Cytoscape Wiki|
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| * ID Mapping (was planned for 2.3) | |
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| * Attribute Based Layout |
* Attribute Based Layout (e.g. cell localization based layout) * editor support for hyperedges * editor support for graphic labels, custom graphical nodes |
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| * Vizmapper map-by-filter value (e.g. color nodes by value of function) | |
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| * Background Task support (for compressing huge session file) |
* Logging system (maybe [http://jakarta.apache.org/commons/logging/ Commons Logging]?), instead of using tons of System.out.print * BioPAX output * editor support for connecting edges to metanodes and their children * editor support for adding "templates" (e.g. metanode templates, network motifs) to canvas * New BioDataServer to fully support entries in OBO and Gene Asociation file. |
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| * Migration to [http://java.sun.com/j2se/1.5.0/index.jsp Java version 5] and lib directory cleanup (especially XML-related files) | |
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| * Define what the Edge ID is | * Define ''Invisible CyAttributes ''(CyAttributes which is not shown on the Browser. Used internally) |
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| * Remove legacy code from GO Server | |
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== Priority for 2.4 Release == 1. Oficially release Metanode plugin 1. Automatic node label position adjustment (place labels outside of the node) 1. ID Mapping 1. [:VisualLegendGenerator:Automatic Visual Legend generator] (code is already available. Needs generic GUI) 1. Immutable/Invisible CyAttributes (mainly for Metanodes) 1. Migration to Java Version 5 * Test core plugins in v5 environments * Replace old library files * Optional: use v5 features (such as generics, extended for loops, etc.) for writing more readable & stable codes |
Features
- Meta Nodes, Phase 2
- ID Mapping (was planned for 2.3)
- Generic Plugin-state saving
- Attribute Based Layout (e.g. cell localization based layout)
- editor support for hyperedges
- editor support for graphic labels, custom graphical nodes
- Multi-colored nodes
- Better hide/show for edges/ nodes
- Real-time vizmapper update
- Vizmapper map-by-filter value (e.g. color nodes by value of function)
- 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
- Complex object (tree, map, etc.) viewer in Attribute Browser
Cytoscape Theme (Skin)
Logging system (maybe [http://jakarta.apache.org/commons/logging/ Commons Logging]?), instead of using tons of System.out.print
- BioPAX output
- editor support for connecting edges to metanodes and their children
- editor support for adding "templates" (e.g. metanode templates, network motifs) to canvas
New BioDataServer to fully support entries in OBO and Gene Asociation file.
- Headless mode, Phase 2 (Web Service?)
Refactoring / Design Issues
Migration to [http://java.sun.com/j2se/1.5.0/index.jsp Java version 5] and lib directory cleanup (especially XML-related files)
New GraphObject class; for nodes/edges
Define Invisible CyAttributes (CyAttributes which is not shown on the Browser. Used internally)
- 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
Expression Matrix must use CyAttribute instead of redundant data structure.
- Unit tests/swing unit tests + more automated build system that includes building of plugins.
Priority for 2.4 Release
- Oficially release Metanode plugin
- Automatic node label position adjustment (place labels outside of the node)
- ID Mapping
[:VisualLegendGenerator:Automatic Visual Legend generator] (code is already available. Needs generic GUI)
Immutable/Invisible CyAttributes (mainly for Metanodes)
- Migration to Java Version 5
- Test core plugins in v5 environments
- Replace old library files
Optional: use v5 features (such as generics, extended for loops, etc.) for writing more readable & stable codes