Url Related Issues

Url Linking in Windows

Clicking on a gene in the dendrogram and karyoscope views is supposed to open a web browser window to a relevant database entry. Unfortunately, there is no standard way to do this in windows. When the linking is bad, typically clicking a gene name launches a DOS terminal window where the window's title equivalent to the URL, but no browser window comes up.

I have tried several things, but nothing works for all versions, and if you are not lucky you will be using one for which the current incarnation does not. Luckily it is easily fixed. Go to start->execute.. and entry "cmd" to get a command line shell. Try the following variants to see how your version of windows likes to do linking:

  1. start http://www.google.com

  2. cmd /c start http://www.google.com

  3. start "http://www.google.com"

  4. cmd /c start "http://www.google.com"

By default, #2 is used in version 1.0.5. If you require something else, you can enter the entire command as the URL string in java treeview, i.e. start http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=HEADER Including the quotes should guard against forbidden characters in the HEADER, as explained in my code: // The problem with the above is that special shell characters, notably & | ( ) < > ^ , // need to be escape, or put in double quotes (which can be doubled to escape them, // but I don't think that's necessary.)

Url Linking on OSX

When OSX tries to open a bad url, sometimes something breaks in the native code. If you run the application from the command line, you will see errors like the following:

2003-03-18 21:41:23.197 java[3492] LSOpenCFURLRef() returned -50 for URL (null) in OsX

This output indicates that an underlying C function failed. The java thread running this just dies without throwing an exception, so there's no way for me to detect it. The symptoms on the user level is that clicking has no effect. If you think this might be the case, double check your Url settings, in particular the preview, and make sure that the url is well formed.