and `type` must use .setAttribute for WWA (#14901) - input.setAttribute( "type", "radio" ); - input.setAttribute( "checked", "checked" ); - input.setAttribute( "name", "t" ); - - div.appendChild( input ); - - // Support: Android <=4.1 only - // Older WebKit doesn't clone checked state correctly in fragments - support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked; - - // Support: IE <=11 only - // Make sure textarea (and checkbox) defaultValue is properly cloned - div.innerHTML = ""; - support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue; -} )(); -var documentElement = document.documentElement; - - - -var - rkeyEvent = /^key/, - rmouseEvent = /^(?:mouse|pointer|contextmenu|drag|drop)|click/, - rtypenamespace = /^([^.]*)(?:\.(.+)|)/; - -function returnTrue() { - return true; -} - -function returnFalse() { - return false; -} - -// Support: IE <=9 only -// See #13393 for more info -function safeActiveElement() { - try { - return document.activeElement; - } catch ( err ) { } -} - -function on( elem, types, selector, data, fn, one ) { - var origFn, type; - - // Types can be a map of types/handlers - if ( typeof types === "object" ) { - - // ( types-Object, selector, data ) - if ( typeof selector !== "string" ) { - - // ( types-Object, data ) - data = data || selector; - selector = undefined; - } - for ( type in types ) { - on( elem, type, selector, data, types[ type ], one ); - } - return elem; - } - - if ( data == null && fn == null ) { - - // ( types, fn ) - fn = selector; - data = selector = undefined; - } else if ( fn == null ) { - if ( typeof selector === "string" ) { - - // ( types, selector, fn ) - fn = data; - data = undefined; - } else { - - // ( types, data, fn ) - fn = data; - data = selector; - selector = undefined; - } - } - if ( fn === false ) { - fn = returnFalse; - } else if ( !fn ) { - return elem; - } - - if ( one === 1 ) { - origFn = fn; - fn = function( event ) { - - // Can use an empty set, since event contains the info - jQuery().off( event ); - return origFn.apply( this, arguments ); - }; - - // Use same guid so caller can remove using origFn - fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ ); - } - return elem.each( function() { - jQuery.event.add( this, types, fn, data, selector ); - } ); -} - -/* - * Helper functions for managing events -- not part of the public interface. - * Props to Dean Edwards' addEvent library for many of the ideas. - */ -jQuery.event = { - - global: {}, - - add: function( elem, types, handler, data, selector ) { - - var handleObjIn, eventHandle, tmp, - events, t, handleObj, - special, handlers, type, namespaces, origType, - elemData = dataPriv.get( elem ); - - // Don't attach events to noData or text/comment nodes (but allow plain objects) - if ( !elemData ) { - return; - } - - // Caller can pass in an object of custom data in lieu of the handler - if ( handler.handler ) { - handleObjIn = handler; - handler = handleObjIn.handler; - selector = handleObjIn.selector; - } - - // Ensure that invalid selectors throw exceptions at attach time - // Evaluate against documentElement in case elem is a non-element node (e.g., document) - if ( selector ) { - jQuery.find.matchesSelector( documentElement, selector ); - } - - // Make sure that the handler has a unique ID, used to find/remove it later - if ( !handler.guid ) { - handler.guid = jQuery.guid++; - } - - // Init the element's event structure and main handler, if this is the first - if ( !( events = elemData.events ) ) { - events = elemData.events = {}; - } - if ( !( eventHandle = elemData.handle ) ) { - eventHandle = elemData.handle = function( e ) { - - // Discard the second event of a jQuery.event.trigger() and - // when an event is called after a page has unloaded - return typeof jQuery !== "undefined" && jQuery.event.triggered !== e.type ? - jQuery.event.dispatch.apply( elem, arguments ) : undefined; - }; - } - - // Handle multiple events separated by a space - types = ( types || "" ).match( rnothtmlwhite ) || [ "" ]; - t = types.length; - while ( t-- ) { - tmp = rtypenamespace.exec( types[ t ] ) || []; - type = origType = tmp[ 1 ]; - namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort(); - - // There *must* be a type, no attaching namespace-only handlers - if ( !type ) { - continue; - } - - // If event changes its type, use the special event handlers for the changed type - special = jQuery.event.special[ type ] || {}; - - // If selector defined, determine special event api type, otherwise given type - type = ( selector ? special.delegateType : special.bindType ) || type; - - // Update special based on newly reset type - special = jQuery.event.special[ type ] || {}; - - // handleObj is passed to all event handlers - handleObj = jQuery.extend( { - type: type, - origType: origType, - data: data, - handler: handler, - guid: handler.guid, - selector: selector, - needsContext: selector && jQuery.expr.match.needsContext.test( selector ), - namespace: namespaces.join( "." ) - }, handleObjIn ); - - // Init the event handler queue if we're the first - if ( !( handlers = events[ type ] ) ) { - handlers = events[ type ] = []; - handlers.delegateCount = 0; - - // Only use addEventListener if the special events handler returns false - if ( !special.setup || - special.setup.call( elem, data, namespaces, eventHandle ) === false ) { - - if ( elem.addEventListener ) { - elem.addEventListener( type, eventHandle ); - } - } - } - - if ( special.add ) { - special.add.call( elem, handleObj ); - - if ( !handleObj.handler.guid ) { - handleObj.handler.guid = handler.guid; - } - } - - // Add to the element's handler list, delegates in front - if ( selector ) { - handlers.splice( handlers.delegateCount++, 0, handleObj ); - } else { - handlers.push( handleObj ); - } - - // Keep track of which events have ever been used, for event optimization - jQuery.event.global[ type ] = true; - } - - }, - - // Detach an event or set of events from an element - remove: function( elem, types, handler, selector, mappedTypes ) { - - var j, origCount, tmp, - events, t, handleObj, - special, handlers, type, namespaces, origType, - elemData = dataPriv.hasData( elem ) && dataPriv.get( elem ); - - if ( !elemData || !( events = elemData.events ) ) { - return; - } - - // Once for each type.namespace in types; type may be omitted - types = ( types || "" ).match( rnothtmlwhite ) || [ "" ]; - t = types.length; - while ( t-- ) { - tmp = rtypenamespace.exec( types[ t ] ) || []; - type = origType = tmp[ 1 ]; - namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort(); - - // Unbind all events (on this namespace, if provided) for the element - if ( !type ) { - for ( type in events ) { - jQuery.event.remove( elem, type + types[ t ], handler, selector, true ); - } - continue; - } - - special = jQuery.event.special[ type ] || {}; - type = ( selector ? special.delegateType : special.bindType ) || type; - handlers = events[ type ] || []; - tmp = tmp[ 2 ] && - new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ); - - // Remove matching events - origCount = j = handlers.length; - while ( j-- ) { - handleObj = handlers[ j ]; - - if ( ( mappedTypes || origType === handleObj.origType ) && - ( !handler || handler.guid === handleObj.guid ) && - ( !tmp || tmp.test( handleObj.namespace ) ) && - ( !selector || selector === handleObj.selector || - selector === "**" && handleObj.selector ) ) { - handlers.splice( j, 1 ); - - if ( handleObj.selector ) { - handlers.delegateCount--; - } - if ( special.remove ) { - special.remove.call( elem, handleObj ); - } - } - } - - // Remove generic event handler if we removed something and no more handlers exist - // (avoids potential for endless recursion during removal of special event handlers) - if ( origCount && !handlers.length ) { - if ( !special.teardown || - special.teardown.call( elem, namespaces, elemData.handle ) === false ) { - - jQuery.removeEvent( elem, type, elemData.handle ); - } - - delete events[ type ]; - } - } - - // Remove data and the expando if it's no longer used - if ( jQuery.isEmptyObject( events ) ) { - dataPriv.remove( elem, "handle events" ); - } - }, - - dispatch: function( nativeEvent ) { - - // Make a writable jQuery.Event from the native event object - var event = jQuery.event.fix( nativeEvent ); - - var i, j, ret, matched, handleObj, handlerQueue, - args = new Array( arguments.length ), - handlers = ( dataPriv.get( this, "events" ) || {} )[ event.type ] || [], - special = jQuery.event.special[ event.type ] || {}; - - // Use the fix-ed jQuery.Event rather than the (read-only) native event - args[ 0 ] = event; - - for ( i = 1; i < arguments.length; i++ ) { - args[ i ] = arguments[ i ]; - } - - event.delegateTarget = this; - - // Call the preDispatch hook for the mapped type, and let it bail if desired - if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) { - return; - } - - // Determine handlers - handlerQueue = jQuery.event.handlers.call( this, event, handlers ); - - // Run delegates first; they may want to stop propagation beneath us - i = 0; - while ( ( matched = handlerQueue[ i++ ] ) && !event.isPropagationStopped() ) { - event.currentTarget = matched.elem; - - j = 0; - while ( ( handleObj = matched.handlers[ j++ ] ) && - !event.isImmediatePropagationStopped() ) { - - // Triggered event must either 1) have no namespace, or 2) have namespace(s) - // a subset or equal to those in the bound event (both can have no namespace). - if ( !event.rnamespace || event.rnamespace.test( handleObj.namespace ) ) { - - event.handleObj = handleObj; - event.data = handleObj.data; - - ret = ( ( jQuery.event.special[ handleObj.origType ] || {} ).handle || - handleObj.handler ).apply( matched.elem, args ); - - if ( ret !== undefined ) { - if ( ( event.result = ret ) === false ) { - event.preventDefault(); - event.stopPropagation(); - } - } - } - } - } - - // Call the postDispatch hook for the mapped type - if ( special.postDispatch ) { - special.postDispatch.call( this, event ); - } - - return event.result; - }, - - handlers: function( event, handlers ) { - var i, handleObj, sel, matchedHandlers, matchedSelectors, - handlerQueue = [], - delegateCount = handlers.delegateCount, - cur = event.target; - - // Find delegate handlers - if ( delegateCount && - - // Support: IE <=9 - // Black-hole SVG instance trees (trac-13180) - cur.nodeType && - - // Support: Firefox <=42 - // Suppress spec-violating clicks indicating a non-primary pointer button (trac-3861) - // https://www.w3.org/TR/DOM-Level-3-Events/#event-type-click - // Support: IE 11 only - // ...but not arrow key "clicks" of radio inputs, which can have `button` -1 (gh-2343) - !( event.type === "click" && event.button >= 1 ) ) { - - for ( ; cur !== this; cur = cur.parentNode || this ) { - - // Don't check non-elements (#13208) - // Don't process clicks on disabled elements (#6911, #8165, #11382, #11764) - if ( cur.nodeType === 1 && !( event.type === "click" && cur.disabled === true ) ) { - matchedHandlers = []; - matchedSelectors = {}; - for ( i = 0; i < delegateCount; i++ ) { - handleObj = handlers[ i ]; - - // Don't conflict with Object.prototype properties (#13203) - sel = handleObj.selector + " "; - - if ( matchedSelectors[ sel ] === undefined ) { - matchedSelectors[ sel ] = handleObj.needsContext ? - jQuery( sel, this ).index( cur ) > -1 : - jQuery.find( sel, this, null, [ cur ] ).length; - } - if ( matchedSelectors[ sel ] ) { - matchedHandlers.push( handleObj ); - } - } - if ( matchedHandlers.length ) { - handlerQueue.push( { elem: cur, handlers: matchedHandlers } ); - } - } - } - } - - // Add the remaining (directly-bound) handlers - cur = this; - if ( delegateCount < handlers.length ) { - handlerQueue.push( { elem: cur, handlers: handlers.slice( delegateCount ) } ); - } - - return handlerQueue; - }, - - addProp: function( name, hook ) { - Object.defineProperty( jQuery.Event.prototype, name, { - enumerable: true, - configurable: true, - - get: jQuery.isFunction( hook ) ? - function() { - if ( this.originalEvent ) { - return hook( this.originalEvent ); - } - } : - function() { - if ( this.originalEvent ) { - return this.originalEvent[ name ]; - } - }, - - set: function( value ) { - Object.defineProperty( this, name, { - enumerable: true, - configurable: true, - writable: true, - value: value - } ); - } - } ); - }, - - fix: function( originalEvent ) { - return originalEvent[ jQuery.expando ] ? - originalEvent : - new jQuery.Event( originalEvent ); - }, - - special: { - load: { - - // Prevent triggered image.load events from bubbling to window.load - noBubble: true - }, - focus: { - - // Fire native event if possible so blur/focus sequence is correct - trigger: function() { - if ( this !== safeActiveElement() && this.focus ) { - this.focus(); - return false; - } - }, - delegateType: "focusin" - }, - blur: { - trigger: function() { - if ( this === safeActiveElement() && this.blur ) { - this.blur(); - return false; - } - }, - delegateType: "focusout" - }, - click: { - - // For checkbox, fire native event so checked state will be right - trigger: function() { - if ( this.type === "checkbox" && this.click && nodeName( this, "input" ) ) { - this.click(); - return false; - } - }, - - // For cross-browser consistency, don't fire native .click() on links - _default: function( event ) { - return nodeName( event.target, "a" ); - } - }, - - beforeunload: { - postDispatch: function( event ) { - - // Support: Firefox 20+ - // Firefox doesn't alert if the returnValue field is not set. - if ( event.result !== undefined && event.originalEvent ) { - event.originalEvent.returnValue = event.result; - } - } - } - } -}; - -jQuery.removeEvent = function( elem, type, handle ) { - - // This "if" is needed for plain objects - if ( elem.removeEventListener ) { - elem.removeEventListener( type, handle ); - } -}; - -jQuery.Event = function( src, props ) { - - // Allow instantiation without the 'new' keyword - if ( !( this instanceof jQuery.Event ) ) { - return new jQuery.Event( src, props ); - } - - // Event object - if ( src && src.type ) { - this.originalEvent = src; - this.type = src.type; - - // Events bubbling up the document may have been marked as prevented - // by a handler lower down the tree; reflect the correct value. - this.isDefaultPrevented = src.defaultPrevented || - src.defaultPrevented === undefined && - - // Support: Android <=2.3 only - src.returnValue === false ? - returnTrue : - returnFalse; - - // Create target properties - // Support: Safari <=6 - 7 only - // Target should not be a text node (#504, #13143) - this.target = ( src.target && src.target.nodeType === 3 ) ? - src.target.parentNode : - src.target; - - this.currentTarget = src.currentTarget; - this.relatedTarget = src.relatedTarget; - - // Event type - } else { - this.type = src; - } - - // Put explicitly provided properties onto the event object - if ( props ) { - jQuery.extend( this, props ); - } - - // Create a timestamp if incoming event doesn't have one - this.timeStamp = src && src.timeStamp || jQuery.now(); - - // Mark it as fixed - this[ jQuery.expando ] = true; -}; - -// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding -// https://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html -jQuery.Event.prototype = { - constructor: jQuery.Event, - isDefaultPrevented: returnFalse, - isPropagationStopped: returnFalse, - isImmediatePropagationStopped: returnFalse, - isSimulated: false, - - preventDefault: function() { - var e = this.originalEvent; - - this.isDefaultPrevented = returnTrue; - - if ( e && !this.isSimulated ) { - e.preventDefault(); - } - }, - stopPropagation: function() { - var e = this.originalEvent; - - this.isPropagationStopped = returnTrue; - - if ( e && !this.isSimulated ) { - e.stopPropagation(); - } - }, - stopImmediatePropagation: function() { - var e = this.originalEvent; - - this.isImmediatePropagationStopped = returnTrue; - - if ( e && !this.isSimulated ) { - e.stopImmediatePropagation(); - } - - this.stopPropagation(); - } -}; - -// Includes all common event props including KeyEvent and MouseEvent specific props -jQuery.each( { - altKey: true, - bubbles: true, - cancelable: true, - changedTouches: true, - ctrlKey: true, - detail: true, - eventPhase: true, - metaKey: true, - pageX: true, - pageY: true, - shiftKey: true, - view: true, - "char": true, - charCode: true, - key: true, - keyCode: true, - button: true, - buttons: true, - clientX: true, - clientY: true, - offsetX: true, - offsetY: true, - pointerId: true, - pointerType: true, - screenX: true, - screenY: true, - targetTouches: true, - toElement: true, - touches: true, - - which: function( event ) { - var button = event.button; - - // Add which for key events - if ( event.which == null && rkeyEvent.test( event.type ) ) { - return event.charCode != null ? event.charCode : event.keyCode; - } - - // Add which for click: 1 === left; 2 === middle; 3 === right - if ( !event.which && button !== undefined && rmouseEvent.test( event.type ) ) { - if ( button & 1 ) { - return 1; - } - - if ( button & 2 ) { - return 3; - } - - if ( button & 4 ) { - return 2; - } - - return 0; - } - - return event.which; - } -}, jQuery.event.addProp ); - -// Create mouseenter/leave events using mouseover/out and event-time checks -// so that event delegation works in jQuery. -// Do the same for pointerenter/pointerleave and pointerover/pointerout -// -// Support: Safari 7 only -// Safari sends mouseenter too often; see: -// https://bugs.chromium.org/p/chromium/issues/detail?id=470258 -// for the description of the bug (it existed in older Chrome versions as well). -jQuery.each( { - mouseenter: "mouseover", - mouseleave: "mouseout", - pointerenter: "pointerover", - pointerleave: "pointerout" -}, function( orig, fix ) { - jQuery.event.special[ orig ] = { - delegateType: fix, - bindType: fix, - - handle: function( event ) { - var ret, - target = this, - related = event.relatedTarget, - handleObj = event.handleObj; - - // For mouseenter/leave call the handler if related is outside the target. - // NB: No relatedTarget if the mouse left/entered the browser window - if ( !related || ( related !== target && !jQuery.contains( target, related ) ) ) { - event.type = handleObj.origType; - ret = handleObj.handler.apply( this, arguments ); - event.type = fix; - } - return ret; - } - }; -} ); - -jQuery.fn.extend( { - - on: function( types, selector, data, fn ) { - return on( this, types, selector, data, fn ); - }, - one: function( types, selector, data, fn ) { - return on( this, types, selector, data, fn, 1 ); - }, - off: function( types, selector, fn ) { - var handleObj, type; - if ( types && types.preventDefault && types.handleObj ) { - - // ( event ) dispatched jQuery.Event - handleObj = types.handleObj; - jQuery( types.delegateTarget ).off( - handleObj.namespace ? - handleObj.origType + "." + handleObj.namespace : - handleObj.origType, - handleObj.selector, - handleObj.handler - ); - return this; - } - if ( typeof types === "object" ) { - - // ( types-object [, selector] ) - for ( type in types ) { - this.off( type, selector, types[ type ] ); - } - return this; - } - if ( selector === false || typeof selector === "function" ) { - - // ( types [, fn] ) - fn = selector; - selector = undefined; - } - if ( fn === false ) { - fn = returnFalse; - } - return this.each( function() { - jQuery.event.remove( this, types, fn, selector ); - } ); - } -} ); - - -var - - /* eslint-disable max-len */ - - // See https://github.com/eslint/eslint/issues/3229 - rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([a-z][^\/\0>\x20\t\r\n\f]*)[^>]*)\/>/gi, - - /* eslint-enable */ - - // Support: IE <=10 - 11, Edge 12 - 13 - // In IE/Edge using regex groups here causes severe slowdowns. - // See https://connect.microsoft.com/IE/feedback/details/1736512/ - rnoInnerhtml = /\s*$/g; - -// Prefer a tbody over its parent table for containing new rows -function manipulationTarget( elem, content ) { - if ( nodeName( elem, "table" ) && - nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ) { - - return jQuery( ">tbody", elem )[ 0 ] || elem; - } - - return elem; -} - -// Replace/restore the type attribute of script elements for safe DOM manipulation -function disableScript( elem ) { - elem.type = ( elem.getAttribute( "type" ) !== null ) + "/" + elem.type; - return elem; -} -function restoreScript( elem ) { - var match = rscriptTypeMasked.exec( elem.type ); - - if ( match ) { - elem.type = match[ 1 ]; - } else { - elem.removeAttribute( "type" ); - } - - return elem; -} - -function cloneCopyEvent( src, dest ) { - var i, l, type, pdataOld, pdataCur, udataOld, udataCur, events; - - if ( dest.nodeType !== 1 ) { - return; - } - - // 1. Copy private data: events, handlers, etc. - if ( dataPriv.hasData( src ) ) { - pdataOld = dataPriv.access( src ); - pdataCur = dataPriv.set( dest, pdataOld ); - events = pdataOld.events; - - if ( events ) { - delete pdataCur.handle; - pdataCur.events = {}; - - for ( type in events ) { - for ( i = 0, l = events[ type ].length; i < l; i++ ) { - jQuery.event.add( dest, type, events[ type ][ i ] ); - } - } - } - } - - // 2. Copy user data - if ( dataUser.hasData( src ) ) { - udataOld = dataUser.access( src ); - udataCur = jQuery.extend( {}, udataOld ); - - dataUser.set( dest, udataCur ); - } -} - -// Fix IE bugs, see support tests -function fixInput( src, dest ) { - var nodeName = dest.nodeName.toLowerCase(); - - // Fails to persist the checked state of a cloned checkbox or radio button. - if ( nodeName === "input" && rcheckableType.test( src.type ) ) { - dest.checked = src.checked; - - // Fails to return the selected option to the default selected state when cloning options - } else if ( nodeName === "input" || nodeName === "textarea" ) { - dest.defaultValue = src.defaultValue; - } -} - -function domManip( collection, args, callback, ignored ) { - - // Flatten any nested arrays - args = concat.apply( [], args ); - - var fragment, first, scripts, hasScripts, node, doc, - i = 0, - l = collection.length, - iNoClone = l - 1, - value = args[ 0 ], - isFunction = jQuery.isFunction( value ); - - // We can't cloneNode fragments that contain checked, in WebKit - if ( isFunction || - ( l > 1 && typeof value === "string" && - !support.checkClone && rchecked.test( value ) ) ) { - return collection.each( function( index ) { - var self = collection.eq( index ); - if ( isFunction ) { - args[ 0 ] = value.call( this, index, self.html() ); - } - domManip( self, args, callback, ignored ); - } ); - } - - if ( l ) { - fragment = buildFragment( args, collection[ 0 ].ownerDocument, false, collection, ignored ); - first = fragment.firstChild; - - if ( fragment.childNodes.length === 1 ) { - fragment = first; - } - - // Require either new content or an interest in ignored elements to invoke the callback - if ( first || ignored ) { - scripts = jQuery.map( getAll( fragment, "script" ), disableScript ); - hasScripts = scripts.length; - - // Use the original fragment for the last item - // instead of the first because it can end up - // being emptied incorrectly in certain situations (#8070). - for ( ; i < l; i++ ) { - node = fragment; - - if ( i !== iNoClone ) { - node = jQuery.clone( node, true, true ); - - // Keep references to cloned scripts for later restoration - if ( hasScripts ) { - - // Support: Android <=4.0 only, PhantomJS 1 only - // push.apply(_, arraylike) throws on ancient WebKit - jQuery.merge( scripts, getAll( node, "script" ) ); - } - } - - callback.call( collection[ i ], node, i ); - } - - if ( hasScripts ) { - doc = scripts[ scripts.length - 1 ].ownerDocument; - - // Reenable scripts - jQuery.map( scripts, restoreScript ); - - // Evaluate executable scripts on first document insertion - for ( i = 0; i < hasScripts; i++ ) { - node = scripts[ i ]; - if ( rscriptType.test( node.type || "" ) && - !dataPriv.access( node, "globalEval" ) && - jQuery.contains( doc, node ) ) { - - if ( node.src ) { - - // Optional AJAX dependency, but won't run scripts if not present - if ( jQuery._evalUrl ) { - jQuery._evalUrl( node.src ); - } - } else { - DOMEval( node.textContent.replace( rcleanScript, "" ), doc ); - } - } - } - } - } - } - - return collection; -} - -function remove( elem, selector, keepData ) { - var node, - nodes = selector ? jQuery.filter( selector, elem ) : elem, - i = 0; - - for ( ; ( node = nodes[ i ] ) != null; i++ ) { - if ( !keepData && node.nodeType === 1 ) { - jQuery.cleanData( getAll( node ) ); - } - - if ( node.parentNode ) { - if ( keepData && jQuery.contains( node.ownerDocument, node ) ) { - setGlobalEval( getAll( node, "script" ) ); - } - node.parentNode.removeChild( node ); - } - } - - return elem; -} - -jQuery.extend( { - htmlPrefilter: function( html ) { - return html.replace( rxhtmlTag, "<$1>" ); - }, - - clone: function( elem, dataAndEvents, deepDataAndEvents ) { - var i, l, srcElements, destElements, - clone = elem.cloneNode( true ), - inPage = jQuery.contains( elem.ownerDocument, elem ); - - // Fix IE cloning issues - if ( !support.noCloneChecked && ( elem.nodeType === 1 || elem.nodeType === 11 ) && - !jQuery.isXMLDoc( elem ) ) { - - // We eschew Sizzle here for performance reasons: https://jsperf.com/getall-vs-sizzle/2 - destElements = getAll( clone ); - srcElements = getAll( elem ); - - for ( i = 0, l = srcElements.length; i < l; i++ ) { - fixInput( srcElements[ i ], destElements[ i ] ); - } - } - - // Copy the events from the original to the clone - if ( dataAndEvents ) { - if ( deepDataAndEvents ) { - srcElements = srcElements || getAll( elem ); - destElements = destElements || getAll( clone ); - - for ( i = 0, l = srcElements.length; i < l; i++ ) { - cloneCopyEvent( srcElements[ i ], destElements[ i ] ); - } - } else { - cloneCopyEvent( elem, clone ); - } - } - - // Preserve script evaluation history - destElements = getAll( clone, "script" ); - if ( destElements.length > 0 ) { - setGlobalEval( destElements, !inPage && getAll( elem, "script" ) ); - } - - // Return the cloned set - return clone; - }, - - cleanData: function( elems ) { - var data, elem, type, - special = jQuery.event.special, - i = 0; - - for ( ; ( elem = elems[ i ] ) !== undefined; i++ ) { - if ( acceptData( elem ) ) { - if ( ( data = elem[ dataPriv.expando ] ) ) { - if ( data.events ) { - for ( type in data.events ) { - if ( special[ type ] ) { - jQuery.event.remove( elem, type ); - - // This is a shortcut to avoid jQuery.event.remove's overhead - } else { - jQuery.removeEvent( elem, type, data.handle ); - } - } - } - - // Support: Chrome <=35 - 45+ - // Assign undefined instead of using delete, see Data#remove - elem[ dataPriv.expando ] = undefined; - } - if ( elem[ dataUser.expando ] ) { - - // Support: Chrome <=35 - 45+ - // Assign undefined instead of using delete, see Data#remove - elem[ dataUser.expando ] = undefined; - } - } - } - } -} ); - -jQuery.fn.extend( { - detach: function( selector ) { - return remove( this, selector, true ); - }, - - remove: function( selector ) { - return remove( this, selector ); - }, - - text: function( value ) { - return access( this, function( value ) { - return value === undefined ? - jQuery.text( this ) : - this.empty().each( function() { - if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { - this.textContent = value; - } - } ); - }, null, value, arguments.length ); - }, - - append: function() { - return domManip( this, arguments, function( elem ) { - if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { - var target = manipulationTarget( this, elem ); - target.appendChild( elem ); - } - } ); - }, - - prepend: function() { - return domManip( this, arguments, function( elem ) { - if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { - var target = manipulationTarget( this, elem ); - target.insertBefore( elem, target.firstChild ); - } - } ); - }, - - before: function() { - return domManip( this, arguments, function( elem ) { - if ( this.parentNode ) { - this.parentNode.insertBefore( elem, this ); - } - } ); - }, - - after: function() { - return domManip( this, arguments, function( elem ) { - if ( this.parentNode ) { - this.parentNode.insertBefore( elem, this.nextSibling ); - } - } ); - }, - - empty: function() { - var elem, - i = 0; - - for ( ; ( elem = this[ i ] ) != null; i++ ) { - if ( elem.nodeType === 1 ) { - - // Prevent memory leaks - jQuery.cleanData( getAll( elem, false ) ); - - // Remove any remaining nodes - elem.textContent = ""; - } - } - - return this; - }, - - clone: function( dataAndEvents, deepDataAndEvents ) { - dataAndEvents = dataAndEvents == null ? false : dataAndEvents; - deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents; - - return this.map( function() { - return jQuery.clone( this, dataAndEvents, deepDataAndEvents ); - } ); - }, - - html: function( value ) { - return access( this, function( value ) { - var elem = this[ 0 ] || {}, - i = 0, - l = this.length; - - if ( value === undefined && elem.nodeType === 1 ) { - return elem.innerHTML; - } - - // See if we can take a shortcut and just use innerHTML - if ( typeof value === "string" && !rnoInnerhtml.test( value ) && - !wrapMap[ ( rtagName.exec( value ) || [ "", "" ] )[ 1 ].toLowerCase() ] ) { - - value = jQuery.htmlPrefilter( value ); - - try { - for ( ; i < l; i++ ) { - elem = this[ i ] || {}; - - // Remove element nodes and prevent memory leaks - if ( elem.nodeType === 1 ) { - jQuery.cleanData( getAll( elem, false ) ); - elem.innerHTML = value; - } - } - - elem = 0; - - // If using innerHTML throws an exception, use the fallback method - } catch ( e ) {} - } - - if ( elem ) { - this.empty().append( value ); - } - }, null, value, arguments.length ); - }, - - replaceWith: function() { - var ignored = []; - - // Make the changes, replacing each non-ignored context element with the new content - return domManip( this, arguments, function( elem ) { - var parent = this.parentNode; - - if ( jQuery.inArray( this, ignored ) < 0 ) { - jQuery.cleanData( getAll( this ) ); - if ( parent ) { - parent.replaceChild( elem, this ); - } - } - - // Force callback invocation - }, ignored ); - } -} ); - -jQuery.each( { - appendTo: "append", - prependTo: "prepend", - insertBefore: "before", - insertAfter: "after", - replaceAll: "replaceWith" -}, function( name, original ) { - jQuery.fn[ name ] = function( selector ) { - var elems, - ret = [], - insert = jQuery( selector ), - last = insert.length - 1, - i = 0; - - for ( ; i <= last; i++ ) { - elems = i === last ? this : this.clone( true ); - jQuery( insert[ i ] )[ original ]( elems ); - - // Support: Android <=4.0 only, PhantomJS 1 only - // .get() because push.apply(_, arraylike) throws on ancient WebKit - push.apply( ret, elems.get() ); - } - - return this.pushStack( ret ); - }; -} ); -var rmargin = ( /^margin/ ); - -var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" ); - -var getStyles = function( elem ) { - - // Support: IE <=11 only, Firefox <=30 (#15098, #14150) - // IE throws on elements created in popups - // FF meanwhile throws on frame elements through "defaultView.getComputedStyle" - var view = elem.ownerDocument.defaultView; - - if ( !view || !view.opener ) { - view = window; - } - - return view.getComputedStyle( elem ); - }; - - - -( function() { - - // Executing both pixelPosition & boxSizingReliable tests require only one layout - // so they're executed at the same time to save the second computation. - function computeStyleTests() { - - // This is a singleton, we need to execute it only once - if ( !div ) { - return; - } - - div.style.cssText = - "box-sizing:border-box;" + - "position:relative;display:block;" + - "margin:auto;border:1px;padding:1px;" + - "top:1%;width:50%"; - div.innerHTML = ""; - documentElement.appendChild( container ); - - var divStyle = window.getComputedStyle( div ); - pixelPositionVal = divStyle.top !