Diff for "Cytoscape_2.4_and_Beyond"

Differences between revisions 15 and 16

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?)

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.

-  ← Revision 15 as of 2006-07-12 22:51:18 →
  Size: 2566
  Editor: KeiichiroOno
  Comment:
+  ← Revision 16 as of 2006-07-12 23:01:43 →
  Size: 1999
  Editor: KeiichiroOno
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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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