Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-06-12

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All times shown according to UTC.

Time Nick Message
04:58 sneumann_ joined #bioclipse
07:03 egonw joined #bioclipse
07:16 Gpox joined #bioclipse
07:17 Gpoks joined #bioclipse
07:27 masak joined #bioclipse
07:34 jonalv joined #bioclipse
07:40 olass joined #bioclipse
07:40 CIA-40 bioclipse: ospjuth * r11270 /bioclipse2/trunk/plugins/net.bioclipse.ds/src/n​et/bioclipse/ds/model/report/ReportHelper.java: Updated to support image creation in different sizes
07:43 CIA-40 bioclipse: goglepox * r11271 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintWidget.java: Moved Highlight generators to be shown above atom/bond
07:46 olass all: please mark all bugs that we will fix today as blocking 1247
07:46 olass 1247 is bug "Release RC2"
07:51 CIA-40 bioclipse: goglepox * r11272 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfedi​tor/handlers/CalculatePropertyHandler.java:
07:51 CIA-40 bioclipse: Added check to not add fingerprints to the moltable vissible columns.
07:51 CIA-40 bioclipse: Fixes bug #1255
07:51 zarah bug #1255 | http://tinyurl.com/l3zxae
07:51 egonw ack
07:59 CIA-40 bioclipse: jonalv * r11273 /bioclipse2/trunk/plugins/net.bioclipse.cor​e/src/net/bioclipse/jobs/BioclipseJob.java: rethrow operation canelled exception and don't present an error dialog for them. Also changed to the error dialog with a stacktrace for other exceptions. Fixes bug: #1264
07:59 zarah bug #1264 | http://tinyurl.com/lrnsp6
08:01 olass_ joined #bioclipse
08:21 shk3 joined #bioclipse
08:56 olass joined #bioclipse
08:56 CIA-40 bioclipse: ospjuth * r11274 /bioclipse2/trunk/plugins/net.bioclipse​.ds/schema/net.bioclipse.ds.test.exsd: The class to extend had gone mising from the Test EP.
09:00 CIA-40 bioclipse: ospjuth * r11275 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Implemented and declares SmartsMatchModel for reporting the SmartsTest in Birt.
09:01 CIA-40 bioclipse: ospjuth * r11276 /bioclipse2/trunk/plugins/net.bioclipse.ds.birt/ (5 files in 2 dirs): Updated report and handlers for adding the SmartsTest and SignSigTest.
09:02 CIA-40 bioclipse: ospjuth * r11277 /bioclipse2/trunk/plugins/net.bioclipse.ds/​src/net/bioclipse/ds/ui/views/DSView.java: The QueryMolecule is rendered a bit larger in the report.
09:04 CIA-40 bioclipse: ospjuth * r11278 /bioclipse2/trunk/plugins/net.bioclipse​.ds.signsig.bursi/src/net/bioclipse/ds/​signsig/bursi/SignSigTestmodel2.java: Implemented SignSigModel for reporting the SignSigTest in Birt.
09:04 masak joined #bioclipse
09:04 CIA-40 bioclipse: ospjuth * r11279 /bioclipse2/trunk/plugins/net.bioclips​e.ds.signsig.bursi/src/net/bioclipse/d​s/signsig/bursi/SignSigTestmodel.java: Renamed SignSigModel since subclipse-- messed things up.
09:05 jonalv olass++ for giving subclipse-- less karma++ :)
09:05 olass lol
09:05 olass there's no doubt that subclipse is really really bad
09:05 CIA-40 bioclipse: ospjuth * r11280 /bioclipse2/trunk/plugins/net​.bioclipse.ds.signsig.bursi/ (5 files in 2 dirs): Removed last remnants of signsic and replaced with signsig (short for Signature Significance)
09:06 olass especially if you run into a problem
09:06 olass it just lacks the power tools to override stuff
09:07 egonw shk3: ping
09:07 shk3 egonw: pong
09:07 zarah shk3: You have new messages. Write '/msg zarah @messages' to read them.
09:08 egonw shk3: are you depending on IMolecule.getSMILES ?
09:08 egonw @msg
09:08 zarah egonw: You have no new messages.
09:08 shk3 don't think so
09:08 egonw zarah: are you making fun of me?!
