Renamed "Order.." to "Sort.."

mzmine · Jul 24, 2019 · 2a83d3a · 2a83d3a
1 parent 277b261
commit 2a83d3a
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Showing 6 changed files with 32 additions and 32 deletions.
diff --git a/src/main/java/net/sf/mzmine/desktop/impl/projecttree/ProjectTreeMouseHandler.java b/src/main/java/net/sf/mzmine/desktop/impl/projecttree/ProjectTreeMouseHandler.java
@@ -35,12 +35,12 @@
 import net.sf.mzmine.datamodel.RawDataFile;
 import net.sf.mzmine.datamodel.Scan;
 import net.sf.mzmine.main.MZmineCore;
-import net.sf.mzmine.modules.peaklistmethods.orderpeaklists.OrderPeakListsModule;
-import net.sf.mzmine.modules.peaklistmethods.orderpeaklists.OrderPeakListsParameters;
+import net.sf.mzmine.modules.peaklistmethods.sortpeaklists.SortPeakListsModule;
+import net.sf.mzmine.modules.peaklistmethods.sortpeaklists.SortPeakListsParameters;
 import net.sf.mzmine.modules.rawdatamethods.exportscans.ExportScansModule;
-import net.sf.mzmine.modules.rawdatamethods.orderdatafiles.OrderDataFilesModule;
-import net.sf.mzmine.modules.rawdatamethods.orderdatafiles.OrderDataFilesParameters;
 import net.sf.mzmine.modules.rawdatamethods.rawdataexport.RawDataExportModule;
+import net.sf.mzmine.modules.rawdatamethods.sortdatafiles.SortDataFilesModule;
+import net.sf.mzmine.modules.rawdatamethods.sortdatafiles.SortDataFilesParameters;
 import net.sf.mzmine.modules.visualization.infovisualizer.InfoVisualizerModule;
 import net.sf.mzmine.modules.visualization.peaklisttable.PeakListTableModule;
 import net.sf.mzmine.modules.visualization.peaksummary.PeakSummaryVisualizerModule;
@@ -169,10 +169,10 @@ public void actionPerformed(ActionEvent e) {
       // save current selection
       TreePath savedSelection[] = tree.getSelectionPaths();
       RawDataFile selectedFiles[] = tree.getSelectedObjects(RawDataFile.class);
-      OrderDataFilesModule module = MZmineCore.getModuleInstance(OrderDataFilesModule.class);
+      SortDataFilesModule module = MZmineCore.getModuleInstance(SortDataFilesModule.class);
       ParameterSet params =
-          MZmineCore.getConfiguration().getModuleParameters(OrderDataFilesModule.class);
-      params.getParameter(OrderDataFilesParameters.dataFiles)
+          MZmineCore.getConfiguration().getModuleParameters(SortDataFilesModule.class);
+      params.getParameter(SortDataFilesParameters.dataFiles)
           .setValue(RawDataFilesSelectionType.SPECIFIC_FILES, selectedFiles);
       module.runModule(MZmineCore.getProjectManager().getCurrentProject(), params,
           new ArrayList<Task>());
@@ -304,10 +304,10 @@ public void actionPerformed(ActionEvent e) {
       // save current selection
       TreePath savedSelection[] = tree.getSelectionPaths();
       PeakList selectedPeakLists[] = tree.getSelectedObjects(PeakList.class);
-      OrderPeakListsModule module = MZmineCore.getModuleInstance(OrderPeakListsModule.class);
+      SortPeakListsModule module = MZmineCore.getModuleInstance(SortPeakListsModule.class);
       ParameterSet params =
-          MZmineCore.getConfiguration().getModuleParameters(OrderPeakListsModule.class);
-      params.getParameter(OrderPeakListsParameters.peakLists)
+          MZmineCore.getConfiguration().getModuleParameters(SortPeakListsModule.class);
+      params.getParameter(SortPeakListsParameters.peakLists)
           .setValue(PeakListsSelectionType.SPECIFIC_PEAKLISTS, selectedPeakLists);
       module.runModule(MZmineCore.getProjectManager().getCurrentProject(), params,
           new ArrayList<Task>());

