Camelia, the Perl 6 bug

IRC log for #cdk, 2008-03-19

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
03:10 CIA-11 jmol: hansonr * r9158 /branches/v11_4/Jmol/src/org/jmol/ (6 files in 4 dirs): version=11.5.19_dev # bug fix: isosurface reading/writing JVXL files having insideout keyword
03:11 CIA-11 jmol: hansonr * r9159 /trunk/Jmol/src/org/jmol/ (6 files in 4 dirs): version=11.5.19_dev # bug fix: isosurface reading/writing JVXL files having insideout keyword
03:57 CIA-11 jmol: hansonr * r9160 /trunk/Jmol/src/org/jmol/ (5 files in 4 dirs): version=11.5.19 # bug fix: null surfaceGenerator causes MO exception
03:57 CIA-11 jmol: hansonr * r9161 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.5.19 VERSION
05:24 jbrefort joined #cdk
05:29 CIA-11 jmol: nicove * r9162 /trunk/Jmol-FAH/projects/ (p4407.xyz.gz p4408.xyz.gz): Folding@Home
07:10 rojasm moin!
07:33 |thomas_ku| joined #cdk
07:33 |thomas_ku| moin
07:40 jpansanel moin
08:19 egonw joined #cdk
08:23 tjeerd joined #cdk
08:43 Annzi joined #cdk
08:52 jonalv joined #cdk
09:00 masak joined #cdk
09:39 egonw_ joined #cdk
10:03 CIA-11 bioclipse: carl_masak * r5119 /bioclipse2/trunk/plugins/net.bioclipse.core​/src/net/bioclipse/core/domain/BioList.java:
10:03 CIA-11 bioclipse: [BioList.java]
10:03 CIA-11 bioclipse: * removed unused imports
10:03 CIA-11 bioclipse: * fixed generic type hiding
10:04 CIA-11 bioclipse: carl_masak * r5120 /bioclipse2/trunk/plugins/net.bioclip​se.core/src/net/bioclipse/recording/ (3 files):
10:04 CIA-11 bioclipse: [IRecordingAdvice.java]
10:04 CIA-11 bioclipse: [JsScriptGenerator.java]
10:04 CIA-11 bioclipse: [ManagerObjectRecord.java]
10:04 CIA-11 bioclipse: * removed unused imports
10:20 CIA-11 bioclipse: Annzi * r5121 /bioclipse2/trunk/plugins/net.bioclipse.moss/ (8 files in 3 dirs): Help and help function were added and some new parameter settings
10:32 CIA-11 cdk: miguelrojasch * r10449 /cdk/branches/miguelrojasch-CMLReact/src/data/cml/ (cmlConciseFormula.cml cmlConciseFormula2.cml): added new cml file. Containing a Molecule with two elemental composition. For cases where is found two different candidates
10:34 CIA-11 cdk: miguelrojasch * r10450 /cdk/branches/miguelrojasch-CMLReact/src/ (2 files in 2 dirs): Added functionality to read formula from CML in put in IMolecule as property (CDKConstants.FORMULA)
10:39 rojasm egonw: what happens when two properties, e.g. IMolecule, have the same key?
10:40 egonw key? id you mean?
10:40 rojasm yes! you have the key and the value
10:40 egonw huh?
10:40 egonw oh...
10:41 egonw the second overwrites the first, I think
10:41 rojasm when I print I print the property I obtain that
10:41 rojasm assertEquals("[C 18 H 21 Cl 2 Mn 1 N 5 O 1, C 4 H 10]", mol.getProperty(CDKConstants.FORMULA).toString());
10:42 rojasm because I set two times as CDKConstants.FORMULA
10:42 rojasm ok, again
10:42 rojasm how I should do it for setting in a IMolecule two different formulas
10:43 rojasm yes!
10:43 egonw good point
10:43 egonw not sure
10:45 egonw tjeerd: around?
10:53 CIA-11 bioclipse: carl_masak * r5122 /bioclipse2/trunk/plugins/net.bioclipse.logging/​src/net/bioclipse/logging/PluginLogManager.java:
10:53 CIA-11 bioclipse: [PluginLogManager.java]
10:53 CIA-11 bioclipse: * added type parametrization
11:00 de_maas joined #cdk
11:18 jbrefort joined #cdk
11:31 carsten joined #cdk
11:35 masak joined #cdk
11:52 CIA-11 bioclipse: carl_masak * r5123 /bioclipse2/trunk/plugins/net.bioclip​se.biojava.business/src/net/bioclipse​/biojava/business/BiojavaHelper.java:
11:52 CIA-11 bioclipse: [BioJavaHelper.java]
11:52 CIA-11 bioclipse: * removed use of Iterator and raw types
12:04 jonalv joined #cdk
12:10 CIA-11 bioclipse: jonalv * r5124 /bioclipse2/trunk/plugins/net.bioclipse.analysis/ (build.properties src/net/bioclipse/analysis/Activator.java): removed unused imports and fixed a warning in build.properties
12:12 CIA-11 bioclipse: jonalv * r5125 /bioclipse2/trunk/plugins/net.bioclipse.bi​ojava.business/src/net/bioclipse/biojava/ (4 files in 2 dirs): organized imports
12:13 CIA-11 bioclipse: jonalv * r5126 /bioclipse2/trunk/plugins/net.bioclipse.biojava.bu​siness.tests/tests/net/bioclipse/biojava/business/ (BiojavaHelperTest.java BiojavaManagerTest.java): organzed imports
12:16 CIA-11 bioclipse: carl_masak * r5127 /bioclipse2/trunk/plugins/net.bioclipse​.biojava.ui/src/net/bioclipse/biojava/u​i/views/SequenceContentProvider.java:
12:16 CIA-11 bioclipse: [SequenceContentProvider.java]
12:16 CIA-11 bioclipse: * whitespace issues
12:16 CIA-11 bioclipse: * removed auto-generated comments
12:19 egonw rojasm: btw: http://cheminfo.informatics.indiana.edu/​~rguha/code/java/nightly/junitdiff.html
12:20 egonw I think that might be a regression to your work?
12:20 CIA-11 bioclipse: carl_masak * r5128 /bioclipse2/trunk/plugins/net.bioclipse.​core.tests/net.bioclipse.recording/net/b​ioclipse/core/domain/BioListTest.java:
12:20 CIA-11 bioclipse: [BioListTest.java]
12:20 CIA-11 bioclipse: * removed error-causing @Override
12:20 CIA-11 bioclipse: * removed unread instance variable
12:22 rojasm ups I think so, thanks egonw
12:26 CIA-11 bioclipse: carl_masak * r5129 /bioclipse2/trunk/plugins/net.bioclipse.​biojava.ui/src/net/bioclipse/biojava/ui/ (8 files in 3 dirs):
12:26 CIA-11 bioclipse: [net.bioclipse.biojava.ui]
12:26 CIA-11 bioclipse: * removed unused imports
12:26 CIA-11 bioclipse: * removed unused instance variables
12:26 CIA-11 bioclipse: * removed unused private methods
12:26 CIA-11 bioclipse: * removed auto-generated TODO comments
12:26 CIA-11 cdk: miguelrojasch * r10451 /cdk/trunk/src/main/org/openscience/cdk/too​ls/manipulator/ReactionSetManipulator.java: Forgot commit for ReactionSetManipulator
12:26 egonw |thomas_ku|: going to submit a Google Summer of Code project to OMII-UK on CDK-Taverna?
12:28 rojasm egonw solved already. I forgot to commit :(
12:29 egonw ack :)
12:31 CIA-11 bioclipse: carl_masak * r5130 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/net​/bioclipse/ui/wizards/NewQSARRProjectWizard.java:
12:31 CIA-11 bioclipse: [NewQSARRProjectWizard.java]
12:31 CIA-11 bioclipse: * commented out unused imports and instance variables
12:41 tjeerd joined #cdk
12:52 |thomas_ku| egonw: what do I need do to for such a submit? #+
12:52 egonw depends on the project, I assume
12:52 egonw but normally you would write up what you would do
12:52 egonw with some time planning
12:52 egonw how Taverna would benefit from it, etc...
12:53 egonw because 21M PubChem/ChemSpider molecules puts some stress on Taverna2, I assume they could be interested
12:54 |thomas_ku| the problem there is the I am not sure if I could package my work there and use this work for my phd thesis than...
12:55 |thomas_ku| and I will not have time to do other stuff beside things for the phd more or less because i have to finish it and the end of this year
12:56 egonw ack, not sure about that either
12:57 |thomas_ku| I will have a look on that...
12:58 |thomas_ku| do you have a web adress?
12:58 |thomas_ku| or is it on the normal google site?
13:00 egonw http://code.google.com/soc/2008/
13:00 egonw http://code.google.com/soc/2008/omii/about.html
13:00 |thomas_ku| thanks
13:01 egonw check the project ideas page
13:01 egonw http://www.omii.ac.uk/wiki/STAFFGoogleSummerOfCode
13:01 egonw but with any project, you can define your own project too
13:04 CIA-11 bioclipse: ospjuth * r5131 /bioclipse2/trunk/plugins/net.bioclipse.bio​java.business/META-INF/spring/context.xml: Reverting 5115 as it overwrote biojava spring context.
