Camelia, the Perl 6 bug

IRC log for #cdk, 2007-11-19

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All times shown according to UTC.

Time Nick Message
05:57 jbrefort joined #cdk
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07:10 rojasm joined #cdk
08:06 CIA-16 cdk: miguelrojasch * r9460 /branches/miguelrojasch/mf/src​/org/openscience/cdk/formula/ (5 files): added JavaDoc documentation
08:08 thomas_ku joined #cdk
08:09 thomas_ku moin
08:23 rojasm moin thomas_ku
08:43 rojas1 joined #cdk
09:03 jpansanel moin
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09:28 rojasm joined #cdk
09:30 egonw koffietijd
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09:50 CIA-16 bioclipse: ospjuth * r4259 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (META-INF/MANIFEST.MF plugin.xml): Use TabbedProperies. Standard layout so far.
10:37 CIA-16 bioclipse: ospjuth * r4260 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.cdk/: Initial import of new CDK plugin for Bioclipse2 hierarchy.
10:38 CIA-16 bioclipse: ospjuth * r4261 /branches/bioclipse2/chemoin​formatics/net.bioclipse.cdk/ (15 files in 9 dirs): Initial import of new CDK plugin for Bioclipse2 hierarchy.
11:02 egonw rojasm: http://metabolomicsinnl.blogspot.com/
11:16 rojasm egonw: interesant!
11:17 rojasm Are you the responsible?
11:18 egonw for that symposium: no
11:18 egonw for the blog: yes
11:18 rojasm ohh
11:19 rojasm ich will transmit for other people!!
11:22 egonw rojasm: ask Theo if he thinks that vacancy he told me about would be suitable for posting it on there as well...
11:25 rojasm ok
11:38 CIA-16 bioclipse: ospjuth * r4262 /branches/bioclipse2/core/plugins/ne​t.bioclipse.ui/src/net/bioclipse/ui/ (3 files in 2 dirs): Refactored workbenchadvisory hack to correct package
12:04 CIA-16 bioclipse: egonw * r4263 /branches/bioclipse2/chemoinfor​matics/net.bioclipse.cdk/jars/: Removed jars to make place for svn:externals
12:07 CIA-16 bioclipse: egonw * r4264 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.cdk/: Get the 3rd party jars from the CDK repos
12:12 CIA-16 bioclipse: egonw * r4265 /branches/bioclipse2/chemoinfor​matics/net.bioclipse.cdk/src/: Get the CDK source directly from the CDK repos
12:22 CIA-16 bioclipse: jonalv * r4266 /branches/bioclipse2/core/plugins/ (net.bioclipse.spring/ spring/):
12:41 Conrad joined #cdk
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12:50 rojasm egonw: make sense to put in MolecularFormula and others extends from ChemObject. It is about setProperties
12:51 CIA-16 bioclipse: carl_masak * r4267 /branches/bioclipse2/core/p​lugins/net.bioclipse.core/ (6 files in 4 dirs):
12:51 CIA-16 bioclipse: [net.bioclipse.core]
12:51 CIA-16 bioclipse: * Added rudimentary js console
12:51 CIA-16 bioclipse: * Window -> Show View -> Scripting -> Javascript Console
12:51 CIA-16 bioclipse: * At present, Java bindings don't work (as they do in bc1)
12:57 egonw rojasm: why do you need setProperties() ?
13:00 rojasm To put for example if it is a validated formula
13:01 rojasm to be possible to iniziate a new instance of ISotope
13:01 rojasm or do you think it is not the correct way
13:02 rojasm I am thinking if IMolecularFormula is able to add isotope that means that it self is also a chemobject
13:04 rojasm egown: I commented Theo you message He will write you he said!
13:05 rojasm Nice Blog apropo
13:13 CIA-16 bioclipse: jonalv * r4268 /branches/bioclipse2/bioinformatics/plugins/ (15 files in 8 dirs): Some work on incorporating biojava.
13:22 rojasm egonw: what do you think?
13:26 egonw mmm... IIsotope is more like a concept, and an instance...
13:29 rojasm so for you not good idea to extends the MolecularFormula and other to chemObject
13:30 egonw correct
13:30 egonw to much overload
13:30 egonw what do you mean with a 'validated formula' ?
13:30 egonw why would you like to flag it as such?
13:31 CIA-16 bioclipse: egonw * r4269 /branches/bioclipse2/chemoin​formatics/net.bioclipse.cdk/ (.classpath META-INF/MANIFEST.MF): Tuned classpath
13:32 rojasm You can create a molecularFormula. But according differents restrictions can be correct or not
13:33 rojasm with properties I thought I could put for what rules ist valid and what not
13:39 egonw OK
13:40 egonw I guess that is useful enough to put in as field...
13:40 CIA-16 bioclipse: ospjuth * r4270 /branches/bioclipse2/core/pl​ugins/net.bioclipse.logging/ (6 files in 2 dirs): Included logging capabilities.
