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 02:46:50
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OK, let me think on your comments and see how far I get.
Thanks!
rb
On Tue, Jul 12, 2011 at 6:35 PM, John David N. Dionisio <do...@lm...>wrote:
> Hi there,
>
> A code-oriented session is OK with me, though this particular question I
> can take a stab at via e-mail.
>
> The trick with full control of a JList is to implement its model (a
> ListModel). For this, I usually create a subclass of AbstractListModel and
> implement the missing methods. This AbstractListModel subclass should be
> able to see the list of species found. Then, the implementations of its
> missing methods would be based on that list of species.
>
> With this ListModel class in hand, keeping the JList up to date is a matter
> of instantiating the JList with this model:
>
> SpeciesListModel speciesListModel = new SpeciesListModel();
> speciesCheckList = new JList(speciesListModel);
>
> If the species list changes, have the species list model fire the
> appropriate list change event (the JavaDoc API has a bunch of fire*
> methods). To keep things simple, there is a "full update" event which just
> says "rebuild the entire JList." That one should be OK. There are
> finer-grained ones like "something got inserted" and "something got
> removed," but that really is more for optimization purposes.
>
> As for the text display, the simplest approach is to implement the toString
> method of the SpeciesProfile class so that they return something that is
> appropriate for a JList. Sometimes that is too limiting though. If you
> want greater flexibility, you will want to implement a ListCellRenderer.
> There is a class called DefaultListCellRenderer that you can extend.
> Typically the subclass would call the superclass's method, which returns a
> JLabel. You can then change the content of the JLabel according to the list
> item that you are trying to display.
>
> See if these leads are enough to go on. If not, I can talk you through
> them more during the call.
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Loyola Marymount University
>
>
> On Jul 12, 2011, at 6:00 PM, Richard Brous wrote:
>
> > 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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