Final Release

This is v1.0.0 of Hygene!

Known Issues

• After extensive interaction with the graph, hovering over and clicking on nodes may result in longer response times than usual.

Alpha 2

v1.0.0-alpha.2

Create README.md

Alpha 1

A preview of the final program.

Demo for Milestone 6

To load the tomato GFA, you should run the program from the command line as follows:

java -Xmx4G -jar hygene-all-0.7.1.jar

Demo for Milestone 5

Run the JAR by double-clicking on it.

Known issues

• Blank screen until first scroll (just scroll a bit to display the nodes and annotations)

Demo for Milestone 4

Extract the src folder to the same directory as the jar.

• hygene-all-0.5.0.zip is our "main" release and has the new layout.
• hygene-all-0.5.0-visual-encoding.zip has visual encodings such as edge thickness and path selection.

Known issues

• Tomato is not displayed after the 1,691,584th node.
• Some nodes are displayed
• Backspace and arrow keys do not work in some input fields.

Demo for Milestone 3

Please pay attention:
There are two JARs in this release: One with ending all which has all navigation capabilities, but the old layout algorithm. The other one does not contain these features, but provides the new, improved layout algorithm.
The two JARs have different file database versions, so please do not forget to delete these file DBs between launches of different versions. Our apologies for the slight delay, this was caused due to unforeseen merging issues.

Known issues

• .gfa files cannot be loaded when a .hygene for that file exists but the version of that database is mismatched. The recommended solution is to delete the corresponding .hygene file.
• Zooming out very far on large genomes will result in a laggy system. This will be fixed when semantic zooming is introduced. The recommended solution is to not zoom out very far.
• Cancelling the load operating (by closing the loading bar) does not actually stop the loading process.
• Pressing the backspace or arrow keys in the centre point query input fields will result in the keys being ignored.
• Edge case of center point queries: Edges to nodes that are not within the radius should not be drawn, but are at the moment. Therefore you sometimes see edges going to 'nothing'.

Demo for Milestone 2

Run by executing java -jar hygene-all-0.3.0.jar --file=filename.gfa

Milestone 1 w/ Improvements

v0.2.1

Add LICENSE

Demo for Milestone 1

v0.2.0

Add LICENSE