13:13 CIA-11 bioclipse: jonalv * r5132 /bioclipse2/trunk/plugins/net.bioclipse.bioja​va.business/META-INF/spring/context-osgi.xml: reverted borken coomit I made earlier. Things should work now... :)
13:26 CIA-11 bioclipse: carl_masak * r5133 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/src/net/bioclipse/ui/ (2 files in 2 dirs):
13:26 CIA-11 bioclipse: [KeywordSourceViewerConfig.java]
13:26 CIA-11 bioclipse: [FileImportWizard.java]
13:26 CIA-11 bioclipse: * removed unused imports
13:29 CIA-11 bioclipse: jonalv * r5134 /bioclipse2/trunk/plugins/net.bioclipse.scripting​/src/net/bioclipse/scripting/JsEnvironment.java: jsscriptingconsole should not crash and burn if not getting all service objects from now on
13:36 CIA-11 bioclipse: ospjuth * r5135 /bioclipse2/trunk/plugins/net.bioclipse.moss/ (5 files in 5 dirs): Refactored job execution to action from performFinish(). Added stub to a job, no progress bar so far.
13:39 * egonw got his OpenRDF toolkit up and running
13:40 egonw which allows his to start toying with SPARQL :)
13:41 CIA-11 bioclipse: ospjuth * r5136 /bioclipse2/trunk/plugins/net.bioc​lipse.moss/src/net/bioclipse/moss/​popup/actions/RunMossAction.java: Added a progress bar for MossAction.
13:45 CIA-11 cdk: miguelrojasch * r10452 /cdk/branches/miguelrojasch-CMLReact/s​rc/main/org/openscience/cdk/tools/mani​pulator/ReactionSetManipulator.java: The method getAllMolecules look for object in different schemes
13:46 CIA-11 cdk: miguelrojasch * r10453 /cdk/branches/miguelrojasch-CMLReact/src/main/or​g/openscience/cdk/reaction/ReactionScheme.java: a scheme accepts IReaction which is apart from IReactionSet
13:48 CIA-11 cdk: miguelrojasch * r10454 /cdk/branches/miguelrojasch-CMLReact/src/main/​org/openscience/cdk/libio/cml/Convertor.java: The method cdkReactionSchemeToCMLReactionScheme analyze IReaction too.
14:23 CIA-11 bioclipse: carl_masak * r5137 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/n​et/bioclipse/ui/views/ScriptingConsoleView.java:
14:23 CIA-11 bioclipse: [ScriptingConsoleView.java]
14:23 CIA-11 bioclipse: * removed line break solution
14:23 CIA-11 bioclipse: * added screening for non-printable characters
14:31 CIA-11 bioclipse: carl_masak * r5138 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/n​et/bioclipse/ui/views/ScriptingConsoleView.java:
14:31 CIA-11 bioclipse: [ScriptingConsoleView.java]
14:31 CIA-11 bioclipse: * trying another way
14:37 CIA-11 bioclipse: carl_masak * r5139 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/n​et/bioclipse/ui/views/ScriptingConsoleView.java:
14:37 CIA-11 bioclipse: [ScriptingConsoleView.java]
14:37 CIA-11 bioclipse: * strings are immutable
14:37 CIA-11 bioclipse: * need to assign to s to make it work
14:37 CIA-11 bioclipse: * removed unused instance variable
14:58 CIA-11 cdk: miguelrojasch * r10455 /cdk/branches/miguelrojasch-CMLReact/src/ (3 files in 3 dirs): When a IMolecule is defined with more of one MolecularFormula it doesn't create a CMLFormula but put all candidates into cdk:properties dict.
15:27 egonw_ joined #cdk
15:29 kde-devel joined #cdk
15:30 kde-devel egonw_: now with a screenie :-) http://cniehaus.livejournal.com/43699.html
15:30 egonw_ was already wondering who kde-devel was ;)
15:30 egonw_ oi, ugly indeed :)
15:30 egonw_ seriously... sounds like fun... don't see much use for it yet...
15:30 egonw_ but at least fun...
15:30 egonw_ chemistry at the desktop...
15:31 egonw_ should blog about it, I gues...
15:31 carsten egonw_: no, only semi-ugly!
15:31 carsten ;-)
15:32 carsten egonw_: purpuse:
15:32 carsten a) fun for me
15:32 carsten b) demo Plasma
15:32 carsten c) quick lookup of BODR
15:33 egonw_ ah, dat is inderdaad wel aardig...
15:34 egonw_ sorry...
15:34 egonw_ yeah, that's indeed nice...
15:34 carsten Das ist in der Tat sehr ...
15:34 egonw_ 'aardig' ist schon
15:35 egonw_ in this context at least...
15:37 carsten http://img80.imageshack.us/m​y.php?image=plasmoid2ml6.png
15:37 egonw_ ah, that's much nicer!
15:37 egonw_ that one is brilliant
15:38 egonw_ just put it at 45% degrees !
