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

[Richard B. <rbr...@gm...>]

OK, submitted new code which added the selected SpeciesProfiles into
selectedSpecies ArrayList. Using this as the argument for:
databaseProfile.setSelectedSpeciesProfile( selectedSpecies );

Thought I would snag each value when surfaced in the Object selection loop
then add to ArrayList.

Richard

On Tue, Aug 2, 2011 at 8:50 AM, Richard Brous <rbr...@gm...> wrote:

> Ah yes, I see why you inlined the conditional and now the code is much more
> elegant.
>
> Btw, neglected to mention i'm starting on chapter 2 in the db textbook
> today.
>
> Look forward to our chat in 15 minutes
> richard
>   On Tue, Aug 2, 2011 at 8:39 AM, John David N. Dionisio <do...@lm...>wrote:
>
>> OK, cool, the changes look good.
>>
>> I committed some comments and little tweaks, mainly for style and
>> succinctness reasons.  The primary logic through-line was not touched.  If
>> you have any questions on those changes, we can discuss that sometime; those
>> are secondary to the main-line issues that you mentioned.
>>
>> John David N. Dionisio, PhD
>> Assistant Professor, Computer Science
>> Loyola Marymount University
>>
>>
>> On Aug 2, 2011, at 12:31 AM, Richard Brous wrote:
>>
>> > Just committed some new code. Mainly adding the logic to append the
>> selected species with either generic or custom in the
>> speciesDescriptionTextArea and cleared out more old comments to keep me
>> focused.
>> >
>> > Also read through the first part of the ExportToGenMAPP class to get a
>> handle on how it is sent the DatabaseProfile databaseProfile with a  single
>> species packaged within. From that effort, I decided to start on the
>> databaseProfile.setSelectedSpeciesProfile method which would be modified for
>> a collection of SpeciesProfiles.
>> >
>> > But I need to create that collection first back on ExportPanel1,
>> proceeding the JList selection/display code. I just need to wrap my head
>> around how to grab them and place them in a newly created SpeciesProfile []
>> selectedProfiles, which would then be used as the argument in
>> databaseProfile.setSelectedSpeciesProfiles(  selectedProfiles );
>> >
>> > We can discuss this further on our call tomorrow.
>> >
>> > Richard
>> >
>> >
>> >
>> >
>> > On Aug 1, 2011, at 11:13 AM, Kam Dahlquist <kda...@lm...> wrote:
>> >
>> >> Hi,
>> >>
>> >> That works for me.  Talk to you tomorrow,
>> >> Kam
>> >>
>> >> At 11:04 AM 8/1/2011, you wrote:
>> >>> Greetings,
>> >>>
>> >>> No worries...for this week the best day turned out to be Tuesday; hope
>> that works well for you also.  So, tomorrow at 9am unless setting else comes
>> up.
>> >>>
>> >>> John David N. Dionisio, PhD
>> >>> Associate Professor, Computer Science
>> >>> Loyola Marymount University
>> >>>
>> >>>
>> >>> On Aug 1, 2011, at 10:46 AM, Kam Dahlquist <kda...@lm...>
>> wrote:
>> >>>
>> >>>> Hi,
>> >>>>
>> >>>> I'm so sorry, I was on my "staycation" last week and just completely
>> forgot about our scheduled phone call.
>> >>>>
>> >>>> I'm back in the office--what are the plans for this week's call?
>> >>>>
>> >>>> Thanks,
>> >>>> Kam
>> >>>>
>> >>>> At 08:30 AM 7/28/2011, you wrote:
>> >>>>> yes fri works for me. thank you!
>> >>>>>
>> >>>>> richard
>> >>>>>
>> >>>>> On Wed, Jul 27, 2011 at 9:42 PM, John David N. Dionisio <
>> do...@lm...> wrote:
>> >>>>> Greetings,
>> >>>>> 3pm Thursday won't work for me unfortunately.  How about 9am Friday?
>>  I can't stay too long even then but it will still be better than not
>> talking at all.
>> >>>>>
>> >>>>> John David N. Dionisio, PhD
>> >>>>> Associate Professor, Computer Science
>> >>>>> Loyola Marymount University
>> >>>>>
>> >>>>> On Jul 27, 2011, at 7:42 PM, Richard Brous <rbr...@gm...>
>> wrote:
>> >>>>>
>> >>>>>> Hi all,
>> >>>>>>
>> >>>>>> Sorry to fall out of touch but with finals and papers due this week
>> and and my mother in law back in the hospital, I'm about at my wits end.
