Other topics that may be of interest: Integrating GenomeView as viewer

Whatever way of communicating you choose, make sure you enable it in the configuration file!

It is important that you set integration:monitorJavaScript=true in your configuration file. Only if you add that line to the configuration file you specify, will communication work.

Controlling GenomeView applet using JavaScript

We have a demo page set up that showcases the various aspects you may want to use when embedding GenomeView as an applet into your web platform.

Supported instruction set, see the demo page for examples on how to use them.

Controlling GenomeView webstart using JavaScript

Include the GenomeView javascript file

In java script, set instanceID='ALL'

Assuming there is a GenomeView webstart instance started, You can now use the java script methods described above to manipulate it.

Controlling GenomeView using a port

The java script is implemented as a local server that listens on port 2223, so you could alternatively directly control GenomeView by sending instructions to that port.

The format of an instruction is GET /genomeview-ALL/[instruction]/[argument]

Some examples:
Load the C. elegans demo instance
GET /genomeview-ALL/session/http://www.broadinstitute.org/software/genomeview/demo/c_elegans/session.php

Position the current visible window to 10000-20000
GET /genomeview-ALL/position/10000:20000

Unload all data:
GET /genomeview-ALL/unload

Full working example code in Java

Socket gv = new Socket("localhost", 2223);
PrintWriter pw=new PrintWriter(gv.getOutputStream());
/*pw.println("GET /genomeview-ALL/session/http://www.broadinstitute.org/software/genomeview/demo/c_elegans/session.php");*/
//pw.println("GET /genomeview-ALL/unload");
pw.println("GET /genomeview-ALL/position/10000:20000");
pw.flush();
gv.close();


Available instructions: