Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-05-22

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Time Nick Message
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08:39 CIA-58 bioclipse: jonalv * r5663 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: implemented cdk.subStructureMatches
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08:56 jonalv egonw, I think substructure search should work from the javascript console now, although it returns an iterator so you would have to do a javascript loop in order to see what you get out...
09:08 rojasm hi. could it be possible if you or I create in bioclipse2/branches the same directories like in trunk but of course empty! so I could start implementing some thing
09:09 masak I'm a bit uncertain whether you can use a Java iterator in a Js loop...
09:09 * masak tries
09:10 olas rojasm: I'm not sure how to do that, ask egonw
09:11 egonw rojasm: you mean an template project?
09:11 rojasm yes
09:12 rojasm like in cdk
09:12 rojasm branches would not break the trunk code!
09:14 egonw ah...
09:14 egonw you want to create a branch of bioclipse2...
09:14 egonw but I guess you just want to set up a plugin?
09:15 egonw no actually hack on BIoclipse2 itself?
09:15 egonw noT actually...
09:16 rojasm ok
09:25 masak re iterators in js: it seems not impossible
09:27 olas egonw: I need assistance with a repaint issue in JCP
09:28 egonw olas: ah, so you broke something? :)
09:28 olas no
09:28 olas it's for SDFileEditor
09:28 olas the second tab will display individual mols in JCP
09:28 egonw yes
09:28 olas but somehow it doesn't get updated
09:28 olas when switched to the tab
09:28 egonw miguel tried that yesterday
09:29 egonw yes, we saw that too
09:29 olas it works if you switch to another editor and back
09:29 CIA-58 bioclipse: ospjuth * r5664 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): Some work to get SingleStructure tab working. Currently, molecules are not repainted.
09:29 olas could you please have a look at that?
09:29 olas And we also need to fix save() of SDFileEditor before end of next week
09:30 olas should not be too hard
09:30 olas but the repaint issue beats me
09:30 olas could you (please) have a look at that?
09:30 olas the thing is: it works if you use the JCPPage from CMLEditor or MDLMOlfileEditor
09:30 olas so it WORKS
09:31 olas it's just that things don't get repainted when called from SDFileEditor onPageChange()
09:31 olas egonw: what you say?
09:31 * egonw is checking...
09:32 egonw olas: where's teh SDF editro?
09:32 olas in plugin net.bioclipse.cdk10.sdfeditor
09:34 egonw oh... /me does not have that plugin in his eclipse yet
09:34 olas check out?
09:34 egonw should have it checked out
09:34 egonw but will do an 'git svn rebase' too
09:38 CIA-58 bioclipse: carl_masak * r5665 /bioclipse2/trunk/plugins/net.bioclipse.ui/sr​c/net/bioclipse/ui/views/JsConsoleView.java: [JsConsoleView] added a final newline at end of progress bar
09:41 egonw he, net.bioclispe.cdk does not compile for me ...
09:41 egonw (hahahaha :)
09:42 jonalv :)
09:58 egonw olas: ok, where should the signal be hooked in?
10:02 egonw lunch time
10:02 egonw olas: when you want to try...
10:02 egonw hook in code like this:
10:04 egonw jcpPage.stateChange(new CHemObjectChangeEvent(jcpPage.get​JcpModel().getRenderer2DModel());
10:04 egonw bbl
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11:20 olas egonw: nope, doesn't help
11:20 olas I've manually added drawingPanel.repaint() and still no luck
11:20 olas how can I force SWT to redraw it all?
11:22 CIA-58 bioclipse: ospjuth * r5666 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.jchempaint/src/net/bioclipse/cdk​10/jchempaint/ui/editor/JCPPage.java: Added repaint() commands that don't work, just to show what I've tried. Egon: please help!
11:22 egonw olas: no idea
11:22 egonw I really don't
11:23 olas can you reproduce it?
11:23 egonw yes, Miguel and I saw that not-updating yesterday too
11:23 olas :-(
11:23 * olas is stuck
11:23 olas will ask masak
11:24 olas masak: help!
11:24 masak yes?
11:24 olas mom, will drop by
11:27 egonw olas: are you sure it is the repaint() that fails?
11:27 egonw and not the setting of the new IChemModel, or so... ?
11:31 CIA-58 bioclipse: jonalv * r5667 /bioclipse2/trunk/plugins/ (4 files in 2 dirs): Added substructuresearch method returning result in a list
12:15 egonw olas: no clue
12:15 egonw I've had a look at it...
12:15 egonw but I can't see any differences...
12:15 egonw and really no idea on how it works...
12:15 egonw too bloody ugly code
12:16 olas solved it :-)
12:16 olas really ugly solution, but hey
12:16 * egonw is looking forward to reading the patch
12:16 egonw wel... really ugly solution... that sounds like JCP, all right
12:17 olas true
12:17 olas I donät mind ugly solutions, if the underlying stuff is ugly
12:18 CIA-58 bioclipse: ospjuth * r5668 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.jchempaint/src/net/bioclipse/cdk​10/jchempaint/ui/editor/JCPPage.java: Force repaint when updating JCPModel by fooling the ControlListener that JCP has been resized. Not beautiful, but works.
12:25 egonw does the job
12:25 egonw I'll verify it's working here too
12:27 egonw no, does not fully work here
12:28 * egonw has a meeting
12:28 egonw olas: first time works...
12:28 egonw ben when I click a second entry...
12:29 egonw ben=but
12:29 egonw then I get a grey background on the second tab
12:29 egonw bbl
12:29 egonw grey BG seems to indicate an incorrectly handle exception somewhere...
12:35 olas egonw: I can't reproduce due to on Mac
12:35 olas please have a look at it
12:35 olas we really need this to work
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13:17 CIA-58 bioclipse: carl_masak * r5669 /bioclipse2/trunk/plugins/ (2 files in 2 dirs):
13:17 CIA-58 bioclipse: [JsThread] added isBusy() method
13:17 CIA-58 bioclipse: [JsConsoleView] now only tab completes on a non-busy js
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13:31 CIA-58 bioclipse: carl_masak * r5670 /bioclipse2/trunk/plugins/net.bioclipse.ui/sr​c/net/bioclipse/ui/editors/ColorManager.java: [ColorManager] brought up to Java 1.5 standards
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13:57 egonw olas: ping
14:00 olas egonw: pong
14:01 egonw it might maybe be the SD file I am looking at...
14:01 egonw what SD file are you testing with?
14:01 olas one of my own
14:02 egonw might you try the .sdf in the demo project/misc ?
14:02 CIA-58 bioclipse: ospjuth * r5671 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10.jchempaint/src/net/bio​clipse/cdk10/jchempaint/ui/editor/ (IJCPbasedMPE.java JCPPage.java): Added interface for JCPbasedMPEs so that JCP can know if contained in an MPE and act upon that.
14:02 olas demo project?
14:02 olas where do I find this demo project?
14:02 olas URL?
14:02 jonalv olas: I think he means the example data
14:02 olas oh
14:03 egonw umm... comes with BC2
14:03 olas egonw: you mean sample data
14:03 olas ok
14:03 CIA-58 bioclipse: egonw * r5672 /bioclipse2/trunk/plugins/net.bioclips​e.cdk10.sdfeditor/src/net/bioclipse/cd​k10/sdfeditor/editor/SDFEditor.java: If the selected entry has not changed, don't update the second view...
14:03 olas egonw: please no commits now
14:03 olas I'm in the middle of refactoring
14:03 egonw oh...
14:04 egonw ok, me will stup hunting that bug then
14:04 olas hmm
14:04 olas I like that you work on it
14:04 olas and maybe it wont disturb me
14:04 jonalv olas: I thought you said that sdf file was borken
14:04 olas ??
14:04 olas please use proper english in this channel
14:04 olas borken =broken?
14:05 olas I donät know
14:05 olas if it's not broken, then the SDFileEditor is
14:05 jonalv you said so last time you where in here. By Masaks computer
14:05 olas egonw: can you confirm that SDFile is OK?
14:05 olas I said MAYBE it's broken
14:05 olas that's a big difference
14:05 jonalv I think we should equip the example project with a few sdf files of different size
14:05 jonalv olas: Okey then I missuderstood you
14:05 olas egonw: could you provide them?
14:06 olas a few SDFiles?
14:06 olas which are confirmed to be OK
14:06 egonw cdk SVN
14:06 olas and not too big
14:06 jonalv and not too small
14:06 jonalv (at least not all of them)
14:07 olas jonalv: you have cdk checked out?
14:07 jonalv olas: I think so yea
14:07 olas add a few from CKD then, please
14:07 jonalv it was HUGE
14:07 egonw jonalv: src/data/mdl
14:08 jonalv Problem is that I don't know where to add them
14:08 olas to sample data project
14:08 olas it should be quite easy to find out where
14:09 jonalv okey, I'll toss it on my TODO queue
14:09 olas ok
14:15 CIA-58 bioclipse: ospjuth * r5673 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.sdf​editor/src/net/bioclipse/cdk10/sdfeditor/editor/ (6 files): Adding index column for SDFileEditor, as requested per RFE 1968729.
14:19 olas egonw: ok, please continue now
14:19 olas my commit is there
14:19 olas others may come, but that was the largest
14:19 egonw ack
14:20 CIA-58 bioclipse: jonalv * r5674 /bioclipse2/trunk/plugins/net.bioclipse.ui/sr​c/net/bioclipse/ui/views/JsConsoleView.java: Cleaned up a bit in ConsoleProgressMonitor
14:20 egonw olas: I suggest sorting on structure == sorting on atom count, bond count, then mass, or so...
