Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-01-31

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All times shown according to UTC.

Time Nick Message
07:32 rojasm joined #bioclipse
07:35 viklund joined #bioclipse
08:30 Annzi joined #bioclipse
08:47 egonw_ joined #bioclipse
08:53 EskilA joined #bioclipse
09:05 masak joined #bioclipse
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09:13 olas joined #bioclipse
09:26 CIA-21 bioclipse: ospjuth * r4852 /branches/bioclipse2/core/plugins/net.bioclipse.c​ore/src/net/bioclipse/core/domain/IMolecule.java: Added IMolecule to core
09:50 CIA-21 bioclipse: ospjuth * r4853 /branches/bioclipse2/chemoinforma​tics/net.bioclipse.cdk.business/: Initial import of CDK business plugin.
09:50 CIA-21 bioclipse: ospjuth * r4854 /branches/bioclipse2/chemoinforma​tics/net.bioclipse.cdk.business/ (21 files in 9 dirs): Initial import of CDK business plugin.
09:51 egonw_ olas: is the reworking of the plugin and dir structures finsihed?
09:51 CIA-21 bioclipse: ospjuth * r4855 /branches/bioclipse2/chemoinformatic​s/net.bioclipse.cdk.business.test/: Initial import of CDK business test plugin.
09:51 viklund joined #bioclipse
09:52 CIA-21 bioclipse: ospjuth * r4856 /branches/bioclipse2/chemoinformati​cs/net.bioclipse.cdk.business.test/ (18 files in 9 dirs): Initial import of CDK business test plugin.
10:01 CIA-21 bioclipse: carl_masak * r4857 /trunk/playground/plugins/net.biocl​ipse.base2/src/net/bioclipse/base2/ (5 files in 2 dirs):
10:01 CIA-21 bioclipse: [Database -> DatabaseImplementation]
10:01 CIA-21 bioclipse: * even in different packages, synonymous class names
10:01 CIA-21 bioclipse:  was a bit too cumbersome
10:01 CIA-21 bioclipse: * note to the Java design people: qualified imports would be nice
10:06 EskilA_ joined #bioclipse
10:10 egonw_ he, guys in Uppsala... you're alright?
10:11 Annz1 :)
10:12 masak just a slight diversion
10:14 jonalv egonw_, we just had some fun in #farmbio (were we use swedish)
10:36 de_maas joined #bioclipse
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10:50 CIA-21 bioclipse: carl_masak * r4858 /trunk/playground/plugins/net.biocl​ipse.base2/src/net/bioclipse/base2/ (5 files in 3 dirs):
10:50 CIA-21 bioclipse: [Base2Database.java]
10:50 CIA-21 bioclipse: [MockDatabase.java]
10:50 CIA-21 bioclipse: * simplified constructor parameters
10:50 CIA-21 bioclipse: [DatabaseImplementation.java]
10:50 CIA-21 bioclipse: * new method getName()
11:16 edrin joined #bioclipse
11:23 steinbeck joined #bioclipse
12:14 EskilA_ joined #bioclipse
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13:59 de_maas joined #bioclipse
14:11 CIA-21 bioclipse: ospjuth * r4859 /branches/bioclipse2/chemoinformatics/net.bi​oclipse.cdk.business/src/net/bioclipse/cdk/ (5 files in 2 dirs): Loading of multiple molecules is now possible, also createMoleculeFromSMILES.
14:14 CIA-21 bioclipse: ospjuth * r4861 /branches/bioclipse2/chemoinformatics/n​et.bioclipse.cdk/META-INF/MANIFEST.MF: Added XOM jar to manifest to get cdk to compile in Eclipse.
14:14 CIA-21 bioclipse: ospjuth * r4862 /branches/bioclipse2/chemoinformatics/n​et.bioclipse.cdk.business/src/net/biocl​ipse/cdk/domain/CDKMoleculeList.java: Updated CDKMoleculeList to extend BioObjectList<IMolecule>
14:14 CIA-21 bioclipse: ospjuth * r4863 /branches/bioclipse2/core/plugins/net.bioclipse.c​ore/src/net/bioclipse/core/domain/IMolecule.java: Updated IMolecule with createSMILES()
14:36 jonalv olas I though we agreed that CDKMoleculeList should not extend BioObjectList<IMolecule>. HAve we changed our mind now?
14:37 jonalv I thought we didn't need a CDKMoleculeList at all...
14:46 CIA-21 bioclipse: ospjuth * r4864 /branches/bioclipse2/core/plugins/n​et.bioclipse.core/src/net/bioclipse​/recording/WrapInProxyAdvice.java: Removed unnecessary @override
15:23 egonw_ [2008-01-31 15:16:58] <CIA-18> bioclipse: ospjuth * r4861 /branches/bioclipse2/chemoinformatics/n​et.bioclipse.cdk/META-INF/MANIFEST.MF: Added XOM jar to manifest to get cdk to compile in Eclipse
