Diff for "Cytoscape_2.4_and_Beyond"

Features

• Meta Nodes, Phase 2
• Generic Plugin-state saving
• 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
• 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

• 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.