Milestone 3

Changes (since milestone 2)

• improved caching:
  • cache now also stores parents and children,
  • original .gfa file is not needed on warm load.
  • cold load time improved.
• better layout algorithm: layered graph drawing.
• bookmarks can now be opened from a different file (opening a bookmark will open the file is if it is not already opened)
• command line arguments:
  • --file=<name>: open file name on startup
  • --clean: clean start, discard the cache for the file you are opening and reparse the .gfa file.
• opening a bookmark will draw it after loading the graph.
• drawing a radius up to 500 is near-instant.
• drawing radius can reach over 3000, but this takes a long time.
• Note: drawing time is very much dependent on the centernode.
  • in TB328, centernode 10000 takes much longer than 20000 (with equal radius)
• Fixed some old bugs, introduced some new ones.

Known issues:

• bookmarks must have at least two characters
• The program does not detect moved files, so bookmarks and recent files don't work when you change/move the files they refer to.
• You can only zoom and pan with the mouse when the cursor is on a node or an edge.
• The graph only shows ancestors / descendants from the centernode, so brothers/sisters etc. (nodes with the same parent as centernode) are not shown.
• clicking on edges does not always give very useful information
• clicking on a horizontal spot of edges does not show information
• edges might clip nodes
• there are some edge crossings.
• There might be duplicates in file -> open recent when opening other files with file -> open. This is only in-memory, so restarting the program fixes it.
• When parsing fails on an outOfMemoryError, it does not give any error message
  • on a related note, tomato cannot be opened yet.