Final Release

The final release for the project.

Sprint 8

This release includes:

• Heatmaps options for the tree
• Heatmap for graph
• Search functionality for annotations
• Color overhaul
• Configurable algorithms*
• Graph-based bubbling*

* (see menu->Settings)

Sprint 7

This release includes:

• More search functionality
• Search pane embedded in the application
• Gene annotations mapped to the graph
• Detection of in-del and point mutations
• Graph zooming optimized: Zooming in and out is perfectly smooth for the 328 data set
• Graph Comparison has been fixed and works now

Sprint 6

In this version:

• Add semantic zoom with grouping (bubbling) of nodes based on phylogeny.
• Add Interactive Search over genomes based on metadata (Ctrl+F to open and close)
• Add legend for that touch of UX
• Common path detection
• enable overview of whole data set by zooming out

Known Bugs:

• Comparing graphs does not work
• Drawing subgraphs (any phylogenetic node other than the root) does not work.
• Bubble detection doesn't work when the tree contains genomes that are not present in the GFA. Please use attached zip file.

Sprint 5

This release adds the following.

• under-the-hood fixes and optimization for the data structures that are used (the model package)
• Visualization of metadata, including genome lineages
• Drag and drop functionality.
• Arbitrary genome set comparison

The beta release contains the latest (visual) functionality.
The stable release contains only well-tested functionality.

Sprint 4

This release

• is able to load the 328 genomes.
• includes visual improvements
• Phylogenetic tree visualization improvements

Sprint 3

The stable version contains tested and documented code.

The prototype release contains the most recent changes, which are not fully tested yet.

The zooming release contains a WIP of semantic zooming.

Sprint 2

A new document regarding manual testing can be found in documentation/testing.md

Sprint 1

The visualisation of the graph and the tree as of now are two separate builds, thus this release is split into two parts.
The jars make us of "340tree.rooted.TKK.nwk" and "TB10.gfa" (embedded into the jar and loaded automatically).