15:38 egonw_ OK, so how do I install that plasmoid on my desktop?
15:38 carsten egonw_: with plasma you can rotate it to any angle you want
15:38 egonw_ crap... got to reboot into a KDE4 session first then :(
15:38 egonw_ carsten: yeah, I know :)
15:38 carsten egonw_: get kdeedu of trunk and buildsyscoca4
15:38 egonw_ one of my PDFs on my desktop is up side down...
15:38 carsten plasmoidviewer kalzium
15:38 egonw_ totally useful, but nice to impress collegues :)
15:38 egonw_ ummm
15:39 egonw_ totalle useless, I meant ;)
15:39 egonw_ oi, that's too difficult...
15:39 egonw_ aren't there these small plasmoid distribs?
15:39 egonw_ like .tgz's or so, which one can just copy/paste?
15:40 egonw_ too difficult -> have to go home in 20 minutes, and still need to blog FOAF #5
15:40 carsten egonw_: get hot new stuff, yes
15:53 egonw_ http://chem-bla-ics.blogspot.com/2008/03/my​-foaf-network-5-sparql-ing-my-network.html
15:53 egonw_ that's all for today
15:53 egonw_ bye all
15:53 egonw_ rojasm: cu tomorrow
16:29 rojasm left #cdk
16:35 CIA-11 bioclipse: jonalv * r5140 /bioclipse2/trunk/plugins/ (8 files in 5 dirs): further work on refactoring usermanager and it's tests
16:44 carsten joined #cdk
17:33 CIA-11 jmol: nicove * r9163 /trunk/Jmol-FAH/projects/p4425.xyz.gz: Folding@Home
17:56 CIA-11 jmol: nicove * r9164 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
17:58 CIA-11 bioclipse: jonalv * r5141 /bioclipse2/trunk/plugins/ (9 files in 8 dirs): more work on Usermanager and tests.
18:45 egonw joined #cdk
19:15 Annzi left #cdk
19:37 man-di egonw: you pingped me for whatever reason without content and my backlog is not long enough...
19:48 egonw oh, don't remember...
19:52 man-di egonw: --- Day changed Sat Mar 08 2008
19:52 man-di 11:12 #cdk: < egonw> man-di: ping... maybe you know?
19:54 egonw [Sat Mar 8 2008] [11:13:21] <egonw> dleidert: do you know the state of a Jmol package?
19:54 egonw [Sat Mar 8 2008] [11:13:38] <egonw> based on the CDK debian/ dir, I think I can set up something for Jmol...
19:54 egonw my log does go back enough...
19:54 egonw I looked at Jmol...
19:54 egonw but seems to require quite a few libs
19:56 man-di I never looked into jmol myself
19:56 egonw ok, that answers the question
19:56 egonw will look at it soon again...
19:58 egonw ok, going offline now...
19:58 egonw thanx for getting back on the ping...
21:02 CIA-11 bioclipse: rklancer * r5142 /bioclipse2/trunk/plugins/n​et.bioclipse.log4jconfig/: Initial import.
21:04 CIA-11 bioclipse: rklancer * r5143 /bioclipse2/trunk/plugins/​net.bioclipse.log4jconfig/ (5 files in 2 dirs): Initial import. NOW REQUIRED FOR MOST LOGGING TO WORK. Fragment project that puts log4j.properties file in log4j's file search path so log4j can configure itself without intervention.
21:06 CIA-11 bioclipse: rklancer * r5144 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/bioclipse.product: Adds newly created net.bioclipse.log4jconfig fragment to product configuration.
21:16 CIA-11 bioclipse: rklancer * r5145 /bioclipse2/trunk/plugins/net.bioclipse.​ui/src/net/bioclipse/ui/Activator.java: Updated to reflect new fragment project method of logging configuration. Used better method for Spring extender startup.
21:37 dleidert joined #cdk
21:44 dleidert left #cdk
22:04 CIA-11 bioclipse: rklancer * r5146 /bioclipse2/trunk/plugins/​net.bioclipse.log4jconfig/ (6 files in 2 dirs):
22:30 CIA-11 bioclipse: rklancer * r5147 /bioclipse2/trunk/plugins/​net.bioclipse.log4jconfig/ (5 files in 2 dirs): Spelling errors.
22:30 CIA-11 jmol: hansonr * r9165 /trunk/Jmol/src/org/jmol/ (5 files in 5 dirs): 11.5.20 # bug fix: zap file > 2 multiple models do not properly delete
22:45 CIA-11 jmol: hansonr * r9166 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.5.20 version
22:54 CIA-11 jmol: hansonr * r9167 /trunk/Jmol/src/org/jmol/mo​delsetbio/BioPolymer.java: DEBUG COMMENT OUT
23:08 CIA-11 jmol: nicove * r9168 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary