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

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

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>
> >>>>>> > >>>>>>>>
> >>>>>> > >>>>>>>>
> >>>>>> > >>>>>>>>
> >>>>>> > >>
> ------------------------------------------------------------------------------
> >>>>>> > >>>>>>>> All of the data generated in your IT infrastructure is
> >>>>>> > >> seriously valuable.
> >>>>>> > >>>>>>>> Why? It contains a definitive record of application
> >>>>>> > >> performance, security
> >>>>>> > >>>>>>>> threats, fraudulent activity, and more. Splunk takes this
> >>>>>> > >> data and makes
> >>>>>> > >>>>>>>> sense of it. IT sense. And common sense.
> >>>>>> > >>>>>>>> http://p.sf.net/sfu/splunk-d2d-c2
> >>>>>> > >>>>>>>> _______________________________________________
> >>>>>> > >>>>>>>> xmlpipedb-developer mailing list
> >>>>>> > >>>>>>>> xml...@li...
> >>>>>> > >>>>>>>>
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>>>>> > >>>>>>>>
> >>>>>> > >>>>>>>> <ATT00001..txt><ATT00002..txt>
> >>>>>> > >>>>>>>
> >>>>>> > >>>>>>>
> >>>>>> > >>>>>>>
> >>>>>> > >>
> ------------------------------------------------------------------------------
> >>>>>> > >>>>>>> AppSumo Presents a FREE Video for the SourceForge
> Community by Eric
> >>>>>> > >>>>>>> Ries, the creator of the Lean Startup Methodology on "Lean
> Startup
> >>>>>> > >>>>>>> Secrets Revealed." This video shows you how to validate
> your ideas,
> >>>>>> > >>>>>>> optimize your ideas and identify your business strategy.
> >>>>>> > >>>>>>> http://p.sf.net/sfu/appsumosfdev2dev
> >>>>>> > >>>>>>> _______________________________________________
> >>>>>> > >>>>>>> xmlpipedb-developer mailing list
> >>>>>> > >>>>>>> xml...@li...
> >>>>>> > >>>>>>>
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>>>>> > >>>>>>
> >>>>>> > >>>>>>
> >>>>>> > >>
> ------------------------------------------------------------------------------
> >>>>>> > >>>>>> AppSumo Presents a FREE Video for the SourceForge Community
> by Eric
> >>>>>> > >>>>>> Ries, the creator of the Lean Startup Methodology on "Lean
> Startup
> >>>>>> > >>>>>> Secrets Revealed." This video shows you how to validate
> your ideas,
> >>>>>> > >>>>>> optimize your ideas and identify your business strategy.
> >>>>>> > >>>>>> http://p.sf.net/sfu/appsumosfdev2dev
> >>>>>> > >>>>>> _______________________________________________
> >>>>>> > >>>>>> xmlpipedb-developer mailing list
> >>>>>> > >>>>>> xml...@li...
> >>>>>> > >>>>>>
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>>>>> > >>>>>
> >>>>>> > >>>>>
> >>>>>> > >>>>>
> >>>>>> > >>
> ------------------------------------------------------------------------------
> >>>>>> > >>>>> Magic Quadrant for Content-Aware Data Loss Prevention
> >>>>>> > >>>>> Research study explores the data loss prevention market.
> >>>>>> > >> Includes in-depth
> >>>>>> > >>>>> analysis on the changes within the DLP market, and the
> criteria used to
> >>>>>> > >>>>> evaluate the strengths and weaknesses of these DLP
> solutions.
> >>>>>> > >>>>> http://www.accelacomm.com/jaw/sfnl/114/51385063/
> >>>>>> > >>>>> _______________________________________________
> >>>>>> > >>>>> xmlpipedb-developer mailing list
> >>>>>> > >>>>> xml...@li...
> >>>>>> > >>>>>
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>>>>> > >>>>
> >>>>>> > >>>> <ATT00001..txt><ATT00002..txt>
> >>>>>> > >>>
> >>>>>> > >>>
> >>>>>> > >>>
> >>>>>> > >>
> ------------------------------------------------------------------------------
> >>>>>> > >>> 10 Tips for Better Web Security
> >>>>>> > >>> Learn 10 ways to better secure your business today. Topics
> covered include:
> >>>>>> > >>> Web security, SSL, hacker attacks & Denial of Service (DoS),
> private keys,
> >>>>>> > >>> security Microsoft Exchange, secure Instant Messaging, and
> much more.
