The sources make up two packages, cobweb and particlesystem. The classes that belong to each package are shown below.
Please Note, that these sources need the processing core, the G4P library and commons codec to work. These libraries (called core.jar, guicomponents.jar and commons-codec-1.4.jar) can be downloaded below (click on "Download Java libraries (jar)").
|Cobweb.java||Main class of the applet, imports the particle system and draws the network|
|GraphFunctions.java||Class that offers some graph-based algorithms|
|GraphMLParser.java||Class to parse GraphML-files and create the network|
|Parameters.java||Class to store parameters like the picture path given in the input file|
|SIFParser.java||Class to parse SIF-files and create the network|
|XGMMLParser.java||Class to parse XGMML-files and create the network|
|Edge.java||Edge between two nodes|
|Integrator.java||Integrator, computes the positions for all nodes|
|Node.java||Class that represents one node|
|ParticleSystem.java||Main class of this package that uses all other classes to represent the network|
|Repulsion.java||Repulsion between two nodes|
|Vector2D.java||Implementation of two dimensional vectors|
|user_col_schema.png||The user-specified colour schema that is used for the control elements|
|font.ttf||The font that is used to show the node names|
|applet.js||Contains a set of functions that is used by the Cobweb applet to communicate with the sidebar.|
Complete example applet. After extracting it to your harddisk opening example.html opens the applet showing an example network. The code of this example applet can be used to understand how the applet can be implemented into a website.
|example.html||Sample html-file showing how the applet can be implemented on a website|
|stylesheet.css||Style rules to define the look of the website|
|applet||Folder containing the applet libraries, for details please click on "Download Java libraries (jar)" above|
|cobweb.jar||Main library for the applet, contains the code for user interaction and network drawing|
|particlesystem.jar||Contains the particle system logic behind the network, computes the nodes positions in the network|
|core.jar||3rd party library containing the core of the processing framework|
|guicomponents.jar||3rd party library for drawing control elements (G4P)|
|commons-codec-1.4.jar||3rd party library offering common encoding functions (Apache commons codec)|
Some example-files can be downloaded here. For general information about the structure of the files please have a look at the tutorial.
|apoptosis.xgmml||The apoptosis example (see here) in XGMML format.|
|apoptosis.graphml||The apoptosis example (see here) in GraphML format.|
|apoptosis.sif||The apoptosis example (see here) in SIF format.|