Milestone 4

Changes (since milestone 3)

Please delete all cache files of previous releases, before loading any new files.

new features

improved caching:
cache now also stores genomes
original .gfa file is now needed on warm load.
cold load time is now slower.

better layout algorithm: Minimal edge crossing.

Drawing:
Node color depends on amount of genomes through node
Siblings of the center node are now also found

Higlights:
Nodes can be highlighted specified by a minimum and maximum genomes, or
nodes can be highlighted specified by genome.
Genome is searchable with regex suggestions.

On click:
Click or Shift+Click on nodes/edges gives information about the sequence in a panel to the right.
Able to compare two nodes/edges, by first clicking the first node and then shift-clicking the second node.
The segments can be copied to clipboard.

Zooming/Panning:
Is not yet dynamic.
It does however feel very intuitive.

known issues

The progress bar fills twice now. Once for cold load parsing, and once for genome loading.
Progress has fallen of the screen. Increase window size to find it.
TB328 is very unpredictable. Performance varies by location (large variation).
Human is also difficult to draw, but it is possible.
Prefers genome selection with highlights over min max number of genomes.
The program does not detect moved files, so bookmarks and recent files don't work when you change/move the files they refer to.
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
Tomato can be opened yet, but will take too long. Cache file is 10gb.