> >>>>>> > >>> http://www.accelacomm.com/jaw/sfnl/114/51426210/
> >>>>>> > >>> _______________________________________________
> >>>>>> > >>> xmlpipedb-developer mailing list
> >>>>>> > >>> xml...@li...
> >>>>>> > >>>
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>>>>> > >>>
> >>>>>> > >>> <ATT00001..txt><ATT00002..txt>
> >>>>>> > >>
> >>>>>> > >>
> >>>>>> > >>
> ------------------------------------------------------------------------------
> >>>>>> > >> 10 Tips for Better Web Security
> >>>>>> > >> Learn 10 ways to better secure your business today. Topics
> covered include:
> >>>>>> > >> Web security, SSL, hacker attacks & Denial of Service (DoS),
> private keys,
> >>>>>> > >> security Microsoft Exchange, secure Instant Messaging, and much
> more.
> >>>>>> > >> http://www.accelacomm.com/jaw/sfnl/114/51426210/
> >>>>>> > >> _______________________________________________
> >>>>>> > >> xmlpipedb-developer mailing list
> >>>>>> > >> xml...@li...
> >>>>>> > >>
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>>>>> > >
> >>>>>> > >
> >>>>>> > >
> ------------------------------------------------------------------------------
> >>>>>> > > 10 Tips for Better Web Security
> >>>>>> > > Learn 10 ways to better secure your business today. Topics
> covered include:
> >>>>>> > > Web security, SSL, hacker attacks & Denial of Service (DoS),
> private keys,
> >>>>>> > > security Microsoft Exchange, secure Instant Messaging, and much
> more.
> >>>>>> > > http://www.accelacomm.com/jaw/sfnl/114/51426210/
> >>>>>> > > _______________________________________________
> >>>>>> > > xmlpipedb-developer mailing list
> >>>>>> > > xml...@li...
> >>>>>> > >
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>>>>> >
> >>>>>> >
> ------------------------------------------------------------------------------
> >>>>>> > 10 Tips for Better Web Security
> >>>>>> > Learn 10 ways to better secure your business today. Topics covered
> include:
> >>>>>> > Web security, SSL, hacker attacks & Denial of Service (DoS),
> private keys,
> >>>>>> > security Microsoft Exchange, secure Instant Messaging, and much
> 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>
> >>>>>>
> >>>>>>
> ------------------------------------------------------------------------------
> >>>>>> 5 Ways to Improve & Secure Unified Communications
> >>>>>> Unified Communications promises greater efficiencies for business.
> UC can
> >>>>>> improve internal communications as well as offer faster, more
> efficient ways
> >>>>>> to interact with customers and streamline customer service. Learn
> more!
> >>>>>> http://www.accelacomm.com/jaw/sfnl/114/51426253/
> >>>>>> _______________________________________________
> >>>>>> xmlpipedb-developer mailing list
> >>>>>> xml...@li...
> >>>>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>>>>>
> >>>>>>
> >>>>>>
> ------------------------------------------------------------------------------
> >>>>>> Got Input?   Slashdot Needs You.
> >>>>>> Take our quick survey online.  Come on, we don't ask for help often.
> >>>>>> Plus, you'll get a chance to win $100 to spend on ThinkGeek.
> >>>>>> http://p.sf.net/sfu/slashdot-survey
> >>>>>> _______________________________________________
> >>>>>> xmlpipedb-developer mailing list
> >>>>>> xml...@li...
> >>>>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>>>>
> ------------------------------------------------------------------------------
> >>>>> Got Input?   Slashdot Needs You.
> >>>>> Take our quick survey online.  Come on, we don't ask for help often.
> >>>>> Plus, you'll get a chance to win $100 to spend on ThinkGeek.
> >>>>> http://p.sf.net/sfu/slashdot-survey
> >>>>> _______________________________________________
> >>>>> 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
> >>>
> >>
> ------------------------------------------------------------------------------
> >> 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
>