New_File_Menu

<Note: Now entire menu refactoring discussion is moved to Refactored_Menu>

New File Menu

In 2.3, the File munu will be re-organized for new features including session saving and XGMML writer. The default save action will be session saving, and other menus will be moved to export menu.

Under File Menu... (Tentative)

• Open (CTRL-O. Warning message will appear since it overwrites current session.)

• Save (Overwrite file, CTRL-S)

• Save as... (File-chooser appears. CTRL-SHIFT-S)

• Import

  • Network File (Supports sif, gml, and xgmml)
  • Attributes...
    • Node Attributes
    • Edge Attributes
    • Expression Matrix
  • Other (Use Template) - This menu item calls Transform class to accept user XSLT.

• Export

  • Network as...
    • XGMML
    • GML
    • SIF
  • Attributes...
    • Node Attributes
    • Edge Attributes
    • (Probably add a new format to include multiple attributes in a file)
  • Network as Graphics (pdf, jpg, etc.)
  • Other (Use Template)

By adding XSL transformer, users and developers can transform network files into all kinds of file formats (for example, HTML). Sample XSL files will be provided. This function will be used when export/import "Other" menu item is selected.

File Format for Networks with Metanodes

Currently, only XGMML file can include metanode information. We need to create new sif format if we allow users to save the network in non-XML format. The import/export function for the new file formats can be implemented by using Transform().

Discussion:

• GaryBader - Jan.13.2006 - You could make the menu simpler by just saying "Save" instead of "Save session". If there is only one save option, it is simpler and you don't have to specify what is saved. Save as... could shortcut to CTRL-SHIFT-S (not very important). Same for 'open session' to 'open'. Also, load could be renamed 'import' - do CYS is the only basic format for Cytoscape and everything else is imported or exported. Also, the import/export should be grouped by data type, so you would have import/export network (GML, XGMML, sif, etc.), annotation (e.g. obo), expression data (e.g. .pvals), image (.png, gif, pdf, etc.). I think that transform could be an option via Cytoscape to make things simpler - so instead of creating a new concept called 'transform' that people must learn, we could just have import and export - they could transform by importing a sif and then exporting to GML. Tranform XSL might be useful as a developer tool, however, so we might want to provide some command line scripts to do common transformations.

• KeiichiroOno - Jan.20.2006 - Updated the document above based on your comment. XSL Transformer already has minimal GUI, which is select source network, template and output file and developers may use it through API (Transform(source network, template, output)). This may be used when we need to create some XML/non-XML files, like extended-sif file that can contain meta-nodes (although we have not finalized the file format). Anyway, I'll re-organize the menu shortly.