>> >>>>>>
>> >>>>>> That said, I was wondering if we could move our con call to
>> tomorrow afternoon if possible instead of 9am? ... Say 3pm 'ish? I don't
>> want to miss it as I would like to discuss a few things but I just can't
>> make it at 9am and then rushing to a 10am final exam.
>> >>>>>>
>> >>>>>> Sorry for the late notice but I hope you both understand... smc
>> classes will be over tomorrow and I can focus much, much more on this
>> afterwards.
>> >>>>>>
>> >>>>>> Richard
>> >>>>>> On Wed, Jul 20, 2011 at 10:38 PM, John David N. Dionisio <
>> do...@lm...> wrote:
>> >>>>>> Hi Rich,
>> >>>>>> Congratulations!  Welcome to the world of Swing GUI programming  :)
>>  It has its share of tics and idiosyncrasies, but with some practice one
>> gets the hang of it.
>> >>>>>> I've reviewed your new code and have interspersed commentary in the
>> context of your notes below.  We don't have a lot of time tomorrow, so
>> perhaps pick and choose the ones that you feel will benefit the most from
>> synchronous discussion.
>> >>>>>> John David N. Dionisio, PhD
>> >>>>>> Associate Professor, Computer Science
>> >>>>>> Loyola Marymount University
>> >>>>>>
>> >>>>>> On Jul 20, 2011, at 9:22 PM, Richard Brous wrote:
>> >>>>>> > Hallelujah!!! - a list box with multiple species of which any
>> combination can be selected now exists!!! Thanks Dondi!! (see attachment)
>> >>>>>> >
>> >>>>>> >
>> >>>>>> > OK, had a chance to review the code corrections, other comments
>> and think on the next steps surrounding the selection of multiple species
>> and their dynamic text updating. Here is where I am at the moment:
>> >>>>>> >
>> >>>>>> > A. Dondis corrections/additions to my last submission
>> >>>>>> >
>> >>>>>> > 1. Creating a private class called SpeciesListModel which
>> extended AbstractListModel
>> >>>>>> >
>> >>>>>> > As soon as I saw your code I realized that I had sort of coded it
>> backwards, thinking about implementing an interface instead of just
>> extending the abstract object and adding methods... duh. My face turned a
>> bit red on that one.
>> >>>>>> >
>> >>>>>> > The idea still of creating a list model to manage the entries in
>> the JList still seems a bit complicated and foreign but I guess the more I
>> work with the  java ui stuff, the better I will become with it.
>> >>>>>>
>> >>>>>> Yes, it can be unwieldy in simple cases (like this one) and can
>> sometimes result in repetitive code.  However, it is very flexible and truly
>> encapsulates the list data from the list presentation (for example, with
>> this approach, you can even create a ListModel that does not have a data
>> structure behind it; or perhaps one that queries for the list contents
>> dynamically).
>> >>>>>> > Additionally I did attempt to add a new method under this class
>> called clearSpeciesProfiles. This was meant to clear the JList of all
>> species found each time the export1 panel was opened instead of aggregating
>> the species in the list. It doesn't seem to be working though so I commented
>> it out for now. Please let me know if I'm adding this functionality in the
>> wrong way and/or in the incorrect location.
>> >>>>>> A couple of notes on this one.  Observe how setSpeciesProfile
>> *replaces* the list of species profiles returned by the list model, and does
>> not add to it.  Thus, I do not think that the duplication occurs at this
>> level --- I believe it occurs at the
>> UniProtDatabaseProfile.checkRequirements method.  Follow the code from
>> GenMAPPBuilder.doExportToGenMAPP and see if you spot the issue.  Remember
>> that the symptom occurs when one tries to export more than once.  Thus, see
>> what the code does to the relevant data structures when
>> GenMAPPBuilder.doExportToGenMAPP is called more than once.
>> >>>>>> > 2. SpringLayout
>> >>>>>> >
>> >>>>>> > I took a look at the website and got a feel for how to adjust
>> panel component locations. Seems like I can use those commands to make the
>> adjustment to the species label that you mentioned in comments.
>> >>>>>> >
>> >>>>>> > Interesting how the leftPanel uses
>> SpringUtilities.makeCompactGrid while the rightPanel uses GridLayout...
>> didn't realize you could combine both kinds on content panel.
>> >>>>>> Yes, this is the power and complexity of Swing layout management
>> --- you can nest them as much as you like, and mix and match them as much as
>> you like.  Powerful and flexible, yes; potentially complicated, yes also.