13:40 egonw what about adding a set/isValidated() field...
13:41 egonw where addIsotope() etc will set it to false again...
13:41 CIA-16 bioclipse: ospjuth * r4271 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (4 files in 3 dirs): Added logging and made a BioclipseActivator to use as base class Activator for all Bioclipse plugins.
13:44 rojasm mmm. I think that validated is not a good method in MolecularFormula because you must not create a valid MolecularFormula. It should be the job of MFValid for example.
13:45 rojasm I am thinking how Atomcontainer has the methods
13:45 rojasm And MFValid should put as properties if it is valid and for what rules is valid or not
13:52 egonw rojasm: you can also subclass the thingy...
13:52 egonw make a sub interface...
13:52 egonw and have MFValidator return that instead of the original...
13:53 egonw then, anyone can do a '? instanceof IValidMolecularFormula' to see if it is valid or not
14:01 rojasm ok
14:03 rojasm and what about clonable and functionallity?
14:03 rojasm -and
14:03 CIA-16 bioclipse: ospjuth * r4272 /branches/bioclipse2/chemoin​formatics/net.bioclipse.cdk/ (.classpath META-INF/MANIFEST.MF build.properties): Export jars
14:05 egonw clonable comes from the Clonable interface...
14:07 CIA-16 bioclipse: egonw * r4273 /branches/bioclipse2/chemoin​formatics/net.bioclipse.cdk/ (.classpath META-INF/MANIFEST.MF build.properties): Reverted Ola's way too greedy patch
14:07 CIA-16 bioclipse: carl_masak * r4274 /branches/bioclipse2/core/p​lugins/net.bioclipse.core/ (6 files in 3 dirs):
14:07 CIA-16 bioclipse: [net.bioclipse.core]
14:07 CIA-16 bioclipse: * added extension capabilities to scripting system
14:10 CIA-16 bioclipse: egonw * r4275 /branches/bioclipse2/chemoin​formatics/net.bioclipse.cdk/ (META-INF/MANIFEST.MF build.properties): Export what should be exported, and nothing more
14:13 rojasm I mean if it makes sense to extends the MolecularFormula to Clonable
14:13 rojasm not extends but implements sorry
14:16 CIA-16 bioclipse: ospjuth * r4276 /branches/bioclipse2/chemoinfo​rmatics/net.bioclipse.cdk.ui/: Initial import.
14:17 egonw there is already add(IMF)
14:18 egonw which basically does the same as clone
14:19 rojasm ok, perfect
14:20 rojasm should the package formula in a new module @cdk.module formula?
14:32 egonw yeah, sounds reasonable...
14:37 CIA-16 cdk: miguelrojasch * r9462 /branches/miguelrojasch/mf/src​/org/openscience/cdk/formula/ (5 files): added @cdk.module formula. Not implimented in build.xml yet
14:37 CIA-16 bioclipse: ospjuth * r4280 /branches/bioclipse2/chemoinfo​rmatics/net.bioclipse.cdk.ui/ (172 files in 21 dirs): Initial import.
14:41 CIA-16 bioclipse: jonalv * r4281 /branches/bioclipse2/core/p​lugins/net.bioclipse.core/ (5 files in 5 dirs): Extensionpoint for aplicationcontext.xml files
14:54 CIA-16 bioclipse: ospjuth * r4282 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (META-INF/MANIFEST.MF src/net/bioclipse/ui/Perspective.java): Added javascript console to default perspective
14:54 CIA-16 bioclipse: carl_masak * r4283 /trunk/plugins/net.bioclips​e.rhino/src/net/bioclipse/ (3 files in 2 dirs):
14:54 CIA-16 bioclipse: [net.bioclipse.plugins.bc_rh​ino.views.RhinoConsoleView]
14:54 CIA-16 bioclipse: [net.bioclipse.views.ScriptingConsoleView]
14:54 CIA-16 bioclipse: * separated scripting console from js
14:54 CIA-16 bioclipse: * this is Very Good(TM) for future console use
14:57 thomas_ku joined #cdk
15:00 CIA-16 bioclipse: egonw * r4284 /trunk/plugins/net.bioclipse.spectr​um.mzdata/src/net/bioclipse/plugins​/extensions/MZDataConvertor.java: Added missing license/copyright statement.
