ProtAnnot source code is available from the Genoviz project hosted at Sourceforge.net.
ProtAnnot uses the Genoviz SDK to implement animated, one-dimensional semantic zooming and several other advanced visualization features that are particularly well-suited for genome browsing. It also uses genomic data models from the Genoviz genometry package.
So if you are interested in building and running ProtAnnot yourself (instead of using Java Web start), you will need to get a copy not only of the ProtAnnot source code, but also the Genoviz SDK and other packages from the repository.
To obtain the source code, visit the Genoviz project page and follow the instructions to check out the code from the subversion source code repository.
Tip: The repository is quite large; we recommend you check out just the trunk (not the various branches). To check out just the trunk, do something like this:
svn co https://genoviz.svn.sourceforge.net/svnroot/genoviz/trunk genoviz
Once you have checked out the source code, you can use the pre-configured NetBeans project that is included in the checkout to build and run ProtAnnot. Just right-click on the IGB project and choose option Protannot to run protannot. Once the program launches, you can click-drag files from the ProtAnnot XML sample files folder directly into the ProtAnnot interface to load and view them.