Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-05-21

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All times shown according to UTC.

Time Nick Message
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07:40 olas egonw: I want a CMLEditor
07:41 olas is it OK with you if I refactor some in cdk10.jcp?
07:41 egonw yeah, me too...
07:41 egonw if you don't break anything, and fix the missing icons for the toolbar... sure! :)
07:41 olas Maybe it's better if you do it
07:41 olas right...
07:41 egonw what d'you had in mind?
07:41 olas missing icons?
07:42 egonw yeah, two icons do not seem to be found...
07:42 Gpox joined #bioclipse
07:42 olas Place MDLMolefileEditor in its own package , for example
07:42 olas and add CMLFileEditor
07:42 egonw please go ahead
07:42 olas ok
07:42 egonw I'll check it tomorrow or so
07:47 olas good
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07:54 CIA-45 bioclipse: ospjuth * r5647 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.jchempaint/ (8 files in 5 dirs): Refactored out MDLFileEditor to its own package.
07:59 CIA-45 bioclipse: ospjuth * r5648 /bioclipse2/trunk/plugins/net.bioclipse.c​dk10.sdfeditor/src/net/bioclipse/cdk10/sd​feditor/editor/StructureTablePage.java: Modified to support refactored MDLFileEditor.
08:08 CIA-45 bioclipse: ospjuth * r5649 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.jchempaint/ (6 files in 5 dirs): Added CMLFileEditor, updated ID for MDLFileEditor, and made Outline use interface IJCPBasedEditor instead of MDLFileEditor.
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08:41 CIA-45 bioclipse: jonalv * r5650 /bioclipse2/trunk/plugins/net.bioclipse.str​ucturedb.tests/tests/net/bioclipse/structur​edb/business/StructuredbManagerTest.java: Substructuresearch returning a list seems to work. Now going for the one returning an iterator (probably much more useful)
09:02 olas egonw: around?
09:03 olas in CMLReader, the read ChemFile returns an IChemFile
09:04 olas there is no method to return a IChemModel, as in MDLV2000Reader
09:04 olas I guess I can construct my own
09:05 olas just wanted to let you know of the differences between the readers
09:12 egonw olas: check accepts()
09:12 olas egonw: how can I turn on pretty printing of CML?
09:12 egonw that allows you to see what the reader can return
09:13 egonw there is no one IChemObject returned, because the file format can contain anything
09:13 olas in the Writer?
09:13 egonw for pretty printing: use the IO options
09:13 olas how?
09:13 olas in the CMLWriter?
09:13 egonw yes\
09:13 egonw mom
09:14 * egonw is looking up the CDK News paper on this
09:14 olas hmm, there's no public method to set IOSettings
09:15 * olas is awaiting egonw's answer
09:15 egonw http://almost.cubic.uni-koeln.de/cdk/cdk_to​p/cdk_news/archive/cdknews1.2.article3.pdf
09:15 egonw grpmh...
09:15 egonw that link might not be working...
09:15 egonw ok, issue 2 of the first CDK News volume
09:16 egonw downloadable from:
09:16 egonw http://sourceforge.net/project/showfiles.​php?group_id=20024&package_id=124796
09:18 olas egonw: doesn't answer my question
09:18 egonw why not?
09:19 olas theres no CML pretty mentioned
09:20 olas it says to look at the source of CMLWriter
09:20 olas which I have done
09:20 egonw sure you do
09:20 egonw net.bioclipse.cdk
09:20 egonw anyway:
09:20 egonw indent = new BooleanIOSetting("Indenting", IOSetting.LOW,
09:20 egonw "Should the output be indented?",
09:20 egonw "true");
09:20 egonw actually, it should indent by default
09:21 olas all is on one long line
09:21 olas how to pass indent to writer?
09:22 egonw see that CDK News article
09:22 olas you are really helpful today, huh?
09:22 olas ok
09:22 olas will not bother you anymore
09:22 egonw sorry... /me is really busy
09:23 * egonw writes CDK News articles, so that he does not have to explain it on IRC anymore :)
10:24 CIA-45 bioclipse: jonalv * r5651 /bioclipse2/trunk/plugins/ (6 files in 3 dirs): Tests and code for substructure iterator in structuredb
10:43 egonw olas: ping
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11:37 rojasm Hi, I updated the bioclipse2 and after iniziate the platform I obtain a error in the javascript console with Registry.osgi.RegistryStrategyOSGI
11:40 masak sounds new
11:41 masak can you pinpoint it to somewhere specific in source?
