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

[John D. N. D. <do...@lm...>]

Hi Rich,

OK, thanks for the discussion setup.  We'll work through this during the call.

John David N. Dionisio, PhD
Associate Professor, Computer Science
Loyola Marymount University



On Jul 6, 2011, at 7:37 PM, Richard Brous wrote:

> Update on status:
>  
> Over the past two weeks I have spent time doing the following:
>  
> 1. Reviewed the taxon id code changes which Don Murphy coded and were merged to create version 2.0 b64
> 2. Reviewed the UniprotDatabaseProfile, UniprotSpeciesProfile, SpeciesProfile, Profile and DatabaseProfile files
> 3. Reviewed and discussed the process by which GenMAPP matches single taxon ids found in a Postgres db with the known species profiles.
>  
> Current actions:
>  
> During the last few days I have started coding in the ability for the species matching functionality to surface multiple taxon ids from within a Postgres db.
>  
> The process being the following steps:
>  
> 1. Grab all the taxon ids from the Postgres db
> The current iteration of the software already does this. In the checkRequirements method in UniprotDatabaseProfile.java, a query of the Postgres db acquires all taxon id's and stores them in ResultSet result variable.
>  
> 2. Check to find match between the taxon ids from Postgres against existing species profiles for known species.
>  
> The current iteration compares each taxon id in ResultSet result variable.
> First taxon id from result:
> If match was found, then that species profile with associated taxon id was added to the speciesProfilesFound arraylist.
> If no match was found, a generic species profile associated with the current taxon id was added to the speciesProfilesFound arraylist.
>  
> Next taxon id from result
> If match was found, then that species profile with associated taxon id was added to the speciesProfilesFound arraylist.
> If no match was found, a generic species profile associated with the current taxon id was added to the speciesProfilesFound arraylist.
>  
> Repeat until no more taxon ids are found in ResultSet result variable.
>  
> 3. Replace the JComboBox with a JList to allow the user to choose a selection of multiple species to export.
>  
> Use the getSelectedIndices method for JList to determine which species have been selected for export.
>  
> 4.  Modify the export process to run a pass for each species selected to generate a multispecies gdb.
> details to be determined.
>  
> -----------------------------------------------------------------------------------------------------------------------------------------------------------
>  
>  
> Discussion for tomorrows call:
>  
>  
> We previously discussed allowing user input to manually add taxon ids and associate them to the generic profile.
>  
> Unless I don't really understand the reasoning behind this, it seems to me that it is unnecessary. Why would we add a taxon id during the export process that isn't already in the Postgres data?
>  
> The current implementation already captures every taxon id in speciesProfilesFound regardless if its a known species or not. So it seems that we don't need to make any modifications in surfacing taxon ids from a Postgres db.
>  
> Then we can go directly to #3 above which I have mostly coded, but can't seem to figure out how and where to populate the JList. In reviewing constructor documentation it indicates 4 ways to instantiate.
>  
> My first choice was to create an empty JList [ JList () ] and populate it later but I don't see a method to do so such as addItems or something similar.
>  
> I then tried to instantiate with speciesProfileFound as an  array argument: JList ( SpeciesProfile[] speciesProfilesFound ) but can't resolve.
>  
>  
> Anyway, I look forward to our call at 9am tomorrow.
>  
> Richard
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