15:23 egonw_ olas: that's what net.bioclipse.xom is for
15:24 egonw_ the lib is used by net.bioclipse.cml too
15:26 egonw_ olas: btw, I'm back... but I guess your worked that out by now :)
15:47 jonalv egonw_, doesn't net.bioclipse.cml depend on net.bioclipse.cdk?
15:50 egonw_ should not
15:50 egonw_ net.bioclipse.cml was just the lib
15:50 egonw_ CML is not just for molecules
15:50 egonw_ but spectra too
15:50 jonalv okey
15:50 jonalv I see
15:50 jonalv I just wondered why it was in a plugin of it's own
15:50 jonalv just curious... :)
15:50 egonw_ check the deps...
15:51 egonw_ can't remember the fine prints
15:51 jonalv I haven't got it checked out so it was faster to ask you :) sry
15:51 jonalv I was running booring DAO tests for Brunn
15:52 jonalv But I wonder whether olas saw you comment...
16:00 CIA-21 bioclipse: ospjuth * r4865 /branches/bioclipse2/chemoinformatics/​net.bioclipse.cdk.business/src/net/bio​clipse/cdk/business/CDKManager.java: Cleanup of javadoc.
16:01 CIA-21 bioclipse: ospjuth * r4866 /branches/bioclipse2/misc/net.bioclipse.data​.sampledata/src/net/bioclipse/data/sampledat​a/wizards/NewSampleDataProjectWizard.java: Fixed so that folders only gets installed when checked.
16:02 egonw_ olas: I'll have to leave in about 30 minutes... do you still like to chat?
16:03 olas welll..
16:03 olas just had some quick questions
16:03 olas please explain this:
16:03 olas How can an IMolecule have several AtomContainers?
16:03 egonw_ it can't
16:03 egonw_ and doens't
16:03 olas ok, good
16:04 egonw_ there is IMoleculeSet too...
16:04 olas yes, I know
16:04 olas just wondered
16:04 egonw_ and IChemFile, which may contain anything
16:04 olas yes
16:04 olas well, I don't think I can ask more questions now, let's take trhem later
16:05 olas gotta commit and then go down to Annzi
16:05 olas and then go to bandy practice
16:05 jonalv take it easy with the noose
16:05 CIA-21 bioclipse: ospjuth * r4867 /branches/bioclipse2/bioinformatics/plugins/n​et.bioclipse.biojava.ui/src/net/bioclipse/bio​java/ui/views/SequenceContentProvider.java: Some code cleanup.
16:06 CIA-21 bioclipse: ospjuth * r4868 /branches/bioclipse2/bioinformatics/plugins/net​.bioclipse.biojava.ui.test/src/net/bioclipse/bi​ojava/ui/test/SequenceContentProviderTest.java: Some more documentation in tests.
16:07 CIA-21 bioclipse: ospjuth * r4869 /branches/bioclipse2/chemoinfo​rmatics/net.bioclipse.cdk.ui/ (6 files in 5 dirs): Updated contentprovider and labelprovider to use and parse into IMolecule.
16:07 jonalv This one is so good: <http://d.yimg.com/us.yimg.com/​p/uc/20080129/ltmcm080129.gif>
16:08 CIA-21 bioclipse: ospjuth * r4870 /branches/bioclipse2/chemoinforma​tics/net.bioclipse.cdk.ui.tests/: Initial import. Tests for CDK UI. Currently tests MoleculeContentProvider.
16:08 CIA-21 bioclipse: ospjuth * r4871 /branches/bioclipse2/chemoinforma​tics/net.bioclipse.cdk.ui.tests/ (21 files in 9 dirs): Initial import. Tests for CDK UI. Currently tests MoleculeContentProvider.
16:27 edrin olas: what is bady practice?
16:37 edrin bandy  practice
16:40 jonalv edrin: <http://en.wikipedia.org/wiki/Bandy>
16:41 edrin ah
16:41 olas http://www.helenelund-bandy.nu/show​Content.asp?type=page&amp;pageID=7
16:41 de_maas left #bioclipse
16:42 olas left #bioclipse
16:46 CIA-21 bioclipse: carl_masak * r4872 /trunk/playground/plugins/net.biocl​ipse.base2/src/net/bioclipse/base2/ (5 files in 2 dirs): * CDF files are now shown alongside other files under a RawBioAssay
16:48 CIA-21 bioclipse: Annzi * r4873 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.moss/ (11 files in 4 dirs): Are now able to read molecules from input file and able to set basic parameters
16:49 Annzi left #bioclipse
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18:11 Annzi left #bioclipse
20:28 edrin left #bioclipse

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