Gsea enhancements

As the software is almost perfect, there are few bugs and little need for enhancements.

Feature Additions for build 3/21

1. Leading edge interactive viewer
2. Added a preferences field for path to user home dir.
3. made native the default space in gsea. Not sure if this is better??
4. default collection of gene sets available via ftp

Found/requested 3/17:

1. Add Command button to Leading Edge page.

Cant do this easilly because of the way the command thing is setup.

2. Leading edge from command line give me fatal errors:
         719  [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\databases    at
              edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)
         719  [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\chip2chip    at  
                        edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)
         799  [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\reports_cache_foo    at
                       edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)

Must set -DGSEA=true flag
So,

java -Xmx ... -DGSEA=true xtools.....

3. MSigDB page, the Find sets that Overlap search gives page with no Export button; make that page more like the
      Find sets that contain this gene page.

Joshs reworked impl will replace this and the export option should be added to it

4. On Run GSEA, change parameter name from "Analyze in the feature space" to "Gene/probe identifier format"

Lets talk.

5. Remove Downloads>Download Gene Sets (no longer needed now that we have MSigDB page).

Done

6. Change first two Help items to "GSEA web site" and "GSEA documentation". First points to home page of web site and
           second points to the doc page of the web site.

Done

Bugs found 3/15/2006 include:

1. Generate a report, go to "Other" section, look at parameters. Error, file cannot be found.

Fixed.

2. Started a pretty long analysis, killed it. It took a few minutes versus a few seconds. If that's expected, perhaps change message to say may take a few minutes.

Whats a long analysis? (for leading edge clustering more than a handful of sets, say 20, is likely pointless)

3. Leading edge report brings up the gct files in a text editor rather than Excel; can't really read them in a text editor.

Opening gct files now works like this: First check prefs to see if excel (or the other programs) exist at location indicated in the prefs. If so, use it. Otherwise issue a generic open file command in windows that will open up the file in whatever editor has been registered by windows for that file type. On the mac, the later mode is always done. On unix i dont know what will happen.