09:08 zarah egonw: are you making fun of me?
09:08 egonw shk3: ack
09:08 shk3 mom
09:08 egonw zarah--
09:08 shk3 checking
09:09 shk3 are you doing rc2 today?
09:09 egonw yes
09:09 shk3 no getSMILES used somewhere
09:10 shk3 ok, then I do the speclipse update site
09:14 egonw jonalv: can you come over for a sec?
09:23 egonw Gpox: can you come over for a sec?
09:23 egonw btw, what is 'celar' ?
09:30 olass egonw: I commented on bug 1230
09:32 egonw @pz 1230
09:32 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1230
09:33 olass jonalv: do you have a bug for the "SMILES in Properties in a job" bug?
09:33 jonalv olass: yes
09:33 olass what no?
09:33 jonalv I made it myself... :)
09:33 olass number?
09:33 jonalv @pz 1267
09:33 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1267
09:34 jonalv olass: I have no idea how to succeed with it though..
09:34 olass right
09:35 shk3 I just found a bug I classified as blocker. Please have a look.
09:35 olass shk3: what number?
09:35 shk3 if you think it's not that bad, just change it.
09:35 olass thanks
09:35 shk3 1271
09:35 olass @pz 1271
09:35 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1271
09:36 olass shk3: this is a known bug
09:36 olass egonw and jonalv spent a lot of time on it
09:36 olass we suspect a bug in eclipse
09:36 egonw shk3: seems to be an Eclipse bug
09:37 egonw shk3: let's hope 3.5 fixes it
09:37 olass yes
09:37 shk3 ok
09:37 shk3 looks like a pretty bad bug for eclipse
09:39 CIA-40 bioclipse: carl_masak * r11281 /bioclipse2/trunk/plugins/net.bioclip​se.doc/html/scriptingBioclipse.html:
09:39 CIA-40 bioclipse: [scriptingBioclipse.html] updated documentation
09:39 CIA-40 bioclipse: It now aligns with <http://wiki.bioclipse.net/index.php?title​=Scripting_in_Bioclipse_2&amp;oldid=3866>.
09:40 zarah CIA-40's link is also http://tinyurl.com/ld5c96
09:40 egonw olass: ack on 1230
09:40 olass shk3: it is the CommonNavigator which has the bug
09:40 olass Eclipse tweaks the CommonNavigator bug time in the Eclipse platform...
09:41 olass shk3: I added it to http://wiki.bioclipse.net/ind​ex.php?title=Intractable_Bugs
09:41 zarah olass's link is also http://tinyurl.com/bfhd57
09:43 * olass is afk for lunch
09:52 egonw @tell ola typo on the 'getting started' page: http://www.bioclipse.net/index.php?option=com​_content&amp;task=view&amp;id=14&amp;Itemid=0 -> whi8ch
09:52 zarah egonw's link is also http://tinyurl.com/ltvwhx
09:52 zarah Consider it noted.
09:58 CIA-40 bioclipse: egonw * r11282 /bioclipse2/trunk/plugins/ (11 files in 9 dirs): IMolecule SMILES was originally designed as a serialization, not a property, and misused as the later later. This patch reinstates the original behavior
09:59 CIA-40 bioclipse: egonw * r11283 /bioclipse2/trunk/plugins/net.bioclipse.core/​src/net/bioclipse/core/domain/IMolecule.java: Added missing JavaDoc: these methods serialize, and are not to be used as properties
10:00 CIA-40 bioclipse: egonw * r11284 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/domain/CDKMolecule.java: Fixed CDKMolecule getSMILES to work as designed: (try to) serialize the IMolecule into SMILES format. Also removed the caching of the SMILES, for which the general setProperty(MolProperty.SMILES) should be used instead.
10:04 CIA-40 bioclipse: egonw * r11285 /bioclipse2/trunk/plugins/ (11 files in 9 dirs): Renamed method to stress the fact that it is a serialization method, not a property
10:07 CIA-40 bioclipse: egonw * r11286 /bioclipse2/trunk/plugins/ (12 files in 10 dirs): Renamed method to stress the fact that it is a serialization method, not a property
10:08 shk3 how can I change an atom in jcp in bc to an unusual element?
10:08 shk3 ie one not in the context menu?
10:09 Gpox @pz 600
10:09 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=600
10:10 Gpox there is a bug
10:12 shk3 hm
10:13 shk3 I think I had a bug on that myself once, but can't find it
10:13 shk3 in any case, this is a blocker, I would say
10:21 shk3 I just did some serious, real world structure editing.
10:21 shk3 What makes it a very bad user experience, is the highlighing of atoms.
10:21 shk3 If you want to attach bonds, merge atoms etc., it virtually don't see where you attach or drop.
10:21 CIA-40 bioclipse: goglepox * r11287 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.business/src/net/bioclipse/cdk/domain/ (CDKMolecule.java CDKMoleculeUtils.java):
10:21 CIA-40 bioclipse: Fixed typo
10:21 CIA-40 bioclipse: Fixes bug #1270
10:22 zarah bug #1270 | http://tinyurl.com/ox7zrm
10:22 shk3 the marker needs to be much more visible.
10:22 CIA-40 bioclipse: goglepox * r11288 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui​.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/ (3 files in 2 dirs): Added the ability to run multiple property calculators at one time via a command
10:27 egonw "Fixes typo reported in bug #1270" ?
10:31 CIA-40 bioclipse: egonw * r11289 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Removed old redundant getSMILES() method implementation which was (incorrectly) using the IMolecule.getSMILES()
10:46 shk3 I found the SWTMouseEventRelay has beed designed to specifcally ignore CTRL+Mouse
10:46 shk3 SWTMouseEventRelay l. 86
10:46 shk3 why so?
10:46 shk3 this is a problem for specmol editor
10:47 shk3 Gpox: seems like you di the SWTMouseEventRelay
10:47 shk3 do you have a second to discuss this?
10:52 shk3 Gpox?
10:53 egonw he's at lunch
10:55 shk3 ah
11:05 CIA-40 bioclipse: egonw * r11290 /bioclipse2/trunk/cdk-externals/tru​nk/org.openscience.cdk.io/src/org/o​penscience/cdk/io/MDLWriter.java:
11:05 CIA-40 bioclipse: Added writer IO option to force writing of 2D coordinates if 3D coordinates are present too, which now are preferably outputted.
11:05 CIA-40 bioclipse: See upstream patch report:
11:05 CIA-40 bioclipse: http://sourceforge.net/tracker/inde​x.php?func=detail&amp;aid=2805271&a​mp;group_id=20024&amp;atid=320024
11:05 zarah CIA-40's link is also http://tinyurl.com/mwb9bd
11:29 Gpox back
11:29 CIA-40 bioclipse: ospjuth * r11291 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.jchempaint/META-INF/MANIFEST.MF: Exported generators package in manifest.
11:32 Gpox shk3: on mac cltr-click brings up the popup menu
11:34 shk3 hm
11:34 shk3 in specmol editor, I need selection of multiple molcules
11:34 shk3 holding ctrl is the obvious choice, i think
11:35 Gpox isn't that platform specific
11:35 shk3 hm
11:35 shk3 might be
11:36 shk3 but than your filtering of click should be for mac only
11:36 shk3 no?
11:36 Gpox I do cmd-click when selecting multiple things on mac
11:36 Gpox yes
11:36 shk3 ok, now it's me for lunch
11:36 shk3 perhaps you can give this a thought
11:36 shk3 and we discuss later
11:36 * shk3 away
11:36 CIA-40 bioclipse: goglepox * r11292 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/domain/CDKMolecule.java:
11:36 CIA-40 bioclipse: Anded check for null for lazy initilaized property map
11:36 CIA-40 bioclipse: Fixes bug #1278
11:37 zarah bug #1278 | http://tinyurl.com/mp947v
11:37 Gpox but IMouseEventRelay dose not handle modifiers
11:47 sneumann shk3: did you check http://msbi.ipb-halle.de/updateSite ?
11:47 zarah sneumann's link is also http://tinyurl.com/l8mwsj
11:48 sneumann It has the massspec_feature, but I am unsure whether it is done properly
11:48 sneumann because testing it my BC2 "install software" mentioned some very old dependencies,
11:48 sneumann exact messages are at home. But if it works for you that'd be great.
11:52 egonw sneumann: there is a RC2 around the corner
11:53 egonw I can test with that release
11:55 CIA-40 bioclipse: egonw * r11293 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java: Fixed 'doi <MANAGER>', which returned an error 'Only do -doi manager.method-' earlier
11:57 sneumann Fine. I think we said earlier that ms_feature is post 2.0, but good to now earlier if it works
11:57 egonw yes
12:06 egonw masak: ping
12:06 masak egonw: pong
12:06 egonw please review patch 11293
12:06 egonw and the upcoming patch by me
12:07 * masak reviews
12:07 jonalv egonw: what does inchi.generate do now?
12:07 egonw generate inchi?
12:07 jonalv egonw: will it caash it on the molecule?
12:07 egonw I hope not
12:08 jonalv egonw: so of what use is the variant taking an BioclispeJobUdatehook?
12:08 egonw it's JNI stuff... if you give it crap, I have no clue what happens
12:08 * shk3 is back
12:08 jonalv egonw: why would I give it crap?
12:08 egonw jonalv: can you come over?
12:08 shk3 sneumann: yes, but needs rc2 it seems
12:09 shk3 will test then
12:09 sneumann I did a svn update of my eclipse-bioclipse workspace as of yesterday evening.
12:09 CIA-40 bioclipse: carl_masak * r11294 /bioclipse2/trunk/plugins/net.bioclipse.jmol/s​rc/net/bioclipse/jmol/editors/JmolEditor.java:
12:09 CIA-40 bioclipse: [JmolEditor.java] comment/whitespace therapy
12:09 CIA-40 bioclipse: Just reading through the code, fixing little things. No changes to
12:09 CIA-40 bioclipse: semantics.
12:10 shk3 well yes, but the update site says rc2 needed
12:10 shk3 which is fine
12:10 shk3 since rc2 will be out today
12:13 masak egonw: looks fine.
12:14 egonw masak: here comes the second commit
12:14 masak :)
12:14 egonw masak: ok, thanx
12:14 egonw it adds 'doi bioclipse'
12:14 masak nice.
12:14 egonw where bioclipse is a pseudo manager
12:14 egonw though we might have a try bioclipse manager
12:14 egonw with bioclipse.copyright()
12:14 egonw bioclipse.authors()
12:14 masak I'll check the commit.
12:14 egonw bioclipse.bugTracker()(
12:15 egonw bioclipse.blog()
12:15 egonw olass: what do you think?
12:15 egonw something post RC2 but pre 2.0.0 ?
12:15 CIA-40 bioclipse: egonw * r11295 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java: Added 'doi bioclipse'
12:16 olass egonw: sounds like a good idea
12:16 masak git++ # we're working on the same file, and it just merges together!
12:16 olass wow
12:16 CIA-40 bioclipse: carl_masak * r11296 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
12:16 CIA-40 bioclipse: [JsConsoleView] minor whitespace therapy
12:16 CIA-40 bioclipse: I have a preference to putting line-breaking binary operators
12:16 CIA-40 bioclipse: first on the new line, not last on the old line.
12:16 olass subclipse can't do that...
12:16 egonw subclipse--
12:16 egonw git++
12:16 olass say that again
12:16 egonw git++
12:17 * olass agrees
12:17 egonw why?
12:17 egonw anyway...
12:17 egonw bioclipse.foo() post RC2, pre 2.0.0 ?
12:17 shk3 Gpox: backt to our ctrl-Issue ;-)
12:21 CIA-40 bioclipse: egonw * r11297 /bioclipse2/trunk/plugins/net.bioclipse.jmol/src​/net/bioclipse/jmol/business/IJmolManager.java: Added DOI for the Jmol manager
12:21 olass egonw: sounds good
12:23 CIA-40 bioclipse: goglepox * r11298 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (3 files in 3 dirs):
12:23 CIA-40 bioclipse: Added support for composit property calculator
12:23 CIA-40 bioclipse: Fixes bug #1279
12:23 zarah bug #1279 | http://tinyurl.com/l2uqsn
12:24 CIA-40 bioclipse: shk3 * r11299 /bioclipse2/trunk/plugins/net.biocl​ipse.specmol/src/net/bioclipse/spec​mol/wizards/NewSpecMolWizard.java: .cml is appended if not there
12:25 shk3 Gpox: what do you think about the ctrl issue?