>> >>>>>> > B. further UI enhancements:
>> >>>>>> >
>> >>>>>> > 1. I dug into export1 design in regard to the text description
>> areas of both the Database and Species profiles. They are both JTextAreas(3,
>> 15) where 3 denotes rows and 15 denotes columns. I changed both fields to be
>> editable and compiled just so I could see how big each text field really is.
>> I was able to type in 23 characters across and 7 rows downward until the
>> next row was cutoff by the bottom edge of the box. I also changed the row
>> and column arguments to JTextAreas(2, 15) and JTextAreas(3, 10) and
>> recompiled but didn't see any change in the volume of text I could enter...
>> must not understand it completely... are the arguments only to manage
>> components placed within the textArea maybe while loose text just starts top
>> left and word/line wraps?
>> >>>>>> >
>> >>>>>> > My reason for fooling with this was to see what would happen of
>> course but really I had the idea that I would shrink the size of the
>> database profileDescriptiontextArea to allow for a larger
>> speciesDescriptionTextArea below it. Also I had been thinking of how to
>> represent the species and its associated custom or default species profile
>> in a way that made the most sense. The species names are pretty long so was
>> going to suggest to simply use taxon id, profile type (custom or default)
>> since the user could cross reference in the JList just to the left.
>> >>>>>>
>> >>>>>> This issue rests in some of the tricks behind Swing layout
>> management.  Unlike conventional GUI design, where components are given
>> fixed, absolute coordinates and sizes, Swing tries to "compute" the layout
>> dynamically, based on a combination of rules, "preferred sizes," and min/max
>> sizes.  The exact algorithm for determining the final layout is placed in
>> the LayoutManager class.  The row/column settings given to JTextArea
>> typically pertain to *preferred* sizing, not final sizing.  As in, the
>> JTextArea "asks" its containing panel that "if possible, I prefer to have
>> this many rows and columns."  The rule of thumb is that a layout manager
>> tries to give its components their preferred sizes *or greater*, if
>> available (the idea being that most UI components wouldn't mind getting more
>> space than they originally asked for).
>> >>>>>> To exercise greater control over this, you'll need to get a better
>> handle on the behavior or the various layout managers.  Certain layout
>> managers *do* cap a UI component's size to no greater than its preference.
>>  This takes some practice, however, and some familiarity with the layout
>> manager "zoo."  My suggestion: let's leave well enough alone here for now,
>> get the functionality done first, then come back to this later.
>> >>>>>> >  2. Dynamic insertion of desired species info into the
>> speciesDescriptionTextArea
>> >>>>>> >
>> >>>>>> > In thinking of how to solve this I went back to code I had
>> commented out in my last submission - the protected method which detected a
>> change in species choice occurred within the JComboBox:
>> speciesProfileSelected( Object selectedItem ) {
>> >>>>>> Yes, the fundamental change that you are making now is that *more
>> than one species profile may be active*.  What you need to do, then, is to
>> maintain the selected species profiles as a collection, and not as a single
>> value.  Then, all the code that used to assume that only a species profile
>> gets selected need to be modified so that they can accommodate a collection
>> of species profiles.  Cases in point...
>> >>>>>> > I had been struggling with what that method really should be
>> doing now that we have a JList where multiple species could be selected. And
>> after some review and then walking away from it for a few, I think it only
>> needs to handle two things:
>> >>>>>> > a. ensure that all the selected species are added to the export
>> dataset. (We then modify the export process itself to account for and
>> properly process multiple species.)
>> >>>>>> ...This is the fundamental change that dominoes through the rest of
>> the export code.  Instead of holding on to a single selected species
>> profile, you need to maintain a collection of them.  Also...
>> >>>>>> > b. use the selected indices to populate/depopulate the
>> speciesDescriptionTextArea dynamically as a selection/deselection is made
>> within the JList.
>> >>>>>> >  I have some ideas but would like to talk them through on the
>> call tomorrow. I'll also submit my latest pass on the code for review.
>> >>>>>> ...This part requires some rewriting so that the generated
>> descriptive text can accommodate a collection of species profiles.  The
>> message generation thus gets a little more complicated.  But it's just
>> additional logic, iterating through the species profiles and incrementally
>> appending a message string until you've gone through all of the selected
>> profiles.  e.g., "This export will use a customized profile for S.
>> typhimurium, a general-purpose profile for B. anthracis, and a customized
>> species profile for H. pylori."  Hope you can see how that string can be
>> computed via iteration through a species profile collection.
>> >>>>>>
>> >>>>>> OK, that would be my 2 cents...let's see what needs live discussion
>> tomorrow morning.
>> >>>>>> > Richard
>> >>>>>> >
>> >>>>>> >
>> >>>>>> >
>> >>>>>> > On Wed, Jul 20, 2011 at 9:00 AM, John David N. Dionisio <
>> do...@lm...> wrote:
>> >>>>>> > Sounds good, talk to everyone Thursday 9am then  :)
>> >>>>>> >
>> >>>>>> > John David N. Dionisio, PhD
>> >>>>>> > Associate Professor, Computer Science
>> >>>>>> > Loyola Marymount University
>> >>>>>> >
>> >>>>>> >
>> >>>>>> > On Jul 20, 2011, at 8:47 AM, Kam Dahlquist <kda...@lm...>
>> wrote:
>> >>>>>> >
>> >>>>>> > > 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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>> >>>>>> > >>>>>>>> _______________________________________________
>> >>>>>> > >>>>>>>> xmlpipedb-developer mailing list
>> >>>>>> > >>>>>>>> xml...@li...
>> >>>>>> > >>>>>>>>
>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> >>>>>> > >>>>>>>>
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>> >>>>>> > >>>>>>> xmlpipedb-developer mailing list
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>> >>>>>> > >>>>>> xmlpipedb-developer mailing list
>> >>>>>> > >>>>>> xml...@li...
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>> >>>>>> > >>> _______________________________________________
>> >>>>>> > >>> xmlpipedb-developer mailing list
>> >>>>>> > >>> xml...@li...
>> >>>>>> > >>>
>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> >>>>>> > >>>
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>> much more.
>> >>>>>> > >> http://www.accelacomm.com/jaw/sfnl/114/51426210/
>> >>>>>> > >> _______________________________________________
>> >>>>>> > >> xmlpipedb-developer mailing list
>> >>>>>> > >> xml...@li...
>> >>>>>> > >>
>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> >>>>>> > >
>> >>>>>> > >
>> >>>>>> > >
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>> >>>>>> > > Learn 10 ways to better secure your business today. Topics
>> covered include:
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>> more.
>> >>>>>> > > http://www.accelacomm.com/jaw/sfnl/114/51426210/
>> >>>>>> > > _______________________________________________
>> >>>>>> > > xmlpipedb-developer mailing list
>> >>>>>> > > xml...@li...
>> >>>>>> > >
>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> >>>>>> >
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>> >>>>>> > Learn 10 ways to better secure your business today. Topics
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>> more.
>> >>>>>> > http://www.accelacomm.com/jaw/sfnl/114/51426210/
>> >>>>>> > _______________________________________________
>> >>>>>> > xmlpipedb-developer mailing list
>> >>>>>> > xml...@li...
>> >>>>>> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> >>>>>> >
>> >>>>>> > <export1-crop.jpg><ATT00001..txt><ATT00002..txt>
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>> >>>>>> _______________________________________________
>> >>>>>> xmlpipedb-developer mailing list
>> >>>>>> xml...@li...
>> >>>>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> >>>>>>
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>> >>>>>>
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>> >>>>>
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>> >>>>> Plus, you'll get a chance to win $100 to spend on ThinkGeek.
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>> >>>>> xmlpipedb-developer mailing list
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>> >>>>
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>> >>>> http://p.sf.net/sfu/rim-blackberry-1
>> >>>> _______________________________________________
>> >>>> xmlpipedb-developer mailing list
>> >>>> xml...@li...
>> >>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> >>>
>> >>
>> ------------------------------------------------------------------------------
>> >> BlackBerry&reg; DevCon Americas, Oct. 18-20, San Francisco, CA
>> >> The must-attend event for mobile developers. Connect with experts.
>> >> Get tools for creating Super Apps. See the latest technologies.
>> >> Sessions, hands-on labs, demos & much more. Register early & save!
>> >> http://p.sf.net/sfu/rim-blackberry-1
>> >> _______________________________________________
>> >> xmlpipedb-developer mailing list
>> >> xml...@li...
>> >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> > <ATT00001..txt><ATT00002..txt>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> BlackBerry&reg; DevCon Americas, Oct. 18-20, San Francisco, CA
>> The must-attend event for mobile developers. Connect with experts.
>> Get tools for creating Super Apps. See the latest technologies.
>> Sessions, hands-on labs, demos & much more. Register early & save!
>> http://p.sf.net/sfu/rim-blackberry-1
>> _______________________________________________
>> xmlpipedb-developer mailing list
>> xml...@li...
>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>
>
>