Table of Contents

  1. Getting started with PathVisio Development
    1. Getting Involved
      1. Obtaining the source code
      2. Where do I add new features? How do I submit it?
    2. Tips on getting started
      1. Q: How do I get a grip on the PathVisio code base?
      2. Q: Where can I ask questions about PathVisio development?
      3. Q: How do I submit a patch?
      4. Q: How to compile PathVisio from the command line on Windows?
      5. Q: How do I compile PathVisio in the eclipse development environment?
    3. Modular structure of PathVisio
      1. Q: Can someone tell me the rationale behind the package structure for …
      2. Troubleshooting Compilation
    4. Coding Style
    5. Additional resources
  2. Gpml Pathway Format
    1. Overview
    2. Naming
    3. Structure of a GPML file
      1. Overview
      2. Root level: Pathway
      3. First level: Pathway Elements
        1. DataNode
        2. Line
        3. Label
        4. Link
        5. Shape
        6. Group
        7. Infobox
        8. Legend
        9. Biopax
      4. Shared attributes and minor elements
        1. Graphics
        2. Comment
        3. GroupIds
        4. GraphRefs/GraphIds
        5. Biopaxref
    4. Schema and Validation
    5. Versioning
    6. History
    7. Future
  3. Code Examples

Code Examples

You can easily create new applications based on the PathVisio code. Rajarshi Guha wrote a small test program that does nothing more than load a pathway and draw it on the screen. It's a good example of the usage of the main classes Pathway and VPathway.

See:  http://blog.rguha.net/?p=394

Here is an example of how to create a simple GPML document using PathVisio code: GpmlJavaExample

An example on how to add a literature reference using PathVisio code can be found here: GpmlLiteratureExample