This is the Application Programming Interface of PIM Walker software.

See:
Description

Packages

com.hybrigenics.pimwalker.core.graph.V25
com.hybrigenics.pimwalker.core.xml.castor	The package com.hybrigenics.pimwalker.core.xml contains the code able to read XML data files based on the MIF.xsd.
com.hybrigenics.pimwalker.core.xml.castor.types	Classes from this package have been automatically generated using Castor source Generator (castor.exolag.org) .
com.hybrigenics.pimwalker.core.xml.castor.V25
com.hybrigenics.pimwalker.core.xml.castor.V25.descriptors
com.hybrigenics.pimwalker.gui	The package com.hybrigenics.pimwalker.gui contains the whole Graphical User Interface of PIM Walker.
com.hybrigenics.pimwalker.resources	The package com.hybrigenics.pimwalker.resouces contains some resources used throughout the Graphical User Interface of PIM Walker.
com.hybrigenics.pimwalker.util	The package com.hybrigenics.pimwalker.util contains utility classes of PIM Walker.

This is the Application Programming Interface of PIM Walker software.

What is PIM Walker ?

    PIM Walker is a viewer of protein-protein interactions map. It is able to
    display such a map as a graph where vertices are the proteins and edges
    represent the known interactions between proteins.

    PIM Walker is able to read data from HUPO/PSI as XML files validated by the
    MIF.xsd. For more information about that file format, please refer to the
    HUPO/PSI web site.

What is the version and what PSI file can it handle ?

    PIM Walker Version 1 (and sub-releases) handles Version 1 PSI files.

The structure of PIM Walker software.

    PIM Walker is made of the following packages:

    1. com.hybrigenics.pimwalker.core.xml : the package contains the code able
       to read XML data files based on the MIF.xsd. The PIM Walker XML reader uses
       the XML Castor framework (see castor.exolag.org). For that purpose, MIF/XML
       'aware' classes have been generated using the Castor SourceGenerator from the
       MIF.xsd. The generated classes are located in sub-package
       com.hybrigenics.pimwalker.core.xml.castor, whereas the xsd file used to generate
       the classes is located in com.hybrigenics.pimwalker.core.xml.xsd.

       Note: generated classes are actually made from a modified release of the MIF.xsd
       file. Indead, this file contains XML Schema declarations that are not supported
       by the Castor class generator. Namely, we made 2 modifications in the original
       MIF.xsd file:

           a. 'unsignedLong' declarations have to be replaced by 'Long',
           b. declaration 'default="free"' has to be removed from the line:
              <xs:element name="availability" type="availabilityType" default="free" minOccurs="0" maxOccurs="unbounded">

       This is the reason why, one could find 'MIF-ver.xsd' and 'MIF-ver-revised.xsd' files
       in package com.hybrigenics.pimwalker.core.xml.xsd; 'ver' denotes the version of the
       MIF.xsd files (exemple: MIF-1.17.xsd). 'revised' file contains the MIF file
       modifications as explained above. Classes are always generated from the latest
       version of the MIF revised file (exemple: MIF-1.17-revised.xsd has been used to
       generate the classes of the PIM Walker release 0.9.2 beta).

    2. com.hybrigenics.pimwalker.core.graph: the package contains the code able
       to handle a data graph made from a XML file containing protein-protein
       interactions. Source code there can be viewed as a gateway between XML data
       and a real graph representation of such data.

    3. com.hybrigenics.pimwalker.gui: the package contains the code of

           a. the Graphical user interface (GUI) of PIM Walker,
           b. the graphical representation of the data graph from
              com.hybrigenics.pimwalker.core.graph.
           c. the graph layouts.

    4. com.hybrigenics.pimwalker.resources: the package contains some resources
       of PIM Walker, like icons and texts used throughout the GUI.

    5. com.hybrigenics.pimwalker.util: the package contains some utility classes
       used elsewhere in PIM Walker, and especially in its gui package.


--
$Id: overview-summary.html,v 1.3 2007/02/01 13:25:52 ameil Exp $
$Revision: 1.3 $
author: P. Durand, A. Meil, Hybrigenics SA (April 2003)