11:48 edrin joined #bioclipse
11:48 egonw edrin: sorry, did not have time to hack in my changes
11:48 edrin hi
11:50 edrin egonw: no problem
11:50 edrin egonw: i read what peter wrote and your, response
11:51 edrin anyone has access to the following pdf: http://www.nature.com/cdd/jou​rnal/v14/n9/abs/4402167a.html ?
11:51 jonalv edrin, do you have a stack trace?
11:51 edrin huh?
11:52 jonalv no sry
11:52 egonw jonalv: I think you meant rojasm
11:52 jonalv rojasm, do you have a stack trace?
11:52 egonw rojasm is working on it...
11:54 egonw rojasm: http://cdk.pastebin.com/
11:54 edrin jonalv: do you have access to this article?
11:54 egonw edrin: /me is checking
11:54 jonalv edrin yea it seems so
11:54 edrin ok :)
11:54 * egonw does not
11:54 jonalv mail?
11:54 rojasm http://cdk.pastebin.com/m539ca524
11:54 edrin maybe one of you can mail it to me?
11:55 rojasm here I put the error
11:55 edrin yes, please :) but only once will be enough of course
11:55 edrin egonw: jonalv has it
11:55 edrin already
11:55 jonalv edrin: you mailadress?
11:55 jonalv *r
11:56 edrin pm
11:57 edrin jonalv: got the mail address ?
11:57 jonalv nope
11:58 edrin johannes.wagener
11:58 edrin at
11:58 edrin med.uni-muenchen.de
11:58 edrin egonw: thank you for also looking
12:01 rojasm some idea about the error?
12:02 jonalv it the new code that runs javascript commans in a separate thread
12:02 edrin jonalv: thanks
12:02 masak rojasm: looking at it right now
12:03 * jonalv is gonna learn spelling some day now...
12:07 egonw any news on the NPE in the JsThread class?
12:09 CIA-45 bioclipse: carl_masak * r5652 /bioclipse2/trunk/plugins/net.bioclipse.script​ing/src/net/bioclipse/scripting/JsThread.java: [JsThread] removed finite wait for actions to be initialized
12:09 masak rojasm: try now
12:09 rojasm ok perfect
12:09 * masak hopes so
12:12 rojasm it works fine no, thanks
12:12 egonw +w
12:12 rojasm know
12:12 rojasm :=
12:12 egonw -k
12:13 egonw :)
12:22 masak here's what we did last week
12:22 masak http://bioclipse.blogspot.com/2008​/05/threading-and-javascript.html
12:24 egonw interesting
12:28 masak essential, even
12:28 masak jonalv++ needed it for some heavy commands he was running
12:29 jonalv yea without that you don't get a status bar when importing sdf file into structuredb, actuall without that the complete bioclipse windows freezes while importing sdf files :)
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13:00 olas egonw: pong
13:00 CIA-45 bioclipse: jonalv * r5653 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: added empty test as a reminder
13:05 egonw olas: don't remember
13:06 olas :-)
13:06 * olas is fixing the SDFEditor
13:07 egonw olas: might you squeeze in column sorting?
13:07 jonalv olas: we both want lazy loading and column sorting ;)
13:08 egonw oh... and a column with the entry number would be nice
13:08 egonw (and easy to implement, I guess...)
13:10 CIA-45 bioclipse: ospjuth * r5654 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.jchempaint/ (5 files in 4 dirs): CMLFileEditor is able to read and show molecules. JCPPage further refactored to support other IJCPBasedEditors.
13:10 CIA-45 bioclipse: ospjuth * r5655 /bioclipse2/trunk/plugins/net.bioclips​e.cdk10.sdfeditor/src/net/bioclipse/cd​k10/sdfeditor/editor/SDFEditor.java: Adapted for API changes in JCPPage. Single Molecule Page not working (yet).
13:11 rojasm olas around
13:11 olas yes
13:11 rojasm ?
13:11 olas !
13:12 masak ¿
13:12 rojasm could you put me as developer in bioclipse again? I thought I was some time ago
13:12 olas hmm, aren't you?
