Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-05-09

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All times shown according to UTC.

Time Nick Message
06:16 malick joined #bioclipse
07:21 olas joined #bioclipse
07:49 CIA-45 bioclipse: ospjuth * r5604 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.​jchempaint/src/net/bioclipse/cdk10/jchempaint/​ui/editor/JCPMultiPageEditorContributor.java:
07:49 CIA-45 bioclipse: Workaround for a ClassCastException that tried to add ICDKChangeListener to the
07:49 CIA-45 bioclipse: IJCPBasedEditor and not to the JCPPAge of it. Occurs if Bioclipse is started
07:49 CIA-45 bioclipse: with an IJCPBasedEditor already open. Placed FIXME in
07:49 CIA-45 bioclipse: JCPMultiPageEditorContributor.
07:55 jonalv joined #bioclipse
08:15 rojasm joined #bioclipse
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09:53 EskilA joined #bioclipse
10:12 malick http://bioconductor.org/pack​ages/2.3/bioc/html/xcms.html
10:32 CIA-45 bioclipse: jonalv * r5605 /bioclipse2/trunk/plugins/ (5 files in 4 dirs): Structuredb instances now survives restart of Bioclipse correctly and can not only be created but also deleted
10:38 olas joined #bioclipse
10:55 CIA-45 bioclipse: ospjuth * r5606 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10.jchempaint/src/net/bio​clipse/cdk10/jchempaint/ui/editor/ (4 files): Updated for getting Coloring to work. Added rePaint() in JCPPage, placed TODO:verify for egonw in stateChanged(...).
11:44 CIA-45 bioclipse: ospjuth * r5607 /bioclipse2/trunk/plugins/net.bioclipse.cd​k10.jchempaint/src/net/bioclipse/cdk10/jch​empaint/ui/editor/MDLMolfileEditor.java: Added EDITOR_ID to class.
13:32 malick joined #bioclipse
13:40 CIA-45 bioclipse: carl_masak * r5608 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java):
13:40 CIA-45 bioclipse: [ICDKManager, CDKManager]
13:40 CIA-45 bioclipse: * name change: createMoleculeFromSMILES -> moleculeFromSmiles
13:40 CIA-45 bioclipse: * whitespace and line length
14:04 ilogger2 joined #bioclipse
14:05 CIA-45 bioclipse: carl_masak * r5609 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java:
14:05 CIA-45 bioclipse: [CDKManagerTest]
14:05 CIA-45 bioclipse: * chased name change: createMoleculeFromSMILES -> moleculeFromSmiles
14:16 olas left #bioclipse
14:27 CIA-45 bioclipse: ospjuth * r5610 /bioclipse2/trunk/plugins/ (11 files in 6 dirs): Working on getting DC on entries in StructureTable open in JCP.
14:45 masak I'm thinking it might be good to write things down
14:45 masak then it'll be logged
14:45 masak and posterity will know what we were thinking :)
14:45 masak a bit like an on-line meeting with an automated secretary
14:46 masak anyway...
14:46 jonalv right
14:47 masak I think that 'retrieveAllStructures', 'retrieveAllFolders' and 'retrieveAllUsers' could be named 'allStructures', 'folders' and 'users' respectively
14:47 masak also, the names of 'createStructure' and 'createUser' do not tell the wholse story
14:47 masak s/wholse/whole/
14:47 jonalv so what are you suggesting we call them instead?
14:48 masak I think they do something more like 'persistStructure'
14:48 masak or at least 'saveStructure'
14:48 jonalv uhm hm not really
14:48 masak no?
14:48 masak the documentation says this: "Creates a structure with the given name from the given cdkmolecule and
14:48 masak * persists it in the database with the given name"
14:49 masak the important step, by me, is not the creating (which CDK and others can do), but the persisting
14:49 jonalv exactly so that name wouldn't be the complete story either only
14:49 jonalv Uhm I disagree
14:49 jonalv I think the persisting is not the important thing but the creation
14:50 masak oki
14:50 jonalv anything that is created in strucutredb is of course persisted
14:50 masak you're right
14:50 masak but I stand by my first suggestion
14:50 jonalv no retrieve?
14:51 masak no retrieve, and in the cases of 'folders' and 'users', no 'all' either
14:51 jonalv there are points in naming methods that does similar things similarly
14:51 masak yes
14:51 masak hm
14:52 masak so maybe 'structures', 'folders', 'users' then
14:52 masak no, on second thought, keep 'all' on those
14:52 masak it's good to know which ones we're getting
14:52 jonalv allStructures, allFolders and allUSers?
14:53 masak yes
14:53 jonalv that sounds good
14:53 masak \o/
14:55 malick left #bioclipse
15:00 CIA-45 bioclipse: jonalv * r5611 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): added cdk.containsSubstructure
15:31 egonw joined #bioclipse
15:41 CIA-45 bioclipse: jonalv * r5612 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Renamed a few methods for structuredb. Hopes this makes things even better :)
15:49 masak jonalv++
15:56 jonalv joined #bioclipse
16:09 CIA-45 bioclipse: jonalv * r5613 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Created test for substructure-search in structuredb
18:20 egonw joined #bioclipse
19:18 egonw_ joined #bioclipse
20:24 rojasm joined #bioclipse
20:49 rojasm joined #bioclipse

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