Re: [XMLPipeDB-developer] GenMAPP multitaxon support - CMSI 486T

[Kam D. <kda...@lm...>]

Hi,

Dondi will have to chime in on this, but I think this is where things 
are going to get tricky.

The final gdb does not actually contain the entire GO, it gets 
trimmed somehow based on the GO associations for a particular 
species.  This is because MAPPFinder cannot handle loading the entire 
GO.  Since there is some type of species-specific trimming going on, 
it's quite possible that this will need to iterate.

However, I don't have the foggiest idea of how this works, so Dondi 
will have to chime in.

Best,
Kam

At 12:09 AM 8/4/2011, you wrote:
>Wednesday 8/3/11 progress:
>
>1. After following the ExportPanel1.java ground zero code of: 
>databaseProfile.setSelectedSpeciesProfile( selectedProfile );
>
>I found the method in DatabaseProfile.java plus a getter method;
>SpeciesProfile setSelectedSpeciesProfile( speciesProfile ) and 
>SpeciesProfile getSelectedSpeciesProfile( speciesProfile )
>
>I created two new methods that each handle List<Object> of 
>SpeciesProfiles argument instead of a single SpeciesProfile; 
>setSelectedSpeciesProfiles and getSelectedSpeciesProfiles.
>
>This enabled the ExportPanel1 ground zero code to become: 
>databaseProfile.setSelectedSpeciesProfiles(selectedSpecies);
>
>2. public static void export() on line 104 in ExportToGenMAPP.java
>
>On line 107 ExportGoData is instantiated which I found in 
>ExportGoData.java and calls a method: public void export(char 
>chosenAspect, int taxon).
>
>Within export, taxon id is required for another method: private void 
>populateGoTables(char chosenAspect, int taxon).
>
>Within populateGoTables, taxon id is required for another method: 
>private void populateUniprotGoTableFromSQL(char chosenAspect, int taxon).
>
>But, if the export to GDB process starts off with exporting GO data, 
>doesn't it only need to do that once no matter how many species are 
>selected? As you probably realize, I'm leading towards not having to 
>iterate through this for each taxon id if possible.
>
>Also, how does the export actually work? How are GO ids and UniProt 
>ids related within the table?
>
>Thanks!
>
>Richard
>
>