Re: [XMLPipeDB-developer] GenMAPP multitaxon support - CMSI 486T
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Re: [XMLPipeDB-developer] GenMAPP multitaxon support - CMSI 486T
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From: Richard B. <rbr...@gm...> - 2011-07-13 01:00:14
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Update for tomorrow 7/13/11:
Clear on what I need to do but can't seem to figure out a way to do it. I
think the best use of our time tomorrow is to make it a code discussion
session (giving Dr. Dahlquist the opportunity to bow out if so inclined)
1. In regard to the JList, I have been working on the best way to implement
it but am getting stuck on how to populate it and where to do so in the
code.
I'm currently working in ExportPanel1.java and have done the following so
far:
imported JList;
imported javax.swing.event.*;
public class ExportPanel1 extends JPanel {
added: private JList speciesCheckList;
private JPanel getContentPanel () {
underneath the species combo box entry // species | JComboBox |
speciesFound |JLabel | Description | ...
added: speciesCheckList = new JList ( speciesProfilesFound );
// registered the listeners
speciesCheckList.addListSelectionListener ( new ListSelectionListener () {
// handle list selection
public void valueChanged ( ListSelectionEvent e ) {
// get selected indices
int [] indices = speciesCheckList.getSelectedIndices ();
}
});
added: //leftPanel.add ( speciesComboBox );
leftPanel.add ( speciesCheckList );
The real issue here is how to populate the JList... I took a look at the
constructors but can't determine a way to populate it after instantiation...
maybe using abstract class somehow?
So instead I have been working to add the speciesProfilesFound [] ArrayList
as a constructor argument. Then I can pre-populate it prior to the
contentPanel being initialized???... or possibly similar to the init()
method which pre-populates the Database profileComboBox?
Once the initital population of the JList is done we can modify it for the
later methods which dynamically alter content in databaseProfileSelected()
and speciesProfileSelected(). This will effect the selectedSpeciesProfile()
method usage and its getter and setter.
Also we can then work on the text indication which dynamically shows
the selected species and whether a custom or generic profile has been
associated.
Dondi - I'm looking forward to your suggestions and assistance!!!
Richard
On Wed, Jul 6, 2011 at 10:58 PM, John David N. Dionisio <do...@lm...>wrote:
> 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
> > <ATT00001..txt><ATT00002..txt>
>
>
>
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