14:21 CIA-58 bioclipse: jonalv * r5675 /bioclipse2/trunk/plugins/ (9 files in 5 dirs): Made progress monitor for substructureSearch
14:25 olas egonw: you broke it!!!
14:25 olas god damn
14:25 jonalv haha
14:26 olas egonw: now fix it, you
14:26 olas or else...
14:26 olas >:)
14:27 masak olas: can't you just update and merge locally?
14:27 egonw olas: fix pending
14:27 egonw oldIx = 0 -> -1
14:27 olas masak: done already
14:28 * olas is awaiting egonw's xommit
14:30 CIA-58 bioclipse: egonw * r5676 /bioclipse2/trunk/plugins/net.bioclips​e.cdk10.sdfeditor/src/net/bioclipse/cd​k10/sdfeditor/editor/SDFEditor.java: Overwrite oldIx at the right place...
14:30 CIA-58 bioclipse: egonw * r5677 /bioclipse2/trunk/plugins/net.bioclips​e.cdk10.sdfeditor/src/net/bioclipse/cd​k10/sdfeditor/editor/SDFEditor.java: Fixed nothing-has-been-selected-previously default (index of structures starts at 0); force a repaint, just in case, but does not help against the grey screen
14:30 CIA-58 bioclipse: egonw * r5678 /bioclipse2/trunk/plugins/net.bioclipse.c​dk10.sdfeditor/src/net/bioclipse/cdk10/sd​feditor/editor/StructureTablePage.java: Missing space; dump error instead of eating it
14:30 olas so no progress?
14:30 egonw yeah, sure...
14:31 egonw already ruled out several causes :)
14:32 olas good
14:33 CIA-58 bioclipse: ospjuth * r5679 /bioclipse2/trunk/plugins/net.bioclips​e.cdk10.sdfeditor/src/net/bioclipse/cd​k10/sdfeditor/editor/SDFEditor.java: On change to StructTablePage, set selection according to currentModel.
14:35 egonw this is fighting against exceptions silently being eaten! :(
14:37 olas oh
14:37 egonw olas: I have no idea where this fails...
14:37 egonw but it is reproducable
14:39 jonalv my computer si to slow for these substructure searches...
14:39 olas egonw: how does the substruct performs?
14:45 egonw it's slow
14:45 egonw how many structures dou you search?
14:45 egonw no idea what the turnaround is...
14:45 egonw but several per second at least...
14:46 egonw excluding format reading etc
14:46 egonw maybe that's slow
14:46 jonalv it was feasible with everyting in a 700kb SDF file but nor realistic in the 6MB file.
14:46 jonalv my question was benzene btw
14:46 egonw this is why one invented fingerprints
14:46 egonw you don't do substructure search on a full database
14:46 jonalv oh I am using fingerprints first :)
14:47 egonw oh...
14:47 olas We need some sort of numbers here
14:47 egonw did you request a YourKit license yet?
14:47 jonalv I sure hope so anyway :)
14:47 olas jonalv: can you make a list of the times for the different steps?
14:47 olas no
14:47 olas hmm
14:47 olas ok, will do that now
14:47 olas or in 5 mins
14:48 * olas has a commit coming along
14:48 jonalv egonw, I am writing on that mail to you with instructions for how to test it.... I need feedback :)
14:49 * egonw has to leave rather shortly...
14:49 egonw will try to work on things over the weekend...
14:49 jonalv cool
14:49 egonw olas, jonalv: please work out priorities...
14:49 egonw and let me know where I should focus my time
14:50 egonw ok, bye for now!
14:50 jonalv I don't want too much of your time but it would be great with a little feedback of what you think about it...
14:50 jonalv k bye
14:51 egonw olas: just stepped through the update of resources for the second tab
14:52 egonw and cannot find anything different between the situation where it works and when it doesn'n... :(
14:52 egonw hope to report more on that later too...
14:57 CIA-58 bioclipse: ospjuth * r5680 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Selections are now synchronized between table and JCPpage in SDFileEditor.
15:42 CIA-58 bioclipse: ospjuth * r5681 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.sdf​editor/src/net/bioclipse/cdk10/sdfeditor/editor/ (3 files): Added sorting when click on headers in SDFileEditor, except on header for Structures. Solves 1968729.
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17:02 CIA-58 bioclipse: ospjuth * r5682 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.sdf​editor/src/net/bioclipse/cdk10/sdfeditor/editor/ (SDFEditor.java StructureTablePage.java): Attempt to fix "grey box bug" when switching to JCPpage in SDFileEditor. Egon: please verify that bug is squashed!
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19:41 CIA-58 bioclipse: ospjuth * r5683 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui/plugin.xml: Commented out cdk.ui contents in navigator, as CDK1o is used for SDF files and CML files.
19:44 CIA-58 bioclipse: ospjuth * r5684 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.ui/: Initial import.

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