== "1%"; - - // Support: Android 4.0 - 4.3 only, Firefox <=3 - 44 - reliableMarginLeftVal = divStyle.marginLeft === "2px"; - boxSizingReliableVal = divStyle.width === "4px"; - - // Support: Android 4.0 - 4.3 only - // Some styles come back with percentage values, even though they shouldn't - div.style.marginRight = "50%"; - pixelMarginRightVal = divStyle.marginRight === "4px"; - - documentElement.removeChild( container ); - - // Nullify the div so it wouldn't be stored in the memory and - // it will also be a sign that checks already performed - div = null; - } - - var pixelPositionVal, boxSizingReliableVal, pixelMarginRightVal, reliableMarginLeftVal, - container = document.createElement( "div" ), - div = document.createElement( "div" ); - - // Finish early in limited (non-browser) environments - if ( !div.style ) { - return; - } - - // Support: IE <=9 - 11 only - // Style of cloned element affects source element cloned (#8908) - div.style.backgroundClip = "content-box"; - div.cloneNode( true ).style.backgroundClip = ""; - support.clearCloneStyle = div.style.backgroundClip === "content-box"; - - container.style.cssText = "border:0;width:8px;height:0;top:0;left:-9999px;" + - "padding:0;margin-top:1px;position:absolute"; - container.appendChild( div ); - - jQuery.extend( support, { - pixelPosition: function() { - computeStyleTests(); - return pixelPositionVal; - }, - boxSizingReliable: function() { - computeStyleTests(); - return boxSizingReliableVal; - }, - pixelMarginRight: function() { - computeStyleTests(); - return pixelMarginRightVal; - }, - reliableMarginLeft: function() { - computeStyleTests(); - return reliableMarginLeftVal; - } - } ); -} )(); - - -function curCSS( elem, name, computed ) { - var width, minWidth, maxWidth, ret, - - // Support: Firefox 51+ - // Retrieving style before computed somehow - // fixes an issue with getting wrong values - // on detached elements - style = elem.style; - - computed = computed || getStyles( elem ); - - // getPropertyValue is needed for: - // .css('filter') (IE 9 only, #12537) - // .css('--customProperty) (#3144) - if ( computed ) { - ret = computed.getPropertyValue( name ) || computed[ name ]; - - if ( ret === "" && !jQuery.contains( elem.ownerDocument, elem ) ) { - ret = jQuery.style( elem, name ); - } - - // A tribute to the "awesome hack by Dean Edwards" - // Android Browser returns percentage for some values, - // but width seems to be reliably pixels. - // This is against the CSSOM draft spec: - // https://drafts.csswg.org/cssom/#resolved-values - if ( !support.pixelMarginRight() && rnumnonpx.test( ret ) && rmargin.test( name ) ) { - - // Remember the original values - width = style.width; - minWidth = style.minWidth; - maxWidth = style.maxWidth; - - // Put in the new values to get a computed value out - style.minWidth = style.maxWidth = style.width = ret; - ret = computed.width; - - // Revert the changed values - style.width = width; - style.minWidth = minWidth; - style.maxWidth = maxWidth; - } - } - - return ret !== undefined ? - - // Support: IE <=9 - 11 only - // IE returns zIndex value as an integer. - ret + "" : - ret; -} - - -function addGetHookIf( conditionFn, hookFn ) { - - // Define the hook, we'll check on the first run if it's really needed. - return { - get: function() { - if ( conditionFn() ) { - - // Hook not needed (or it's not possible to use it due - // to missing dependency), remove it. - delete this.get; - return; - } - - // Hook needed; redefine it so that the support test is not executed again. - return ( this.get = hookFn ).apply( this, arguments ); - } - }; -} - - -var - - // Swappable if display is none or starts with table - // except "table", "table-cell", or "table-caption" - // See here for display values: https://developer.mozilla.org/en-US/docs/CSS/display - rdisplayswap = /^(none|table(?!-c[ea]).+)/, - rcustomProp = /^--/, - cssShow = { position: "absolute", visibility: "hidden", display: "block" }, - cssNormalTransform = { - letterSpacing: "0", - fontWeight: "400" - }, - - cssPrefixes = [ "Webkit", "Moz", "ms" ], - emptyStyle = document.createElement( "div" ).style; - -// Return a css property mapped to a potentially vendor prefixed property -function vendorPropName( name ) { - - // Shortcut for names that are not vendor prefixed - if ( name in emptyStyle ) { - return name; - } - - // Check for vendor prefixed names - var capName = name[ 0 ].toUpperCase() + name.slice( 1 ), - i = cssPrefixes.length; - - while ( i-- ) { - name = cssPrefixes[ i ] + capName; - if ( name in emptyStyle ) { - return name; - } - } -} - -// Return a property mapped along what jQuery.cssProps suggests or to -// a vendor prefixed property. -function finalPropName( name ) { - var ret = jQuery.cssProps[ name ]; - if ( !ret ) { - ret = jQuery.cssProps[ name ] = vendorPropName( name ) || name; - } - return ret; -} - -function setPositiveNumber( elem, value, subtract ) { - - // Any relative (+/-) values have already been - // normalized at this point - var matches = rcssNum.exec( value ); - return matches ? - - // Guard against undefined "subtract", e.g., when used as in cssHooks - Math.max( 0, matches[ 2 ] - ( subtract || 0 ) ) + ( matches[ 3 ] || "px" ) : - value; -} - -function augmentWidthOrHeight( elem, name, extra, isBorderBox, styles ) { - var i, - val = 0; - - // If we already have the right measurement, avoid augmentation - if ( extra === ( isBorderBox ? "border" : "content" ) ) { - i = 4; - - // Otherwise initialize for horizontal or vertical properties - } else { - i = name === "width" ? 1 : 0; - } - - for ( ; i < 4; i += 2 ) { - - // Both box models exclude margin, so add it if we want it - if ( extra === "margin" ) { - val += jQuery.css( elem, extra + cssExpand[ i ], true, styles ); - } - - if ( isBorderBox ) { - - // border-box includes padding, so remove it if we want content - if ( extra === "content" ) { - val -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles ); - } - - // At this point, extra isn't border nor margin, so remove border - if ( extra !== "margin" ) { - val -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); - } - } else { - - // At this point, extra isn't content, so add padding - val += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles ); - - // At this point, extra isn't content nor padding, so add border - if ( extra !== "padding" ) { - val += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); - } - } - } - - return val; -} - -function getWidthOrHeight( elem, name, extra ) { - - // Start with computed style - var valueIsBorderBox, - styles = getStyles( elem ), - val = curCSS( elem, name, styles ), - isBorderBox = jQuery.css( elem, "boxSizing", false, styles ) === "border-box"; - - // Computed unit is not pixels. Stop here and return. - if ( rnumnonpx.test( val ) ) { - return val; - } - - // Check for style in case a browser which returns unreliable values - // for getComputedStyle silently falls back to the reliable elem.style - valueIsBorderBox = isBorderBox && - ( support.boxSizingReliable() || val === elem.style[ name ] ); - - // Fall back to offsetWidth/Height when value is "auto" - // This happens for inline elements with no explicit setting (gh-3571) - if ( val === "auto" ) { - val = elem[ "offset" + name[ 0 ].toUpperCase() + name.slice( 1 ) ]; - } - - // Normalize "", auto, and prepare for extra - val = parseFloat( val ) || 0; - - // Use the active box-sizing model to add/subtract irrelevant styles - return ( val + - augmentWidthOrHeight( - elem, - name, - extra || ( isBorderBox ? "border" : "content" ), - valueIsBorderBox, - styles - ) - ) + "px"; -} - -jQuery.extend( { - - // Add in style property hooks for overriding the default - // behavior of getting and setting a style property - cssHooks: { - opacity: { - get: function( elem, computed ) { - if ( computed ) { - - // We should always get a number back from opacity - var ret = curCSS( elem, "opacity" ); - return ret === "" ? "1" : ret; - } - } - } - }, - - // Don't automatically add "px" to these possibly-unitless properties - cssNumber: { - "animationIterationCount": true, - "columnCount": true, - "fillOpacity": true, - "flexGrow": true, - "flexShrink": true, - "fontWeight": true, - "lineHeight": true, - "opacity": true, - "order": true, - "orphans": true, - "widows": true, - "zIndex": true, - "zoom": true - }, - - // Add in properties whose names you wish to fix before - // setting or getting the value - cssProps: { - "float": "cssFloat" - }, - - // Get and set the style property on a DOM Node - style: function( elem, name, value, extra ) { - - // Don't set styles on text and comment nodes - if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) { - return; - } - - // Make sure that we're working with the right name - var ret, type, hooks, - origName = jQuery.camelCase( name ), - isCustomProp = rcustomProp.test( name ), - style = elem.style; - - // Make sure that we're working with the right name. We don't - // want to query the value if it is a CSS custom property - // since they are user-defined. - if ( !isCustomProp ) { - name = finalPropName( origName ); - } - - // Gets hook for the prefixed version, then unprefixed version - hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ]; - - // Check if we're setting a value - if ( value !== undefined ) { - type = typeof value; - - // Convert "+=" or "-=" to relative numbers (#7345) - if ( type === "string" && ( ret = rcssNum.exec( value ) ) && ret[ 1 ] ) { - value = adjustCSS( elem, name, ret ); - - // Fixes bug #9237 - type = "number"; - } - - // Make sure that null and NaN values aren't set (#7116) - if ( value == null || value !== value ) { - return; - } - - // If a number was passed in, add the unit (except for certain CSS properties) - if ( type === "number" ) { - value += ret && ret[ 3 ] || ( jQuery.cssNumber[ origName ] ? "" : "px" ); - } - - // background-* props affect original clone's values - if ( !support.clearCloneStyle && value === "" && name.indexOf( "background" ) === 0 ) { - style[ name ] = "inherit"; - } - - // If a hook was provided, use that value, otherwise just set the specified value - if ( !hooks || !( "set" in hooks ) || - ( value = hooks.set( elem, value, extra ) ) !== undefined ) { - - if ( isCustomProp ) { - style.setProperty( name, value ); - } else { - style[ name ] = value; - } - } - - } else { - - // If a hook was provided get the non-computed value from there - if ( hooks && "get" in hooks && - ( ret = hooks.get( elem, false, extra ) ) !== undefined ) { - - return ret; - } - - // Otherwise just get the value from the style object - return style[ name ]; - } - }, - - css: function( elem, name, extra, styles ) { - var val, num, hooks, - origName = jQuery.camelCase( name ), - isCustomProp = rcustomProp.test( name ); - - // Make sure that we're working with the right name. We don't - // want to modify the value if it is a CSS custom property - // since they are user-defined. - if ( !isCustomProp ) { - name = finalPropName( origName ); - } - - // Try prefixed name followed by the unprefixed name - hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ]; - - // If a hook was provided get the computed value from there - if ( hooks && "get" in hooks ) { - val = hooks.get( elem, true, extra ); - } - - // Otherwise, if a way to get the computed value exists, use that - if ( val === undefined ) { - val = curCSS( elem, name, styles ); - } - - // Convert "normal" to computed value - if ( val === "normal" && name in cssNormalTransform ) { - val = cssNormalTransform[ name ]; - } - - // Make numeric if forced or a qualifier was provided and val looks numeric - if ( extra === "" || extra ) { - num = parseFloat( val ); - return extra === true || isFinite( num ) ? num || 0 : val; - } - - return val; - } -} ); - -jQuery.each( [ "height", "width" ], function( i, name ) { - jQuery.cssHooks[ name ] = { - get: function( elem, computed, extra ) { - if ( computed ) { - - // Certain elements can have dimension info if we invisibly show them - // but it must have a current display style that would benefit - return rdisplayswap.test( jQuery.css( elem, "display" ) ) && - - // Support: Safari 8+ - // Table columns in Safari have non-zero offsetWidth & zero - // getBoundingClientRect().width unless display is changed. - // Support: IE <=11 only - // Running getBoundingClientRect on a disconnected node - // in IE throws an error. - ( !elem.getClientRects().length || !elem.getBoundingClientRect().width ) ? - swap( elem, cssShow, function() { - return getWidthOrHeight( elem, name, extra ); - } ) : - getWidthOrHeight( elem, name, extra ); - } - }, - - set: function( elem, value, extra ) { - var matches, - styles = extra && getStyles( elem ), - subtract = extra && augmentWidthOrHeight( - elem, - name, - extra, - jQuery.css( elem, "boxSizing", false, styles ) === "border-box", - styles - ); - - // Convert to pixels if value adjustment is needed - if ( subtract && ( matches = rcssNum.exec( value ) ) && - ( matches[ 3 ] || "px" ) !== "px" ) { - - elem.style[ name ] = value; - value = jQuery.css( elem, name ); - } - - return setPositiveNumber( elem, value, subtract ); - } - }; -} ); - -jQuery.cssHooks.marginLeft = addGetHookIf( support.reliableMarginLeft, - function( elem, computed ) { - if ( computed ) { - return ( parseFloat( curCSS( elem, "marginLeft" ) ) || - elem.getBoundingClientRect().left - - swap( elem, { marginLeft: 0 }, function() { - return elem.getBoundingClientRect().left; - } ) - ) + "px"; - } - } -); - -// These hooks are used by animate to expand properties -jQuery.each( { - margin: "", - padding: "", - border: "Width" -}, function( prefix, suffix ) { - jQuery.cssHooks[ prefix + suffix ] = { - expand: function( value ) { - var i = 0, - expanded = {}, - - // Assumes a single number if not a string - parts = typeof value === "string" ? value.split( " " ) : [ value ]; - - for ( ; i < 4; i++ ) { - expanded[ prefix + cssExpand[ i ] + suffix ] = - parts[ i ] || parts[ i - 2 ] || parts[ 0 ]; - } - - return expanded; - } - }; - - if ( !rmargin.test( prefix ) ) { - jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber; - } -} ); - -jQuery.fn.extend( { - css: function( name, value ) { - return access( this, function( elem, name, value ) { - var styles, len, - map = {}, - i = 0; - - if ( Array.isArray( name ) ) { - styles = getStyles( elem ); - len = name.length; - - for ( ; i < len; i++ ) { - map[ name[ i ] ] = jQuery.css( elem, name[ i ], false, styles ); - } - - return map; - } - - return value !== undefined ? - jQuery.style( elem, name, value ) : - jQuery.css( elem, name ); - }, name, value, arguments.length > 1 ); - } -} ); - - -function Tween( elem, options, prop, end, easing ) { - return new Tween.prototype.init( elem, options, prop, end, easing ); -} -jQuery.Tween = Tween; - -Tween.prototype = { - constructor: Tween, - init: function( elem, options, prop, end, easing, unit ) { - this.elem = elem; - this.prop = prop; - this.easing = easing || jQuery.easing._default; - this.options = options; - this.start = this.now = this.cur(); - this.end = end; - this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" ); - }, - cur: function() { - var hooks = Tween.propHooks[ this.prop ]; - - return hooks && hooks.get ? - hooks.get( this ) : - Tween.propHooks._default.get( this ); - }, - run: function( percent ) { - var eased, - hooks = Tween.propHooks[ this.prop ]; - - if ( this.options.duration ) { - this.pos = eased = jQuery.easing[ this.easing ]( - percent, this.options.duration * percent, 0, 1, this.options.duration - ); - } else { - this.pos = eased = percent; - } - this.now = ( this.end - this.start ) * eased + this.start; - - if ( this.options.step ) { - this.options.step.call( this.elem, this.now, this ); - } - - if ( hooks && hooks.set ) { - hooks.set( this ); - } else { - Tween.propHooks._default.set( this ); - } - return this; - } -}; - -Tween.prototype.init.prototype = Tween.prototype; - -Tween.propHooks = { - _default: { - get: function( tween ) { - var result; - - // Use a property on the element directly when it is not a DOM element, - // or when there is no matching style property that exists. - if ( tween.elem.nodeType !== 1 || - tween.elem[ tween.prop ] != null && tween.elem.style[ tween.prop ] == null ) { - return tween.elem[ tween.prop ]; - } - - // Passing an empty string as a 3rd parameter to .css will automatically - // attempt a parseFloat and fallback to a string if the parse fails. - // Simple values such as "10px" are parsed to Float; - // complex values such as "rotate(1rad)" are returned as-is. - result = jQuery.css( tween.elem, tween.prop, "" ); - - // Empty strings, null, undefined and "auto" are converted to 0. - return !result || result === "auto" ? 0 : result; - }, - set: function( tween ) { - - // Use step hook for back compat. - // Use cssHook if its there. - // Use .style if available and use plain properties where available. - if ( jQuery.fx.step[ tween.prop ] ) { - jQuery.fx.step[ tween.prop ]( tween ); - } else if ( tween.elem.nodeType === 1 && - ( tween.elem.style[ jQuery.cssProps[ tween.prop ] ] != null || - jQuery.cssHooks[ tween.prop ] ) ) { - jQuery.style( tween.elem, tween.prop, tween.now + tween.unit ); - } else { - tween.elem[ tween.prop ] = tween.now; - } - } - } -}; - -// Support: IE <=9 only -// Panic based approach to setting things on disconnected nodes -Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = { - set: function( tween ) { - if ( tween.elem.nodeType && tween.elem.parentNode ) { - tween.elem[ tween.prop ] = tween.now; - } - } -}; - -jQuery.easing = { - linear: function( p ) { - return p; - }, - swing: function( p ) { - return 0.5 - Math.cos( p * Math.PI ) / 2; - }, - _default: "swing" -}; - -jQuery.fx = Tween.prototype.init; - -// Back compat <1.8 extension point -jQuery.fx.step = {}; - - - - -var - fxNow, inProgress, - rfxtypes = /^(?:toggle|show|hide)$/, - rrun = /queueHooks$/; - -function schedule() { - if ( inProgress ) { - if ( document.hidden === false && window.requestAnimationFrame ) { - window.requestAnimationFrame( schedule ); - } else { - window.setTimeout( schedule, jQuery.fx.interval ); - } - - jQuery.fx.tick(); - } -} - -// Animations created synchronously will run synchronously -function createFxNow() { - window.setTimeout( function() { - fxNow = undefined; - } ); - return ( fxNow = jQuery.now() ); -} - -// Generate parameters to create a standard animation -function genFx( type, includeWidth ) { - var which, - i = 0, - attrs = { height: type }; - - // If we include width, step value is 1 to do all cssExpand values, - // otherwise step value is 2 to skip over Left and Right - includeWidth = includeWidth ? 1 : 0; - for ( ; i < 4; i += 2 - includeWidth ) { - which = cssExpand[ i ]; - attrs[ "margin" + which ] = attrs[ "padding" + which ] = type; - } - - if ( includeWidth ) { - attrs.opacity = attrs.width = type; - } - - return attrs; -} - -function createTween( value, prop, animation ) { - var tween, - collection = ( Animation.tweeners[ prop ] || [] ).concat( Animation.tweeners[ "*" ] ), - index = 0, - length = collection.length; - for ( ; index < length; index++ ) { - if ( ( tween = collection[ index ].call( animation, prop, value ) ) ) { - - // We're done with this property - return tween; - } - } -} - -function defaultPrefilter( elem, props, opts ) { - var prop, value, toggle, hooks, oldfire, propTween, restoreDisplay, display, - isBox = "width" in props || "height" in props, - anim = this, - orig = {}, - style = elem.style, - hidden = elem.nodeType && isHiddenWithinTree( elem ), - dataShow = dataPriv.get( elem, "fxshow" ); - - // Queue-skipping animations hijack the fx hooks - if ( !opts.queue ) { - hooks = jQuery._queueHooks( elem, "fx" ); - if ( hooks.unqueued == null ) { - hooks.unqueued = 0; - oldfire = hooks.empty.fire; - hooks.empty.fire = function() { - if ( !hooks.unqueued ) { - oldfire(); - } - }; - } - hooks.unqueued++; - - anim.always( function() { - - // Ensure the complete handler is called before this completes - anim.always( function() { - hooks.unqueued--; - if ( !jQuery.queue( elem, "fx" ).length ) { - hooks.empty.fire(); - } - } ); - } ); - } - - // Detect show/hide animations - for ( prop in props ) { - value = props[ prop ]; - if ( rfxtypes.test( value ) ) { - delete props[ prop ]; - toggle = toggle || value === "toggle"; - if ( value === ( hidden ? "hide" : "show" ) ) { - - // Pretend to be hidden if this is a "show" and - // there is still data from a stopped show/hide - if ( value === "show" && dataShow && dataShow[ prop ] !== undefined ) { - hidden = true; - - // Ignore all other no-op show/hide data - } else { - continue; - } - } - orig[ prop ] = dataShow && dataShow[ prop ] || jQuery.style( elem, prop ); - } - } - - // Bail out if this is a no-op like .hide().hide() - propTween = !jQuery.isEmptyObject( props ); - if ( !propTween && jQuery.isEmptyObject( orig ) ) { - return; - } - - // Restrict "overflow" and "display" styles during box animations - if ( isBox && elem.nodeType === 1 ) { - - // Support: IE <=9 - 11, Edge 12 - 13 - // Record all 3 overflow attributes because IE does not infer the shorthand - // from identically-valued overflowX and overflowY - opts.overflow = [ style.overflow, style.overflowX, style.overflowY ]; - - // Identify a display type, preferring old show/hide data over the CSS cascade - restoreDisplay = dataShow && dataShow.display; - if ( restoreDisplay == null ) { - restoreDisplay = dataPriv.get( elem, "display" ); - } - display = jQuery.css( elem, "display" ); - if ( display === "none" ) { - if ( restoreDisplay ) { - display = restoreDisplay; - } else { - - // Get nonempty value(s) by temporarily forcing visibility - showHide( [ elem ], true ); - restoreDisplay = elem.style.display || restoreDisplay; - display = jQuery.css( elem, "display" ); - showHide( [ elem ] ); - } - } - - // Animate inline elements as inline-block - if ( display === "inline" || display === "inline-block" && restoreDisplay != null ) { - if ( jQuery.css( elem, "float" ) === "none" ) { - - // Restore the original display value at the end of pure show/hide animations - if ( !propTween ) { - anim.done( function() { - style.display = restoreDisplay; - } ); - if ( restoreDisplay == null ) { - display = style.display; - restoreDisplay = display === "none" ? "" : display; - } - } - style.display = "inline-block"; - } - } - } - - if ( opts.overflow ) { - style.overflow = "hidden"; - anim.always( function() { - style.overflow = opts.overflow[ 0 ]; - style.overflowX = opts.overflow[ 1 ]; - style.overflowY = opts.overflow[ 2 ]; - } ); - } - - // Implement show/hide animations - propTween = false; - for ( prop in orig ) { - - // General show/hide setup for this element animation - if ( !propTween ) { - if ( dataShow ) { - if ( "hidden" in dataShow ) { - hidden = dataShow.hidden; - } - } else { - dataShow = dataPriv.access( elem, "fxshow", { display: restoreDisplay } ); - } - - // Store hidden/visible for toggle so `.stop().toggle()` "reverses" - if ( toggle ) { - dataShow.hidden = !hidden; - } - - // Show elements before animating them - if ( hidden ) { - showHide( [ elem ], true ); - } - - /* eslint-disable no-loop-func */ - - anim.done( function() { - - /* eslint-enable no-loop-func */ - - // The final step of a "hide" animation is actually hiding the element - if ( !hidden ) { - showHide( [ elem ] ); - } - dataPriv.remove( elem, "fxshow" ); - for ( prop in orig ) { - jQuery.style( elem, prop, orig[ prop ] ); - } - } ); - } - - // Per-property setup - propTween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim ); - if ( !( prop in dataShow ) ) { - dataShow[ prop ] = propTween.start; - if ( hidden ) { - propTween.end = propTween.start; - propTween.start = 0; - } - } - } -} - -function propFilter( props, specialEasing ) { - var index, name, easing, value, hooks; - - // camelCase, specialEasing and expand cssHook pass - for ( index in props ) { - name = jQuery.camelCase( index ); - easing = specialEasing[ name ]; - value = props[ index ]; - if ( Array.isArray( value ) ) { - easing = value[ 1 ]; - value = props[ index ] = value[ 0 ]; - } - - if ( index !== name ) { - props[ name ] = value; - delete props[ index ]; - } - - hooks = jQuery.cssHooks[ name ]; - if ( hooks && "expand" in hooks ) { - value = hooks.expand( value ); - delete props[ name ]; - - // Not quite $.extend, this won't overwrite existing keys. - // Reusing 'index' because we have the correct "name" - for ( index in value ) { - if ( !( index in props ) ) { - props[ index ] = value[ index ]; - specialEasing[ index ] = easing; - } - } - } else { - specialEasing[ name ] = easing; - } - } -} - -function Animation( elem, properties, options ) { - var result, - stopped, - index = 0, - length = Animation.prefilters.length, - deferred = jQuery.Deferred().always( function() { - - // Don't match elem in the :animated selector - delete tick.elem; - } ), - tick = function() { - if ( stopped ) { - return false; - } - var currentTime = fxNow || createFxNow(), - remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ), - - // Support: Android 2.3 only - // Archaic crash bug won't allow us to use `1 - ( 0.5 || 0 )` (#12497) - temp = remaining / animation.duration || 0, - percent = 1 - temp, - index = 0, - length = animation.tweens.length; - - for ( ; index < length; index++ ) { - animation.tweens[ index ].run( percent ); - } - - deferred.notifyWith( elem, [ animation, percent, remaining ] ); - - // If there's more to do, yield - if ( percent < 1 && length ) { - return remaining; - } - - // If this was an empty animation, synthesize a final progress notification - if ( !length ) { - deferred.notifyWith( elem, [ animation, 1, 0 ] ); - } - - // Resolve the animation and report its conclusion - deferred.resolveWith( elem, [ animation ] ); - return false; - }, - animation = deferred.promise( { - elem: elem, - props: jQuery.extend( {}, properties ), - opts: jQuery.extend( true, { - specialEasing: {}, - easing: jQuery.easing._default - }, options ), - originalProperties: properties, - originalOptions: options, - startTime: fxNow || createFxNow(), - duration: options.duration, - tweens: [], - createTween: function( prop, end ) { - var tween = jQuery.Tween( elem, animation.opts, prop, end, - animation.opts.specialEasing[ prop ] || animation.opts.easing ); - animation.tweens.push( tween ); - return tween; - }, - stop: function( gotoEnd ) { - var index = 0, - - // If we are going to the end, we want to run all the tweens - // otherwise we skip this part - length = gotoEnd ? animation.tweens.length : 0; - if ( stopped ) { - return this; - } - stopped = true; - for ( ; index < length; index++ ) { - animation.tweens[ index ].run( 1 ); - } - - // Resolve when we played the last frame; otherwise, reject - if ( gotoEnd ) { - deferred.notifyWith( elem, [ animation, 1, 0 ] ); - deferred.resolveWith( elem, [ animation, gotoEnd ] ); - } else { - deferred.rejectWith( elem, [ animation, gotoEnd ] ); - } - return this; - } - } ), - props = animation.props; - - propFilter( props, animation.opts.specialEasing ); - - for ( ; index < length; index++ ) { - result = Animation.prefilters[ index ].call( animation, elem, props, animation.opts ); - if ( result ) { - if ( jQuery.isFunction( result.stop ) ) { - jQuery._queueHooks( animation.elem, animation.opts.queue ).stop = - jQuery.proxy( result.stop, result ); - } - return result; - } - } - - jQuery.map( props, createTween, animation ); - - if ( jQuery.isFunction( animation.opts.start ) ) { - animation.opts.start.call( elem, animation ); - } - - // Attach callbacks from options - animation - .progress( animation.opts.progress ) - .done( animation.opts.done, animation.opts.complete ) - .fail( animation.opts.fail ) - .always( animation.opts.always ); - - jQuery.fx.timer( - jQuery.extend( tick, { - elem: elem, - anim: animation, - queue: animation.opts.queue - } ) - ); - - return animation; -} - -jQuery.Animation = jQuery.extend( Animation, { - - tweeners: { - "*": [ function( prop, value ) { - var tween = this.createTween( prop, value ); - adjustCSS( tween.elem, prop, rcssNum.exec( value ), tween ); - return tween; - } ] - }, - - tweener: function( props, callback ) { - if ( jQuery.isFunction( props ) ) { - callback = props; - props = [ "*" ]; - } else { - props = props.match( rnothtmlwhite ); - } - - var prop, - index = 0, - length = props.length; - - for ( ; index < length; index++ ) { - prop = props[ index ]; - Animation.tweeners[ prop ] = Animation.tweeners[ prop ] || []; - Animation.tweeners[ prop ].unshift( callback ); - } - }, - - prefilters: [ defaultPrefilter ], - - prefilter: function( callback, prepend ) { - if ( prepend ) { - Animation.prefilters.unshift( callback ); - } else { - Animation.prefilters.push( callback ); - } - } -} ); - -jQuery.speed = function( speed, easing, fn ) { - var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : { - complete: fn || !fn && easing || - jQuery.isFunction( speed ) && speed, - duration: speed, - easing: fn && easing || easing && !jQuery.isFunction( easing ) && easing - }; - - // Go to the end state if fx are off - if ( jQuery.fx.off ) { - opt.duration = 0; - - } else { - if ( typeof opt.duration !