Cytoscape Wiki|
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| Deletions are marked like this. | Additions are marked like this. |
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| * Visual Legend | * Visual Legend automatic generator |
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| * Tree Object Support in CyAttributes (for GO data) |
* Tree Object viewer in Browser (For GO data, etc.) * ''Cytoscape Theme (Skin)'' * Background Task support (for compressing huge session file) |
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* Define what the Edge ID is * Performance tuning for save/load huge sessions |
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| * Unit tests/swing unit tests + more automated build system that includes building of plugins. |
Features
- Meta Nodes, Phase 2
- Attribute Based Layout
- Multi-colored nodes
- Better hide/show for edges/ nodes
- Real-time vizmapper update
- KEGG Reader / Reaction node + editor
- Expression Matrix reader for more data formats (MIAME)
- Interactive Slider Widget
- Visual Legend automatic generator
- Standardize context menus for nodes/edges
- Network specific node and edge attributes
- Generic Preference System and inteligent UI for the new preference data structure
- Tree Object viewer in Browser (For GO data, etc.)
Cytoscape Theme (Skin)
- Background Task support (for compressing huge session file)
- Headless mode, Phase 2 (Web Service?)
Refactoring / Design Issues
New GraphObject class; for nodes/edges
- Define what the Edge ID is
- Performance tuning for save/load huge sessions
- Formalize what goes in the core
- Improving / Refactoring Event Model
- Remove the "GO Level" idea from Gene Ontology Server
- Remove legacy code from GO Server
Expression Matrix must use CyAttribute instead of redundant data structure.
- Unit tests/swing unit tests + more automated build system that includes building of plugins.