13:12 olas sure
13:12 olas what do you plan to do?
13:12 rojasm I would like to put some tracker first
13:12 egonw write a competitor and destroy BC2 ... what else ? :)
13:13 olas haha
13:13 olas tracker?
13:13 olas what is that?
13:13 egonw bug 'track' system ?
13:13 rojasm I wanted to put some
13:13 rojasm thanks
13:14 olas oh, sure
13:14 olas you are still there
13:14 rojasm but I remember I commit one month ago some thing
13:14 olas but somehow credentials for bugs is missing
13:14 olas will add it back
13:14 egonw ah... ok, I think I understand the problem
13:14 egonw right
13:15 olas hmm
13:15 egonw he needs to be allowed BTS rights
13:15 egonw let me check
13:15 olas it says rechnician on bugs
13:15 olas will add to feature requests as well
13:15 egonw also for feature reqyest?
13:15 egonw ok, good
13:15 olas done
13:16 egonw thanx
13:16 rojasm thanks olas
13:19 jonalv olas: I think we should remove boolean has3dCoords() from IMolecule
13:19 egonw why?
13:19 egonw it's important for deciding to open JCP or Jmol
13:19 egonw I'd say...
13:20 jonalv because IMolecule does not define any way fro getting those 3dcoords so you must do a instanceof check to figure that out anyway
13:23 egonw ah, ic...
13:23 egonw for CDK, cdk.geometry.GeometryTools has the method for checking for 3D coords
13:23 olas I know
13:23 olas but an IMolecule is as small as possible
13:24 olas so yes, I second jonalvs proposal (for now)
13:24 masak me too
13:24 olas it is never used
13:24 olas (AFAIK)
13:24 egonw who am I to argue then...
13:24 jonalv if we get rid it an IMolecule only says that a molecule has a SMiles
13:25 olas I know
13:25 olas well, afaik it's the simplest molecule repr there is
13:25 olas so it's a start
13:25 masak it's one simplest molecule repr
13:25 olas if we find reasons to extend it later, we can (and should)
13:26 egonw olas: simplest??
13:26 masak just like a graph would be
13:26 jonalv egonw: what is simpler than smils?
13:26 olas egonw: it's a String
13:57 CIA-45 bioclipse: jonalv * r5656 /bioclipse2/trunk/plugins/net.biocli​pse.biojava.business/src/net/bioclip​se/biojava/business/Activator.java: cleaned up a bit
14:19 CIA-45 bioclipse: ospjuth * r5657 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.jchempaint/src/net/bioclipse/cdk​10/jchempaint/ui/editor/JCPPage.java:
14:19 CIA-45 bioclipse: Tried to refactor out initialization so that JCPPage can be initialized as a
14:19 CIA-45 bioclipse: second tab in the SDFileEditor. Still no luck, but I don't think I have broken
14:19 CIA-45 bioclipse: anything in the CMLEditor and MDLEditor. Functionality moved from
14:19 CIA-45 bioclipse: createPartControl() to updateJCPModel(). Egonw: Please verify I have not broken
14:19 CIA-45 bioclipse: anything.
14:20 * olas need to run now, must give brother a ride
14:20 olas will be back later this evening
14:20 olas bye
14:20 olas left #bioclipse
14:48 CIA-45 bioclipse: jonalv * r5658 /bioclipse2/trunk/plugins/net.bioclipse.core/ (9 files in 5 dirs): Wrote a molecule manager but I can't get it to show up in the console. /me feels a bit silly. Perhaps someone can see what I made wrong? :)
14:50 CIA-45 bioclipse: jonalv * r5659 /bioclipse2/trunk/plugins/net.biocl​ipse.structuredb/src/net/bioclipse/​structuredb/domain/Structure.java: Removed has3dCoords from Structure
15:17 CIA-45 bioclipse: jonalv * r5660 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Added createFromMolecule to cdk manager
16:06 CIA-45 bioclipse: jonalv * r5661 /bioclipse2/trunk/plugins/ (4 files in 2 dirs): Wrote toCDKMolecule( Structure s) in structuredb and switched to using it on a few places
16:08 CIA-45 bioclipse: jonalv * r5662 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/domain/CDKMolecule.java: Addded all-params constructor to cdkMolecule
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