== "number" ) { - if ( opt.duration in jQuery.fx.speeds ) { - opt.duration = jQuery.fx.speeds[ opt.duration ]; - - } else { - opt.duration = jQuery.fx.speeds._default; - } - } - } - - // Normalize opt.queue - true/undefined/null -> "fx" - if ( opt.queue == null || opt.queue === true ) { - opt.queue = "fx"; - } - - // Queueing - opt.old = opt.complete; - - opt.complete = function() { - if ( jQuery.isFunction( opt.old ) ) { - opt.old.call( this ); - } - - if ( opt.queue ) { - jQuery.dequeue( this, opt.queue ); - } - }; - - return opt; -}; - -jQuery.fn.extend( { - fadeTo: function( speed, to, easing, callback ) { - - // Show any hidden elements after setting opacity to 0 - return this.filter( isHiddenWithinTree ).css( "opacity", 0 ).show() - - // Animate to the value specified - .end().animate( { opacity: to }, speed, easing, callback ); - }, - animate: function( prop, speed, easing, callback ) { - var empty = jQuery.isEmptyObject( prop ), - optall = jQuery.speed( speed, easing, callback ), - doAnimation = function() { - - // Operate on a copy of prop so per-property easing won't be lost - var anim = Animation( this, jQuery.extend( {}, prop ), optall ); - - // Empty animations, or finishing resolves immediately - if ( empty || dataPriv.get( this, "finish" ) ) { - anim.stop( true ); - } - }; - doAnimation.finish = doAnimation; - - return empty || optall.queue === false ? - this.each( doAnimation ) : - this.queue( optall.queue, doAnimation ); - }, - stop: function( type, clearQueue, gotoEnd ) { - var stopQueue = function( hooks ) { - var stop = hooks.stop; - delete hooks.stop; - stop( gotoEnd ); - }; - - if ( typeof type !== "string" ) { - gotoEnd = clearQueue; - clearQueue = type; - type = undefined; - } - if ( clearQueue && type !== false ) { - this.queue( type || "fx", [] ); - } - - return this.each( function() { - var dequeue = true, - index = type != null && type + "queueHooks", - timers = jQuery.timers, - data = dataPriv.get( this ); - - if ( index ) { - if ( data[ index ] && data[ index ].stop ) { - stopQueue( data[ index ] ); - } - } else { - for ( index in data ) { - if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) { - stopQueue( data[ index ] ); - } - } - } - - for ( index = timers.length; index--; ) { - if ( timers[ index ].elem === this && - ( type == null || timers[ index ].queue === type ) ) { - - timers[ index ].anim.stop( gotoEnd ); - dequeue = false; - timers.splice( index, 1 ); - } - } - - // Start the next in the queue if the last step wasn't forced. - // Timers currently will call their complete callbacks, which - // will dequeue but only if they were gotoEnd. - if ( dequeue || !gotoEnd ) { - jQuery.dequeue( this, type ); - } - } ); - }, - finish: function( type ) { - if ( type !== false ) { - type = type || "fx"; - } - return this.each( function() { - var index, - data = dataPriv.get( this ), - queue = data[ type + "queue" ], - hooks = data[ type + "queueHooks" ], - timers = jQuery.timers, - length = queue ? queue.length : 0; - - // Enable finishing flag on private data - data.finish = true; - - // Empty the queue first - jQuery.queue( this, type, [] ); - - if ( hooks && hooks.stop ) { - hooks.stop.call( this, true ); - } - - // Look for any active animations, and finish them - for ( index = timers.length; index--; ) { - if ( timers[ index ].elem === this && timers[ index ].queue === type ) { - timers[ index ].anim.stop( true ); - timers.splice( index, 1 ); - } - } - - // Look for any animations in the old queue and finish them - for ( index = 0; index < length; index++ ) { - if ( queue[ index ] && queue[ index ].finish ) { - queue[ index ].finish.call( this ); - } - } - - // Turn off finishing flag - delete data.finish; - } ); - } -} ); - -jQuery.each( [ "toggle", "show", "hide" ], function( i, name ) { - var cssFn = jQuery.fn[ name ]; - jQuery.fn[ name ] = function( speed, easing, callback ) { - return speed == null || typeof speed === "boolean" ? - cssFn.apply( this, arguments ) : - this.animate( genFx( name, true ), speed, easing, callback ); - }; -} ); - -// Generate shortcuts for custom animations -jQuery.each( { - slideDown: genFx( "show" ), - slideUp: genFx( "hide" ), - slideToggle: genFx( "toggle" ), - fadeIn: { opacity: "show" }, - fadeOut: { opacity: "hide" }, - fadeToggle: { opacity: "toggle" } -}, function( name, props ) { - jQuery.fn[ name ] = function( speed, easing, callback ) { - return this.animate( props, speed, easing, callback ); - }; -} ); - -jQuery.timers = []; -jQuery.fx.tick = function() { - var timer, - i = 0, - timers = jQuery.timers; - - fxNow = jQuery.now(); - - for ( ; i < timers.length; i++ ) { - timer = timers[ i ]; - - // Run the timer and safely remove it when done (allowing for external removal) - if ( !timer() && timers[ i ] === timer ) { - timers.splice( i--, 1 ); - } - } - - if ( !timers.length ) { - jQuery.fx.stop(); - } - fxNow = undefined; -}; - -jQuery.fx.timer = function( timer ) { - jQuery.timers.push( timer ); - jQuery.fx.start(); -}; - -jQuery.fx.interval = 13; -jQuery.fx.start = function() { - if ( inProgress ) { - return; - } - - inProgress = true; - schedule(); -}; - -jQuery.fx.stop = function() { - inProgress = null; -}; - -jQuery.fx.speeds = { - slow: 600, - fast: 200, - - // Default speed - _default: 400 -}; - - -// Based off of the plugin by Clint Helfers, with permission. -// https://web.archive.org/web/20100324014747/http://blindsignals.com/index.php/2009/07/jquery-delay/ -jQuery.fn.delay = function( time, type ) { - time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time; - type = type || "fx"; - - return this.queue( type, function( next, hooks ) { - var timeout = window.setTimeout( next, time ); - hooks.stop = function() { - window.clearTimeout( timeout ); - }; - } ); -}; - - -( function() { - var input = document.createElement( "input" ), - select = document.createElement( "select" ), - opt = select.appendChild( document.createElement( "option" ) ); - - input.type = "checkbox"; - - // Support: Android <=4.3 only - // Default value for a checkbox should be "on" - support.checkOn = input.value !== ""; - - // Support: IE <=11 only - // Must access selectedIndex to make default options select - support.optSelected = opt.selected; - - // Support: IE <=11 only - // An input loses its value after becoming a radio - input = document.createElement( "input" ); - input.value = "t"; - input.type = "radio"; - support.radioValue = input.value === "t"; -} )(); - - -var boolHook, - attrHandle = jQuery.expr.attrHandle; - -jQuery.fn.extend( { - attr: function( name, value ) { - return access( this, jQuery.attr, name, value, arguments.length > 1 ); - }, - - removeAttr: function( name ) { - return this.each( function() { - jQuery.removeAttr( this, name ); - } ); - } -} ); - -jQuery.extend( { - attr: function( elem, name, value ) { - var ret, hooks, - nType = elem.nodeType; - - // Don't get/set attributes on text, comment and attribute nodes - if ( nType === 3 || nType === 8 || nType === 2 ) { - return; - } - - // Fallback to prop when attributes are not supported - if ( typeof elem.getAttribute === "undefined" ) { - return jQuery.prop( elem, name, value ); - } - - // Attribute hooks are determined by the lowercase version - // Grab necessary hook if one is defined - if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) { - hooks = jQuery.attrHooks[ name.toLowerCase() ] || - ( jQuery.expr.match.bool.test( name ) ? boolHook : undefined ); - } - - if ( value !== undefined ) { - if ( value === null ) { - jQuery.removeAttr( elem, name ); - return; - } - - if ( hooks && "set" in hooks && - ( ret = hooks.set( elem, value, name ) ) !== undefined ) { - return ret; - } - - elem.setAttribute( name, value + "" ); - return value; - } - - if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) { - return ret; - } - - ret = jQuery.find.attr( elem, name ); - - // Non-existent attributes return null, we normalize to undefined - return ret == null ? undefined : ret; - }, - - attrHooks: { - type: { - set: function( elem, value ) { - if ( !support.radioValue && value === "radio" && - nodeName( elem, "input" ) ) { - var val = elem.value; - elem.setAttribute( "type", value ); - if ( val ) { - elem.value = val; - } - return value; - } - } - } - }, - - removeAttr: function( elem, value ) { - var name, - i = 0, - - // Attribute names can contain non-HTML whitespace characters - // https://html.spec.whatwg.org/multipage/syntax.html#attributes-2 - attrNames = value && value.match( rnothtmlwhite ); - - if ( attrNames && elem.nodeType === 1 ) { - while ( ( name = attrNames[ i++ ] ) ) { - elem.removeAttribute( name ); - } - } - } -} ); - -// Hooks for boolean attributes -boolHook = { - set: function( elem, value, name ) { - if ( value === false ) { - - // Remove boolean attributes when set to false - jQuery.removeAttr( elem, name ); - } else { - elem.setAttribute( name, name ); - } - return name; - } -}; - -jQuery.each( jQuery.expr.match.bool.source.match( /\w+/g ), function( i, name ) { - var getter = attrHandle[ name ] || jQuery.find.attr; - - attrHandle[ name ] = function( elem, name, isXML ) { - var ret, handle, - lowercaseName = name.toLowerCase(); - - if ( !isXML ) { - - // Avoid an infinite loop by temporarily removing this function from the getter - handle = attrHandle[ lowercaseName ]; - attrHandle[ lowercaseName ] = ret; - ret = getter( elem, name, isXML ) != null ? - lowercaseName : - null; - attrHandle[ lowercaseName ] = handle; - } - return ret; - }; -} ); - - - - -var rfocusable = /^(?:input|select|textarea|button)$/i, - rclickable = /^(?:a|area)$/i; - -jQuery.fn.extend( { - prop: function( name, value ) { - return access( this, jQuery.prop, name, value, arguments.length > 1 ); - }, - - removeProp: function( name ) { - return this.each( function() { - delete this[ jQuery.propFix[ name ] || name ]; - } ); - } -} ); - -jQuery.extend( { - prop: function( elem, name, value ) { - var ret, hooks, - nType = elem.nodeType; - - // Don't get/set properties on text, comment and attribute nodes - if ( nType === 3 || nType === 8 || nType === 2 ) { - return; - } - - if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) { - - // Fix name and attach hooks - name = jQuery.propFix[ name ] || name; - hooks = jQuery.propHooks[ name ]; - } - - if ( value !== undefined ) { - if ( hooks && "set" in hooks && - ( ret = hooks.set( elem, value, name ) ) !== undefined ) { - return ret; - } - - return ( elem[ name ] = value ); - } - - if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) { - return ret; - } - - return elem[ name ]; - }, - - propHooks: { - tabIndex: { - get: function( elem ) { - - // Support: IE <=9 - 11 only - // elem.tabIndex doesn't always return the - // correct value when it hasn't been explicitly set - // https://web.archive.org/web/20141116233347/http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/ - // Use proper attribute retrieval(#12072) - var tabindex = jQuery.find.attr( elem, "tabindex" ); - - if ( tabindex ) { - return parseInt( tabindex, 10 ); - } - - if ( - rfocusable.test( elem.nodeName ) || - rclickable.test( elem.nodeName ) && - elem.href - ) { - return 0; - } - - return -1; - } - } - }, - - propFix: { - "for": "htmlFor", - "class": "className" - } -} ); - -// Support: IE <=11 only -// Accessing the selectedIndex property -// forces the browser to respect setting selected -// on the option -// The getter ensures a default option is selected -// when in an optgroup -// eslint rule "no-unused-expressions" is disabled for this code -// since it considers such accessions noop -if ( !support.optSelected ) { - jQuery.propHooks.selected = { - get: function( elem ) { - - /* eslint no-unused-expressions: "off" */ - - var parent = elem.parentNode; - if ( parent && parent.parentNode ) { - parent.parentNode.selectedIndex; - } - return null; - }, - set: function( elem ) { - - /* eslint no-unused-expressions: "off" */ - - var parent = elem.parentNode; - if ( parent ) { - parent.selectedIndex; - - if ( parent.parentNode ) { - parent.parentNode.selectedIndex; - } - } - } - }; -} - -jQuery.each( [ - "tabIndex", - "readOnly", - "maxLength", - "cellSpacing", - "cellPadding", - "rowSpan", - "colSpan", - "useMap", - "frameBorder", - "contentEditable" -], function() { - jQuery.propFix[ this.toLowerCase() ] = this; -} ); - - - - - // Strip and collapse whitespace according to HTML spec - // https://html.spec.whatwg.org/multipage/infrastructure.html#strip-and-collapse-whitespace - function stripAndCollapse( value ) { - var tokens = value.match( rnothtmlwhite ) || []; - return tokens.join( " " ); - } - - -function getClass( elem ) { - return elem.getAttribute && elem.getAttribute( "class" ) || ""; -} - -jQuery.fn.extend( { - addClass: function( value ) { - var classes, elem, cur, curValue, clazz, j, finalValue, - i = 0; - - if ( jQuery.isFunction( value ) ) { - return this.each( function( j ) { - jQuery( this ).addClass( value.call( this, j, getClass( this ) ) ); - } ); - } - - if ( typeof value === "string" && value ) { - classes = value.match( rnothtmlwhite ) || []; - - while ( ( elem = this[ i++ ] ) ) { - curValue = getClass( elem ); - cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " ); - - if ( cur ) { - j = 0; - while ( ( clazz = classes[ j++ ] ) ) { - if ( cur.indexOf( " " + clazz + " " ) < 0 ) { - cur += clazz + " "; - } - } - - // Only assign if different to avoid unneeded rendering. - finalValue = stripAndCollapse( cur ); - if ( curValue !== finalValue ) { - elem.setAttribute( "class", finalValue ); - } - } - } - } - - return this; - }, - - removeClass: function( value ) { - var classes, elem, cur, curValue, clazz, j, finalValue, - i = 0; - - if ( jQuery.isFunction( value ) ) { - return this.each( function( j ) { - jQuery( this ).removeClass( value.call( this, j, getClass( this ) ) ); - } ); - } - - if ( !arguments.length ) { - return this.attr( "class", "" ); - } - - if ( typeof value === "string" && value ) { - classes = value.match( rnothtmlwhite ) || []; - - while ( ( elem = this[ i++ ] ) ) { - curValue = getClass( elem ); - - // This expression is here for better compressibility (see addClass) - cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " ); - - if ( cur ) { - j = 0; - while ( ( clazz = classes[ j++ ] ) ) { - - // Remove *all* instances - while ( cur.indexOf( " " + clazz + " " ) > -1 ) { - cur = cur.replace( " " + clazz + " ", " " ); - } - } - - // Only assign if different to avoid unneeded rendering. - finalValue = stripAndCollapse( cur ); - if ( curValue !== finalValue ) { - elem.setAttribute( "class", finalValue ); - } - } - } - } - - return this; - }, - - toggleClass: function( value, stateVal ) { - var type = typeof value; - - if ( typeof stateVal === "boolean" && type === "string" ) { - return stateVal ? this.addClass( value ) : this.removeClass( value ); - } - - if ( jQuery.isFunction( value ) ) { - return this.each( function( i ) { - jQuery( this ).toggleClass( - value.call( this, i, getClass( this ), stateVal ), - stateVal - ); - } ); - } - - return this.each( function() { - var className, i, self, classNames; - - if ( type === "string" ) { - - // Toggle individual class names - i = 0; - self = jQuery( this ); - classNames = value.match( rnothtmlwhite ) || []; - - while ( ( className = classNames[ i++ ] ) ) { - - // Check each className given, space separated list - if ( self.hasClass( className ) ) { - self.removeClass( className ); - } else { - self.addClass( className ); - } - } - - // Toggle whole class name - } else if ( value === undefined || type === "boolean" ) { - className = getClass( this ); - if ( className ) { - - // Store className if set - dataPriv.set( this, "__className__", className ); - } - - // If the element has a class name or if we're passed `false`, - // then remove the whole classname (if there was one, the above saved it). - // Otherwise bring back whatever was previously saved (if anything), - // falling back to the empty string if nothing was stored. - if ( this.setAttribute ) { - this.setAttribute( "class", - className || value === false ? - "" : - dataPriv.get( this, "__className__" ) || "" - ); - } - } - } ); - }, - - hasClass: function( selector ) { - var className, elem, - i = 0; - - className = " " + selector + " "; - while ( ( elem = this[ i++ ] ) ) { - if ( elem.nodeType === 1 && - ( " " + stripAndCollapse( getClass( elem ) ) + " " ).indexOf( className ) > -1 ) { - return true; - } - } - - return false; - } -} ); - - - - -var rreturn = /\r/g; - -jQuery.fn.extend( { - val: function( value ) { - var hooks, ret, isFunction, - elem = this[ 0 ]; - - if ( !arguments.length ) { - if ( elem ) { - hooks = jQuery.valHooks[ elem.type ] || - jQuery.valHooks[ elem.nodeName.toLowerCase() ]; - - if ( hooks && - "get" in hooks && - ( ret = hooks.get( elem, "value" ) ) !== undefined - ) { - return ret; - } - - ret = elem.value; - - // Handle most common string cases - if ( typeof ret === "string" ) { - return ret.replace( rreturn, "" ); - } - - // Handle cases where value is null/undef or number - return ret == null ? "" : ret; - } - - return; - } - - isFunction = jQuery.isFunction( value ); - - return this.each( function( i ) { - var val; - - if ( this.nodeType !== 1 ) { - return; - } - - if ( isFunction ) { - val = value.call( this, i, jQuery( this ).val() ); - } else { - val = value; - } - - // Treat null/undefined as ""; convert numbers to string - if ( val == null ) { - val = ""; - - } else if ( typeof val === "number" ) { - val += ""; - - } else if ( Array.isArray( val ) ) { - val = jQuery.map( val, function( value ) { - return value == null ? "" : value + ""; - } ); - } - - hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ]; - - // If set returns undefined, fall back to normal setting - if ( !hooks || !( "set" in hooks ) || hooks.set( this, val, "value" ) === undefined ) { - this.value = val; - } - } ); - } -} ); - -jQuery.extend( { - valHooks: { - option: { - get: function( elem ) { - - var val = jQuery.find.attr( elem, "value" ); - return val != null ? - val : - - // Support: IE <=10 - 11 only - // option.text throws exceptions (#14686, #14858) - // Strip and collapse whitespace - // https://html.spec.whatwg.org/#strip-and-collapse-whitespace - stripAndCollapse( jQuery.text( elem ) ); - } - }, - select: { - get: function( elem ) { - var value, option, i, - options = elem.options, - index = elem.selectedIndex, - one = elem.type === "select-one", - values = one ? null : [], - max = one ? index + 1 : options.length; - - if ( index < 0 ) { - i = max; - - } else { - i = one ? index : 0; - } - - // Loop through all the selected options - for ( ; i < max; i++ ) { - option = options[ i ]; - - // Support: IE <=9 only - // IE8-9 doesn't update selected after form reset (#2551) - if ( ( option.selected || i === index ) && - - // Don't return options that are disabled or in a disabled optgroup - !option.disabled && - ( !option.parentNode.disabled || - !nodeName( option.parentNode, "optgroup" ) ) ) { - - // Get the specific value for the option - value = jQuery( option ).val(); - - // We don't need an array for one selects - if ( one ) { - return value; - } - - // Multi-Selects return an array - values.push( value ); - } - } - - return values; - }, - - set: function( elem, value ) { - var optionSet, option, - options = elem.options, - values = jQuery.makeArray( value ), - i = options.length; - - while ( i-- ) { - option = options[ i ]; - - /* eslint-disable no-cond-assign */ - - if ( option.selected = - jQuery.inArray( jQuery.valHooks.option.get( option ), values ) > -1 - ) { - optionSet = true; - } - - /* eslint-enable no-cond-assign */ - } - - // Force browsers to behave consistently when non-matching value is set - if ( !optionSet ) { - elem.selectedIndex = -1; - } - return values; - } - } - } -} ); - -// Radios and checkboxes getter/setter -jQuery.each( [ "radio", "checkbox" ], function() { - jQuery.valHooks[ this ] = { - set: function( elem, value ) { - if ( Array.isArray( value ) ) { - return ( elem.checked = jQuery.inArray( jQuery( elem ).val(), value ) > -1 ); - } - } - }; - if ( !support.checkOn ) { - jQuery.valHooks[ this ].get = function( elem ) { - return elem.getAttribute( "value" ) === null ? "on" : elem.value; - }; - } -} ); - - - - -// Return jQuery for attributes-only inclusion - - -var rfocusMorph = /^(?:focusinfocus|focusoutblur)$/; - -jQuery.extend( jQuery.event, { - - trigger: function( event, data, elem, onlyHandlers ) { - - var i, cur, tmp, bubbleType, ontype, handle, special, - eventPath = [ elem || document ], - type = hasOwn.call( event, "type" ) ? event.type : event, - namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split( "." ) : []; - - cur = tmp = elem = elem || document; - - // Don't do events on text and comment nodes - if ( elem.nodeType === 3 || elem.nodeType === 8 ) { - return; - } - - // focus/blur morphs to focusin/out; ensure we're not firing them right now - if ( rfocusMorph.test( type + jQuery.event.triggered ) ) { - return; - } - - if ( type.indexOf( "." ) > -1 ) { - - // Namespaced trigger; create a regexp to match event type in handle() - namespaces = type.split( "." ); - type = namespaces.shift(); - namespaces.sort(); - } - ontype = type.indexOf( ":" ) < 0 && "on" + type; - - // Caller can pass in a jQuery.Event object, Object, or just an event type string - event = event[ jQuery.expando ] ? - event : - new jQuery.Event( type, typeof event === "object" && event ); - - // Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true) - event.isTrigger = onlyHandlers ? 2 : 3; - event.namespace = namespaces.join( "." ); - event.rnamespace = event.namespace ? - new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ) : - null; - - // Clean up the event in case it is being reused - event.result = undefined; - if ( !event.target ) { - event.target = elem; - } - - // Clone any incoming data and prepend the event, creating the handler arg list - data = data == null ? - [ event ] : - jQuery.makeArray( data, [ event ] ); - - // Allow special events to draw outside the lines - special = jQuery.event.special[ type ] || {}; - if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) { - return; - } - - // Determine event propagation path in advance, per W3C events spec (#9951) - // Bubble up to document, then to window; watch for a global ownerDocument var (#9724) - if ( !onlyHandlers && !special.noBubble && !jQuery.isWindow( elem ) ) { - - bubbleType = special.delegateType || type; - if ( !rfocusMorph.test( bubbleType + type ) ) { - cur = cur.parentNode; - } - for ( ; cur; cur = cur.parentNode ) { - eventPath.push( cur ); - tmp = cur; - } - - // Only add window if we got to document (e.g., not plain obj or detached DOM) - if ( tmp === ( elem.ownerDocument || document ) ) { - eventPath.push( tmp.defaultView || tmp.parentWindow || window ); - } - } - - // Fire handlers on the event path - i = 0; - while ( ( cur = eventPath[ i++ ] ) && !event.isPropagationStopped() ) { - - event.type = i > 1 ? - bubbleType : - special.bindType || type; - - // jQuery handler - handle = ( dataPriv.get( cur, "events" ) || {} )[ event.type ] && - dataPriv.get( cur, "handle" ); - if ( handle ) { - handle.apply( cur, data ); - } - - // Native handler - handle = ontype && cur[ ontype ]; - if ( handle && handle.apply && acceptData( cur ) ) { - event.result = handle.apply( cur, data ); - if ( event.result === false ) { - event.preventDefault(); - } - } - } - event.type = type; - - // If nobody prevented the default action, do it now - if ( !onlyHandlers && !event.isDefaultPrevented() ) { - - if ( ( !special._default || - special._default.apply( eventPath.pop(), data ) === false ) && - acceptData( elem ) ) { - - // Call a native DOM method on the target with the same name as the event. - // Don't do default actions on window, that's where global variables be (#6170) - if ( ontype && jQuery.isFunction( elem[ type ] ) && !jQuery.isWindow( elem ) ) { - - // Don't re-trigger an onFOO event when we call its FOO() method - tmp = elem[ ontype ]; - - if ( tmp ) { - elem[ ontype ] = null; - } - - // Prevent re-triggering of the same event, since we already bubbled it above - jQuery.event.triggered = type; - elem[ type ](); - jQuery.event.triggered = undefined; - - if ( tmp ) { - elem[ ontype ] = tmp; - } - } - } - } - - return event.result; - }, - - // Piggyback on a donor event to simulate a different one - // Used only for `focus(in | out)` events - simulate: function( type, elem, event ) { - var e = jQuery.extend( - new jQuery.Event(), - event, - { - type: type, - isSimulated: true - } - ); - - jQuery.event.trigger( e, null, elem ); - } - -} ); - -jQuery.fn.extend( { - - trigger: function( type, data ) { - return this.each( function() { - jQuery.event.trigger( type, data, this ); - } ); - }, - triggerHandler: function( type, data ) { - var elem = this[ 0 ]; - if ( elem ) { - return jQuery.event.trigger( type, data, elem, true ); - } - } -} ); - - -jQuery.each( ( "blur focus focusin focusout resize scroll click dblclick " + - "mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " + - "change select submit keydown keypress keyup contextmenu" ).split( " " ), - function( i, name ) { - - // Handle event binding - jQuery.fn[ name ] = function( data, fn ) { - return arguments.length > 0 ? - this.on( name, null, data, fn ) : - this.trigger( name ); - }; -} ); - -jQuery.fn.extend( { - hover: function( fnOver, fnOut ) { - return this.mouseenter( fnOver ).mouseleave( fnOut || fnOver ); - } -} ); - - - - -support.focusin = "onfocusin" in window; - - -// Support: Firefox <=44 -// Firefox doesn't have focus(in | out) events -// Related ticket - https://bugzilla.mozilla.org/show_bug.cgi?id=687787 -// -// Support: Chrome <=48 - 49, Safari <=9.0 - 9.1 -// focus(in | out) events fire after focus & blur events, -// which is spec violation - http://www.w3.org/TR/DOM-Level-3-Events/#events-focusevent-event-order -// Related ticket - https://bugs.chromium.org/p/chromium/issues/detail?id=449857 -if ( !support.focusin ) { - jQuery.each( { focus: "focusin", blur: "focusout" }, function( orig, fix ) { - - // Attach a single capturing handler on the document while someone wants focusin/focusout - var handler = function( event ) { - jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ) ); - }; - - jQuery.event.special[ fix ] = { - setup: function() { - var doc = this.ownerDocument || this, - attaches = dataPriv.access( doc, fix ); - - if ( !attaches ) { - doc.addEventListener( orig, handler, true ); - } - dataPriv.access( doc, fix, ( attaches || 0 ) + 1 ); - }, - teardown: function() { - var doc = this.ownerDocument || this, - attaches = dataPriv.access( doc, fix ) - 1; - - if ( !attaches ) { - doc.removeEventListener( orig, handler, true ); - dataPriv.remove( doc, fix ); - - } else { - dataPriv.access( doc, fix, attaches ); - } - } - }; - } ); -} -var location = window.location; - -var nonce = jQuery.now(); - -var rquery = ( /\?/ ); - - - -// Cross-browser xml parsing -jQuery.parseXML = function( data ) { - var xml; - if ( !data || typeof data !== "string" ) { - return null; - } - - // Support: IE 9 - 11 only - // IE throws on parseFromString with invalid input. - try { - xml = ( new window.DOMParser() ).parseFromString( data, "text/xml" ); - } catch ( e ) { - xml = undefined; - } - - if ( !xml || xml.getElementsByTagName( "parsererror" ).length ) { - jQuery.error( "Invalid XML: " + data ); - } - return xml; -}; - - -var - rbracket = /\[\]$/, - rCRLF = /\r?\n/g, - rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i, - rsubmittable = /^(?:input|select|textarea|keygen)/i; - -function buildParams( prefix, obj, traditional, add ) { - var name; - - if ( Array.isArray( obj ) ) { - - // Serialize array item. - jQuery.each( obj, function( i, v ) { - if ( traditional || rbracket.test( prefix ) ) { - - // Treat each array item as a scalar. - add( prefix, v ); - - } else { - - // Item is non-scalar (array or object), encode its numeric index. - buildParams( - prefix + "[" + ( typeof v === "object" && v != null ? i : "" ) + "]", - v, - traditional, - add - ); - } - } ); - - } else if ( !traditional && jQuery.type( obj ) === "object" ) { - - // Serialize object item. - for ( name in obj ) { - buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add ); - } - - } else { - - // Serialize scalar item. - add( prefix, obj ); - } -} - -// Serialize an array of form elements or a set of -// key/values into a query string -jQuery.param = function( a, traditional ) { - var prefix, - s = [], - add = function( key, valueOrFunction ) { - - // If value is a function, invoke it and use its return value - var value = jQuery.isFunction( valueOrFunction ) ? - valueOrFunction() : - valueOrFunction; - - s[ s.length ] = encodeURIComponent( key ) + "=" + - encodeURIComponent( value == null ? "" : value ); - }; - - // If an array was passed in, assume that it is an array of form elements. - if ( Array.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) { - - // Serialize the form elements - jQuery.each( a, function() { - add( this.name, this.value ); - } ); - - } else { - - // If traditional, encode the "old" way (the way 1.3.2 or older - // did it), otherwise encode params recursively. - for ( prefix in a ) { - buildParams( prefix, a[ prefix ], traditional, add ); - } - } - - // Return the resulting serialization - return s.join( "&" ); -}; - -jQuery.fn.extend( { - serialize: function() { - return jQuery.param( this.serializeArray() ); - }, - serializeArray: function() { - return this.map( function() { - - // Can add propHook for "elements" to filter or add form elements - var elements = jQuery.prop( this, "elements" ); - return elements ? jQuery.makeArray( elements ) : this; - } ) - .filter( function() { - var type = this.type; - - // Use .is( ":disabled" ) so that fieldset[disabled] works - return this.name && !jQuery( this ).is( ":disabled" ) && - rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) && - ( this.checked || !rcheckableType.test( type ) ); - } ) - .map( function( i, elem ) { - var val = jQuery( this ).val(); - - if ( val == null ) { - return null; - } - - if ( Array.isArray( val ) ) { - return jQuery.map( val, function( val ) { - return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; - } ); - } - - return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; - } ).get(); - } -} ); - - -var - r20 = /%20/g, - rhash = /#.*$/, - rantiCache = /([?&])_=[^&]*/, - rheaders = /^(.*?):[ \t]*([^\r\n]*)$/mg, - - // #7653, #8125, #8152: local protocol detection - rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/, - rnoContent = /^(?:GET|HEAD)$/, - rprotocol = /^\/\//, - - /* Prefilters - * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example) - * 2) These are called: - * - BEFORE asking for a transport - * - AFTER param serialization (s.data is a string if s.processData is true) - * 3) key is the dataType - * 4) the catchall symbol "*" can be used - * 5) execution will start with transport dataType and THEN continue down to "*" if needed - */ - prefilters = {}, - - /* Transports bindings - * 1) key is the dataType - * 2) the catchall symbol "*" can be used - * 3) selection will start with transport dataType and THEN go to "*" if needed - */ - transports = {}, - - // Avoid comment-prolog char sequence (#10098); must appease lint and evade compression - allTypes = "*/".concat( "*" ), - - // Anchor tag for parsing the document origin - originAnchor = document.createElement( "a" ); - originAnchor.href = location.href; - -// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport -function addToPrefiltersOrTransports( structure ) { - - // dataTypeExpression is optional and defaults to "*" - return function( dataTypeExpression, func ) { - - if ( typeof dataTypeExpression !== "string" ) { - func = dataTypeExpression; - dataTypeExpression = "*"; - } - - var dataType, - i = 0, - dataTypes = dataTypeExpression.toLowerCase().match( rnothtmlwhite ) || []; - - if ( jQuery.isFunction( func ) ) { - - // For each dataType in the dataTypeExpression - while ( ( dataType = dataTypes[ i++ ] ) ) { - - // Prepend if requested - if ( dataType[ 0 ] === "+" ) { - dataType = dataType.slice( 1 ) || "*"; - ( structure[ dataType ] = structure[ dataType ] || [] ).unshift( func ); - - // Otherwise append - } else { - ( structure[ dataType ] = structure[ dataType ] || [] ).push( func ); - } - } - } - }; -} - -// Base inspection function for prefilters and transports -function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR ) { - - var inspected = {}, - seekingTransport = ( structure === transports ); - - function inspect( dataType ) { - var selected; - inspected[ dataType ] = true; - jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) { - var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR ); - if ( typeof dataTypeOrTransport === "string" && - !seekingTransport && !inspected[ dataTypeOrTransport ] ) { - - options.dataTypes.unshift( dataTypeOrTransport ); - inspect( dataTypeOrTransport ); - return false; - } else if ( seekingTransport ) { - return !( selected = dataTypeOrTransport ); - } - } ); - return selected; - } - - return inspect( options.dataTypes[ 0 ] ) || !inspected[ "*" ] && inspect( "*" ); -} - -// A special extend for ajax options -// that takes "flat" options (not to be deep extended) -// Fixes #9887 -function ajaxExtend( target, src ) { - var key, deep, - flatOptions = jQuery.ajaxSettings.flatOptions || {}; - - for ( key in src ) { - if ( src[ key ] !== undefined ) { - ( flatOptions[ key ] ? target : ( deep || ( deep = {} ) ) )[ key ] = src[ key ]; - } - } - if ( deep ) { - jQuery.extend( true, target, deep ); - } - - return target; -} - -/* Handles responses to an ajax request: - * - finds the right dataType (mediates between content-type and expected dataType) - * - returns the corresponding response - */ -function ajaxHandleResponses( s, jqXHR, responses ) { - - var ct, type, finalDataType, firstDataType, - contents = s.contents, - dataTypes = s.dataTypes; - - // Remove auto dataType and get content-type in the process - while ( dataTypes[ 0 ] === "*" ) { - dataTypes.shift(); - if ( ct === undefined ) { - ct = s.mimeType || jqXHR.getResponseHeader( "Content-Type" ); - } - } - - // Check if we're dealing with a known content-type - if ( ct ) { - for ( type in contents ) { - if ( contents[ type ] && contents[ type ].test( ct ) ) { - dataTypes.unshift( type ); - break; - } - } - } - - // Check to see if we have a response for the expected dataType - if ( dataTypes[ 0 ] in responses ) { - finalDataType = dataTypes[ 0 ]; - } else { - - // Try convertible dataTypes - for ( type in responses ) { - if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[ 0 ] ] ) { - finalDataType = type; - break; - } - if ( !firstDataType ) { - firstDataType = type; - } - } - - // Or just use first one - finalDataType = finalDataType || firstDataType; - } - - // If we found a dataType - // We add the dataType to the list if needed - // and return the corresponding response - if ( finalDataType ) { - if ( finalDataType !== dataTypes[ 0 ] ) { - dataTypes.unshift( finalDataType ); - } - return responses[ finalDataType ]; - } -} - -/* Chain conversions given the request and the original response - * Also sets the responseXXX fields on the jqXHR instance - */ -function ajaxConvert( s, response, jqXHR, isSuccess ) { - var conv2, current, conv, tmp, prev, - converters = {}, - - // Work with a copy of dataTypes in case we need to modify it for conversion - dataTypes = s.dataTypes.slice(); - - // Create converters map with lowercased keys - if ( dataTypes[ 1 ] ) { - for ( conv in s.converters ) { - converters[ conv.toLowerCase() ] = s.converters[ conv ]; - } - } - - current = dataTypes.shift(); - - // Convert to each sequential dataType - while ( current ) { - - if ( s.responseFields[ current ] ) { - jqXHR[ s.responseFields[ current ] ] = response; - } - - // Apply the dataFilter if provided - if ( !prev && isSuccess && s.dataFilter ) { - response = s.dataFilter( response, s.dataType ); - } - - prev = current; - current = dataTypes.shift(); - - if ( current ) { - - // There's only work to do if current dataType is non-auto - if ( current === "*" ) { - - current = prev; - - // Convert response if prev dataType is non-auto and differs from current - } else if ( prev !== "*" && prev !== current ) { - - // Seek a direct converter - conv = converters[ prev + " " + current ] || converters[ "* " + current ]; - - // If none found, seek a pair - if ( !conv ) { - for ( conv2 in converters ) { - - // If conv2 outputs current - tmp = conv2.split( " " ); - if ( tmp[ 1 ] === current ) { - - // If prev can be converted to accepted input - conv = converters[ prev + " " + tmp[ 0 ] ] || - converters[ "* " + tmp[ 0 ] ]; - if ( conv ) { - - // Condense equivalence converters - if ( conv === true ) { - conv = converters[ conv2 ]; - - // Otherwise, insert the intermediate dataType - } else if ( converters[ conv2 ] !== true ) { - current = tmp[ 0 ]; - dataTypes.unshift( tmp[ 1 ] ); - } - break; - } - } - } - } - - // Apply converter (if not an equivalence) - if ( conv !== true ) { - - // Unless errors are allowed to bubble, catch and return them - if ( conv && s.throws ) { - response = conv( response ); - } else { - try { - response = conv( response ); - } catch ( e ) { - return { - state: "parsererror", - error: conv ? e : "No conversion from " + prev + " to " + current - }; - } - } - } - } - } - } - - return { state: "success", data: response }; -} - -jQuery.extend( { - - // Counter for holding the number of active queries - active: 0, - - // Last-Modified header cache for next request - lastModified: {}, - etag: {}, - - ajaxSettings: { - url: location.href, - type: "GET", - isLocal: rlocalProtocol.test( location.protocol ), - global: true, - processData: true, - async: true, - contentType: "application/x-www-form-urlencoded; charset=UTF-8", - - /* - timeout: 0, - data: null, - dataType: null, - username: null, - password: null, - cache: null, - throws: false, - traditional: false, - headers: {}, - */ - - accepts: { - "*": allTypes, - text: "text/plain", - html: "text/html", - xml: "application/xml, text/xml", - json: "application/json, text/javascript" - }, - - contents: { - xml: /\bxml\b/, - html: /\bhtml/, - json: /\bjson\b/ - }, - - responseFields: { - xml: "responseXML", - text: "responseText", - json: "responseJSON" - }, - - // Data converters - // Keys separate source (or catchall "*") and destination types with a single space - converters: { - - // Convert anything to text - "* text": String, - - // Text to html (true = no transformation) - "text html": true, - - // Evaluate text as a json expression - "text json": JSON.parse, - - // Parse text as xml - "text xml": jQuery.parseXML - }, - - // For options that shouldn't be deep extended: - // you can add your own custom options here if - // and when you create one that shouldn't be - // deep extended (see ajaxExtend) - flatOptions: { - url: true, - context: true - } - }, - - // Creates a full fledged settings object into target - // with both ajaxSettings and settings fields. - // If target is omitted, writes into ajaxSettings. - ajaxSetup: function( target, settings ) { - return settings ? - - // Building a settings object - ajaxExtend( ajaxExtend( target, jQuery.ajaxSettings ), settings ) : - - // Extending ajaxSettings - ajaxExtend( jQuery.ajaxSettings, target ); - }, - - ajaxPrefilter: addToPrefiltersOrTransports( prefilters ), - ajaxTransport: addToPrefiltersOrTransports( transports ), - - // Main method - ajax: function( url, options ) { - - // If url is an object, simulate pre-1.5 signature - if ( typeof url === "object" ) { - options = url; - url = undefined; - } - - // Force options to be an object - options = options || {}; - - var transport, - - // URL without anti-cache param - cacheURL, - - // Response headers - responseHeadersString, - responseHeaders, - - // timeout handle - timeoutTimer, - - // Url cleanup var - urlAnchor, - - // Request state (becomes false upon send and true upon completion) - completed, - - // To know if global events are to be dispatched - fireGlobals, - - // Loop variable - i, - - // uncached part of the url - uncached, - - // Create the final options object - s = jQuery.ajaxSetup( {}, options ), - - // Callbacks context - callbackContext = s.context || s, - - // Context for global events is callbackContext if it is a DOM node or jQuery collection - globalEventContext = s.context && - ( callbackContext.nodeType || callbackContext.jquery ) ? - jQuery( callbackContext ) : - jQuery.event, - - // Deferreds - deferred = jQuery.Deferred(), - completeDeferred = jQuery.Callbacks( "once memory" ), - - // Status-dependent callbacks - statusCode = s.statusCode || {}, - - // Headers (they are sent all at once) - requestHeaders = {}, - requestHeadersNames = {}, - - // Default abort message - strAbort = "canceled", - - // Fake xhr - jqXHR = { - readyState: 0, - - // Builds headers hashtable if needed - getResponseHeader: function( key ) { - var match; - if ( completed ) { - if ( !responseHeaders ) { - responseHeaders = {}; - while ( ( match = rheaders.exec( responseHeadersString ) ) ) { - responseHeaders[ match[ 1 ].toLowerCase() ] = match[ 2 ]; - } - } - match = responseHeaders[ key.toLowerCase() ]; - } - return match == null ? null : match; - }, - - // Raw string - getAllResponseHeaders: function() { - return completed ? responseHeadersString : null; - }, - - // Caches the header - setRequestHeader: function( name, value ) { - if ( completed == null ) { - name = requestHeadersNames[ name.toLowerCase() ] = - requestHeadersNames[ name.toLowerCase() ] || name; - requestHeaders[ name ] = value; - } - return this; - }, - - // Overrides response content-type header - overrideMimeType: function( type ) { - if ( completed == null ) { - s.mimeType = type; - } - return this; - }, - - // Status-dependent callbacks - statusCode: function( map ) { - var code; - if ( map ) { - if ( completed ) { - - // Execute the appropriate callbacks - jqXHR.always( map[ jqXHR.status ] ); - } else { - - // Lazy-add the new callbacks in a way that preserves old ones - for ( code in map ) { - statusCode[ code ] = [ statusCode[ code ], map[ code ] ]; - } - } - } - return this; - }, - - // Cancel the request - abort: function( statusText ) { - var finalText = statusText || strAbort; - if ( transport ) { - transport.abort( finalText ); - } - done( 0, finalText ); - return this; - } - }; - - // Attach deferreds - deferred.promise( jqXHR ); - - // Add protocol if not provided (prefilters might expect it) - // Handle falsy url in the settings object (#10093: consistency with old signature) - // We also use the url parameter if available - s.url = ( ( url || s.url || location.href ) + "" ) - .replace( rprotocol, location.protocol + "//" ); - - // Alias method option to type as per ticket #12004 - s.type = options.method || options.type || s.method || s.type; - - // Extract dataTypes list - s.dataTypes = ( s.dataType || "*" ).toLowerCase().match( rnothtmlwhite ) || [ "" ]; - - // A cross-domain request is in order when the origin doesn't match the current origin. - if ( s.crossDomain == null ) { - urlAnchor = document.createElement( "a" ); - - // Support: IE <=8 - 11, Edge 12 - 13 - // IE throws exception on accessing the href property if url is malformed, - // e.g. http://example.com:80x/ - try { - urlAnchor.href = s.url; - - // Support: IE <=8 - 11 only - // Anchor's host property isn't correctly set when s.url is relative - urlAnchor.href = urlAnchor.href; - s.crossDomain = originAnchor.protocol + "//" + originAnchor.host !== - urlAnchor.protocol + "//" + urlAnchor.host; - } catch ( e ) { - - // If there is an error parsing the URL, assume it is crossDomain, - // it can be rejected by the transport if it is invalid - s.crossDomain = true; - } - } - - // Convert data if not already a string - if ( s.data && s.processData && typeof s.data !== "string" ) { - s.data = jQuery.param( s.data, s.traditional ); - } - - // Apply prefilters - inspectPrefiltersOrTransports( prefilters, s, options, jqXHR ); - - // If request was aborted inside a prefilter, stop there - if ( completed ) { - return jqXHR; - } - - // We can fire global events as of now if asked to - // Don't fire events if jQuery.event is undefined in an AMD-usage scenario (#15118) - fireGlobals = jQuery.event && s.global; - - // Watch for a new set of requests - if ( fireGlobals && jQuery.active++ === 0 ) { - jQuery.event.trigger( "ajaxStart" ); - } - - // Uppercase the type - s.type = s.type.toUpperCase(); - - // Determine if request has content - s.hasContent = !rnoContent.test( s.type ); - - // Save the URL in case we're toying with the If-Modified-Since - // and/or If-None-Match header later on - // Remove hash to simplify url manipulation - cacheURL = s.url.replace( rhash, "" ); - - // More options handling for requests with no content - if ( !s.hasContent ) { - - // Remember the hash so we can put it back - uncached = s.url.slice( cacheURL.length ); - - // If data is available, append data to url - if ( s.data ) { - cacheURL += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data; - - // #9682: remove data so that it's not used in an eventual retry - delete s.data; - } - - // Add or update anti-cache param if needed - if ( s.cache === false ) { - cacheURL = cacheURL.replace( rantiCache, "$1" ); - uncached = ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + ( nonce++ ) + uncached; - } - - // Put hash and anti-cache on the URL that will be requested (gh-1732) - s.url = cacheURL + uncached; - - // Change '%20' to '+' if this is encoded form body content (gh-2658) - } else if ( s.data && s.processData && - ( s.contentType || "" ).indexOf( "application/x-www-form-urlencoded" ) === 0 ) { - s.data = s.data.replace( r20, "+" ); - } - - // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. - if ( s.ifModified ) { - if ( jQuery.lastModified[ cacheURL ] ) { - jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ cacheURL ] ); - } - if ( jQuery.etag[ cacheURL ] ) { - jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ cacheURL ] ); - } - } - - // Set the correct header, if data is being sent - if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) { - jqXHR.setRequestHeader( "Content-Type", s.contentType ); - } - - // Set the Accepts header for the server, depending on the dataType - jqXHR.setRequestHeader( - "Accept", - s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[ 0 ] ] ? - s.accepts[ s.dataTypes[ 0 ] ] + - ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) : - s.accepts[ "*" ] - ); - - // Check for headers option - for ( i in s.headers ) { - jqXHR.setRequestHeader( i, s.headers[ i ] ); - } - - // Allow custom headers/mimetypes and early abort - if ( s.beforeSend && - ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || completed ) ) { - - // Abort if not done already and return - return jqXHR.abort(); - } - - // Aborting is no longer a cancellation - strAbort = "abort"; - - // Install callbacks on deferreds - completeDeferred.add( s.complete ); - jqXHR.done( s.success ); - jqXHR.fail( s.error ); - - // Get transport - transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR ); - - // If no transport, we auto-abort - if ( !transport ) { - done( -1, "No Transport" ); - } else { - jqXHR.readyState = 1; - - // Send global event - if ( fireGlobals ) { - globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] ); - } - - // If request was aborted inside ajaxSend, stop there - if ( completed ) { - return jqXHR; - } - - // Timeout - if ( s.async && s.timeout > 0 ) { - timeoutTimer = window.setTimeout( function() { - jqXHR.abort( "timeout" ); - }, s.timeout ); - } - - try { - completed = false; - transport.send( requestHeaders, done ); - } catch ( e ) { - - // Rethrow post-completion exceptions - if ( completed ) { - throw e; - } - - // Propagate others as results - done( -1, e ); - } - } - - // Callback for when everything is done - function done( status, nativeStatusText, responses, headers ) { - var isSuccess, success, error, response, modified, - statusText = nativeStatusText; - - // Ignore repeat invocations - if ( completed ) { - return; - } - - completed = true; - - // Clear timeout if it exists - if ( timeoutTimer ) { - window.clearTimeout( timeoutTimer ); - } - - // Dereference transport for early garbage collection - // (no matter how long the jqXHR object will be used) - transport = undefined; - - // Cache response headers - responseHeadersString = headers || ""; - - // Set readyState - jqXHR.readyState = status > 0 ? 4 : 0; - - // Determine if successful - isSuccess = status >= 200 && status < 300 || status === 304; - - // Get response data - if ( responses ) { - response = ajaxHandleResponses( s, jqXHR, responses ); - } - - // Convert no matter what (that way responseXXX fields are always set) - response = ajaxConvert( s, response, jqXHR, isSuccess ); - - // If successful, handle type chaining - if ( isSuccess ) { - - // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. - if ( s.ifModified ) { - modified = jqXHR.getResponseHeader( "Last-Modified" ); - if ( modified ) { - jQuery.lastModified[ cacheURL ] = modified; - } - modified = jqXHR.getResponseHeader( "etag" ); - if ( modified ) { - jQuery.etag[ cacheURL ] = modified; - } - } - - // if no content - if ( status === 204 || s.type === "HEAD" ) { - statusText = "nocontent"; - - // if not modified - } else if ( status === 304 ) { - statusText = "notmodified"; - - // If we have data, let's convert it - } else { - statusText = response.state; - success = response.data; - error = response.error; - isSuccess = !error; - } - } else { - - // Extract error from statusText and normalize for non-aborts - error = statusText; - if ( status || !statusText ) { - statusText = "error"; - if ( status < 0 ) { - status = 0; - } - } - } - - // Set data for the fake xhr object - jqXHR.status = status; - jqXHR.statusText = ( nativeStatusText || statusText ) + ""; - - // Success/Error - if ( isSuccess ) { - deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] ); - } else { - deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] ); - } - - // Status-dependent callbacks - jqXHR.statusCode( statusCode ); - statusCode = undefined; - - if ( fireGlobals ) { - globalEventContext.trigger( isSuccess ? "ajaxSuccess" : "ajaxError", - [ jqXHR, s, isSuccess ? success : error ] ); - } - - // Complete - completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] ); - - if ( fireGlobals ) { - globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] ); - - // Handle the global AJAX counter - if ( !( --jQuery.active ) ) { - jQuery.event.trigger( "ajaxStop" ); - } - } - } - - return jqXHR; - }, - - getJSON: function( url, data, callback ) { - return jQuery.get( url, data, callback, "json" ); - }, - - getScript: function( url, callback ) { - return jQuery.get( url, undefined, callback, "script" ); - } -} ); - -jQuery.each( [ "get", "post" ], function( i, method ) { - jQuery[ method ] = function( url, data, callback, type ) { - - // Shift arguments if data argument was omitted - if ( jQuery.isFunction( data ) ) { - type = type || callback; - callback = data; - data = undefined; - } - - // The url can be an options object (which then must have .url) - return jQuery.ajax( jQuery.extend( { - url: url, - type: method, - dataType: type, - data: data, - success: callback - }, jQuery.isPlainObject( url ) && url ) ); - }; -} ); - - -jQuery._evalUrl = function( url ) { - return jQuery.ajax( { - url: url, - - // Make this explicit, since user can override this through ajaxSetup (#11264) - type: "GET", - dataType: "script", - cache: true, - async: false, - global: false, - "throws": true - } ); -}; - - -jQuery.fn.extend( { - wrapAll: function( html ) { - var wrap; - - if ( this[ 0 ] ) { - if ( jQuery.isFunction( html ) ) { - html = html.call( this[ 0 ] ); - } - - // The elements to wrap the target around - wrap = jQuery( html, this[ 0 ].ownerDocument ).eq( 0 ).clone( true ); - - if ( this[ 0 ].parentNode ) { - wrap.insertBefore( this[ 0 ] ); - } - - wrap.map( function() { - var elem = this; - - while ( elem.firstElementChild ) { - elem = elem.firstElementChild; - } - - return elem; - } ).append( this ); - } - - return this; - }, - - wrapInner: function( html ) { - if ( jQuery.isFunction( html ) ) { - return this.each( function( i ) { - jQuery( this ).wrapInner( html.call( this, i ) ); - } ); - } - - return this.each( function() { - var self = jQuery( this ), - contents = self.contents(); - - if ( contents.length ) { - contents.wrapAll( html ); - - } else { - self.append( html ); - } - } ); - }, - - wrap: function( html ) { - var isFunction = jQuery.isFunction( html ); - - return this.each( function( i ) { - jQuery( this ).wrapAll( isFunction ? html.call( this, i ) : html ); - } ); - }, - - unwrap: function( selector ) { - this.parent( selector ).not( "body" ).each( function() { - jQuery( this ).replaceWith( this.childNodes ); - } ); - return this; - } -} ); - - -jQuery.expr.pseudos.hidden = function( elem ) { - return !jQuery.expr.pseudos.visible( elem ); -}; -jQuery.expr.pseudos.visible = function( elem ) { - return !!( elem.offsetWidth || elem.offsetHeight || elem.getClientRects().length ); -}; - - - - -jQuery.ajaxSettings.xhr = function() { - try { - return new window.XMLHttpRequest(); - } catch ( e ) {} -}; - -var xhrSuccessStatus = { - - // File protocol always yields status code 0, assume 200 - 0: 200, - - // Support: IE <=9 only - // #1450: sometimes IE returns 1223 when it should be 204 - 1223: 204 - }, - xhrSupported = jQuery.ajaxSettings.xhr(); - -support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported ); -support.ajax = xhrSupported = !!xhrSupported; - -jQuery.ajaxTransport( function( options ) { - var callback, errorCallback; - - // Cross domain only allowed if supported through XMLHttpRequest - if ( support.cors || xhrSupported && !options.crossDomain ) { - return { - send: function( headers, complete ) { - var i, - xhr = options.xhr(); - - xhr.open( - options.type, - options.url, - options.async, - options.username, - options.password - ); - - // Apply custom fields if provided - if ( options.xhrFields ) { - for ( i in options.xhrFields ) { - xhr[ i ] = options.xhrFields[ i ]; - } - } - - // Override mime type if needed - if ( options.mimeType && xhr.overrideMimeType ) { - xhr.overrideMimeType( options.mimeType ); - } - - // X-Requested-With header - // For cross-domain requests, seeing as conditions for a preflight are - // akin to a jigsaw puzzle, we simply never set it to be sure. - // (it can always be set on a per-request basis or even using ajaxSetup) - // For same-domain requests, won't change header if already provided. - if ( !options.crossDomain && !headers[ "X-Requested-With" ] ) { - headers[ "X-Requested-With" ] = "XMLHttpRequest"; - } - - // Set headers - for ( i in headers ) { - xhr.setRequestHeader( i, headers[ i ] ); - } - - // Callback - callback = function( type ) { - return function() { - if ( callback ) { - callback = errorCallback = xhr.onload = - xhr.onerror = xhr.onabort = xhr.onreadystatechange = null; - - if ( type === "abort" ) { - xhr.abort(); - } else if ( type === "error" ) { - - // Support: IE <=9 only - // On a manual native abort, IE9 throws - // errors on any property access that is not readyState - if ( typeof xhr.status !== "number" ) { - complete( 0, "error" ); - } else { - complete( - - // File: protocol always yields status 0; see #8605, #14207 - xhr.status, - xhr.statusText - ); - } - } else { - complete( - xhrSuccessStatus[ xhr.status ] || xhr.status, - xhr.statusText, - - // Support: IE <=9 only - // IE9 has no XHR2 but throws on binary (trac-11426) - // For XHR2 non-text, let the caller handle it (gh-2498) - ( xhr.responseType || "text" ) !== "text" || - typeof xhr.responseText !== "string" ? - { binary: xhr.response } : - { text: xhr.responseText }, - xhr.getAllResponseHeaders() - ); - } - } - }; - }; - - // Listen to events - xhr.onload = callback(); - errorCallback = xhr.onerror = callback( "error" ); - - // Support: IE 9 only - // Use onreadystatechange to replace onabort - // to handle uncaught aborts - if ( xhr.onabort !== undefined ) { - xhr.onabort = errorCallback; - } else { - xhr.onreadystatechange = function() { - - // Check readyState before timeout as it changes - if ( xhr.readyState === 4 ) { - - // Allow onerror to be called first, - // but that will not handle a native abort - // Also, save errorCallback to a variable - // as xhr.onerror cannot be accessed - window.setTimeout( function() { - if ( callback ) { - errorCallback(); - } - } ); - } - }; - } - - // Create the abort callback - callback = callback( "abort" ); - - try { - - // Do send the request (this may raise an exception) - xhr.send( options.hasContent && options.data || null ); - } catch ( e ) { - - // #14683: Only rethrow if this hasn't been notified as an error yet - if ( callback ) { - throw e; - } - } - }, - - abort: function() { - if ( callback ) { - callback(); - } - } - }; - } -} ); - - - - -// Prevent auto-execution of scripts when no explicit dataType was provided (See gh-2432) -jQuery.ajaxPrefilter( function( s ) { - if ( s.crossDomain ) { - s.contents.script = false; - } -} ); - -// Install script dataType -jQuery.ajaxSetup( { - accepts: { - script: "text/javascript, application/javascript, " + - "application/ecmascript, application/x-ecmascript" - }, - contents: { - script: /\b(?:java|ecma)script\b/ - }, - converters: { - "text script": function( text ) { - jQuery.globalEval( text ); - return text; - } - } -} ); - -// Handle cache's special case and crossDomain -jQuery.ajaxPrefilter( "script", function( s ) { - if ( s.cache === undefined ) { - s.cache = false; - } - if ( s.crossDomain ) { - s.type = "GET"; - } -} ); - -// Bind script tag hack transport -jQuery.ajaxTransport( "script", function( s ) { - - // This transport only deals with cross domain requests - if ( s.crossDomain ) { - var script, callback; - return { - send: function( _, complete ) { - script = jQuery( " - - - - - - - - - - - - - - - - - - - - - - -
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Changelog

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0.7.2 (2020-07-18)

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0.7.1 (2020-06-27)

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0.7.0 (2020-01-18)

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  • new tool: OTTER
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  • unit test for OTTER
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  • tweaks for compatibility of gpuPANDA with cupy
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0.6.2 (Stockholm) (2020-05-15)

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  • Added gpuPANDA, which is a gpu-accelerated implementation of PANDA
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  • Added gpuLIONESS
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  • Added a gpuPANDA and gpuLIONESS tutorial
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  • Fixed condor dependency to python-igraph (still under investigation in #82 )
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0.6.1 (2020-01-18)

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  • sambar tutorial
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  • condor tutorial
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  • added 3.8 to Ubunutu test server (along with 3.6 and 3.7 )
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    • Union: adds rows for genes/TFs that are missing in at least one prior (expression, ppi, motif)
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    • Intersection: removes TF/genes that missing in at least one prior
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    • Legacy: previous data processing behavior
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  • The default was set to union in netZooM, netZooR, netZooPy as it is the default in netZooC.
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0.5.0 (2019-11-22)

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0.4.0 (2019-11-18)

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0.3.0 (2019-11-14)

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0.2.0 (2019-11-13)

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0.1.1 (2019-9-3)

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0.1.0 (2019-7-26)

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  • transition to python 3
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  • pypanda: original import and NaN values in normalized matrices are replaced with values normalized by the overall z-score. This allows running the Toy Data provided in this repository.
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Functions

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netZooPy.panda

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analyze_panda

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class AnalyzePanda

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 AnalyzePanda(Panda)
- Network plot.
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top_network_plot

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 top_network_plot(self, top = 100, file = 'panda_top_100.png')
- Select top genes
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shape_plot_network

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__shape_plot_network(self, subset_panda_results, file = 'panda.png')
-Create plot
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create_plot

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__create_plot(self, unique_genes, links, file = 'panda.png')
-Run plot
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run_panda

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Description:
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-    Run PANDA algorithm from the command line.
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-Usage:
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-    -h, --help: help
-    -e, --expression: expression values
-    -m, --motif: pair file of motif edges, or Pearson correlation matrix when not provided
-    -p, --ppi: pair file of PPI edges
-    -o, --out: output file
-    -r, --rm_missing
-    -q, --lioness: output for Lioness single sample networks
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-Example:
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-    python run_panda.py -e ./ToyData/ToyExpressionData.txt -m ./ToyData/ToyMotifData.txt -p ./ToyData/ToyPPIData.txt -o test_panda.txt -q output_panda.txt
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panda

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class Panda

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Panda(object)
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-Description:
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-	Using PANDA to infer gene regulatory network.
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-Usage:
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-	1. Reading in input data (expression data, motif prior, TF PPI data)
-	2. Computing coexpression network
-	3. Normalizing networks
-	4. Running PANDA algorithm
-	5. Writing out PANDA network
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-Authors: 
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-cychen, davidvi, alessandromarin
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init
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init__(self, expression_file, motif_file, ppi_file, save_memory = False, save_tmp=True, remove_missing=False, keep_expression_matrix = False):
-    # =====================================================================
-    # Data loading
-    # =====================================================================
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remove_missing
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remove_missing(self)
-    Remove genes and tfs not present in all files.
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normalize_network
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normalize_network(self, x)
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panda_loop
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panda_loop(self, correlation_matrix, motif_matrix, ppi_matrix)
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t_function
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update_diagonal
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update_diagonal(diagonal_matrix, num, alpha, step)
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pearson_results_data_frame
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pearson_results_data_frame(self)
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save_panda_results
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save_panda_results(self, path='panda.npy')
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top_network_plot
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top_network_plot(self, top = 100, file = 'panda_top_100.png')
-    Select top genes.
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shape_plot_network
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shape_plot_network(self, subset_panda_results, file = 'panda.png')
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create_plot
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create_plot(self, unique_genes, links, file = 'panda.png')
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split_label
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split_label(label)
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return_panda_indegree
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return_panda_indegree(self)
-    Return Panda indegree.
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return_panda_outdegree
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return_panda_outdegree(self)
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netZooPy.lioness

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run_lioness

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Description:
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-    Run LIONESS algorithm from the command line.
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-Usage:
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-    -h, --help: help
-    -e, --expression: expression matrix (.npy)
-    -m, --motif: motif matrix, normalized (.npy)
-    -p, --ppi: ppi matrix, normalized (.npy)
-    -n, --npy: PANDA network (.npy)
-    -o, --out: output folder
-    -f, --format: output format (txt, npy, or mat)
-    start: to start from nth sample (optional)
-    end: to end at nth sample (optional, must with start)
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-Example:
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-    python run_lioness.py -e expression.npy -m motif.npy -p ppi.npy -n panda.npy -o /tmp -f npy 1 100
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lioness

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class Lioness

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Lioness(Panda)
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-Description:
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-   Using LIONESS to infer single-sample gene regulatory networks.
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-Usage:
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-   1. Reading in PANDA network and preprocessed middle data
-   2. Computing coexpression network
-   3. Normalizing coexpression network
-   4. Running PANDA algorithm
-   5. Writing out LIONESS networks
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-Authors:
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-   cychen, davidvi
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init
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init__(self, obj, start=1, end=None, save_dir='lioness_output', save_fmt='npy')
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lioness_loop
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lioness_loop(self)
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save_lioness_results
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save_lioness_results(self, file='lioness.txt')
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analyze_lioness

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class AnalyzeLioness

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AnalyzeLioness(Lioness)
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init
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init__(self, lioness_data)
-Load variables from lioness.
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top_network_plot
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top_network_plot(self, column = 0, top = 100, file = 'lioness_top_100.png')
-Select top genes.
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lioness_for_puma

-
-

class LionessPuma

-
LionessPuma(Puma)
-
-Description:
-     Using LIONESS to infer single-sample gene regulatory networks.
-
-Usage:
-    1. Reading in PUMA network and preprocessed middle data
-    2. Computing coexpression network
-    3. Normalizing coexpression network
-    4. Running PUMA algorithm
-    5. Writing out LIONESS networks
-
-Authors:
-    cychen, davidvi
-
-
-
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init
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init__(self, obj, start=1, end=None, save_dir='lioness_output', save_fmt='npy')
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lioness_loop
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 lioness_loop(self)
-
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save_lioness_results
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 save_lioness_results(self, file='lioness.txt')
-
-
-
-
-
-
-
-

netZooPy.puma

-
-

run_puma

-
Description:
-    Run PUMA algorithm from the command line.
-
-Usage:
-    run_puma
-    -h, --help: help
-    -e, --expression: expression values
-    -m, --motif: pair file of motif edges, or Pearson correlation matrix when not provided
-    -p, --ppi: pair file of PPI edges
-    -i, --mir (required): miR file
-    -o, --out: output file
-    -r, --rm_missing
-    -q, --lioness: output for Lioness single sample networks
-
- Example:
-     python run_puma.py -e ./ToyData/ToyExpressionData.txt -m ./ToyData/ToyMotifData.txt -p ./ToyData/ToyPPIData.txt -i ToyData/ToyMiRList.txt -o test_puma.txt -q output_lioness.txt
-
-
-
-
-

puma

-
-

class Puma

-
Puma(object)
-
-Description:
-    Using PUMA to infer gene regulatory network.
-
-Usage:
-    1. Reading in input data (expression data, motif prior, TF PPI data, miR)
-    2. Computing coexpression network
-    3. Normalizing networks
-    4. Running PUMA algorithm
-    5. Writing out PUMA network
-
-Authors:
-    cychen, davidvi, alessandromarin
-
-
-
-
init
-
init__(self, expression_file, motif_file, ppi_file, mir_file, save_memory = False, save_tmp=True, remove_missing=False, keep_expression_matrix = False)
-# =====================================================================
-# Data loading
-# =====================================================================
-
-
-
-
-
remove_missing
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remove_missing(self)
-Remove genes and tfs not present in all files.
-
-
-
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normalize_network
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normalize_network(self, x)
-
-
-
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puma_loop
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puma_loop(self, correlation_matrix, motif_matrix, ppi_matrix)
-Puma algorithm
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-
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t_function
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t_function(x, y=None)
-T function
-
-
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update_diagonal
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update_diagonal(diagonal_matrix, num, alpha, step)
-Update diagoanl
-
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pearson_results_data_frame
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pearson_results_data_frame(self)
-Results to data frame
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pearson_results_data_frame
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pearson_results_data_frame(self)
-Results to data frame.
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save_puma_results
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save_puma_results(self, path='puma.npy')
-
-
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top_network_plot
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top_network_plot(self, top = 100, file = 'puma_top_100.png')
-Select top genes.
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shape_plot_network
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shape_plot_network(self, subset_puma_results, file = 'puma.png')
-Create plot
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-
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create_plot
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create_plot(self, unique_genes, links, file = 'puma.png')
-Run plot
-
-
-
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split_label
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split_label(label)
-
-
-
-
-
-
return_puma_indegree
-
return_puma_indegree(self)
-Return Puma indegree
-
-
-
-
-
return_puma_outdegree
-
 return_puma_outdegree(self)
- Return Puma outdegree
-
-
-
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Home

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netZooPy is a catalog of methods for the reconstruction and analysis of gene regulatory networks.

-

netZooPy has started as a merge of the following repositories and forks:

-
    -
  • pypanda from David Van Ijzendorn,
    • -
  • Alessandro Marin’s pypanda and Marieke Kuijjer’s pypuma fork, and
    • -
  • Cho-Yi Chen’s fork.
    • -
  • Genis Calderer’s pysambar and pycondor
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Installation guide

-

To install netZooPy on your computer, please check the following requirements:

-
-

Requirements

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    -
  • Python 3
    • -
-

In addition to the following pip packages:

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    -
  • networkx
    • -
  • numpy
    • -
  • pandas
    • -
  • matplotlib
    • -
  • scipy
    • -
  • python-igraph
    • -
-
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Install

-
    -
  • git clone https://github.com/netZoo/netZooPy.git
    • -
  • cd netZooPy
    • -
  • pip3 install -e .
    • -
  • Then you can import netZooPy in your code through import netZooPy
    • -
-
-
-

Troubleshooting

-
    -

  • If you experience installation issues with igraph on MacOs. Please install igraph through brew install igraph.

    -

    Please refer to the detailed error fix for MacOs and Ubuntu here.

    -

    Refer to the igraph instrallation manual

    -
    • -

  • To report any installation issue or function bug, please report through opening an issue on github.

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Tutorials

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Tutorials in netZooPy use Jupter notebooks.

