Diff for "IdekerLabProgress"

December 2009 Sprint

• Allow Nested Network Model by adding getNetwork/setNetwork methods to CyNode

• Network Browser - Network attr indicating its parents, node attr indicating its children
• File I/O support for nested networks (NNF Reader, XGMML Reader/Writer, and refactoring for session reader/writer)
• Network Editing - Add an icon in editor that allows a network to dropped on a node or on the canvas (where a node would be created)
• Network Editing - Add a right-click option to the node menu allowing a network to be added/removed
• Right click on a node menu option to jump to nested network
• Rendering - recursive rendering (a nested network will be rendered within the bounds of a node by a recursively defined renderer.) Assuming rendering only, NO user interaction

• Label Wrap - add an option to LabelPosition that allows a node/edge label width to be specified and automatically wraps lines when the text is longer than the width

• GenomeSpace analysis task requirements (due in Jan)

• Add new edge types to Cytoscape (dotted [circles, not dashes], dot-dash, ////, sine wave, parallel lines, ->->->->, parallel lines with single sided arrows)

• Editor - update editor instructions
• Editor - add check box that allows node id to be specified when node is dropped (mantis 2087)

• BioMart plugin maintenance

• A PSIQUIC client release (This works with 2.7)
• Maintenance release for Scripting plugins
• Select all nodes/edges is very slow
• Bug - Fiddling with default visual style and node label position broke all of the control panel.
• Add newlines in the attr browser by either adding \n manually or by typing alt-enter, some combination. Do whatever excel does. (mantis 2088) toggling between large networks can be slow (mantis 2068)

• Bug: In PluginManager Dialog, "Released by" field is missing for some installed plugins

• Bug: In Pluginmanager dialog, some plugins are labeled "out-of-date" incorrectly

January 2010 Sprint

• Port MCode - Edges in overview graph can be used to indicate that nodes in nested networks exist in both nested networks.
• Port JActiveModules - Edges in overview graph can be used to indicate that nodes in nested networks exist in both nested networks.

• Implement Rohith/Greg/Sourav/PLoS CompBio 2008 code

• Write a demonstration plugin that provides the ability to visualize the edges that exist between nodes that are in nested networks (providing a DualLayout type of visualization).

• Apply visual style to multiple networks (selected in NetworkPanel)

• Make Network Panel pop-up commands consistent (allow user to apply commands to selected networks)

• Allow ArrowHead color to inherit from Edge Color. Provide an option for coupling and decoupling this feature.

• RFC for feature to allow functions in AttributeBrowser cells.

• A visual property that will determine whether to display the nested network or not and add VizMap GUI support for boolean properties.

• Fix looping problems with NNF formats (2123, 2122)
• Write a mini-review of Cytoscape in English and translate it into Chinese.

• Prepare for BioHackathon 2010. Make RDFScape work with the trunk code (2.7.0).

• Encode width of columns persistence in order and in CyAttributesBrowser (code is in coreplugins/browser).

• Attribute browser code to allow editing list attributes.
• Bug 0002109: Apply Visual style on wrong view when import XGMML file.
• Filters Bug: Colons in filter string breaks filter restoration.
• Old Filters: save defined filters (properties) to session.

• QuickFind bug: Null pointer exception when many subnetworks are created.