Examples aren't working ?
Try the unsigned applet demos

Quick Links to jars for example:
jalviewApplet.jar and JmolApplet.jar

JalviewLite API Demo

Using the Javascript API to fill out forms using data from JalviewLite
Click the Javascript buttons below to interact with the Applet instance on the page.

View the source in your browser to see how it has been done.
View the full JalviewLite API documentation.

Using the Jalview Applet for Input to an HTML Form

Make a new View and Get and Set Group Display List