12:25 shk3 on many platforms (ie win+linux) holding ctrl for multiple selections is common.
12:26 shk3 right now, this is blocked for all platforms.
12:27 masak egonw: if we do add a real manager called 'bioclipse', the 'pseudo' manager will override the real one, as the code stands now.
12:27 masak egonw: but maybe that's not such big a deal...
12:31 egonw yes, indeed
12:31 egonw that last patch will have to be reverted when that happens
12:31 egonw will add a note about that
12:32 egonw masak: @pz 1284
12:32 masak @pz 1284
12:32 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1284
12:33 masak goodie. worksforme.
12:36 CIA-40 bioclipse: egonw * r11300 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: More accurate manager description
12:37 shk3 is Gpox round?
12:40 olass shk3: Gpox is helping me
12:41 olass sorry but I need him for RC2
12:41 Gpox shk3: < Gpox> but IMouseEventRelay dose not handle modifiers
12:45 shk3 the SWTMouseEventRelay does
12:45 shk3 that's the problem for me right now
12:47 CIA-40 bioclipse: ospjuth * r11301 /bioclipse2/trunk/plugins/net.bi​oclipse.ds/src/net/bioclipse/ds/ (model/report/ReportHelper.java ui/views/DSView.java): Added support for highlighting substructures in DS report.
12:49 * egonw sees no other option than to add yet another saveMolecule() method
12:49 egonw 34 is not enough
12:59 shk3 joined #bioclipse
13:21 CIA-40 bioclipse: ospjuth * r11302 /bioclipse2/trunk/plugins/net.bioclipse.ds/src/net​/bioclipse/ds/business/DSConsensusCalculator.java: Added a stub for a consensus calculator for DS.
13:21 olass Gpox: committed in r11302
13:40 CIA-40 bioclipse: goglepox * r11303 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui​.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/ (3 files in 2 dirs):
13:40 CIA-40 bioclipse: Removed IPropertyCalculatorComposite
13:40 CIA-40 bioclipse: Mulitplied progress in calculateProperties with 1000
13:40 Gpox olass: committed in r11303
13:42 CIA-40 bioclipse: goglepox * r11304 /bioclipse2/trunk/plugins/net.bioclipse.ds/src/net​/bioclipse/ds/business/DSConsensusCalculator.java: Added some stubs to consensus calculator
13:51 CIA-40 bioclipse: shk3 * r11305 /bioclipse2/trunk/plugins/net.biocli​pse.nmrshiftdb/src/net/bioclipse/nmr​shiftdb/wizards/SubmitWizard.java: fixes bug in submit
13:54 CIA-40 bioclipse: egonw * r11306 /bioclipse2/trunk/plugins/net.biocli​pse.cdk.debug/src/net/bioclipse/cdkd​ebug/business/CDKDebugManager.java: Fixed 'implements': manager implementations should not implement the matching manager interfaces, but simply IBioclipseManager
13:55 CIA-40 bioclipse: egonw * r11307 /bioclipse2/trunk/ (5 files in 4 dirs): Added cdx.listReaderOptions(IChemFormat) and cdx.listWriterOptions(IChemFormat)
14:01 CIA-40 bioclipse: goglepox * r11308 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfedi​tor/handlers/CalculatePropertyHandler.java: Added the ability to add more than one calculator to an action
14:07 egonw is anyone using CDKManager.save() ?
14:10 egonw finger crossed
14:10 egonw +s
14:10 egonw it's not broken
14:16 jonalv egonw: could you come over when you ahve a second?
14:22 egonw jonalv: quick question
14:23 egonw should a manager interface method that takes a BioclipseUIJob be published
14:23 egonw ?
14:26 jonalv egonw: no
14:26 egonw ack
14:26 egonw that explains a failing unit test
14:27 jonalv egonw: good
14:27 egonw shk3: please take notice for future reference
14:29 jonalv who wrote the property stuff on ICDKMolecule? It's not thread safe
14:30 shk3 egonw: what exactly?
14:31 CIA-40 bioclipse: egonw * r11309 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): Extended save API to support writer options
14:31 egonw shk3:
14:31 egonw [16:23:23] <egonw> should a manager interface method that takes a BioclipseUIJob be published
14:31 egonw [16:23:24] <egonw> ?
14:31 egonw [16:26:40] <jonalv> egonw: no
14:31 egonw [16:26:49] <egonw> ack
14:31 egonw [16:26:55] <egonw> that explains a failing unit test
14:31 egonw [16:27:12] <jonalv> egonw: good
14:32 shk3 hm
14:32 shk3 ok
14:50 jonalv yey it's working!
14:50 egonw ha, cool!
14:50 egonw here too!
14:51 jonalv egonw: sry?
14:51 jonalv egonw: what works for you? :)
14:52 egonw huh?
14:52 egonw what works for you then?
14:52 egonw (hahahaha)
14:52 jonalv the calculate inchi as a job in the backgournd stuff
14:52 egonw saveAs MDL molfile 2D coordinates
14:52 jonalv and if failed show failed to calculate...
14:52 CIA-40 bioclipse: egonw * r11310 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Force saving MDL V2000 molfile as 2D (fixes #1237)
14:52 zarah bug #1237 |
14:52 jonalv egonw: aha nice
14:59 CIA-40 bioclipse: jonalv * r11311 /bioclipse2/trunk/plugins/net.bioclipse.i​nchi/src/net/bioclipse/inchi/InChI.java: Added FAILED_TO_CALCULATE as an InChI instance
15:01 CIA-40 bioclipse: jonalv * r11312 /bioclipse2/trunk/plugins/ (3 files in 2 dirs):
15:01 CIA-40 bioclipse: Generate InChi in a job in the background a CDKMolecule lacks InChi and then update the properties view. Also if InChi generation fails use InChI ionstance representing failed to calculate.
15:01 CIA-40 bioclipse: fixes bug: #1267.
15:01 zarah bug #1267 |
15:02 shk3 how is rd2 doing?
15:04 CIA-40 bioclipse: shk3 * r11313 /bioclipse2/trunk/plugins/net.bioclips​e.nmrshiftdb/src/net/bioclipse/nmrshif​tdb/business/INmrshiftdbManager.java: removed published from methods with bioclipseuijob
15:09 CIA-40 bioclipse: goglepox * r11314 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/JCPCellPainter.java:
15:09 CIA-40 bioclipse: Made compact shape oval in sdf editor
15:09 CIA-40 bioclipse: Fixes bug #1288
15:09 Gpox shk3: about ctrl-click
15:09 CIA-40 bioclipse: ospjuth * r11315 /bioclipse2/trunk/plugins/net.bioclipse.ds​/src/net/bioclipse/ds/model/TestRun.java: Make TestRun implement ICOlorProvider to allow for coloring text and background in a MolTable cell.
15:09 Gpox @pz 759
15:10 zarah bug #1288 | http://tinyurl.com/poaw2l
15:10 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=759
15:10 Gpox @pz 768
15:10 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=768
15:11 shk3 hm ok
15:11 shk3 I implemented this multiple selection for specmol editor
15:11 shk3 I made it to work if any key is pressed
15:11 shk3 but due to filtering of ctrl, this is now left out
15:12 shk3 which is bad in win and linux, since ctrl is standard there for multiple selections
15:12 shk3 if you do it jcp, you will have the same problem, I suppose
15:14 shk3 but since you said in mac ctrl+click is right click, this sounds really like it needs platform-specific treatment
15:18 CIA-40 bioclipse: goglepox * r11316 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintView.java:
15:18 CIA-40 bioclipse: Filter out CDKChemObject form selections in JChemPaintView
15:18 CIA-40 bioclipse: Sovles bug #1258
15:18 zarah bug #1258 | http://tinyurl.com/nz9kvd
15:21 CIA-40 bioclipse: shk3 * r11317 /bioclipse2/trunk/ (6 files in 6 dirs): preparing rc2
15:27 shk3 Gpox: what do you think?
15:28 egonw he left 10 minutes ago
15:29 egonw can you please file a bug report and indicate which patch broke the SpecMol editor functionality?
