In this tutorial, we will demonstrate how to create nodes and edges in the plug-in. We use two examples to illustrate these functions. The simple one simply adds three nodes and the edges between them, with some customization of the node properties; while the complicated one is modified from the VisANT parser of edge-list, which reads the file of an edge-list, parse it, and create the corresponding network. In both example, the network is presented using circle layout.


Here is the step-by-step explanation of the plug-in:



Compiling: Download EdgeListPlugin, and put it in the same directory as VisAnt.jar, open a does/shell window and go to the directory where there is VisAnt.jar, use following command to compile:


javac -classpath .;VisAnt.jar EdgeListPlugin.java


Packaging the plug-in: if you do not have a sub-directory named "plugins" under current directory, create it. Then run following command to package (the name of the package is your choice, we use creator.jar here):


jar -cf plugins\creator.jar EdgeListPlugin.class


This command will create creator.jar under plugins directory,


Running VisANT: VisANT can be started by double-mouse-clicking. If that does not work, run following command to start (always using following command to run VisANT if you need to debug your plug-in) :


java -jar  VisAnt.jar


The EdgeListPlugin should be automatically loaded into VisANT and you will find the corresponding menu under Plugins menu in VisANT.


For questions/suggestions about this tutorials, please email VisANT@zlab.bu.edu.


Note: 1. It is worthy to point out that the illustrated customization only change the visual properties of the node (color, size etc) and each node has one DataPoint object that stores the properties of the biological entity represented by the node, which includes the name and alias, functional annotations, ids of external databases, expression values etc. Therefore to add functional annotation you must get the DataPoint of the nodes and change it through corresponding method.


2. Similar to nodes, each edge has a corresponding Linkage object that stores biological meaningful properties of the edge except the visual ones. Because in general these biological properties are part of properties of corresponding biological entity, the Linkage objects are stored in DataPoint object.