Add MeV Analysis file as a file type for bioassay sets

[Nicklas Nordborg]

The scenario is this. A users uses the MeV extension to export and download data to MeV. In MeV some analysis steps are done and saved as a MeV analysis file. The file is uploaded to BASE and the Manual transform plug-in is used to register the work done in MeV as a new bioassay set. The analysis file is attached to the new bioassay set and can later be downloaded and opened in MeV in the same way as as the original data.

This ticket is a preparation for a more automated procedure that should implement a "Save to BASE" function directly in MeV (see #242).

This ticket replaces #125.

[Nicklas Nordborg]

Bad news. It seem like MeV doesn't support opening analysis files from the command line/java web start. The file is downloaded from BASE correctly, but then a NullPointerException is displayed. After that it is however possible to manually go to File -> Open analysis and open the downloaded file without problems.

But... I think we can solve this problem... We are going to need a startup wrapper for inserting the "Save to BASE" menu item (see #242), and I think we can also use this wrapper to take care of all the file handling. Eg. downloading the data file from BASE to the local computer. The wrapper will then start MeV without command line parameters and as a last step invoke various methods for loading the data files. It seems that some of the methods that we may need to call are private but there are ways around that using reflection. Not very elegant but it allows us to work around some of the limitations in the MeV API.

[Nicklas Nordborg]

(In [1156]) References #241: Add MeV Analysis file as a file type for bioassay sets

The MeV analysis file type is now supported by the launch functionality. There is still no automatic installation. This must be done manually. Eg. create a data file type with external id=mev.anl; name=MeV analysis file; extension=anl; generic file type=Spot data; Item type=Bioassay set.

Also, MeV is not able to open the file yet. We need the wrapper for that.

[Nicklas Nordborg]

(In [1157]) References #241: Add MeV Analysis file as a file type for bioassay sets

Restructured the source code. Added wrapper that allows us to download and start MeV with an analysis file.

[Nicklas Nordborg]

(In [1159]) References #241: Add MeV Analysis file as a file type for bioassay sets

Added an "Installation" plug-in that is used to register data file types needed by the MeV package. Updated the installation instructions. This should complete this ticket, but I want to do some more tests.

[Nicklas Nordborg]

(In [1160]) References #241: Add MeV Analysis file as a file type for bioassay sets

Corrected a mistake when naming file types. I think the installation plug-in also should create a "MeV Analysis" configuration for the "Manual transform" plug-in. I keep having to redo that all the time. Other than that, everything seem to work as expected.

[Nicklas Nordborg]

(In [1161]) Fixes #241: Add MeV Analysis file as a file type for bioassay sets

The installation now adds a "MeV analysis" configuration for the manual transform plug-in.

[Nicklas Nordborg]

(In [1180]) References #241: Add MeV Analysis file as a file type for bioassay sets

The first part of the installation must be committed before the second part can take place.

[Nicklas Nordborg]

(In [1181]) References #241: Add MeV Analysis file as a file type for bioassay sets

The "Launch MeV" dialog failed with a PermissionDeniedException if one of the files attached to the bioassay set was not readable by the current user.