15:29 egonw the uppsala team (and Arvid in particular) is focusing on a really important demo next week
15:30 egonw and he has very little time for other things right now
15:30 egonw shk3: to get stuff working for speclipse for rc2 is the following:
15:30 egonw (it's a workaround)
15:31 egonw make an feature update which includes a jchempaint feature that removes the filtering ot Ctrl
15:31 egonw or better
15:31 egonw make the 'customized' cdk.jchempaint plugins part of the RC2 Speclipse feature
15:31 egonw I have no clue what functionality depends on the Ctrl to be filtered out,
15:32 egonw but this allows you to release a working Speclipse for the RC2
15:32 CIA-40 bioclipse: ospjuth * r11318 /bioclipse2/trunk/plugins/net.bi​oclipse.ds/src/net/bioclipse/ds/ (business/ConsensusCalculator.java model/TestRun.java): Refactored out calculation of consensus into a ConsensusCalculator.
15:39 CIA-40 bioclipse: ospjuth * r11319 /bioclipse2/trunk/plugins/net.bioclip​se.ds/src/net/bioclipse/ds/business/ (ConsensusCalculator.java DSConsensusCalculator.java): Call consensus calculation in DSConsensusCalculator.
15:40 CIA-40 bioclipse: ospjuth * r11320 /bioclipse2/trunk/plugins/net.bioclipse.ds/src/n​et/bioclipse/ds/model/report/ReportHelper.java: Added support for roundtripping between ITestResults and string serialization
15:41 shk3 egonw: it still works with any other key than ctrl, so I will leave it right now and we will look for a solution once there is time for this.
15:41 CIA-40 bioclipse: shk3 * r11321 /bioclipse2/trunk/plugins/net.bioclip​se.cdk.jchempaint/doc/molecules.html: improved doc
15:44 CIA-40 bioclipse: shk3 * r11322 /bioclipse2/trunk/net.bioclipse​.speclipse-updatesite/site.xml: updated the update site
15:46 CIA-40 bioclipse: ospjuth * r11323 /bioclipse2/trunk/plugins/ (5 files in 3 dirs): API change: Status > Classification.
15:46 olass need to run to train now
15:46 olass RC2 will be released in the evening
15:46 CIA-40 bioclipse: ospjuth * r11324 /bioclipse2/trunk/plugins/net.bioclipse.ds/ (8 files in 3 dirs): API change implemented: Status > Classification.
15:46 olass in the worst case, tomorrow morning
15:46 egonw I need 4 minutes
15:46 olass sry
15:46 olass train won't wait
15:47 olass anjd jonalv needs at least 10 minutes as well
15:47 olass so will build at home and upload over night
15:50 CIA-40 bioclipse: egonw * r11325 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Now asks confirmation about 3D coordinate info loss (fixes #1233)
15:50 zarah bug #1233 |
15:51 CIA-40 bioclipse: egonw * r11326 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: Methods taking a bioclipse job should not be published
15:52 jonalv egonw: "" is actually a correct smiles...
15:53 egonw sure
15:53 egonw a set of zero atoms
15:53 jonalv the cdkmoleculepropertysource translated that one to N/A
15:53 egonw which makes sense though
15:53 egonw I guess
15:56 * egonw exits Eclipse
15:56 egonw enough bioclipse hacking for today
16:00 Gpox joined #bioclipse
16:25 CIA-40 bioclipse: jonalv * r11327 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): moved SMILES generation from JChempaint editor to a job initialized from the CDKMoleculePropertySource just like inchi.
16:29 Gpox joined #bioclipse
16:34 CIA-40 bioclipse: goglepox * r11328 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui.sdfeditor/plugin.xml:
16:34 CIA-40 bioclipse: Added Open before Additions in context menu
16:34 CIA-40 bioclipse: Solves bug #1281
16:34 zarah bug #1281 |
16:46 jonalv @pz 1281
16:46 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1281
17:35 egonw joined #bioclipse
17:39 egonw_ joined #bioclipse
17:44 CIA-40 bioclipse: ospjuth * r11329 /bioclipse2/trunk/plugins/net.bioclipse.ds​/src/net/bioclipse/ds/model/TestRun.java: Fixed a NPE if no results available.
17:44 sneumann_ joined #bioclipse
18:00 sneumann__ joined #bioclipse
20:07 CIA-40 bioclipse: ospjuth * r11330 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): Updated DSSIngleReport with a bioclipse logo.

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