CytoscapeEditor_Palette_3_0

TableOfContents([2])

Proposal

• Generalize the mechanism for generating the Cytoscape Editor's palette so that the full range of Cytoscape visual properties is accommodated in the palette

Background

The current Cytoscape mechanism for constructing palettes in the Cytoscape Editor is driven by the current Visual Style. Discrete mappings for Node fill color and shape are used to generate a set of palette entries with varying shapes and colors. Discrete mappings for Edge target arrow are used to generate a set of palette entries with varying target arrow shapes. This limitation is arbitrary and doesn't take advantage of the broad range of Node shapes, colors, size, border characteristics, and other visual properties that can be defined via the vizmapper. Likewise, for edges, the broad range of visual properties available include line width, line style, source arrow. The generation of the palette should be generalized so that any visual property that is defined in the vizmapper can be utilized and reflected in the editing tool.

Use Cases

This enhanced editor functionality would be necessary for editing Molecular Interaction Networks (MiMs). A description of the technical issues related to supporting MiMs in Cytoscape can be found in the RFC MolecularInteractionNetworks. The figure below shows a portion of a molecular interaction network for XXXXX. Note the different shapes, sizes, border characteristics and what they imply for the task of editing such a network interactively. attachment:mims_sample.png

Implementation Plan

Outline and describe the process and major issues related to implementing this proposal. Illustrate your plan when possible. Try this free online tool for making diagrams -> [http://www.best4c.com/editor/NetMapApplication.jsp Best4c] (draw; save; then insert hyperlink into this page)

Project Management

Project Timeline

Provide a timeline for implementation. Insert a graphic if you can. Try this free online tool for making project timelines -> [http://www.helpuplan.com/index.asp Help-u-Plan] (create a new chart; modify; right-click to save gif; then attach to this page)

Tasks and Milestones

Outline the major milestones and tasks involved in implementation.

1. Milestone 1: …

   1. Task 1: ...
   2. Task 2: ...

2. Milestone 2: …

Project Dependencies

Outline and projects that depend on this project, link to relevant RFC's and note at what point dependent projects could be started.

Related RFCs

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Issues

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Comments

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