15:06 CIA-16 bioclipse: carl_masak * r4285 /branches/bioclipse2/core/plugins/net.bio​clipse.core/src/net/bioclipse/core/views/ (RhinoConsoleView.java ScriptingConsoleView.java):
15:06 CIA-16 bioclipse: [net.bioclipse.core.views]
15:06 CIA-16 bioclipse: * separated RhinoConsoleView from ScriptingConsoleView
15:06 CIA-16 bioclipse: * basically a model feature stolen from bc1
15:08 CIA-16 bioclipse: egonw * r4286 /trunk/plugins/net.bioclipse.spectrum/src/​net/bioclipse/model/SpectrumResource.java: Added extra NPE test
15:08 CIA-16 bioclipse: egonw * r4287 /trunk/plugins/net.bioclipse.st​atistics/META-INF/MANIFEST.MF: There are no views
15:14 CIA-16 bioclipse: egonw * r4288 /trunk/plugins/de.ipbhalle.msbi.mzdata/.project: Can't find that jpox builder
15:29 CIA-16 bioclipse: ospjuth * r4289 /branches/bioclipse2/core/plugins/ne​t.bioclipse.ui/META-INF/MANIFEST.MF: Added deps
15:48 CIA-16 bioclipse: egonw * r4290 /trunk/plugins/net.bioclipse.spectrum/src/​net/bioclipse/model/SpectrumResource.java: NPE debugging is *impossible* if all exceptions are silently catched and disregarded... I hate any language that allows that
15:49 CIA-16 bioclipse: egonw * r4291 /trunk/plugins/de.ipbhalle.msbi.mzd​ata.editor/src/de/ipbhalle/msbi/Mzd​ata/presentation/MzdataEditor.java: Fixed switching from TextEditor to MzdataEditor
16:06 CIA-16 bioclipse: egonw * r4292 /trunk/plugins/ (5 files in 2 dirs): More NPE debugging, but no trace of the source :(
16:07 rojasm egonw: you said that add(IMF) is the same as clone. But that is not exactly true. Because add is a sum of previously IMF. CH3 + add(CH3) = return C2H6
16:07 egonw sure
16:07 egonw clone() equals new MF().add(oldMF)
16:08 rojasm ok. But I think that is now so clear like oldMF.clone()
16:09 egonw then implement Clonable
16:10 rojasm I ask only. For me is easier because I am working with but if somebody tried to understand maybe it is not too easy
16:18 CIA-16 bioclipse: ospjuth * r4293 /branches/bioclipse2/core/plugins/net.bi​oclipse.ui/src/net/bioclipse/ui/editors/ (14 files in 3 dirs): Added old PDBEditor and KeywordEditor
16:18 CIA-16 bioclipse: ospjuth * r4294 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (3 files in 2 dirs): Got logger working for other plugins as well
16:19 egonw rojasm: I'm fine with adding .clone()
16:19 CIA-16 bioclipse: ospjuth * r4295 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/: Initial import.
16:20 CIA-16 bioclipse: ospjuth * r4296 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/ (19 files in 9 dirs): Initial import. Only dummy editor working so far.
16:47 CIA-16 bioclipse: ospjuth * r4297 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/ (10 files in 4 dirs): Work on a MPE with Jmol on first tab and source on second. Does not work due to errors with CdkJmolAdapter. Egonw: Help!
17:01 CIA-16 cdk: miguelrojasch * r9463 /branches/miguelrojasch/mf/src​/org/openscience/cdk/formula/ (6 files): added clone functionality. Not as superclass of chemObject.
17:02 CIA-16 cdk: miguelrojasch * r9464 /branches/miguelrojasch/mf/src/o​rg/openscience/cdk/test/formula/ (4 files): added test for formula package
17:03 CIA-16 bioclipse: egonw * r4298 /trunk/plugins/de.ipbhalle.msbi.mzd​ata.editor/src/de/ipbhalle/msbi/Mzd​ata/presentation/MzdataEditor.java: OK, getString() is broken, but don't complain about it. As I hate these NPEs, hiding a few more wont hurt :)
17:05 rojasm left #cdk
18:02 rojasm joined #cdk
18:22 CIA-16 bioclipse: jonalv * r4299 /branches/bioclipse2/core/plugi​ns/net.bioclipse.spring.osgi/: Initial import.
18:22 CIA-16 bioclipse: jonalv * r4300 /branches/bioclipse2/core/plug​ins/net.bioclipse.spring.osgi/ (18 files in 10 dirs): Initial import.
18:35 shk3 joined #cdk
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19:21 egonw hi shk3
19:22 egonw hi others
19:35 shk3_ joined #cdk
19:36 egonw hi shk3_
19:38 shk3_ problems with connection
19:40 egonw yeah, noticed :)
19:44 shk3_ thanks for looking at the mzdata stuff
19:44 egonw yeah, I'm reasonably happy with the outcome...
19:44 egonw the plugin is working again...
19:44 shk3_ I will forward you message to steffen just to make him aware of the problem
19:44 egonw OK
19:44 egonw I will further discuss it with him...
19:45 egonw BC2 will be able to use true Eclipse plugins...
19:45 egonw basically making your work obsolete...
19:45 egonw that is...
19:45 egonw given that the code *is* upgraded for EMF 2.3
20:03 egonw bye all
22:54 rojasm left #cdk

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