diff --git a/src/main/java/net/sf/mzmine/main/MZmineModulesList.java b/src/main/java/net/sf/mzmine/main/MZmineModulesList.java
@@ -77,13 +77,13 @@
 import net.sf.mzmine.modules.peaklistmethods.normalization.linear.LinearNormalizerModule;
 import net.sf.mzmine.modules.peaklistmethods.normalization.rtnormalizer.RTNormalizerModule;
 import net.sf.mzmine.modules.peaklistmethods.normalization.standardcompound.StandardCompoundNormalizerModule;
-import net.sf.mzmine.modules.peaklistmethods.orderpeaklists.OrderPeakListsModule;
 import net.sf.mzmine.modules.peaklistmethods.peakpicking.adap3decompositionV1_5.ADAP3DecompositionV1_5Module;
 import net.sf.mzmine.modules.peaklistmethods.peakpicking.adap3decompositionV2.ADAP3DecompositionV2Module;
 import net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.DeconvolutionModule;
 import net.sf.mzmine.modules.peaklistmethods.peakpicking.peakextender.PeakExtenderModule;
 import net.sf.mzmine.modules.peaklistmethods.peakpicking.shapemodeler.ShapeModelerModule;
 import net.sf.mzmine.modules.peaklistmethods.peakpicking.smoothing.SmoothingModule;
+import net.sf.mzmine.modules.peaklistmethods.sortpeaklists.SortPeakListsModule;
 import net.sf.mzmine.modules.projectmethods.projectclose.ProjectCloseModule;
 import net.sf.mzmine.modules.projectmethods.projectload.ProjectLoadModule;
 import net.sf.mzmine.modules.projectmethods.projectsave.ProjectSaveAsModule;
@@ -97,14 +97,14 @@
 import net.sf.mzmine.modules.rawdatamethods.filtering.scanfilters.ScanFiltersModule;
 import net.sf.mzmine.modules.rawdatamethods.filtering.scansmoothing.ScanSmoothingModule;
 import net.sf.mzmine.modules.rawdatamethods.merge.RawFileMergeModule;
-import net.sf.mzmine.modules.rawdatamethods.orderdatafiles.OrderDataFilesModule;
 import net.sf.mzmine.modules.rawdatamethods.peakpicking.gridmass.GridMassModule;
 import net.sf.mzmine.modules.rawdatamethods.peakpicking.manual.ManualPeakPickerModule;
 import net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetectionModule;
 import net.sf.mzmine.modules.rawdatamethods.peakpicking.msms.MsMsPeakPickerModule;
 import net.sf.mzmine.modules.rawdatamethods.peakpicking.targetedpeakdetection.TargetedPeakDetectionModule;
 import net.sf.mzmine.modules.rawdatamethods.rawdataexport.RawDataExportModule;
 import net.sf.mzmine.modules.rawdatamethods.rawdataimport.RawDataImportModule;
+import net.sf.mzmine.modules.rawdatamethods.sortdatafiles.SortDataFilesModule;
 import net.sf.mzmine.modules.tools.isotopepatternpreview.IsotopePatternPreviewModule;
 import net.sf.mzmine.modules.tools.msmsspectramerge.MsMsSpectraMergeModule;
 import net.sf.mzmine.modules.tools.mzrangecalculator.MzRangeFormulaCalculatorModule;
@@ -158,10 +158,10 @@ public class MZmineModulesList {
       // Not ready for prime time: ADAP3DModule.class,
       GridMassModule.class, ManualPeakPickerModule.class, MsMsPeakPickerModule.class,
       ScanFiltersModule.class, CropFilterModule.class, BaselineCorrectionModule.class,
-      AlignScansModule.class, ScanSmoothingModule.class, OrderDataFilesModule.class,
+      AlignScansModule.class, ScanSmoothingModule.class, SortDataFilesModule.class,
 
       // Alignment
-      OrderPeakListsModule.class, JoinAlignerModule.class, HierarAlignerGcModule.class,
+      SortPeakListsModule.class, JoinAlignerModule.class, HierarAlignerGcModule.class,
 
       RansacAlignerModule.class, ADAP3AlignerModule.class,
       // PathAlignerModule.class,

diff --git a/.../orderpeaklists/OrderPeakListsModule.java → ...ds/sortpeaklists/SortPeakListsModule.java b/.../orderpeaklists/OrderPeakListsModule.java → ...ds/sortpeaklists/SortPeakListsModule.java
@@ -16,7 +16,7 @@
  * USA
  */
 
-package net.sf.mzmine.modules.peaklistmethods.orderpeaklists;
+package net.sf.mzmine.modules.peaklistmethods.sortpeaklists;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -45,12 +45,12 @@
  * This is a very simple module which reorders feature lists alphabetically
  * 
  */
-public class OrderPeakListsModule implements MZmineProcessingModule {
+public class SortPeakListsModule implements MZmineProcessingModule {
 
   private Logger logger = Logger.getLogger(this.getClass().getName());
 
-  private static final String MODULE_NAME = "Order feature lists";
-  private static final String MODULE_DESCRIPTION = "Order selected feature lists alphabetically";
+  private static final String MODULE_NAME = "Sort feature lists";
+  private static final String MODULE_DESCRIPTION = "Sort selected feature lists alphabetically";
 
   @Override
   public @Nonnull String getName() {
@@ -68,7 +68,7 @@ public ExitCode runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet
       @Nonnull Collection<Task> tasks) {
 
     List<PeakList> peakLists = Arrays.asList(parameters
-        .getParameter(OrderPeakListsParameters.peakLists).getValue().getMatchingPeakLists());
+        .getParameter(SortPeakListsParameters.peakLists).getValue().getMatchingPeakLists());
 
 
     PeakListTreeModel model = null;
@@ -133,7 +133,7 @@ public int compare(DefaultMutableTreeNode o1, DefaultMutableTreeNode o2) {
 
   @Override
   public @Nonnull Class<? extends ParameterSet> getParameterSetClass() {
-    return OrderPeakListsParameters.class;
+    return SortPeakListsParameters.class;
   }
 
 }
diff --git a/...erpeaklists/OrderPeakListsParameters.java → ...ortpeaklists/SortPeakListsParameters.java b/...erpeaklists/OrderPeakListsParameters.java → ...ortpeaklists/SortPeakListsParameters.java
@@ -16,17 +16,17 @@
  * USA
  */
 
-package net.sf.mzmine.modules.peaklistmethods.orderpeaklists;
+package net.sf.mzmine.modules.peaklistmethods.sortpeaklists;
 
 import net.sf.mzmine.parameters.Parameter;
 import net.sf.mzmine.parameters.impl.SimpleParameterSet;
 import net.sf.mzmine.parameters.parametertypes.selectors.PeakListsParameter;
 
-public class OrderPeakListsParameters extends SimpleParameterSet {
+public class SortPeakListsParameters extends SimpleParameterSet {
 
   public static final PeakListsParameter peakLists = new PeakListsParameter();
 
-  public OrderPeakListsParameters() {
+  public SortPeakListsParameters() {
     super(new Parameter[] {peakLists});
   }
 

diff --git a/.../orderdatafiles/OrderDataFilesModule.java → ...ds/sortdatafiles/SortDataFilesModule.java b/.../orderdatafiles/OrderDataFilesModule.java → ...ds/sortdatafiles/SortDataFilesModule.java
@@ -16,7 +16,7 @@
  * USA
  */
 
-package net.sf.mzmine.modules.rawdatamethods.orderdatafiles;
+package net.sf.mzmine.modules.rawdatamethods.sortdatafiles;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -43,10 +43,10 @@
 /**
  * This is a very simple module which reorders data files alphabetically
  */
-public class OrderDataFilesModule implements MZmineProcessingModule {
+public class SortDataFilesModule implements MZmineProcessingModule {
 
-  private static final String MODULE_NAME = "Order raw data files";
-  private static final String MODULE_DESCRIPTION = "Order selected raw data files alphabetically";
+  private static final String MODULE_NAME = "Sort raw data files";
+  private static final String MODULE_DESCRIPTION = "Sort selected raw data files alphabetically";
 
   @Override
   public @Nonnull String getName() {
@@ -64,7 +64,7 @@ public ExitCode runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet
       @Nonnull Collection<Task> tasks) {
 
     List<RawDataFile> dataFiles = Arrays.asList(parameters
-        .getParameter(OrderDataFilesParameters.dataFiles).getValue().getMatchingRawDataFiles());
+        .getParameter(SortDataFilesParameters.dataFiles).getValue().getMatchingRawDataFiles());
 
 
     RawDataTreeModel model = null;
@@ -128,7 +128,7 @@ public int compare(DefaultMutableTreeNode o1, DefaultMutableTreeNode o2) {
 
   @Override
   public @Nonnull Class<? extends ParameterSet> getParameterSetClass() {
-    return OrderDataFilesParameters.class;
+    return SortDataFilesParameters.class;
   }
 
 }
diff --git a/...erdatafiles/OrderDataFilesParameters.java → ...ortdatafiles/SortDataFilesParameters.java b/...erdatafiles/OrderDataFilesParameters.java → ...ortdatafiles/SortDataFilesParameters.java
@@ -16,17 +16,17 @@
  * USA
  */
 
-package net.sf.mzmine.modules.rawdatamethods.orderdatafiles;
+package net.sf.mzmine.modules.rawdatamethods.sortdatafiles;
 
 import net.sf.mzmine.parameters.Parameter;
 import net.sf.mzmine.parameters.impl.SimpleParameterSet;
 import net.sf.mzmine.parameters.parametertypes.selectors.RawDataFilesParameter;
 
-public class OrderDataFilesParameters extends SimpleParameterSet {
+public class SortDataFilesParameters extends SimpleParameterSet {
 
   public static final RawDataFilesParameter dataFiles = new RawDataFilesParameter();
 
-  public OrderDataFilesParameters() {
+  public SortDataFilesParameters() {
     super(new Parameter[] {dataFiles});
   }