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

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Hi,

I'm OK for Thursday, too.  Sorry, I don't generally check my e-mail 
at night.  Hope everything is OK.  In the future, don't hesitate to 
move things if I'm not responding, I'll catch up eventually :)

Best,
Kam

At 08:29 AM 7/20/2011, John David N. Dionisio wrote:
>OK, acknowledged.  Take care.
>
>John David N. Dionisio, PhD
>Associate Professor, Computer Science
>Loyola Marymount University
>
>
>
>On Jul 20, 2011, at 8:25 AM, Richard Brous wrote:
>
> > OK, I am forced to push to tomorrow now because our nanny is 
> stuck in traffic, christina is back at the hospital and I have to 
> drive my boys to MDR for their camp.
> >
> > I'm sorry this is so crazy but all is upside down atm.
> >
> > I already have a bunch of questions which I will lay out via 
> email since they are more high level than can be placed in code 
> comments... at least I think so atm.
> >
> > Either way come hell or high-water I'll get another iteration on 
> this prior to a call.
> >
> > rb
> >
> > On Tue, Jul 19, 2011 at 11:21 PM, John David N. Dionisio 
> <do...@lm...> wrote:
> > Hi Rich,
> >
> > Sorry to hear about your mother-in-law.  Hospital wait states are 
> never fun.
> >
> > I can do Thursday morning at 9am if needed.  Let's watch the 
> e-mail in the morning to see if Kam can do that too; if so, then 
> Thursday it is, but if not, then we can still push for Wednesday 9am.
> >
> > John David N. Dionisio, PhD
> > Associate Professor, Computer Science
> > Loyola Marymount University
> >
> >
> >
> > On Jul 19, 2011, at 10:26 PM, Richard Brous wrote:
> >
> > > ok, can't get a break... sitting in the ER after admitting my 
> mother in law at St. Johns in Santa Monica. We are waiting to get 
> her a bed but not sure how long it will take.
> > >
> > > Luckily I have my laptop with me so I was able to scan the new 
> code with all the Dondi comments and compile a build which runs. I 
> will review Dondi's changes as best I can from here but likely 
> won't be able to do much with it by our call tomorrow.
> > >
> > > I'm happy to push our call to Thursday morning instead of 
> tomorrow to allow more time... but it is late so unless I hear 
> otherwise, tomorrow at 9am is still a go.
> > >
> > > Richard
> > >
> > > On Tue, Jul 19, 2011 at 3:00 PM, Richard Brous 
> <rbr...@gm...> wrote:
> > > Thanks will review later this afternoon. Sorry got hung up on 
> this but continuing forward comments in code should speed this way up.
> > >
> > > Rb
> > >
> > > Sent from my iPhone
> > >
> > > On Jul 19, 2011, at 12:04 AM, "John David N. Dionisio" 
> <do...@lm...> wrote:
> > >
> > > > Greetings,
> > > >
> > > > OK, my responses are committed.  As noted in my "Dondi -" 
> comments, you were fairly close.  The main miss was how 
> AbstractListModel was to be used.  Give it a gander and holler if 
> anything else remains unclear.
> > > >
> > > > At this point, you'll need to start managing what should 
> happen as the user selects/deselects species.  You'll also want 
> that little informational panel on the right that summarizes (for 
> tech types) whether the selected species will be using a customized 
> species profile or the generic one.
> > > >
> > > > Carry on, see how this goes.  :)
> > > >
> > > > John David N. Dionisio, PhD
> > > > Associate Professor, Computer Science
> > > > Loyola Marymount University
> > > >
> > > >
> > > > On Jul 18, 2011, at 10:14 AM, Richard Brous wrote:
> > > >
> > > >> Ok , took the code as far as I could and submitted export 1 
> - unfortunately   broken code even though I made a point not to by 
> commenting out unfinished blocks. Take a look at the commit comments for info.
> > > >>
> > > >> I look forward to your comments which I'm sure will help 
> straighten this out!
> > > >>
> > > >> Rb
> > > >>
> > > >> Sent from my iPhone
> > > >>
> > > >> On 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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