| Time |
Nick |
Message |
| 07:32 |
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rojasm joined #bioclipse |
| 07:35 |
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viklund joined #bioclipse |
| 08:30 |
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Annzi joined #bioclipse |
| 08:47 |
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| 08:53 |
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EskilA joined #bioclipse |
| 09:05 |
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masak joined #bioclipse |
| 09:05 |
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jonalv joined #bioclipse |
| 09:13 |
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olas joined #bioclipse |
| 09:26 |
CIA-21 |
bioclipse: ospjuth * r4852 /branches/bioclipse2/core/plugins/net.bioclipse.core/src/net/bioclipse/core/domain/IMolecule.java: Added IMolecule to core |
| 09:50 |
CIA-21 |
bioclipse: ospjuth * r4853 /branches/bioclipse2/chemoinformatics/net.bioclipse.cdk.business/: Initial import of CDK business plugin. |
| 09:50 |
CIA-21 |
bioclipse: ospjuth * r4854 /branches/bioclipse2/chemoinformatics/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/chemoinformatics/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/chemoinformatics/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.bioclipse.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 |
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| 10:37 |
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de_maas left #bioclipse |
| 10:50 |
CIA-21 |
bioclipse: carl_masak * r4858 /trunk/playground/plugins/net.bioclipse.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 |
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steinbeck joined #bioclipse |
| 12:14 |
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EskilA_ joined #bioclipse |
| 13:14 |
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EskilA joined #bioclipse |
| 13:59 |
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de_maas joined #bioclipse |
| 14:11 |
CIA-21 |
bioclipse: ospjuth * r4859 /branches/bioclipse2/chemoinformatics/net.bioclipse.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/net.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/net.bioclipse.cdk.business/src/net/bioclipse/cdk/domain/CDKMoleculeList.java: Updated CDKMoleculeList to extend BioObjectList<IMolecule> |
| 14:14 |
CIA-21 |
bioclipse: ospjuth * r4863 /branches/bioclipse2/core/plugins/net.bioclipse.core/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/net.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/net.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/bioclipse/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/sampledata/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/net.bioclipse.biojava.ui/src/net/bioclipse/biojava/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/biojava/ui/test/SequenceContentProviderTest.java: Some more documentation in tests. |
| 16:07 |
CIA-21 |
bioclipse: ospjuth * r4869 /branches/bioclipse2/chemoinformatics/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/chemoinformatics/net.bioclipse.cdk.ui.tests/: Initial import. Tests for CDK UI. Currently tests MoleculeContentProvider. |
| 16:08 |
CIA-21 |
bioclipse: ospjuth * r4871 /branches/bioclipse2/chemoinformatics/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/showContent.asp?type=page&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.bioclipse.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/chemoinformatics/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 |
| 17:37 |
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Annzi joined #bioclipse |
| 18:11 |
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Annzi left #bioclipse |
| 20:28 |
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edrin left #bioclipse |