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- - - - - - - - - - - - \ No newline at end of file diff --git a/docs/_static/netZoo_logo_v14.png b/docs/_static/netZoo_logo_v14.png new file mode 100644 index 00000000..f9c382ea Binary files /dev/null and b/docs/_static/netZoo_logo_v14.png differ diff --git a/docs/_static/netZoo_logo_v14_nobcg.png b/docs/_static/netZoo_logo_v14_nobcg.png new file mode 100644 index 00000000..aa412573 Binary files /dev/null and b/docs/_static/netZoo_logo_v14_nobcg.png differ diff --git a/docs/_templates/layout.html b/docs/_templates/layout.html new file mode 100644 index 00000000..2def3782 --- /dev/null +++ b/docs/_templates/layout.html @@ -0,0 +1,19 @@ +{% extends "!layout.html" %} + {% block footer %} {{ super() }} + + +{% endblock %} \ No newline at end of file diff --git a/docs/changelog.rst b/docs/changelog.rst index ac0e993c..099459ff 100644 --- a/docs/changelog.rst +++ b/docs/changelog.rst @@ -3,6 +3,22 @@ Changelog ========== +0.9.2 (2022-02-25) +------------------ +- added command line interface (panda, lioness) +- updating documentation + +0.9.0 (2022-02-11) +------------------ +- we fixed the panda-lioness and puma-lioness behavior ( panda was passing the updated motif to lioness ). The results are now compatible with the ones of netzooR. +- removed py3.6 support +- updated version on anaconda.org + +0.8.0 (2021-06-08) +------------------- +- support for Python v3.9 +- addition of DRAGON + unit tests +tutorial and many bug fixes that Daniel and Marouen have been doing as a user requests + 0.7.2 (2020-07-18) ------------------ diff --git a/docs/conf.py b/docs/conf.py index 1bdd7de3..3e68367e 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -12,9 +12,13 @@ # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # -# import os -# import sys -# sys.path.insert(0, os.path.abspath('.')) +import os +import sys +sys.path.insert(0, os.path.abspath('.')) +sys.path.insert(0, os.path.abspath('../..')) +sys.path.insert(0, os.path.abspath("../../netZooPy")) +sys.path.insert(0, os.path.abspath("../netZooPy")) +sys.path.insert(0, os.path.abspath("../../netZooPy/docs/")) # -- Project information ----------------------------------------------------- @@ -24,7 +28,7 @@ author = u'netZoo' # The short X.Y version -__version__ = "0.1.1" +__version__ = "0.9.1" version = ".".join(__version__.split(".")[:2]) # The full version, including alpha/beta/rc tags release = __version__ @@ -39,12 +43,28 @@ # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. -extensions = ['releases'] +#extensions = ['releases','myst_parser'] + +extensions = [ + 'myst_parser', + 'sphinx.ext.intersphinx', + 'sphinx.ext.mathjax', + 'sphinx.ext.ifconfig', + 'sphinx.ext.viewcode', + 'sphinx.ext.todo', + 'sphinx.ext.viewcode', + 'sphinx.ext.githubpages', + 'sphinx.ext.autodoc', + 'sphinx.ext.coverage', + 'sphinx.ext.napoleon', + 'sphinx_rtd_theme', + 'sphinx_click', + 'sphinx.ext.autosectionlabel'] # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] -releases_github_path = "netZoo/netZooPy" # NOTE Change to "velocyto-team/velocyto.py" upon public release -releases_unstable_prehistory = True +#releases_github_path = "netZoo/netZooPy" # NOTE Change to "velocyto-team/velocyto.py" upon public release +#releases_unstable_prehistory = True # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: @@ -87,11 +107,27 @@ # # html_theme_options = {} + # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] +html_logo = "_static/netZoo_logo_v14_nobcg.png" +html_theme_options = { + 'canonical_url': '', + 'logo_only': False, + 'display_version': True, + 'prev_next_buttons_location': 'bottom', + 'style_external_links': False, + # Toc options + 'collapse_navigation': True, + 'sticky_navigation': True, + 'navigation_depth': 4, + 'includehidden': True, + 'titles_only': False, + +} # Custom sidebar templates, must be a dictionary that maps document names # to template names. # @@ -160,10 +196,15 @@ ] -from recommonmark.parser import CommonMarkParser +#from recommonmark.parser import CommonMarkParser -source_parsers = { - '.md': CommonMarkParser, -} +#source_parsers = { +# '.md': CommonMarkParser, +#} -source_suffix = ['.rst', '.md'] +#source_suffix = ['.rst', '.md'] +source_suffix = { + '.rst': 'restructuredtext', + '.txt': 'markdown', + '.md': 'markdown', +} diff --git a/docs/functions/api.rst b/docs/functions/api.rst new file mode 100644 index 00000000..84865576 --- /dev/null +++ b/docs/functions/api.rst @@ -0,0 +1,73 @@ +The Animals (API) +------------------- + + +Panda +====== + +.. autoclass:: netZooPy.panda.panda.Panda + :members: + :undoc-members: + :inherited-members: + :private-members: + +.. autoclass:: netZooPy.panda.analyze_panda.AnalyzePanda + :members: + :undoc-members: + :private-members: + +Condor +====== + +.. autoclass:: netZooPy.condor.condor.condor_object + :members: + :undoc-members: + :inherited-members: + :private-members: + +Other function +~~~~~~~~~~~~~~~ +.. autofunction:: netZooPy.condor.run_condor + +Lioness +========= + + +.. autoclass:: netZooPy.lioness.lioness.Lioness + :members: + :undoc-members: + :inherited-members: + :private-members: + +.. autoclass:: netZooPy.lioness.analyze_lioness.AnalyzeLioness + :members: + :undoc-members: + :private-members: + +Puma +===== + +.. autoclass:: netZooPy.puma.puma.Puma + :members: + :undoc-members: + :inherited-members: + :private-members: + +Sambar +====== + +.. autofunction:: netZooPy.sambar.sambar + +Extra sambar functions +~~~~~~~~~~~~~~~~~~~~~~~~ + +.. autofunction:: netZooPy.sambar.corgenelength + +.. autofunction:: netZooPy.sambar.convertgmt + +.. autofunction:: netZooPy.sambar.desparsify + +.. autofunction:: netZooPy.sambar.binomial_dist + +.. autofunction:: netZooPy.sambar.clustering + diff --git a/docs/functions/cli.rst b/docs/functions/cli.rst new file mode 100644 index 00000000..9810d5a3 --- /dev/null +++ b/docs/functions/cli.rst @@ -0,0 +1,41 @@ +Command Line Interface +----------------------- + + +Netzoopy also has a command line interface that allows to run the animal methods +from the command line, for example: + +.. code-block:: + + netzoopy panda --e expression.txt --m motif.txt --p ppi.txt --o output_panda.txt + +The command above would run the panda message passing method using the expression, +motif and ppi data passed as input, and returning an output file containing the +panda weighted edges. + +While we expect to provide most animals from CLI, so far you can use: panda,lioness. + +If you want to use the previous command line calls (python run_panda.py), check the +:ref:`Run functions (legacy)` + +Commands +========================= + +.. click:: netZooPy.cli:cli + :prog: netzoopy + :commands: panda,lioness,condor + :nested: full + + +Run functions (legacy) +========================= + +Panda +~~~~~~~ + +.. autofunction:: netZooPy.panda.run_panda.main + +Lioness +~~~~~~~~~ + +.. autofunction:: netZooPy.lioness.run_lioness.main diff --git a/docs/index.rst b/docs/index.rst index 7e2a2481..516507d2 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -13,7 +13,10 @@ Home netZooPy is a catalog of methods for the reconstruction and analysis of gene regulatory networks. -netZooPy has started as a merge of the following repositories and forks: +Available animals are: (gpu)PANDA, (gpu)LIONESS, (gpu)PUMA, SAMBAR, CONDOR, OTTER, and DRAGON. + + +netZooPy has merged of the following repositories and forks: - `pypanda `_ from David Van Ijzendorn, @@ -23,13 +26,9 @@ netZooPy has started as a merge of the following repositories and forks: - Genis Calderer's `pysambar `_ and `pycondor `_ -Contents -======== - -.. toctree:: - :hidden: - self +Getting started +------------------ .. toctree:: @@ -37,16 +36,34 @@ Contents .. toctree:: - functions/index + tutos/index + +Documentation +------------- + +Netzoopy also has a command line interface that allows to run the animal methods +from the command line, for example: + +.. code-block:: + + netzoopy panda --e expression.txt --m motif.txt --p ppi.txt --o output_panda.txt + +Check the documentation below for a full list of options. .. toctree:: + functions/cli + +.. toctree:: + + functions/api - tutos/index .. toctree:: changelog + + Indices and tables ================== diff --git a/docs/install/index.md b/docs/install/index.md index 45018d41..1a010fd6 100644 --- a/docs/install/index.md +++ b/docs/install/index.md @@ -1,8 +1,11 @@ # Installation guide -To install netZooPy on your computer, please check the following requirements: +You can install netZooPy through pip or through conda. Below, you will find +all the steps and requirements for both cases. -## Requirements +## PIP installation + +### Requirements - Python 3 @@ -20,7 +23,7 @@ In addition to the following pip packages: - python-igraph -## Install +### Install - `git clone https://github.com/netZoo/netZooPy.git` @@ -30,7 +33,7 @@ In addition to the following pip packages: - Then you can import netZooPy in your code through `import netZooPy` -## Troubleshooting +### Troubleshooting - If you experience installation issues with igraph on MacOs. Please install igraph through `brew install igraph`. @@ -39,3 +42,14 @@ In addition to the following pip packages: Refer to the igraph instrallation [manual](https://igraph.org/python/#pyinstallosx) - To report any installation issue or function bug, please report through opening an [issue](https://github.com/netZoo/netZooPy/issues) on github. + + +## Conda installation + +On anaconda.org you will find the conda recipes for all platforms. We recommend using conda environments to keep your analyses self-contained and reproducible. + +To install netzoopy through conda: + +```bash +conda install -c netzoo -c conda-forge netzoopy +``` \ No newline at end of file diff --git a/docs/requirements.txt b/docs/requirements.txt index b8c14be9..bdcf2ee5 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1 +1,6 @@ +-e . releases +recommonmark +numpydoc +myst-parser +sphinx-click diff --git a/docs/tutos/index.md b/docs/tutos/index.md index 11a54e8d..e7a3605f 100644 --- a/docs/tutos/index.md +++ b/docs/tutos/index.md @@ -1,5 +1,7 @@ # Tutorials +You will find a comprehensive tutorial for all the animals at [https://netzoo.github.io/](https://netzoo.github.io/) + Tutorials in netZooPy use [Jupter](https://jupyter.org/) notebooks. - [Up_and_running_with_PANDA_and_netZooPy](https://github.com/netZoo/netZooPy/tree/master/tutorials/panda) by Daniel C. Morgan. diff --git a/netZooPy/cli.py b/netZooPy/cli.py new file mode 100755 index 00000000..8d872914 --- /dev/null +++ b/netZooPy/cli.py @@ -0,0 +1,13 @@ +#!/usr/bin/python3 + +import click + +from netZooPy import command_line as cl + +@click.group() +def cli(): + pass + +cli.add_command(cl.panda) +cli.add_command(cl.lioness) +cli.add_command(cl.condor) diff --git a/netZooPy/command_line.py b/netZooPy/command_line.py new file mode 100755 index 00000000..140fa454 --- /dev/null +++ b/netZooPy/command_line.py @@ -0,0 +1,206 @@ +#!/usr/bin/env python + +import sys +import getopt +import click +from netZooPy.panda.panda import Panda +from netZooPy.lioness import Lioness +from netZooPy.condor import condor_object + +############################################################################# +# PANDA ##################################################################### +############################################################################# + +@click.command() +@click.option('-e', '--expression', 'expression', type=str, required=True, + help='Path to file containing the gene expression data. By default, \ + the expression file does not have a header, and the cells are separated by a tab.') +@click.option('-m', '--motif', 'motif', type=str, required=True, + help='Path to pair file containing the transcription factor DNA binding motif edges in the form of TF-gene-weight(0/1). If not provided, the gene coexpression matrix is returned as a result network.') +@click.option('-p', '--ppi', 'ppi', type=str, required=True, + help='Path to pair file containing the PPI edges. The PPI can be symmetrical, if not, it will be transformed into a symmetrical adjacency matrix.') +@click.option('-o', '--out', 'output', type=str, required=True, + help='Output panda file. Format as txt') +@click.option('--computing', type=str, show_default=True, default='cpu', + help='computing option, choose one between cpu and gpu') +@click.option('--precision', type=str, show_default=True, default='double', + help='precision option') +@click.option('--save_memory', is_flag=True, show_default=True, + help='panda option. When true the result network is weighted adjacency matrix of size (nTFs, nGenes).\ + when false The result network has 4 columns in the form gene - TF - weight in motif prior - PANDA edge.') +@click.option('--save_tmp', is_flag=True, show_default=True, + help='panda option') +@click.option('--rm_missing', is_flag=True, show_default=False, + help='Removes the genes and TFs that are not present in one of the priors. Works only if modeProcess=legacy') +@click.option('--keep_expr', is_flag=True, show_default=True, + help='Keeps the input expression matrix in the result') +@click.option('--mode_process', type=str, default='union', show_default=True, + help='panda option for input data processing. Choose between union(default), \ + legacy and intersection') +@click.option('--alpha', type=float, default=0.1, show_default=True, + help='panda and lioness first sample') +@click.option('--start', type=int, default=1, show_default=True, + help='panda first sample') +@click.option('--end', type=int, default=None, show_default=True, + help='panda last sample') +def panda(expression, motif, ppi, output, computing='cpu', precision='double', save_memory=False, save_tmp=False, rm_missing=False, keep_expr=False, mode_process='union', alpha=0.1, start=1, end=None): + """ Run panda using expression, motif and ppi data. + Use flags to modify the function behavior. By default, boolean flags are false. + Output is a text file, with the TF, Gene, Motif, Force columns, where TF and Gene + are the nodes of the network considered, Motif is the prior and force is + the actual panda score. + + warning: To keep the command line call clean, we have set all booleans to false as default. To set a boolean to True, + from command line you just have to add the respective flag + >>> netzoopy panda .... --rm_missing --save_tmp + In this case rm_missing and save_tmp are set to True. + To replicate the Panda class default behavior pass --save_memory and --save_tmp + + + Example: + + netzoopy panda -e tests/puma/ToyData/ToyExpressionData.txt -m tests/puma/ToyData/ToyMotifData.txt -p tests/puma/ToyData/ToyPPIData.txt -o test_panda.txt + + + Reference: + + Glass, Kimberly, et al. "Passing messages between biological networks to refine predicted interactions." PloS one 8.5 (2013): e64832. + + + """ + print('Input data:') + print('Expression:', expression) + print('Motif data:', motif) + print('PPI data:', ppi) + + # Run PANDA + print('Start Panda run ...') + panda_obj = Panda(expression, motif, ppi, computing=computing,precision = precision, save_tmp=True, remove_missing=rm_missing, keep_expression_matrix=keep_expr, save_memory=save_memory,modeProcess=mode_process, alpha=alpha,start=start, end=end) + panda_obj.save_panda_results(output) + +############################################################################# +# LIONESS ################################################################### +############################################################################# + +@click.command() +@click.option('-e', '--expression', 'expression', type=str, required=True, + help='Path to file containing the gene expression data. By default, \ + the expression file does not have a header, and the cells are separated by a tab.') +@click.option('-m', '--motif', 'motif', type=str, required=True, + help='Path to pair file containing the transcription factor DNA binding motif edges in the form of TF-gene-weight(0/1). If not provided, the gene coexpression matrix is returned as a result network.') +@click.option('-p', '--ppi', 'ppi', type=str, required=True, + help='Path to pair file containing the PPI edges. The PPI can be symmetrical, if not, it will be transformed into a symmetrical adjacency matrix.') +@click.option('-op', '--out-panda', 'output_panda', type=str, required=True, + help='Output panda file. Format as txt') +@click.option('-ol', '--out-lioness', 'output_lioness', type=str, required=True, + help='Output lioness folder') +@click.option('--fmt', type=str, show_default=True, default='npy', + help='Lioness network files output format. Choose one between .npy,.txt,.mat') +@click.option('--computing', type=str, show_default=True, default='cpu', + help='computing option, choose one between cpu and gpu') +@click.option('--precision', type=str, show_default=True, default='double', + help='precision option') +@click.option('--ncores', type=int, show_default=True, default=1, + help='Number of cores. Lioness CPU parallelizes over ncores') +@click.option('--save_memory', is_flag=True, show_default=False, + help='panda option. When true the result network is weighted adjacency matrix of size (nTFs, nGenes).\ + when false The result network has 4 columns in the form gene - TF - weight in motif prior - PANDA edge.') +@click.option('--save_tmp', is_flag=True, show_default=True, + help='panda option') +@click.option('--rm_missing', is_flag=True, show_default=False, + help='Removes the genes and TFs that are not present in one of the priors. Works only if modeProcess=legacy') +@click.option('--mode_process', type=str, default='union', show_default=True, + help='panda option for input data processing. Choose between union(default), \ + legacy and intersection') +@click.option('--output_type', type=str, default='network', show_default=True, + help='lioness option for output format. Choose one between network, gene_targeting, tf_targeting') +@click.option('--alpha', type=float, default=0.1, show_default=True, + help='panda and lioness first sample') +@click.option('--start', type=int, default=1, show_default=True, + help='panda and lioness first sample') +@click.option('--end', type=int, default=None, show_default=True, + help='panda and lioness last sample') +def lioness(expression, motif, ppi, output_panda, output_lioness, fmt, computing, precision, ncores, save_memory, save_tmp, rm_missing, mode_process,output_type, alpha, start, end): + """Run Lioness to extract single-sample networks. + First runs panda using expression, motif and ppi data. + Then runs lioness and puts results in the output_lioness folder. + Use flags to modify the function behavior. By default, boolean flags are false. + + Example: + + netzoopy lioness -e tests/puma/ToyData/ToyExpressionData.txt -m tests/puma/ToyData/ToyMotifData.txt -p tests/puma/ToyData/ToyPPIData.txt -op test_panda.txt -ol lioness/ + + Reference: + Kuijjer, Marieke Lydia, et al. "Estimating sample-specific regulatory networks." Iscience 14 (2019): 226-240. + + """ + + print('Input data:') + print('Expression:', expression) + print('Motif data:', motif) + print('PPI data:', ppi) + print('Output panda:', output_panda) + print('Lioness folder:', output_lioness) + + # Run PANDA + print('Start Panda run ...') + + panda_obj = Panda(expression, motif, ppi, computing=computing, save_tmp=save_tmp, remove_missing=rm_missing, keep_expression_matrix=True, save_memory=save_memory, modeProcess=mode_process, start=start, end=end) + print('Panda saved. Computing Lioness...') + Lioness(panda_obj, computing=computing, precision=precision,ncores=ncores, save_dir=output_lioness, save_fmt=fmt, output = output_type, alpha = alpha) + print('All done!') + + + +@click.command() +@click.option('-n', '--network_file', 'network', type=str, required=True, + help='Path to file encoding an edgelist.') +@click.option('--sep', type=str, show_default=True, default=',', + help='network file separator') +@click.option('--index_col', type=int, show_default=True, default=0, + help='Column that stores the index of the edgelist. E.g. None, 0...') +@click.option('--header', type=int, show_default=True, default=0, + help='Row that stores the header of the edgelist. E.g. None, 0...') +@click.option('--initial_method', type=str, show_default=True, default='LCS', + help='Method to determine intial community assignment. (By default Multilevel method)') +@click.option('--initial_project', is_flag=True, show_default=True, + help='Whether to project the network onto one of the bipartite sets for\ + the initial community detection.') +@click.option('--com_num', type=str, show_default=True, default='def', + help='Max number of communities. It is recomended to leave this to default,\ + otherwise if the initial community assignement is bigger the program will crash.') +@click.option('--delta_qmin', type=str, show_default=True, default='def', + help='Difference modularity threshold for stopping the iterative process.') +@click.option('--resolution', type=int, show_default=True, default=1, + help='Not yet implemented') +@click.option('--tar_output', type=str, show_default=True, default='tar_memb.txt', + help='Filename for saving the tar node final membership.') +@click.option('--reg_output', type=str, show_default=True, default='reg_memb.txt', + help='Filename for saving the reg node final membership.') +def condor( + network_file, + sep=",", + index_col=0, + header=0, + initial_method="LCS", + initial_project=False, + com_num="def", + delta_qmin="def", + resolution=1, + tar_output="tar_memb.txt", + reg_output="reg_memb.txt", +): + """ + Computation of the whole condor process. It creates a condor object and runs all the steps of BRIM on it. The function outputs + Note: The edgelist is assumed to contain a bipartite network. The program will relabel the nodes so that the edgelist represents a bipartite network anyway. + It is on the user to know that the network they are using is suitable for the method. + + tar and reg final memberships are saved to csv + """ + + co = condor_object(network_file, sep, index_col, header) + co.initial_community(initial_method, initial_project) + co.brim(delta_qmin, com_num, resolution) + co.tar_memb.to_csv(tar_output) + co.reg_memb.to_csv(reg_output) + diff --git a/netZooPy/condor/condor.py b/netZooPy/condor/condor.py index 7c29f2f2..2f217f8b 100644 --- a/netZooPy/condor/condor.py +++ b/netZooPy/condor/condor.py @@ -4,390 +4,510 @@ from .timer import Timer class condor_object: - def __init__(self, network_file = None,sep=",",index_col=0,header=0,dataframe = None): - """ - Description: - Initialization of the condor object. The function gets a network in edgelist format as a path to a file or encoded in a pandas dataframe. - Builds a condor_object with an edgelist,an igraph network, names of the targets and regulators. + """ + Initialization of the condor object. The function gets a network + in edgelist format as a path to a file or encoded in a pandas dataframe. + Builds a condor_object with an edgelist,an igraph network, names of the + targets and regulators. + + Note: The edgelist is assumed to contain a bipartite network. + The program will relabel the nodes so that the edgelist represents a bipartite network anyway. + It is on the user to know that the network they are using is suitable for the method. + + Parameters + ------------ + + network_file: str + Path to file encoding an edgelist. + sep: str + Separator used in the file. + index_col: int + Column that stores the index of the edgelist. E.g. None, 0... + header: int + Row that stores the header of the edgelist. E.g. None, 0... + dataframe: dataFrame + Pandas DataFrame containing the edgelist. Use as alternative + to filename + + Returns + --------- + + condor_object : object + The object has the following attributes: + - net: Contains the network edgelist as a pandas DataFrame. + - graph: iGraph object containing the bipartite network. + - reg_names: list of the nodes in the first column. + - tar_names: list of the nodes in the second column. + - index_dict: dictionary keeping track of the indices in the "graph" variable and the actual names of the nodes. + + warning: + Condor uses iGraph for the node assignment. For the initialization of the + assignment, there is some stochasticity involved, that can be somehow controlled + by setting the python random seed. - Note: The edgelist is assumed to contain a bipartite network. The program will relabel the nodes so that the edgelist represents a bipartite network anyway. - It is on the user to know that the network they are using is suitable for the method. - Inputs: - network_file: Path to file encoding an edgelist. - sep: Separator used in the file. - index_col: Column that stores the index of the edgelist. E.g. None, 0... - header: Row that stores the header of the edgelist. E.g. None, 0... - dataframe: Pandas DataFrame containing the edgelist. - Outputs: - condor_object is built with the following variables: - net: Contains the network edgelist as a pandas DataFrame. - graph: iGraph object containing the bipartite network. - reg_names: list of the nodes in the first column. - tar_names: list of the nodes in the second column. - index_dict: dictionary keeping track of the indices in the "graph" variable and the actual names of the nodes. - """ - - #Checks that either a dataframe or a path to an edgelist are provided, and not to both at the same time. - assert (dataframe is not None or network_file is not None), "Could not create condor object. Edgelist must be passed either as a pandas DataFrame or path to file." - assert (dataframe is None or network_file is None), "Could not create condor object. Either pass a DataFrame or a file path. Not both." - + For instance, running condor twice + on the same dataset, in the same python process, might result in slightly different assignments. + To avoid this behavior, you can set the seed ( random.seed(0) ) before calling + condor. + + >>> import random + >>> random.seed(1) + >>> c1 = condor(...) + >>> random.seed(1) + >>> c2 = condor(...) + + In this case c1 and c2 are exactly the same. + + On the contrary, if condor is called twice during two different python calls, you will + have the exact same results, as the random seed will have resetted. + Instead, the stochasticity of the initial assignment can be kept by setting + a random seed at the beginning + + >>> import random + >>> random.seed(random.randint(1,10000000)) + >>> condor(...) + + """ + + def __init__( + self, network_file=None, sep=",", index_col=0, header=0, dataframe=None + ): + + # Checks that either a dataframe or a path to an edgelist are provided, and not to both at the same time. + assert ( + dataframe is not None or network_file is not None + ), "Could not create condor object. Edgelist must be passed either as a pandas DataFrame or path to file." + assert ( + dataframe is None or network_file is None + ), "Could not create condor object. Either pass a DataFrame or a file path. Not both." + if network_file is not None: - #Reads the edgelist and creates a DataFrame - self.net = pd.read_csv(network_file,sep=sep,index_col=index_col,header=header) - + # Reads the edgelist and creates a DataFrame + self.net = pd.read_csv( + network_file, sep=sep, index_col=index_col, header=header + ) + if dataframe is not None: - #Checks that the dataframe has the proper format. - assert dataframe.shape[1]<4, "DataFrame must have at most three columns. Two containing vertices and an additional one containing edgeweights." - if dataframe.shape[1]==3: - assert pd.api.types.is_numeric_dtype(dataframe.iloc[:,2]), "Weight column must contain numeric values." + # Checks that the dataframe has the proper format. + assert ( + dataframe.shape[1] < 4 + ), "DataFrame must have at most three columns. Two containing vertices and an additional one containing edgeweights." + if dataframe.shape[1] == 3: + assert pd.api.types.is_numeric_dtype( + dataframe.iloc[:, 2] + ), "Weight column must contain numeric values." self.net = dataframe - - - #Forces the edgelist to induce a bipartite network by renaming the columns. - self.net.iloc[:,0] = "reg_" + self.net.iloc[:,0] - self.net.iloc[:,1] = "tar_" + self.net.iloc[:,1] - #self.net.columns = ["V1","V2","weight"] + + # Forces the edgelist to induce a bipartite network by renaming the columns. + cnames = self.net.columns + self.net = self.net.astype({cnames[0]: str, cnames[1]: str}) + self.net.iloc[:, 0] = "reg_" + self.net.iloc[:, 0] + self.net.iloc[:, 1] = "tar_" + self.net.iloc[:, 1] + # self.net.columns = ["V1","V2","weight"] with Timer("Object creation:"): - #Checks that the DataFrame gives rise to a well-defined bipartite network. + # Checks that the DataFrame gives rise to a well-defined bipartite network. assert not self.net.isnull().any().any(), "NaN values detected." - assert not ("" in list(self.net.iloc[:,0]) or "" in list(self.net.iloc[:,1])), "Empty strings detected." - - #Checks if weights are provided. If not, a column with 1s is added to the DataFrame. - if self.net.shape[1] != 3: + assert not ( + "" in list(self.net.iloc[:, 0]) or "" in list(self.net.iloc[:, 1]) + ), "Empty strings detected." + + # Checks if weights are provided. If not, a column with 1s is added to the DataFrame. + if self.net.shape[1] != 3: print("Unweighted network. Weights initialized as 1.") self.net["weight"] = 1 - - #Creates iGraph object from the DataFrame. - self.graph = Graph.DataFrame(self.net,directed=False) - - - self.reg_names = sorted(set(self.net.iloc[:,0])) - self.tar_names = sorted(set(self.net.iloc[:,1])) - - #By construction of the graph object, and the fact that reg_ is sorted in front of tar_ - #we have that the graph nodes are sorted by first the reg nodes and then the tar nodes. - types = [0]*len(self.reg_names) - types.extend([1]*len(self.tar_names)) + + self.net.columns = ["V1", "V2", "weight"] + # Creates iGraph object from the DataFrame. + self.graph = Graph.DataFrame(self.net, directed=False) + + self.reg_names = sorted(set(self.net.iloc[:, 0])) + self.tar_names = sorted(set(self.net.iloc[:, 1])) + + # By construction of the graph object, and the fact that reg_ is sorted in front of tar_ + # we have that the graph nodes are sorted by first the reg nodes and then the tar nodes. + types = [0] * len(self.reg_names) + types.extend([1] * len(self.tar_names)) self.graph.vs["type"] = types - + # Dictionary to keep track of node indices and node names should they be rearranged. # TO-DO: Check if this is really necessary. - self.index_dict = {node.index: node["name"] for node in self.graph.vs } - + self.index_dict = {node.index: node["name"] for node in self.graph.vs} + self.modularity = None self.reg_memb = None self.tar_memb = None self.Qcoms = None - - - - - def initial_community(self, method = "LCS", project=False): + + def initial_community(self, method="LCS", project=False): """ - Description: - Computation of the initial community structure based on unipartite methods. - - Inputs: - self : condor object. - method : Method to determine intial community assignment. - "LCS": Multilevel method. - "LEC": Leading Eigenvector method. - "FG" : Fast Greedy method. - "LDN": Leiden method - project: Whether to apply the initial community structure on the bipartite network disregarding the bipartite structure - or apply it to the unipartite network resulting from the projection onto one of these nodes. + Computation of the initial community structure based on unipartite methods. + + Parameters + ----------- + + method : str + Method to determine intial community assignment. + - "LCS": Multilevel method. + - "LEC": Leading Eigenvector method. + - "FG" : Fast Greedy method. + - "LDN": Leiden method + project: bool + Whether to apply the initial community structure on the bipartite network + disregarding the bipartite structure or apply it to the unipartite network resulting from the projection onto + one of these nodes. Outputs: self : updates condor object with tar_memb: DataFrame of initial target node membership. reg_memb: DataFrame of initial reg node membership. - """ + """ + weights_id = self.net.columns[2] if project: with Timer("Initial community structure with projection:"): - - #Obtains bipartite projection onto target subset. + + # Obtains bipartite projection onto target subset. projected_graph = self.graph.bipartite_projection(which=1) - - if method=="LCS": - vc = Graph.community_multilevel(projected_graph,weights=weights_id) - if method=="LEC": - vc = Graph.community_leading_eigenvector(projected_graph,weights=weights_id) - if method=="FG": - vc = Graph.community_fastgreedy(projected_graph,weights=weights_id).as_clustering() - if method=="LDN": - vc = Graph.community_leiden(projected_graph,weights=weights_id).as_clustering() - + + if method == "LCS": + vc = Graph.community_multilevel(projected_graph, weights=weights_id) + if method == "LEC": + vc = Graph.community_leading_eigenvector( + projected_graph, weights=weights_id + ) + if method == "FG": + vc = Graph.community_fastgreedy( + projected_graph, weights=weights_id + ).as_clustering() + if method == "LDN": + vc = Graph.community_leiden( + projected_graph, weights=weights_id + ).as_clustering() + self.modularity = vc.modularity - print("Initial modularity: ",self.modularity) - + print("Initial modularity: ", self.modularity) + tar_index = [i.index for i in self.graph.vs.select(type_in=[1])] - #By the ordering on the indices, the target nodes indices begin at len(co.reg_names) - #in order not to mess with the indices in vc we substract that starting value. - tar_memb = [vc.membership[i-len(self.reg_names)] for i in tar_index] - T0 = pd.DataFrame(zip(tar_index,tar_memb)) - T0.columns = ["index","community"] + # By the ordering on the indices, the target nodes indices begin at len(co.reg_names) + # in order not to mess with the indices in vc we substract that starting value. + tar_memb = [vc.membership[i - len(self.reg_names)] for i in tar_index] + T0 = pd.DataFrame(zip(tar_index, tar_memb)) + T0.columns = ["index", "community"] self.tar_memb = T0 - - #Here we have only computed the community structure for the target nodes. We initialize a properly sized dataframe for the reg nodes. + + # Here we have only computed the community structure for the target nodes. We initialize a properly sized dataframe for the reg nodes. reg_index = [i.index for i in self.graph.vs.select(type_in=[0])] - #By the ordering on the indices, the target nodes indices begin at len(co.reg_names) - #in order not to mess with the indices in vc we substract that starting value. + # By the ordering on the indices, the target nodes indices begin at len(co.reg_names) + # in order not to mess with the indices in vc we substract that starting value. reg_memb = [0 for i in reg_index] - R0 = pd.DataFrame(zip(reg_index,reg_memb)) - R0.columns = ["index","community"] + R0 = pd.DataFrame(zip(reg_index, reg_memb)) + R0.columns = ["index", "community"] self.reg_memb = R0 - - #Sort of the same as above but without projecting. The bipartite network is treated as a unipartite network. + # Sort of the same as above but without projecting. The bipartite network is treated as a unipartite network. else: with Timer("Initial community structure without projection:"): - if method=="LCS": - vc = Graph.community_multilevel(self.graph,weights=weights_id) - if method=="LEC": - vc = Graph.community_leading_eigenvector(self.graph,weights=weights_id) - if method=="FG": - vc = Graph.community_fastgreedy(self.graph,weights=weights_id).as_clustering() - if method=="LDN": - vc = Graph.community_leiden(self.graph,weights=weights_id).as_clustering() - + if method == "LCS": + vc = Graph.community_multilevel(self.graph, weights=weights_id) + if method == "LEC": + vc = Graph.community_leading_eigenvector( + self.graph, weights=weights_id + ) + if method == "FG": + vc = Graph.community_fastgreedy( + self.graph, weights=weights_id + ).as_clustering() + if method == "LDN": + vc = Graph.community_leiden( + self.graph, weights=weights_id + ).as_clustering() + self.modularity = vc.modularity - print("Initial modularity: ",self.modularity) + print("Initial modularity: ", self.modularity) - tar_index = [i.index for i in self.graph.vs.select(type_in=[1])] tar_memb = [vc.membership[i] for i in tar_index] tar_index = [self.index_dict[i] for i in tar_index] - T0 = pd.DataFrame(zip(tar_index,tar_memb)) - T0.columns = ["index","community"] + T0 = pd.DataFrame(zip(tar_index, tar_memb)) + T0.columns = ["index", "community"] self.tar_memb = T0 - + reg_index = [i.index for i in self.graph.vs.select(type_in=[0])] reg_memb = [vc.membership[i] for i in reg_index] reg_index = [self.index_dict[i] for i in reg_index] - R0 = pd.DataFrame(zip(reg_index,reg_memb)) - R0.columns = ["index","community"] + R0 = pd.DataFrame(zip(reg_index, reg_memb)) + R0.columns = ["index", "community"] self.reg_memb = R0 + + def bipartite_modularity(self, B, m, R, T): + """ Computation of the bipartite modularity as described in + Michael J. Barber. Modularity and community detection in bipartite networks. + + Parameters + ------------ + B : array + modularity matrix. + m : array + sum of the weights (or number of edges in the unweighted case). + R : array + community assignement matrix for reg nodes. + T : array + community assignement matrix for tar nodes. - - - - - def bipartite_modularity(self,B,m,R,T): - """Computation of the bipartite modularity as described in ""Modularity and community detection in bipartite networks" by Michael J. Barber." - Inputs: - self : condor object. - B : modularity matrix. - m : sum of the weights (or number of edges in the unweighted case. - R : community assignement matrix for reg nodes. - T : community assignement matrix for tar nodes. - Outputs: - self : updates condor object with - Qcoms: Modularity contribution by each community. - Q: Modularity score. - Q : Modularity score. - + Returns + -------- + Q: _ + Modularity score. + Notes + -------- + self.Qcoms: _ + Modularity contribution by each community. + self.modularity: _ + Modularity score. + + References + ----------- + .. [1]__ Michael J. Barber. Modularity and community detection in bipartite networks. + """ RtBT = T.transpose().dot(B.dot(R)) - Qcoms = (1/m)*(np.diagonal(RtBT)) + Qcoms = (1 / m) * (np.diagonal(RtBT)) Q = sum(Qcoms) - self.Qcoms = Qcoms[Qcoms>0] + self.Qcoms = Qcoms[Qcoms > 0] self.modularity = Q return Q - - - - - def matrices(self,c): - """Computation of modularity matrix and initial community matrix. - Inputs: - self : condor object. - c : max number of communities. - Outputs: - B : Modularity matrix. - m : Sum of the weights (or number of edges in the unweighted case. - T0 : Initial community structure matrix for target nodes. - R0 : Initial community structure matrix for reg nodes. - gn : Index dictionary for tar node names. - rg : Index dictionary for reg node names. - - """ - - + def matrices(self, c): + """ Computation of modularity matrix and initial community matrix. + + Parameters + ------------ + c : int + max number of communities. + Returns + ---------- + B : array + Modularity matrix. + m : int + Sum of the weights (or number of edges in the unweighted case. + T0 : array + Initial community structure matrix for target nodes. + R0 : array + Initial community structure matrix for reg nodes. + gn : dict + Index dictionary for tar node names. + rg : dict + Index dictionary for reg node names. + + """ + with Timer("Matrix computation:"): - - #Dimensions of the matrix + + # Dimensions of the matrix p = len(self.tar_names) q = len(self.reg_names) - - #Index dictionaries for the matrix. Note that this set of indices is different of that in the condor object (that one is for the igraph network.) - rg = {self.reg_names[i]: i for i in range(0,q)} - gn = {self.tar_names[i]: i for i in range(0,p)} - + + # Index dictionaries for the matrix. Note that this set of indices is different of that in the condor object (that one is for the igraph network.) + rg = {self.reg_names[i]: i for i in range(0, q)} + gn = {self.tar_names[i]: i for i in range(0, p)} + # Computes weighted biadjacency matrix. - A = np.matrix(np.zeros((p,q))) + A = np.matrix(np.zeros((p, q))) for edge in self.net.iterrows(): - A[gn[edge[1][1]],rg[edge[1][0]]] = edge[1][2] - + A[gn[edge[1][1]], rg[edge[1][0]]] = edge[1][2] + # Computes node degrees for the nodesets. ki = A.sum(1) - dj = A.sum(0) - #Computes sum of edges and bimodularity matrix. + dj = A.sum(0) + # Computes sum of edges and bimodularity matrix. m = float(sum(ki)) - B = A - ((ki@dj)/m) - - #d = self.index_dict - + B = A - ((ki @ dj) / m) + + # d = self.index_dict + # Computation of initial modularity matrix for tar and reg nodes from the membership dataframe. - T_ed = zip([gn[j] for j in [i for i in self.tar_memb.iloc[:,0]]],self.tar_memb.iloc[:,1]) - T0 = np.zeros((p,c)) + T_ed = zip( + [gn[j] for j in [i for i in self.tar_memb.iloc[:, 0]]], + self.tar_memb.iloc[:, 1], + ) + T0 = np.zeros((p, c)) for edge in T_ed: - T0[edge]=1 - - R_ed = zip([rg[j] for j in [i for i in self.reg_memb.iloc[:,0]]],self.reg_memb.iloc[:,1]) - R0 = np.zeros((q,c)) + T0[edge] = 1 + + R_ed = zip( + [rg[j] for j in [i for i in self.reg_memb.iloc[:, 0]]], + self.reg_memb.iloc[:, 1], + ) + R0 = np.zeros((q, c)) for edge in R_ed: - R0[edge]=1 - - - return B,m,T0,R0,gn,rg - - - - + R0[edge] = 1 + + return B, m, T0, R0, gn, rg + + def brim(self, deltaQmin="def", c="def", resolution=1): + + """ Implementation of the BRIM algorithm to iteratively maximize + bipartite modularity. Note that c is the maximum number of communities. + Dynamic choice of c is not yet implemented. + + Parameters + ------------ + deltaQmin: str + Difference modularity threshold for stopping the iterative process + c : int + max number of communities. + resolution: int + Not yet implemented option - def brim(self,deltaQmin="def",c="def",resolution=1): - """Implementation of the BRIM algorithm to iteratively maximize bipartite modularity. - Note that c is the maximum number of communities. Dynamic choice of c is not yet implemented. - - Inputs: - self : condor object. - deltaQmin: Difference modularity threshold for stopping the iterative process - c : max number of communities. - resolution: Not yet implemented option - Outputs: - self : Updates condor object with the following: - modularity: Modularity score for the final assignement. - tar_memb: Final community assignement for tar nodes. - reg_memb: Final community assignement for reg nodes. - + Notes + --------- + Updates condor object with the following: + - self.modularity: Modularity score for the final assignement. + - self.tar_memb: Final community assignement for tar nodes. + - self.reg_memb: Final community assignement for reg nodes. + Note: c : Has to be bigger than the number of communities given by the initial community assignement. Otherwise the program will crash. The default option gives room for 20% more communities which rarely fails. - """ - - + """ + if c == "def": - c = int(len(self.tar_memb["community"].unique())*1.2) - - B,m,T0,R0,gn,rg = self.matrices(c) - - #Default deltaQmin. - if(deltaQmin == "def"): - deltaQmin = min(1/m,1e-5) - + c = int(len(self.tar_memb["community"].unique()) * 1.2) + + B, m, T0, R0, gn, rg = self.matrices(c) + + + # Default deltaQmin. + if deltaQmin == "def": + deltaQmin = min(1 / m, 1e-5) + with Timer("BRIM: "): Qnow = 0 deltaQ = 1 - p,q = B.shape - while(deltaQ>deltaQmin): - #Right sweep + p, q = B.shape + while deltaQ > deltaQmin: + # Right sweep Tp = T0.transpose().dot(B) - R = np.zeros((q,c)) + R = np.zeros((q, c)) am = np.array(np.argmax(Tp.transpose(), axis=1)) - for i in range(0,len(am)): - R[i,am[i][0]]=1 + for i in range(0, len(am)): + R[i, am[i][0]] = 1 - - #Left sweep + # Left sweep Rp = B.dot(R) - T = np.zeros((p,c)) + T = np.zeros((p, c)) am = np.array(np.argmax(Rp, axis=1)) - for i in range(0,len(am)): - T[i,am[i][0]]=1 + + for i in range(0, len(am)): + T[i, am[i][0]] = 1 T0 = T Qthen = Qnow - Qnow = self.bipartite_modularity(B,m,R,T) - deltaQ = Qnow-Qthen + Qnow = self.bipartite_modularity(B, m, R, T) + deltaQ = Qnow - Qthen print(Qnow) self.modularity = Qnow - - - - self.tar_memb = pd.DataFrame(list(zip(list(gn),[T[i,:].argmax() for i in range(0,len(gn))]))) - self.reg_memb = pd.DataFrame(list(zip(list(rg),[R[i,:].argmax() for i in range(0,len(rg))]))) - self.tar_memb.columns = ["tar","com"] - self.reg_memb.columns = ["reg","com"] - - - - - def qscores(self): - """Computes the qscores (contribution of a vertex to its community modularity) - for each vertex in the network.""" + self.tar_memb = pd.DataFrame( + list(zip(list(gn), [T[i, :].argmax() for i in range(0, len(gn))])) + ) + self.reg_memb = pd.DataFrame( + list(zip(list(rg), [R[i, :].argmax() for i in range(0, len(rg))])) + ) + self.tar_memb.columns = ["tar", "com"] + self.reg_memb.columns = ["reg", "com"] + + def qscores(self): + """ + Computes the qscores (contribution of a vertex to its community modularity) + for each vertex in the network. + """ + c = 1 + max(self.reg_memb["com"]) - B,m,T,R,gn,rg = self.matrices(c) - self.Qscores={"reg_qscores":None,"tar_qscores":None} + B, m, T, R, gn, rg = self.matrices(c) + self.Qscores = {"reg_qscores": None, "tar_qscores": None} - #Qscores for the targets: - Rq = B.dot(R)/(2*m) + # Qscores for the targets: + Rq = B.dot(R) / (2 * m) Qj = list() - for j,r in self.tar_memb.iterrows(): - Qjh = Rq[j,r["com"]]/self.Qcoms[r["com"]] + for j, r in self.tar_memb.iterrows(): + Qjh = Rq[j, r["com"]] / self.Qcoms[r["com"]] Qj.append(Qjh) - self.Qscores["tar_qscores"]=self.tar_memb.copy() + self.Qscores["tar_qscores"] = self.tar_memb.copy() self.Qscores["tar_qscores"]["qscore"] = Qj - #Qscores for the regulators: - Tq = T.transpose().dot(B)/(2*m) + # Qscores for the regulators: + Tq = T.transpose().dot(B) / (2 * m) Qi = list() - for i,r in self.reg_memb.iterrows(): - Qih = Tq[r["com"],i]/self.Qcoms[r["com"]] + for i, r in self.reg_memb.iterrows(): + Qih = Tq[r["com"], i] / self.Qcoms[r["com"]] Qi.append(Qih) - self.Qscores["reg_qscores"]=self.reg_memb.copy() + self.Qscores["reg_qscores"] = self.reg_memb.copy() self.Qscores["reg_qscores"]["qscore"] = Qi - - - - - -def run_condor(network_file,sep=",",index_col=0,header=0,initial_method="LCS",initial_project=False,com_num="def",deltaQmin="def",resolution=1,return_output=False,tar_output="tar_memb.txt",reg_output="reg_memb.txt"): + + +def run_condor( + network_file, + sep=",", + index_col=0, + header=0, + initial_method="LCS", + initial_project=False, + com_num="def", + deltaQmin="def", + resolution=1, + return_output=False, + tar_output="tar_memb.txt", + reg_output="reg_memb.txt", +): """ - Description: - Computation of the whole condor process. It creates a condor object and runs all the steps of BRIM on it. The function outputs - - Note: The edgelist is assumed to contain a bipartite network. The program will relabel the nodes so that the edgelist represents a bipartite network anyway. - It is on the user to know that the network they are using is suitable for the method. - Inputs: - network_file: Path to file encoding an edgelist. - sep: Separator used in the file. - index_col: Column that stores the index of the edgelist. E.g. None, 0... - header: Row that stores the header of the edgelist. E.g. None, 0... - initial_method: Method to determine intial community assignment. (By default Multilevel method). - initial_project: Whether to project the network onto one of the bipartite sets for the initial community detection. - com_num: Max number of communities. It is recomended to leave this to default, otherwise if the initial community assignement is bigger the program will crash. - deltaQmin: Difference modularity threshold for stopping the iterative process. - resolution: Not yet implemented. - return_output: Whether the function returns the created condor object. - tar_output: Filename for saving the tar node final membership. - reg_output: Filename for saving the reg node final membership. - - Outputs: - condor_object (if return_output=True) - Files "tar_memb.txt" and "reg_memb.txt" encoding the final tar and reg node membership. - """ - + Computation of the whole condor process. It creates a condor object and runs all the steps of BRIM on it. The function outputs + + Note: The edgelist is assumed to contain a bipartite network. The program will relabel the nodes so that the edgelist represents a bipartite network anyway. + It is on the user to know that the network they are using is suitable for the method. - co = condor_object(network_file,sep,index_col,header) - co.initial_community(initial_method,initial_project) - co.brim(deltaQmin,com_num,resolution) + Parameters + ----------- + network_file: str + Path to file encoding an edgelist. + sep: str + Separator used in the file. + index_col: int + Column that stores the index of the edgelist. E.g. None, 0... + header: int + Row that stores the header of the edgelist. E.g. None, 0... + initial_method: str + Method to determine intial community assignment. (By default Multilevel method). + initial_project: bool + Whether to project the network onto one of the bipartite sets for the initial community detection. + com_num: int + Max number of communities. It is recomended to leave this to default, otherwise if the initial community assignement is bigger the program will crash. + deltaQmin: float + Difference modularity threshold for stopping the iterative process. + resolution: int + Not yet implemented. + return_output: bool + Whether the function returns the created condor object. + tar_output: str + Filename for saving the tar node final membership. + reg_output: str + Filename for saving the reg node final membership. + + Returns + -------- + Files "tar_memb.txt" and "reg_memb.txt" encoding the final tar and reg node membership. + """ + + co = condor_object(network_file, sep, index_col, header) + co.initial_community(initial_method, initial_project) + + co.brim(deltaQmin, com_num, resolution) co.tar_memb.to_csv(tar_output) co.reg_memb.to_csv(reg_output) - if return_output == True: return co + + if return_output == True: + return co diff --git a/netZooPy/lioness/analyze_lioness.py b/netZooPy/lioness/analyze_lioness.py index 2a90c6cc..96aca0b6 100755 --- a/netZooPy/lioness/analyze_lioness.py +++ b/netZooPy/lioness/analyze_lioness.py @@ -12,36 +12,34 @@ class AnalyzeLioness(Lioness): """ - Description: Plots LIONESS network. - Inputs: - Panda: LIONESS object. + Parameters + ------------ + lioness_data: object + lioness object. - Methods: - __init__ : Intialize instance of AnalyzePanda class. - top_network_plot : Selects top genes. """ def __init__(self, lioness_data): """ - Description: + Intialize instance of AnalyzeLioness class and load variables. - - Inputs: - lioness_data : LIONESS object """ self.export_panda_results = lioness_data.export_panda_results self.lioness_results = lioness_data.export_lioness_results return None def top_network_plot(self, index = 0, top = 100, file = 'lioness_top_100.png'): """ - Description: - Selects top genes. + Network of top genes. - Inputs: - column: Index of sample to plot. - top : Top number of genes to plot. - file : File to save the network plot. + Parameters + ----------- + index: int (defaults to 0) + Index of sample to plot. + top : int (defaults to 100) + Top number of genes to plot. + file : str + File to save the network plot. """ self.export_panda_results[['force']] = self.lioness_results.iloc[index,:] plot = AnalyzePanda(self) diff --git a/netZooPy/lioness/lioness.py b/netZooPy/lioness/lioness.py index 0c007dac..61ff27ae 100755 --- a/netZooPy/lioness/lioness.py +++ b/netZooPy/lioness/lioness.py @@ -13,51 +13,83 @@ from netZooPy.panda.calculations import compute_panda class Lioness(Panda): - """ - Description: - Using LIONESS to infer single-sample gene regulatory networks. + """ Using LIONESS to infer single-sample gene regulatory networks. 1. Reading in PANDA network and preprocessed middle data 2. Computing coexpression network 3. Normalizing coexpression network 4. Running PANDA algorithm 5. Writing out LIONESS networks - Inputs: - Panda: Panda object. - - Methods: - __init__ : Intialize instance of Lioness class and load data. - __lioness_loop : The LIONESS algorithm. - save_lioness_results : Saves LIONESS network. - - Example: - from netZooPy.lioness.lioness import Lioness - To run the Lioness algorithm for single sample networks, first run PANDA using the keep_expression_matrix flag, then use Lioness as follows: - panda_obj = Panda('../../tests/ToyData/ToyExpressionData.txt', '../../tests/ToyData/ToyMotifData.txt', '../../tests/ToyData/ToyPPIData.txt', remove_missing=False, keep_expression_matrix=True) - lioness_obj = Lioness(panda_obj) - - Save Lioness results: - lioness_obj.save_lioness_results('Toy_Lioness.txt') - Return a network plot for one of the Lioness single sample networks: - plot = AnalyzeLioness(lioness_obj) - plot.top_network_plot(column= 0, top=100, file='top_100_genes.png') - - Example lioness output: - Sample1 Sample2 Sample3 Sample4 - ------------------------------- - -0.667452814003 -1.70433776179 -0.158129613892 -0.655795512803 - -0.843366539284 -0.733709815256 -0.84849895139 -0.915217389738 - 3.23445386464 2.68888472802 3.35809757371 3.05297381396 - 2.39500370135 1.84608635425 2.80179804094 2.67540878165 - -0.117475863987 0.494923925853 0.0518448588965 -0.0584810456421 - + Parameters + ---------- + + obj : object + PANDA object, generated with keep_expression_matrix=True. + computing : str + 'cpu' uses Central Processing Unit (CPU) to run PANDA + 'gpu' use the Graphical Processing Unit (GPU) to run PANDA + precision : str + 'double' computes the regulatory network in double precision (15 decimal digits). + 'single' computes the regulatory network in single precision (7 decimal digits) which is fastaer, requires half the memory but less accurate. + start : int + Index of first sample to compute the network. + end : int + Index of last sample to compute the network. + save_dir : str + Directory to save the networks. + save_fmt : str + Save format. + - '.npy': (Default) Numpy file. + - '.txt': Text file. + - '.mat': MATLAB file. + output : str + - 'network' returns all networks in a single edge-by-sample matrix (lioness_obj.total_lioness_network). For large sample sizes, this variable requires large RAM memory. + - 'gene_targeting' returns gene targeting scores for all networks in a single gene-by-sample matrix (lioness_obj.total_lioness_network). + - 'tf_targeting' returns tf targeting scores for all networks in a single gene-by-sample matrix (lioness_obj.total_lioness_network). + alpha : float + learning rate, set to 0.1 by default but has to be changed manually to match the learning rate of the PANDA object. + + Returns + -------- + export_lioness_results : _ + Depeding on the output argument, this can be either all the lioness + networks or their gene/tf targeting scores. + + Notes + ------- + Example on how to use Lioness and plot the network + + >>> from netZooPy.lioness.lioness import Lioness + >>> #To run the Lioness algorithm for single sample networks, first run PANDA using the keep_expression_matrix flag, then use Lioness as follows: + >>> panda_obj = Panda('../../tests/ToyData/ToyExpressionData.txt', '../../tests/ToyData/ToyMotifData.txt', '../../tests/ToyData/ToyPPIData.txt', remove_missing=False, keep_expression_matrix=True) + >>> lioness_obj = Lioness(panda_obj) + + >>> #Save Lioness results: + >>> lioness_obj.save_lioness_results('Toy_Lioness.txt') + >>> #Return a network plot for one of the Lioness single sample networks: + >>> plot = AnalyzeLioness(lioness_obj) + >>> plot.top_network_plot(column= 0, top=100, file='top_100_genes.png') + + Example lioness output: TF, Gene and Motif order is identical to the panda output file. - Authors: - Cho-Yi Chen, David Vi, Daniel Morgan + - Sample1 Sample2 Sample3 Sample4\n + - -------------------------------\n + - -0.667452814003 -1.70433776179 -0.158129613892 -0.655795512803\n + - -0.843366539284 -0.733709815256 -0.84849895139 -0.915217389738\n + - 3.23445386464 2.68888472802 3.35809757371 3.05297381396\n + - 2.39500370135 1.84608635425 2.80179804094 2.67540878165\n + - -0.117475863987 0.494923925853 0.0518448588965 -0.0584810456421\n + + - Reference: - Kuijjer, Marieke Lydia, et al. "Estimating sample-specific regulatory networks." Iscience 14 (2019): 226-240. + References + ----------- + + .. [1]__ Kuijjer, Marieke Lydia, et al. "Estimating sample-specific regulatory networks." + Iscience 14 (2019): 226-240. + + Authors: Cho-Yi Chen, David Vi, Daniel Morgan """ def __init__( @@ -73,32 +105,7 @@ def __init__( output="network", alpha=0.1, ): - """ - Description: - Initialize instance of Lioness class and load data. - - Inputs: - obj : PANDA object, generated with keep_expression_matrix=True. - obj.motif_matrix: TF DNA motif binding data in tf-by-gene format. - If set to None, Lioness will be performed on gene coexpression network. - computing : 'cpu' uses Central Processing Unit (CPU) to run PANDA - 'gpu' use the Graphical Processing Unit (GPU) to run PANDA - precision : 'double' computes the regulatory network in double precision (15 decimal digits). - 'single' computes the regulatory network in single precision (7 decimal digits) which is fastaer, requires half the memory but less accurate. - start : Index of first sample to compute the network. - end : Index of last sample to compute the network. - save_dir : Directory to save the networks. - save_fmt : Save format. - '.npy': (Default) Numpy file. - '.txt': Text file. - '.mat': MATLAB file. - output : 'network' returns all networks in a single edge-by-sample matrix (lioness_obj.total_lioness_network). For large sample sizes, this variable requires large RAM memory. - 'gene_targeting' returns gene targeting scores for all networks in a single gene-by-sample matrix (lioness_obj.total_lioness_network). - 'tf_targeting' returns tf targeting scores for all networks in a single gene-by-sample matrix (lioness_obj.total_lioness_network). - alpha : learning rate, set to 0.1 by default but has to be changed manually to match the learning rate of the PANDA object. - - Output: - export_lioness_results : Depeding on the output argument, this can be either all the lioness networks or their gene/tf targeting scores. + """ Initialize instance of Lioness class and load data. """ # Load data with Timer("Loading input data ..."): @@ -181,12 +188,12 @@ def __init__( self.save_lioness_results() def __lioness_loop(self, i): - """ - Description: - Initialize instance of Lioness class and load data. + """ Initialize instance of Lioness class and load data. - Outputs: - self.total_lioness_network: An edge-by-sample matrix containing sample-specific networks. + Returns + -------- + self.total_lioness_network: array + An edge-by-sample matrix containing sample-specific networks. """ # for i in self.indexes: print("Running LIONESS for sample %d:" % (i + 1)) @@ -269,12 +276,12 @@ def __lioness_loop(self, i): @delayed @wrap_non_picklable_objects def __par_lioness_loop(self, i, output): - """ - Description: - Initialize instance of Lioness class and load data. + """ Initialize instance of Lioness class and load data. - Outputs: - self.total_lioness_network: An edge-by-sample matrix containing sample-specific networks. + Returns + --------- + self.total_lioness_network: array + An edge-by-sample matrix containing sample-specific networks. """ # for i in self.indexes: print("Running LIONESS for sample %d:" % (i + 1)) @@ -350,12 +357,9 @@ def __par_lioness_loop(self, i, output): return self.total_lioness_network def save_lioness_results(self): - """ - Description: - Saves LIONESS network. - - Outputs: - file: Path to save the network. + """ Saves LIONESS network. + Uses self.save_fmt, self.save_dir to save the data + into self.total_lioness_network """ # self.lioness_network.to_csv(file, index=False, header=False, sep="\t") fullpath = os.path.join(self.save_dir, "lioness.%s" % (self.save_fmt)) @@ -375,14 +379,16 @@ def save_lioness_results(self): return None def export_lioness_table(self, output_filename="lioness_table.txt", header=False): - """ - Description: + """ Saves LIONESS network with edge names. This saves a dataframe with the corresponding header and indexes. - So far we - Outputs: - output_filename: Path to save the network. Specify relative path - and format. Choose between .csv, .tsv and .txt. (Defaults to .lioness_table.txt)) + + Parameters + ------------ + output_filename: str + Path to save the network. Specify relative path + and format. Choose between .csv, .tsv and .txt. + (Defaults to .lioness_table.txt)) """ df = self.export_lioness_results df = df.sort_values(by=['tf','gene']) diff --git a/netZooPy/otter/otter.py b/netZooPy/otter/otter.py index 2a1f232c..46b2a496 100755 --- a/netZooPy/otter/otter.py +++ b/netZooPy/otter/otter.py @@ -3,26 +3,36 @@ def otter(W, P, C, lam=0.035, gamma=0.335, Iter=60, eta=0.00001, bexp=1): - """ - Description: - OTTER infers gene regulatory networks using TF DNA binding + """ + OTTER infers gene regulatory networks using TF DNA binding motif (W), TF PPI (P), and gene coexpression (C) through minimzing the following objective: min f(W) with f(W) = (1-lam)/4*||WW' - P||^2 + (lam/4)*||W'W - C||^2 + (gamma/2)*||W||^2 - Inputs: - W : TF-gene regulatory network based on TF motifs as a - matrix of size (t,g), g=number of genes, t=number of TFs - P : TF-TF protein interaction network as a matrix of size (t,t) - C : gene coexpression as a matrix of size (g,g) - lam : it should be in [0,1]. - gamma : penalization term - Iter : number of iterations of the algorithm - eta : the learning rate - Outputs: - W : Predicted TF-gene complete regulatory network as an adjacency matrix of size (t,g). - Reference: - Weighill, Deborah, et al. "Gene Regulatory Network Inference as Relaxed Graph Matching." BioRxiv (2020). + Parameters + ----------- + W : array + TF-gene regulatory network based on TF motifs as a + matrix of size (t,g), g=number of genes, t=number of TFs + P : array + TF-TF protein interaction network as a matrix of size (t,t) + C : array + gene coexpression as a matrix of size (g,g) + lam : float + it should be in [0,1]. + gamma : float + penalization term + Iter : int + number of iterations of the algorithm + eta : float + the learning rate + Returns + --------- + W : array + Predicted TF-gene complete regulatory network as an adjacency matrix of size (t,g). + References + ------------- + .. [1] Weighill, Deborah, et al. "Gene Regulatory Network Inference as Relaxed Graph Matching." AAAI Conference (2021). """ b1 = 0.9 b2 = 0.999 @@ -51,4 +61,4 @@ def otter(W, P, C, lam=0.035, gamma=0.335, Iter=60, eta=0.00001, bexp=1): alpha = eta * sqrt(1 - b2t) / (1 - b1t) epst = eps * sqrt((1 - b2t)) W = W - alpha * (m / (epst + np.sqrt(v))) - return W \ No newline at end of file + return W diff --git a/netZooPy/panda/analyze_panda.py b/netZooPy/panda/analyze_panda.py index 130c19dd..ea53e6b1 100644 --- a/netZooPy/panda/analyze_panda.py +++ b/netZooPy/panda/analyze_panda.py @@ -6,26 +6,18 @@ import matplotlib.pyplot as plt class AnalyzePanda(Panda): + """ - Description: Plots PANDA network. - Inputs: - Panda: PANDA object. - - Methods: - __init__ : Intialize instance of AnalyzePanda class. - top_network_plot : Selects top genes. - __shape_plot_network: Creates plot. - __create_plot : Runs plot. + Parameters + ----------- + panda_data : object + PANDA object """ def __init__(self, panda_data): """ - Description: Intialize instance of AnalyzePanda class. - - Inputs: - panda_data : PANDA object """ if not hasattr(panda_data,'export_panda_results'): print() @@ -39,12 +31,14 @@ def __init__(self, panda_data): def top_network_plot(self, top = 100, file = 'panda_top_100.png'): """ - Description: Selects top genes. - Inputs: - top : Top number of genes to plot. - file: File to save the network plot. + Parameters + ----------- + top : int (Defaults to 100) + Top number of genes to plot. + file: str (Defaults to panda_top_100.png) + File to save the network plot. """ subset_panda_results = self.panda_results.sort_values(by=['force'], ascending=False) subset_panda_results = subset_panda_results[subset_panda_results.tf != subset_panda_results.gene] @@ -54,12 +48,14 @@ def top_network_plot(self, top = 100, file = 'panda_top_100.png'): def __shape_plot_network(self, subset_panda_results, file = 'panda.png'): """ - Description: Creates plot. - Inputs: - subset_panda_results : Reduced PANDA network to the top genes. - file : File to save the network plot. + Parameters + ___________ + subset_panda_results : array + Reduced PANDA network to the top genes. + file : str (Defaults to panda.png) + File to save the network plot. """ #reshape data for networkx unique_genes = list(set(list(subset_panda_results['tf'])+list(subset_panda_results['gene']))) @@ -78,13 +74,16 @@ def __shape_plot_network(self, subset_panda_results, file = 'panda.png'): def __create_plot(self, unique_genes, links, file = 'panda.png'): """ - Description: - Runs the plot. + Plot panda network on specified genes and edges - Inputs: - unique_genes : Unique list of PANDA genes. - links : Edgdes of the subset PANDA network to the top genes. - file : File to save the network plot. + Parameters + ___________ + unique_genes : list + Unique list of PANDA genes. + links : edges + Edgdes of the subset PANDA network to the top genes. + file : str (Defaults to panda.png) + File to save the network plot. """ #plot g = nx.Graph() diff --git a/netZooPy/panda/panda.py b/netZooPy/panda/panda.py index c363c77c..ea3a41a4 100755 --- a/netZooPy/panda/panda.py +++ b/netZooPy/panda/panda.py @@ -1,5 +1,4 @@ from __future__ import print_function - import math import time import pandas as pd @@ -10,65 +9,93 @@ class Panda(object): - """ - Description: - Using PANDA to infer gene regulatory network. + """ + Using PANDA to infer gene regulatory network. 1. Reading in input data (expression data, motif prior, TF PPI data) 2. Computing coexpression network 3. Normalizing networks 4. Running PANDA algorithm 5. Writing out PANDA network - Inputs: - object: Panda object. - - Outputs: - object: Panda result object - object.panda_network: adjacency matrix of resulting network - - Methods: - __init__ : Intialize instance of Panda class. - __remove_missing : Removes the gens and TFs that are not present in one of the priors. Works only if modeProcess='legacy'. - _normalize_network : Standardizes the input data matrices. - processData : Processes data files into data matrices. - panda_loop : The PANDA algorithm. - __pearson_results_data_frame: Saves PANDA network in edges format. - save_panda_results : Saves PANDA network. - top_network_plot : Selects top genes to plot. - __shape_plot_network : Creates network plot. - __create_plot : Runs network plot. - return_panda_indegree : computes indegree of panda network, only if save_memory = False. - return_panda_outdegree : computes outdegree of panda network, only if save_memory = False. - - Example: - Import the classes in the pypanda library: - from netZooPy.panda.panda import Panda - Run the Panda algorithm, leave out motif and PPI data to use Pearson correlation network: - panda_obj = Panda('../../tests/ToyData/ToyExpressionData.txt', '../../tests/ToyData/ToyMotifData.txt', '../../tests/ToyData/ToyPPIData.txt', remove_missing=False) - Save the results: - panda_obj.save_panda_results('Toy_Panda.pairs.txt') - Return a network plot: - panda_obj.top_network_plot(top=70, file='top_genes.png') - Calculate in- and outdegrees for further analysis: - indegree = panda_obj.return_panda_indegree() - outdegree = panda_obj.return_panda_outdegree() - Toy data: - The example gene expression data that we have available here contains gene expression profiles for different samples in the columns. Of note, this is just a small subset of a larger gene expression dataset. We provided these "toy" data so that the user can test the method. - However, if you plan to model gene regulatory networks on your own dataset, you should use your own expression data as input. - Sample PANDA results: - TF Gene Motif Force - --------------------- - CEBPA AACSL 0.0 -0.951416589143 - CREB1 AACSL 0.0 -0.904241609324 - DDIT3 AACSL 0.0 -0.956471642313 - E2F1 AACSL 1.0 3.6853160511 - EGR1 AACSL 0.0 -0.695698519643 - - Authors: - Cho-Yi Chen, David Vi, Alessandro Marin, Marouen Ben Guebila, Daniel Morgan - - Reference: - Glass, Kimberly, et al. "Passing messages between biological networks to refine predicted interactions." PloS one 8.5 (2013): e64832. + + Parameters + ---------- + + expression_file : str + Path to file containing the gene expression data or pandas dataframe. By default, the expression file does not have a header, and the cells ares separated by a tab. + motif_file : str + Path to file containing the transcription factor DNA binding motif data in the form of + TF-gene-weight(0/1) or pandas dataframe. + If set to none, the gene coexpression matrix is returned as a result network. + ppi_file : str + Path to file containing the PPI data. or pandas dataframe. + The PPI can be symmetrical, if not, it will be transformed into a symmetrical adjacency matrix. + computing : str + 'cpu' uses Central Processing Unit (CPU) to run PANDA. + 'gpu' use the Graphical Processing Unit (GPU) to run PANDA. + precision : str + - 'double' computes the regulatory network in double precision (15 decimal digits). + - 'single' computes the regulatory network in single precision (7 decimal digits) which is fastaer, requires half the memory but less accurate. + save_memory : bool + - True : removes temporary results from memory. The result network is weighted adjacency matrix of size (nTFs, nGenes). + - False: keeps the temporary files in memory. The result network has 4 columns in the form gene - TF - weight in motif prior - PANDA edge. + save_tmp : bool + Save temporary variables. + remove_missing : bool + Removes the gens and TFs that are not present in one of the priors. Works only if modeProcess='legacy'. + keep_expression_matrix : bool + Keeps the input expression matrix in the result Panda object. + modeProcess : str + The input data processing mode. + - 'legacy': refers to the processing mode in netZooPy<=0.5 + - (Default)'union': takes the union of all TFs and genes across priors and fills the missing genes in the priors with zeros. + - 'intersection': intersects the input genes and TFs across priors and removes the missing TFs/genes. + alpha : str + Learning rate (default: 0.1) + start : int + First sample of the expression dataset. This replicates the behavior of Lioness (default : 1) + end : int + Last sample of the expression dataset. This replicates the behavior of Lioness (default : None ) + + Examples + -------- + + >>> #Import the classes in the pypanda library: + >>> from netZooPy.panda.panda import Panda + >>> #Run the Panda algorithm, leave out motif and PPI data to use Pearson correlation network: + >>> panda_obj = Panda('../../tests/ToyData/ToyExpressionData.txt', '../../tests/ToyData/ToyMotifData.txt', '../../tests/ToyData/ToyPPIData.txt', remove_missing=False) + >>> #Save the results: + >>> panda_obj.save_panda_results('Toy_Panda.pairs.txt') + >>> #Return a network plot: + >>> panda_obj.top_network_plot(top=70, file='top_genes.png') + >>> #Calculate in- and outdegrees for further analysis: + >>> indegree = panda_obj.return_panda_indegree() + >>> outdegree = panda_obj.return_panda_outdegree() + + + Notes + ------ + + Toy data:The example gene expression data that we have available here contains gene expression profiles + for different samples in the columns. Of note, this is just a small subset of a larger gene + expression dataset. We provided these "toy" data so that the user can test the method. + + + Sample PANDA results:\b + - TF Gene Motif Force\n + - CEBPA AACSL 0.0 -0.951416589143\n + - CREB1 AACSL 0.0 -0.904241609324\n + - DDIT3 AACSL 0.0 -0.956471642313\n + - E2F1 AACSL 1.0 3.685316051\n + - EGR1 AACSL 0.0 -0.695698519643 + + References + ---------- + .. [1]__ Glass, Kimberly, et al. "Passing messages between biological networks to refine predicted interactions." + PloS one 8.5 (2013): e64832. + + Authors: Cho-Yi Chen, David Vi, Alessandro Marin, Marouen Ben Guebila, Daniel Morgan + """ def __init__( @@ -87,31 +114,7 @@ def __init__( start=1, end=None, ): - """ - Description: - Intialize instance of Panda class and load data. - - Inputs: - expression_file : Path to file containing the gene expression data or pandas dataframe. By default, the expression file does not have a header, and the cells ares separated by a tab. - motif_file : Path to file containing the transcription factor DNA binding motif data in the form of TF-gene-weight(0/1) or pandas dataframe. - If set to none, the gene coexpression matrix is returned as a result network. - ppi_file : Path to file containing the PPI data. or pandas dataframe. The PPI can be symmetrical, if not, it will be transformed into a symmetrical adjacency matrix. - computing : 'cpu' uses Central Processing Unit (CPU) to run PANDA. - 'gpu' use the Graphical Processing Unit (GPU) to run PANDA. - precision : 'double' computes the regulatory network in double precision (15 decimal digits). - 'single' computes the regulatory network in single precision (7 decimal digits) which is fastaer, requires half the memory but less accurate. - save_memory : True : removes temporary results from memory. The result network is weighted adjacency matrix of size (nTFs, nGenes). - False: keeps the temporary files in memory. The result network has 4 columns in the form gene - TF - weight in motif prior - PANDA edge. - save_tmp : Save temporary variables. - remove_missing : Removes the gens and TFs that are not present in one of the priors. Works only if modeProcess='legacy'. - keep_expression_matrix: Keeps the input expression matrix in the result Panda object. - modeProcess : The input data processing mode. - 'legacy': refers to the processing mode in netZooPy<=0.5 - (Default)'union': takes the union of all TFs and genes across priors and fills the missing genes in the priors with zeros. - 'intersection': intersects the input genes and TFs across priors and removes the missing TFs/genes. - alpha : Learning rate (default: 0.1) - start : First sample of the expression dataset. This replicates the behavior of Lioness (default : 1) - end : Last sample of the expression dataset. This replicates the behavior of Lioness (default : None ) + """ Intialize instance of Panda class and load data. """ # Read data self.processData( @@ -124,6 +127,7 @@ def __init__( start=start, end=end ) + print(modeProcess,motif_file,expression_file,ppi_file,save_memory,remove_missing,keep_expression_matrix) if hasattr(self, "export_panda_results"): return @@ -146,7 +150,8 @@ def __init__( # Clean up useless variables to release memory # ===================================================================== self.tfs, self.genes = self.unique_tfs, self.gene_names - if save_memory: + + if (save_memory==True): print("Clearing motif and ppi data, unique tfs, and gene names for speed") del self.unique_tfs, self.gene_names, self.motif_matrix_unnormalized @@ -188,9 +193,7 @@ def __init__( ) def __remove_missing(self): - """ - Description: - Removes the gens and TFs that are not present in one of the priors. Works only if modeProcess='legacy'. + """ Removes the genes and TFs that are not present in one of the priors. Works only if modeProcess='legacy'. """ if self.expression_data is not None: print("Remove expression not in motif:") @@ -237,15 +240,17 @@ def __remove_missing(self): return None def _normalize_network(self, x): - """ - Description: - Standardizes the input data matrices. + """Standardizes the input data matrices. - Inputs: - x : Input adjacency matrix. + Parameters + ---------- + x : array + Input adjacency matrix. - Outputs: - normalized_matrix: Standardized adjacency matrix. + Returns + ------- + normalized_matrix: array + Standardized adjacency matrix. """ normalized_matrix = calc.normalize_network(x) return normalized_matrix @@ -261,19 +266,31 @@ def processData( start=1, end=None, ): + """ Processes data files into data matrices. + + Parameters + ---------- + + expression_file : str + Path to file containing the gene expression data or pandas dataframe. By default, the expression file does not have a header, and the cells ares separated by a tab. + motif_file : str + Path to file containing the transcription factor DNA binding motif data in the form of + TF-gene-weight(0/1) or pandas dataframe. + If set to none, the gene coexpression matrix is returned as a result network. + ppi_file : str + Path to file containing the PPI data. or pandas dataframe. + The PPI can be symmetrical, if not, it will be transformed into a symmetrical adjacency matrix. + remove_missing : bool + Removes the gens and TFs that are not present in one of the priors. Works only if modeProcess='legacy'. + keep_expression_matrix : bool + Keeps the input expression matrix in the result Panda object. + modeProcess : str + The input data processing mode. + - 'legacy': refers to the processing mode in netZooPy<=0.5 + - (Default)'union': takes the union of all TFs and genes across priors and fills the missing genes in the priors with zeros. + - 'intersection': intersects the input genes and TFs across priors and removes the missing TFs/genes. """ - Description: - Processes data files into data matrices. - - Inputs: - modeProcess : Input adjacency matrix. - expression_file : Path to file containing the gene expression data. - motif_file : Path to file containing the transcription factor DNA binding motif data in the form of TF-gene-weight(0/1). - If set to none, the gene coexpression matrix is returned as a result network. - ppi_file : Path to file containing the PPI data. - remove_missing : Removes the gens and TFs that are not present in one of the priors. Works only if modeProcess='legacy'. - keep_expression_matrix: Keeps the input expression matrix in the result Panda object. - """ + # if modeProcess=="legacy": # ===================================================================== # Data loading @@ -369,6 +386,7 @@ def processData( if modeProcess == "legacy" and remove_missing and motif_file is not None: self.__remove_missing() + print('new case') if modeProcess == "legacy" and remove_missing==False: if expression_file is not None: self.gene_names = ( @@ -484,22 +502,19 @@ def processData( def panda_loop( self, correlation_matrix, motif_matrix, ppi_matrix, computing="cpu", alpha=0.1 ): - """ - Description: - The PANDA algorithm. - - Inputs: - correlation_matrix: Input coexpression matrix. - motif_matrix : Input motif regulation prior network. - ppi_matrix : Input PPI matrix. - computing : 'cpu' uses Central Processing Unit (CPU) to run PANDA. - 'gpu' use the Graphical Processing Unit (GPU) to run PANDA. - - Methods (these are no longer used here, but defined in calculations.py): - t_function : Continuous Tanimoto similarity function computed on the CPU. - update_diagonal : Updates the diagonal of the input matrix in the message passing computed on the CPU. - gt_function : Continuous Tanimoto similarity function computed on the GPU. - gupdate_diagonal: Updates the diagonal of the input matrix in the message passing computed on the GPU. + """ The PANDA algorithm. + + Parameters + ---------- + correlation_matrix: array + Input coexpression matrix. + motif_matrix : array + Input motif regulation prior network. + ppi_matrix : array + Input PPI matrix. + computing : str + 'cpu' uses Central Processing Unit (CPU) to run PANDA. + 'gpu' use the Graphical Processing Unit (GPU) to run PANDA. """ @@ -528,18 +543,13 @@ def panda_loop( return motif_matrix def __pearson_results_data_frame(self): - """ - Description: - Saves PANDA network in edges format. + """ Saves PANDA network in edges format. """ genes_1 = np.tile(self.gene_names, (len(self.gene_names), 1)).flatten() genes_2 = ( np.tile(self.gene_names, (len(self.gene_names), 1)).transpose().flatten() ) self.flat_panda_network = self.panda_network.transpose().flatten() - print(genes_1) - print(genes_2) - print((self.flat_panda_network).shape) self.export_panda_results = pd.DataFrame( {"tf": genes_1, "gene": genes_2, "force": self.flat_panda_network} ) @@ -547,12 +557,12 @@ def __pearson_results_data_frame(self): return None def save_panda_results(self, path="panda.npy"): - """ - Description: - Saves PANDA network. + """ Saves PANDA network. - Inputs: - path: Path to save the network. + Parameters + ---------- + path: str + Path to save the network. """ with Timer("Saving PANDA network to %s ..." % path): # Because there are two modes of operation (save_memory), save to file will be different @@ -571,14 +581,16 @@ def save_panda_results(self, path="panda.npy"): np.save(path, toexport) def top_network_plot(self, top=100, file="panda_top_100.png", plot_bipart=False): - """ - Description: - Selects top genes. - - Inputs: - top : Top number of genes to plot. - file : File to save the network plot. - plot_bipart: Plot the network as a bipartite layout. + """ Selects top genes. + + Parameters + ---------- + top : int + Top number of genes to plot. + file : str + File to save the network plot. + plot_bipart: bool + Plot the network as a bipartite layout. """ if not hasattr(self, "export_panda_results"): raise AttributeError( @@ -606,14 +618,16 @@ def top_network_plot(self, top=100, file="panda_top_100.png", plot_bipart=False) def __shape_plot_network( self, subset_panda_results, file="panda.png", plot_bipart=False ): - """ - Description: - Creates plot. - - Inputs: - subset_panda_results : Reduced PANDA network to the top genes. - file : File to save the network plot. - plot_bipart: Plot the network as a bipartite layout. + """ Creates plot. + + Parameters + ----------- + subset_panda_results : array + Reduced PANDA network to the top genes. + file : str + File to save the network plot. + plot_bipart: bool + Plot the network as a bipartite layout. """ # reshape data for networkx unique_genes = list( @@ -643,17 +657,21 @@ def __shape_plot_network( return None def __create_plot(self, unique_genes, links, file="panda.png", plot_bipart=False): - """ - Description: - Runs the plot. - - Inputs: - unique_genes : Unique list of PANDA genes. - links : Edges of the subset PANDA network to the top genes. - file : File to save the network plot. - plot_bipart : Plot the network as a bipartite layout. - - Methods: + """ Runs the plot. + + Parameters + ---------- + unique_genes : list + Unique list of PANDA genes. + links : list + Edges of the subset PANDA network to the top genes. + file : str + File to save the network plot. + plot_bipart : bool + Plot the network as a bipartite layout. + + Notes + ----- split_label: Splits the plot label over several lines for plotting purposes. """ import networkx as nx @@ -680,14 +698,15 @@ def __create_plot(self, unique_genes, links, file="panda.png", plot_bipart=False labels = {} def split_label(label): - """ - Description: Splits the plot label over several lines for plotting purposes. + """ Splits the plot label over several lines for plotting purposes. - Inputs: + Parameters + ---------- label: Input label text. - Outputs: - label: Output label text divided over several lines. + Returns: + label: _ + Output label text divided over several lines. """ ll = len(label) if ll > 6: @@ -730,9 +749,7 @@ def split_label(label): return None def return_panda_indegree(self): - """ - Description: - computes indegree of PANDA network, only if save_memory = False. + """ Computes indegree of PANDA network, only if save_memory = False. """ export_panda_results_pd = pd.DataFrame( self.export_panda_results, columns=["tf", "gene", "motif", "force"] @@ -742,9 +759,7 @@ def return_panda_indegree(self): return self.panda_indegree def return_panda_outdegree(self): - """ - Description: - computes outdegree of PANDA network, only if save_memory = False. + """ computes outdegree of PANDA network, only if save_memory = False. """ export_panda_results_pd = pd.DataFrame( self.export_panda_results, columns=["tf", "gene", "motif", "force"] diff --git a/netZooPy/puma/puma.py b/netZooPy/puma/puma.py index a2c62869..02fd7173 100755 --- a/netZooPy/puma/puma.py +++ b/netZooPy/puma/puma.py @@ -12,40 +12,67 @@ class Puma(object): """ - Description: - Using PUMA to infer gene regulatory network. + Using PUMA to infer gene regulatory network. 1. Reading in input data (expression data, motif prior, TF PPI data, miR) 2. Computing coexpression network 3. Normalizing networks 4. Running PUMA algorithm 5. Writing out PUMA network - Inputs: - object: Puma object. - - Methods: - __init__ : Intialize instance of Puma class. - __remove_missing : Removes the gens and TFs that are not present in one of the priors. Works only if modeProcess='legacy'. - _normalize_network : Standardizes the input data matrices. - puma_loop : The PUMA algorithm. - __pearson_results_data_frame: Saves PUMA network in edges format. - save_puma_results : Saves PUMA network. - top_network_plot : Selects top genes to plot. - __shape_plot_network : Creates network plot. - __create_plot : Runs network plot. - return_puma_indegree : computes indegree of puma network, only if save_memory = False. - return_puma_outdegree : computes outdegree of puma network, only if save_memory = False. - - Example: + Parameters + ------------ + + expression_file : str + Path to file containing the gene expression data. + motif_file : str + Path to file containing the regulation prior. This can be a miRNA-Gene predicted network from TargetScan/miRanda. + However, this can be combined with transcription factor DNA binding motif data in the form of TF-gene-weight(0/1) to estimate gene regulation by TF and miRNA. + If set to none, the gene coexpression matrix is returned as a result network. + ppi_file : str + Path to file containing the TF PPI data. This can be provided as 'None' if no TF data is given and PUMA will estimate a miRNA-Gene networks. + mir_file : str + Path to file containing miRNA list. + computing : str + - 'cpu' uses Central Processing Unit (CPU) to run PANDA. + - 'gpu' use the Graphical Processing Unit (GPU) to run PANDA. + precision : str + 'double' computes the regulatory network in double precision (15 decimal digits). + 'single' computes the regulatory network in single precision (7 decimal digits) which is fastaer, requires half the memory but less accurate. + save_memory : bool + True : removes temporary results from memory. The result network is weighted adjacency matrix of size (nTFs, nGenes). + False: keeps the temporary files in memory. The result network has 4 columns in the form gene - TF - weight in motif prior - PUMA edge. + save_tmp : bool + Save temporary variables. + remove_missing : bool + Removes the gens and TFs that are not present in one of the priors. Works only if modeProcess='legacy'. + keep_expression_matrix: bool + Keeps the input expression matrix in the result Puma object. + modeProcess : str + The input data processing mode. + - 'legacy': refers to the processing mode in netZooPy<=0.5 + - (Default)'union': takes the union of all TFs and genes across priors and fills the missing genes in the priors with zeros. + - 'intersection': intersects the input genes and TFs across priors and removes the missing TFs/genes. + alpha : float + Learning rate (default: 0.1) + start : int + first sample of expression (default 1) + end : int + last sample of expression (default None) + + Examples + -------- Run the PUMA algorithm, leave out motif and PPI data to use Pearson correlation network: from netZooPy.puma.puma import Puma puma_obj = Puma('../../tests/ToyData/ToyExpressionData.txt', '../../tests/ToyData/ToyMotifData.txt', '../../tests/ToyData/ToyPPIData.txt','../../tests/ToyData/ToyMiRList.txt') - Authors: - cychen, davidvi, alessandromarin + - Reference: - Kuijjer, Marieke L., et al. "PUMA: PANDA Using MicroRNA Associations." BioRxiv (2019). + References + ---------- + + ..[1]__ Kuijjer, Marieke L., et al. "PUMA: PANDA Using MicroRNA Associations." OUP Bioinformatics (2019). + + Authors:cychen, davidvi, alessandromarin """ def __init__( @@ -66,33 +93,7 @@ def __init__( end=None, ): """ - Description: Intialize instance of Puma class and load data. - - Inputs: - expression_file : Path to file containing the gene expression data. - motif_file : Path to file containing the regulation prior. This can be a miRNA-Gene predicted network from TargetScan/miRanda. - However, this can be combined with transcription factor DNA binding motif data in the form of TF-gene-weight(0/1) to estimate gene regulation by TF and miRNA. - If set to none, the gene coexpression matrix is returned as a result network. - ppi_file : Path to file containing the TF PPI data. This can be provided as 'None' if no TF data is given and PUMA will estimate a miRNA-Gene networks. - mir_file : Path to file containing miRNA list. - computing : 'cpu' uses Central Processing Unit (CPU) to run PANDA. - 'gpu' use the Graphical Processing Unit (GPU) to run PANDA. - precision : 'double' computes the regulatory network in double precision (15 decimal digits). - 'single' computes the regulatory network in single precision (7 decimal digits) which is fastaer, requires half the memory but less accurate. - - save_memory : True : removes temporary results from memory. The result network is weighted adjacency matrix of size (nTFs, nGenes). - False: keeps the temporary files in memory. The result network has 4 columns in the form gene - TF - weight in motif prior - PUMA edge. - save_tmp : Save temporary variables. - remove_missing : Removes the gens and TFs that are not present in one of the priors. Works only if modeProcess='legacy'. - keep_expression_matrix: Keeps the input expression matrix in the result Puma object. - modeProcess : The input data processing mode. - 'legacy': refers to the processing mode in netZooPy<=0.5 - (Default)'union': takes the union of all TFs and genes across priors and fills the missing genes in the priors with zeros. - 'intersection': intersects the input genes and TFs across priors and removes the missing TFs/genes. - alpha : Learning rate (default: 0.1) - start : first sample of expression (default 1) - end : last sample of expression (default None) """ # ===================================================================== # Data loading @@ -220,7 +221,6 @@ def __init__( def __remove_missing(self): """ - Description: Removes the gens and TFs that are not present in one of the priors. Works only if modeProcess='legacy'. """ if self.expression_data is not None: @@ -269,14 +269,17 @@ def __remove_missing(self): def _normalize_network(self, x): """ - Description: Standardizes the input data matrices. - Inputs: - x : Input adjacency matrix. + Parameters + ---------- + x : array + Input adjacency matrix. - Outputs: - normalized_matrix: Standardized adjacency matrix. + Returns + -------- + normalized_matrix: array + Standardized adjacency matrix. """ return calc.normalize_network(x) @@ -284,21 +287,20 @@ def puma_loop( self, correlation_matrix, motif_matrix, ppi_matrix, computing="cpu", alpha=0.1 ): """ - Description: - The PUMA algorithm. - - Inputs: - correlation_matrix: Input coexpression matrix. - motif_matrix : Input motif regulation prior network. - ppi_matrix : Input PPI matrix. - computing : 'cpu' uses Central Processing Unit (CPU) to run PANDA. - 'gpu' use the Graphical Processing Unit (GPU) to run PANDA. - - Methods: - t_function : Continuous Tanimoto similarity function computed on the CPU. - update_diagonal : Updates the diagonal of the input matrix in the message passing computed on the CPU. - gt_function : Continuous Tanimoto similarity function computed on the GPU. - gupdate_diagonal: Updates the diagonal of the input matrix in the message passing computed on the GPU. + The PUMA algorithm. + + Parameters + ------------ + correlation_matrix: array + Input coexpression matrix. + motif_matrix : array + Input motif regulation prior network. + ppi_matrix : array + Input PPI matrix. + computing : str + - 'cpu' uses Central Processing Unit (CPU) to run PANDA. + - 'gpu' use the Graphical Processing Unit (GPU) to run PANDA. + """ puma_loop_time = time.time() @@ -327,7 +329,6 @@ def puma_loop( def __pearson_results_data_frame(self): """ - Description: Saves PUMA network in edges format. """ genes_1 = np.tile(self.gene_names, (len(self.gene_names), 1)).flatten() @@ -343,11 +344,12 @@ def __pearson_results_data_frame(self): def save_puma_results(self, path="puma.npy"): """ - Description: - Saves PUMA network. + Saves PUMA network. - Inputs: - path: Path to save the network. + Parameters + ------------- + path: str + Path to save the network. """ with Timer("Saving PUMA network to %s ..." % path): # Because there are two modes of operation (save_memory), save to file will be different @@ -367,13 +369,14 @@ def save_puma_results(self, path="puma.npy"): def top_network_plot(self, top=100, file="puma_top_100.png"): """ - Description: - Selects top genes. - - Inputs: - top : Top number of genes to plot. - file : File to save the network plot. - plot_bipart: Plot the network as a bipartite layout. + Selects top genes and plot network + + Parameters + ---------- + top : int + Top number of genes to plot. + file : str + File to save the network plot. """ if not hasattr(self, "export_puma_results"): raise AttributeError( @@ -396,13 +399,13 @@ def top_network_plot(self, top=100, file="puma_top_100.png"): def __shape_plot_network(self, subset_puma_results, file="puma.png"): """ - Description: - Creates plot. + Creates plot. - Inputs: - subset_puma_results : Reduced PUMA network to the top genes. - file : File to save the network plot. - plot_bipart : Plot the network as a bipartite layout. + Paramters: + subset_puma_results : array + Reduced PUMA network to the top genes. + file : str + File to save the network plot. """ # reshape data for networkx unique_genes = list( @@ -429,17 +432,17 @@ def __shape_plot_network(self, subset_puma_results, file="puma.png"): def __create_plot(self, unique_genes, links, file="puma.png"): """ - Description: - Runs the plot. + Runs the plot. - Inputs: - unique_genes : Unique list of PUMA genes. - links : Edges of the subset PUMA network to the top genes. - file : File to save the network plot. - plot_bipart : Plot the network as a bipartite layout. + Parameters + ----------- + unique_genes : list + Unique list of PUMA genes. + links : list + Edges of the subset PUMA network to the top genes. + file : str + File to save the network plot. - Methods: - split_label: Splits the plot label over several lines for plotting purposes. """ import networkx as nx import matplotlib.pyplot as plt @@ -462,13 +465,17 @@ def __create_plot(self, unique_genes, links, file="puma.png"): def split_label(label): """ - Description: Splits the plot label over several lines for plotting purposes. + Splits the plot label over several lines for plotting purposes. - Inputs: - label: Input label text. + Parameters + ---------- + label: str + Input label text. - Outputs: - label: Output label text divided over several lines. + Returns + ------- + label: str + Output label text divided over several lines. """ ll = len(label) if ll > 6: @@ -499,8 +506,7 @@ def split_label(label): def return_puma_indegree(self): """ - Description: - computes indegree of PUMA network, only if save_memory = False. + Computes indegree of PUMA network, only if save_memory = False. """ # subset_indegree = self.export_puma_results.loc[:,['gene','force']] subset_indegree = self.puma_results.loc[:, ["gene", "force"]] @@ -509,8 +515,7 @@ def return_puma_indegree(self): def return_puma_outdegree(self): """ - Description: - computes outdegree of PUMA network, only if save_memory = False. + Computes outdegree of PUMA network, only if save_memory = False. """ export_puma_results_pd = pd.DataFrame( self.export_puma_results, columns=["tf", "gene", "motif", "force"] diff --git a/netZooPy/sambar/sambar.py b/netZooPy/sambar/sambar.py index fc476034..69f6d8b4 100644 --- a/netZooPy/sambar/sambar.py +++ b/netZooPy/sambar/sambar.py @@ -47,22 +47,29 @@ def corgenelength(mut,cangenes,esize,normbysample=True,subcangenes=True): """ - Description: Function to normalize gene mutation scores by gene length. mut should be a dataframe of mutation scores with genes as columns and samples as rows. (VERY IMPORTANT, IF OTHERWISE MATRIX SHOULD BE TRANSPOSED OR IT WON'T WORK!!!) - Inputs: - mut : Mutation scores. - cangenes : A set of cancer associated genes. - esize : A dataframe of gene lengths. - normbysample: True : Normalizes the gene mutation scores in a sample by the total mutations within the sample. - False: Deactivate normalization. - subcangenes : True: Subsets mutation data to cancer-associated genes. - False: Takes all genes. + Parameters + -------------- + mut : list + Mutation scores. + cangenes : list + A set of cancer associated genes. + esize : dataFrame + A dataframe of gene lengths. + normbysample: bool + - True : Normalizes the gene mutation scores in a sample by the total mutations within the sample. + - False: Deactivate normalization. + subcangenes : bool + - True: Subsets mutation data to cancer-associated genes. + - False: Takes all genes. - Outputs: - mut : Mutation scores normalized by gene length. + Returns + -------------- + mut:_ + Mutation scores normalized by gene length. """ #Subsets mutation data to cancer-associated genes. if(subcangenes): @@ -92,23 +99,29 @@ def corgenelength(mut,cangenes,esize,normbysample=True,subcangenes=True): return mut[sorted(mut.columns)] def convertgmt(gmtfile, cangenes,gmtMSigDB=True,subcangenes=True): - """ - Description: - This function takes as input the name of a gmt file containing lists of genes associated to pathways. - It outputs an adjacency matrix of genes and pathways. - It also subsets the genes to a list of cancer-associated genes. + """ + This function takes as input the name of a gmt file containing lists of genes associated to pathways. + It outputs an adjacency matrix of genes and pathways. + It also subsets the genes to a list of cancer-associated genes. - Inputs: - gmtfile : Path the gmt file. - cangenes : A set of cancer associated genes. - gmtMSigDB : True : gmt file from MSigDB - False: file not form MSigDB - subcangenes: True : Subsets mutation data to cancer-associated genes. - False: Takes all genes. + Parameters + ----------- + gmtfile: str + Path the gmt file. + cangenes:list + A set of cancer associated genes. + gmtMSigDB : bool, optional + If true: gmt file from MSigDB . Defaults to True. + subcangenes : bool, optional + If true: Subsets mutation data to cancer-associated genes. + otherwise takes all genes. Defaults to True. + + Returns + -------- + sign_matrix: _ + Adjacency matrix of genes and pathways. + """ - Outputs: - sign_matrix: Adjacency matrix of genes and pathways. - """ file = open(gmtfile) # Loads the gmt file pw = file.readlines() #Reads file into list of strings @@ -147,11 +160,10 @@ def convertgmt(gmtfile, cangenes,gmtMSigDB=True,subcangenes=True): return sign_matrix[sorted(sign_matrix.columns)] def desparsify(mutdata,exonsize,gmtfile,cangenes,normMut=True,gmtMSigDB=True,subcangenes=True): - """ - Description: - Applies the sambar method to de-sparcify the mutation data using the pathway signatures in the gmtfile. + """ + Applies the sambar method to de-sparsify the mutation data using the pathway signatures in the gmtfile. - Inputs: + Args: mutdata : Mutation scores. exonsize : A dataframe of gene lengths. gmtfile : Path the gmt file. @@ -162,10 +174,12 @@ def desparsify(mutdata,exonsize,gmtfile,cangenes,normMut=True,gmtMSigDB=True,sub False: file not form MSigDB subcangenes : True : Subsets mutation data to cancer-associated genes. False: Takes all genes. - - Outputs: - mt : Genes in both pathways and mutation data. - pathway_scores: Pathway scores. + Returns + ------- + mt : _ + Genes in both pathways and mutation data + pathway_scores : _ + Pathway scores. """ tinit = time.time() @@ -208,16 +222,17 @@ def desparsify(mutdata,exonsize,gmtfile,cangenes,normMut=True,gmtMSigDB=True,sub return mt,pathway_scores def binomial_dist(u,v): - """ - Description: - Implementation of the binomial dissimilarity funcion or Millar distance from the vegan:vegdist package in R. + """Implementation of the binomial dissimilarity funcion or Millar distance from the vegan:vegdist package in R. - Inputs: + Parameters + ---------- u : First vector to compare distance from. v : Second vector to compare distance to. - Outputs: - bd: binomial dissimilarity. + Returns + ------- + bd: _ + binomial dissimilarity. """ np.seterr(divide='ignore', invalid='ignore') #The following steps raise divide by zero errors. This avoids the error to show up as it is not a problem since it is processed afterwards. x,y= u,v @@ -231,19 +246,20 @@ def binomial_dist(u,v): return bd def clustering(pt, kmin,kmax,distance,linkagem): - """ - Description: - Computes the clustering for the pathways matrix and returns a dataframe with the groups with k clusters from kmin to kmax. + """Computes the clustering for the pathways matrix and returns a dataframe with the groups with k clusters from kmin to kmax. - Inputs: + Parameters + ---------- pt : Pathway scores. kmin : Min number of groups in the clustering. kmax : Max number of groups in the clustering. distance: Similarity metric for the clustering. Default is binomial distance but any distance from scipy.spatial.distance can be used. linkagem: Linkage method. Default is complete. - Outputs: - df : Cluster assignement dataframe. + Returns + ------- + df: _ + Cluster assignement dataframe. """ tinit = time.time() if(distance=="binomial"): @@ -265,11 +281,10 @@ def clustering(pt, kmin,kmax,distance,linkagem): return df.transpose() def sambar(mut_file=mut,esize_file=esize,genes_file=genes,gmtfile=sign,normPatient=True,kmin=2,kmax=4,gmtMSigDB=True,subcangenes=True,distance="binomial",linkagem="complete",cluster=True): - """ - Description: - Runs SAMBAR and outputs the pt matrix, the mt matrix and the clustering matrix. + """Runs SAMBAR and outputs the pt matrix, the mt matrix and the clustering matrix. - Inputs: + Parameters + ------------------ mutfile : matrix of mutations with genes as columns and samples as rows. Format CSV. esize_file : file with genes and their length. genes_file : file with list of cancer-associated genes. @@ -282,13 +297,20 @@ def sambar(mut_file=mut,esize_file=esize,genes_file=genes,gmtfile=sign,normPatie linkagem : Linkage method. Default is complete. cluster : Whether the clustering has to be compute or the output will just be the pathway mutation scores. - Outputs: - pt : the pathway matrix. - groups : the groups dataframe as python objects. - mt_out.csv : processed gene mutation scores. - pt_out.csv : pathway mutation scores - clustergroups.csv: matrix of pertinence to a group in the clustering. - dist_matrix.csv : Computation of the distance matrix is resource-consuming so the matrix is writen so it doesn't have to be computed again. + Returns + ------- + pt :_ + the pathway matrix. + groups :_ + the groups dataframe as python objects. + mt_out.csv :_ + processed gene mutation scores. + pt_out.csv:_ + pathway mutation scores + clustergroups.csv: _ + matrix of pertinence to a group in the clustering. + dist_matrix.csv : _ + Computation of the distance matrix is resource-consuming so the matrix is writen so it doesn't have to be computed again. Reference: Kuijjer, Marieke Lydia, et al. "Cancer subtype identification using somatic mutation data." British journal of cancer 118.11 (2018): 1492-1501. diff --git a/requirements.txt b/requirements.txt index a9a054b2..047ecd0e 100755 --- a/requirements.txt +++ b/requirements.txt @@ -6,3 +6,4 @@ scipy python-igraph joblib statsmodels +click diff --git a/setup.py b/setup.py index c42b412e..2ec81f10 100755 --- a/setup.py +++ b/setup.py @@ -1,11 +1,11 @@ from setuptools import setup, find_packages setup(name='netZooPy', - version='0.9.0', + version='0.9.2', description='Python implementation of netZoo.', url='https://github.com/netZoo/netZooPy', author='netZoo team', - author_email='twangxx@hsph.harvard.edu', + author_email='vfanfani@hsph.harvard.edu', license='GPL-3', packages=find_packages(), install_requires=['pandas', @@ -15,6 +15,13 @@ 'scipy', 'python-igraph', 'joblib', - 'statsmodels' + 'statsmodels', + 'click' ], - zip_safe=False) + zip_safe=False, + # add cli interface + entry_points={ + 'console_scripts': [ + 'netzoopy=netZooPy.cli:cli' + ], + }, ) diff --git a/tests/test_condor.py b/tests/test_condor.py index 227a4593..81d480f1 100644 --- a/tests/test_condor.py +++ b/tests/test_condor.py @@ -4,6 +4,12 @@ import pandas as pd import numpy as np import random +import subprocess +import netZooPy.command_line as cmd + +np.random.seed(0) +import random +random.seed(0) def test_condor(): print('Start Condor run ...') @@ -14,11 +20,33 @@ def test_condor(): gt_file1 ='tests/condor/gh_tar_memb.txt' gt_file2 ='tests/condor/gh_reg_memb.txt' - #1. Condor + print('finished extra comparison') condor.run_condor(network) - res1=pd.read_csv(output_file1, sep=' ', header=None) - res2=pd.read_csv(output_file2, sep=' ', header=None) - gt1 =pd.read_csv(gt_file1, sep=' ', header=None) - gt2 =pd.read_csv(gt_file2, sep=' ', header=None) + res1=pd.read_csv(output_file1, sep=',', header=None) + res2=pd.read_csv(output_file2, sep=',', header=None) + gt1 =pd.read_csv(gt_file1, sep=',', header=None) + gt2 =pd.read_csv(gt_file2, sep=',', header=None) pd.testing.assert_frame_equal(res1,gt1,check_less_precise=False,check_exact=False) pd.testing.assert_frame_equal(res2,gt2,check_less_precise=False,check_exact=False) + print('finished condor test') + + np.random.seed(0) + random.seed(0) + + ## Test command line call + result = subprocess.run(["netzoopy", "condor", "--help"], capture_output=False) + assert result.returncode == 0 + + # 1. Test command line + cmd.condor.callback(network, tar_output="tar2.txt",reg_output="reg2.txt") + res1=pd.read_csv('tar2.txt', sep=',', header=None) + res2=pd.read_csv('reg2.txt', sep=',', header=None) + gt1 =pd.read_csv(gt_file1, sep=',', header=None) + gt2 =pd.read_csv(gt_file2, sep=',', header=None) + + print(res1.columns) + print(gt1.columns) + pd.testing.assert_frame_equal(res1,gt1,check_less_precise=False,check_exact=False) + pd.testing.assert_frame_equal(res2,gt2,check_less_precise=False,check_exact=False) + + print('finished comparison with command line') \ No newline at end of file diff --git a/tests/test_lioness.py b/tests/test_lioness.py index 4a199b83..43fc4e14 100644 --- a/tests/test_lioness.py +++ b/tests/test_lioness.py @@ -5,6 +5,8 @@ import pandas as pd import numpy as np import glob +import subprocess +import netZooPy.command_line as cmd def test_lioness(): @@ -33,8 +35,10 @@ def test_lioness(): end = 4 ) # Set parameters - lioness_obj = Lioness(panda_obj, start=1, end = 4) + lioness_obj = Lioness(panda_obj,save_dir = "lioness_output", start=1, end = 4) + panda_obj.save_panda_results('panda_remove.txt') lioness_obj.export_lioness_table(output_table) + # Check that the correlation matrix for Panda and Lioness are the same (there is no update by Panda or Lioness) np.allclose(panda_obj.correlation_matrix, lioness_obj.correlation_matrix) np.allclose(panda_obj.motif_matrix, lioness_obj.motif_matrix) @@ -45,7 +49,17 @@ def test_lioness(): pydf = pd.read_csv(output_table, sep = ' ', header=None).iloc[:,0:3] pd.testing.assert_frame_equal(rdf, pydf, rtol=5e-1, atol= 99e-2, check_exact=False) + + ## Test command line call + result = subprocess.run(["netzoopy", "lioness", "--help"], capture_output=False) + assert result.returncode == 0 + # 1. Test command line + #positional: expression, motif, ppi, output_panda, output_lioness, fmt, computing, precision, ncores, save_memory, save_tmp, rm_missing, mode_process,output_type, alpha, start, end): + cmd.lioness.callback(expression_data, motif, ppi, 'panda.txt','lioness_output_cmd','npy','cpu','double',1,False,True,rm_missing,'legacy','network',0.1,1,4) + res = np.load("lioness_output/lioness.1.npy") + gt = res = np.load("lioness_output_cmd/lioness.1.npy") + assert np.allclose(gt, res) # 2. Testing Lioness with motif set to None to compute Lioness on coexpression networks motif = None diff --git a/tests/test_panda.py b/tests/test_panda.py index 665ed4fb..b261836d 100644 --- a/tests/test_panda.py +++ b/tests/test_panda.py @@ -3,7 +3,8 @@ from netZooPy.panda.panda import Panda import pandas as pd import numpy as np - +import subprocess +import netZooPy.command_line as cmd def test_panda(): # print(os.getcwd()) @@ -18,6 +19,10 @@ def test_panda(): gt_file_inter = "tests/panda/inter_test_panda.txt" gt_file_rm = "tests/panda/rm_test_panda.txt" + ## Test command line call + result = subprocess.run(["netzoopy", "panda", "--help"], capture_output=False) + assert result.returncode == 0 + # 0. Intersection panda_obj = Panda( expression_data, @@ -28,11 +33,18 @@ def test_panda(): keep_expression_matrix=bool(lioness_file), modeProcess="intersection", ) + panda_obj.save_panda_results(output_file) res = pd.read_csv(output_file, sep=" ", header=None) gt = pd.read_csv(gt_file_inter, sep=" ", header=None) pd.testing.assert_frame_equal(res, gt, rtol=1e-5, check_exact=False) + # 0.b Intersection from command line + cmd.panda.callback(expression_data, motif, ppi, output_file, rm_missing = rm_missing, keep_expr=bool(lioness_file),mode_process='intersection', save_memory = True) + res = pd.read_csv(output_file, sep=" ", header=None) + gt = pd.read_csv(gt_file_inter, sep=" ", header=None) + pd.testing.assert_frame_equal(res, gt, rtol=1e-5, check_exact=False) + # 0.1 Intersection via DataFrame expression = pd.read_csv(expression_data, sep="\t", header=None, index_col=0) motif_data = pd.read_csv(motif, sep="\t", names=["source", "target", "w"]) @@ -85,6 +97,16 @@ def test_panda(): gt = pd.read_csv(gt_file, sep=" ", header=None) pd.testing.assert_frame_equal(res, gt, rtol=1e-5, check_exact=False) + + # 1.b Union from command line + + cmd.panda.callback(expression_data, motif, ppi, output_file, rm_missing = rm_missing, keep_expr=bool(lioness_file),mode_process='union', save_memory = True) + + res = pd.read_csv(output_file, sep=" ", header=None) + gt = pd.read_csv(gt_file, sep=" ", header=None) + pd.testing.assert_frame_equal(res, gt, rtol=1e-5, check_exact=False) + + # 2. In-degree and out-degree panda_obj = Panda( expression_data, @@ -164,9 +186,7 @@ def test_panda(): + ".txt" ) gt = pd.read_csv(gt_test_panda + str(i) + ".txt", sep=" ", header=None) - pd.testing.assert_frame_equal( - res, gt, rtol=1e-5, check_exact=False - ) + pd.testing.assert_frame_equal(res, gt, rtol=1e-5, check_exact=False) # PPI i = i + 1 panda_obj = Panda( @@ -188,9 +208,7 @@ def test_panda(): + ".txt" ) gt = pd.read_csv(gt_test_panda + str(i) + ".txt", sep=" ", header=None) - pd.testing.assert_frame_equal( - res, gt, rtol=1e-5, check_exact=False - ) + pd.testing.assert_frame_equal(res, gt, rtol=1e-5, check_exact=False) # Expression i = i + 1 panda_obj = Panda( @@ -212,9 +230,7 @@ def test_panda(): + ".txt" ) gt = pd.read_csv(gt_test_panda + str(i) + ".txt", sep=" ", header=None) - pd.testing.assert_frame_equal( - res, gt, rtol=1e-5, check_exact=False - ) + pd.testing.assert_frame_equal(res, gt, rtol=1e-5, check_exact=False) # Expression and PPI i = i + 1 panda_obj = Panda( @@ -236,6 +252,4 @@ def test_panda(): + ".txt" ) gt = pd.read_csv(gt_test_panda + str(i) + ".txt", sep=" ", header=None) - pd.testing.assert_frame_equal( - res, gt, rtol=1e-5, check_exact=False - ) + pd.testing.assert_frame_equal(res, gt, rtol=1e-5, check_exact=False)