Perforce JViews Diagrammer Sample: Bionetwork Viewer

Description

This sample displays Systems Biology Markup Language (SBML) files using Perforce JViews Diagrammer.

How to Use the Sample

• The Reaction Network pane displays all the reactions contained in the current file.
• The Selected Reaction pane shows a single reaction and allows you to navigate through the network diagram.
• Use the toolbar at the top of the window to zoom or pan the diagram.
• Select a node in the Reaction Network pane. The Selected Reaction pane is updated automatically to show the currently selected reaction.
• Click the up and down arrows in the Selected Reaction panel to move to the reaction that produced this species or to the next reaction in which this species is a reactant.
• Click the left and right arrows (if any) to go to the previous or next reaction involving this species.
• Select a new node in the Reaction Network pane. The Selected Reaction pane is updated automatically to show the newly selected reaction.
• Use the right and left arrow buttons in the toolbar to go back and forth in the history of selected reactions.
• You can open a different SBML file using the Open button in the toolbar.

How to Run the Sample as an Application

This sample can be run as an application. The installation directory contains an executable JAR file, diagrammer-bionetwork.jar, that allows you to execute the sample with a double click from a file browser. Note that if you are using Internet Explorer, you can open the installation directory and execute the JAR file from the browser. This technique may not work in other Web browsers.

Alternatively, you can run the sample application from the command line. First check that the Ant utility is properly configured. If not, see the instructions on how to configure Ant for Perforce JViews.

Then, go to the installation directory of the sample and type:

ant run

Topics Covered

• Large diagram navigation.

Detailed Description

This sample displays Systems Biology Markup Language (SBML) files using Perforce JViews Diagrammer.

Installation Directory

The Bionetwork Viewer sample is installed here.

Classes Involved

• ilog.views.diagrammer.IlvDiagrammer

  The main class of the diagram component.

Source Files

• bionetwork.BioNetwork

  The entry point of the sample.

• bionetwork.SBMLReader

  The reader of SBML files into SDM models.