Camelia, the Perl 6 bug

IRC log for #cdk, 2008-04-28

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All times shown according to UTC.

Time Nick Message
02:54 CIA-30 jmol: hansonr * r9327 /trunk/Jmol/test/org/jmol/adapter/s​marter/TestSmarterJmolAdapter.java: TestSmarter fix
02:55 CIA-30 jmol: hansonr * r9328 /trunk/Jmol/test/org/jmol/adapter/s​marter/TestSmarterJmolAdapter.java: TestSmarter fix
03:12 CIA-30 jmol: hansonr * r9329 /trunk/Jmol/src/org/jmol/ (7 files in 4 dirs): (log message trimmed)
03:12 CIA-30 jmol: version=11.5.32
03:12 CIA-30 jmol: # new feature: isosurface ELLIPSOID id
03:12 CIA-30 jmol: # AXES {ix iy iz} {jx jy jz} {kx ky kz}
03:12 CIA-30 jmol: # CENTER {x y z}
03:12 CIA-30 jmol: # SCALE n.m
03:12 CIA-30 jmol: # COLOR [translucent [x.y] |opaque] [color]
05:03 egonw joined #cdk
05:27 jbrefort joined #cdk
05:58 CIA-30 bioclipse: egonw * r5496 /bioclipse2/trunk/plugins/net.bioclipse.cdk/ (.classpath META-INF/MANIFEST.MF): Synched dir name (jars -> jar), to make life easier with a git checkout, where svn:imports is not automatically used, and I have to do a manual svn co
05:58 CIA-30 bioclipse: egonw * r5497 /bioclipse2/trunk/plugins/net.bio​clipse.core/META-INF/MANIFEST.MF: Made plugin 'singleton', which is required by Eclipse3.4 (please email if this gives trouble in 3.3)
05:58 CIA-30 bioclipse: egonw * r5498 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10/.classpath: Fixed CP problems
05:58 CIA-30 bioclipse: egonw * r5499 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10/.classpath: Reordering.
05:59 CIA-30 bioclipse: egonw * r5500 /bioclipse2/trunk/plugins/net.bioclipse.cd​k10.jchempaint/src/net/bioclipse/cdk10/jch​empaint/ui/editor/MDLMolfileEditor.java: Added class JavaDoc
06:15 carsten joined #cdk
07:19 CIA-30 jmol: hansonr * r9330 /trunk/Jmol/src/org/jmol/ (6 files in 3 dirs): (log message trimmed)
07:19 CIA-30 jmol: version=11.5.32
07:19 CIA-30 jmol: # new feature: load [file info] FILTER "[filter string]"
07:19 CIA-30 jmol: # new feature: load [file info] FILTER "BIOMOLECULE n"
07:19 CIA-30 jmol: # new feature: load [file info] FILTER "BIOMOLECULE n;APPLY SYMMETRY"
07:19 CIA-30 jmol: # new feature: load [file info] FILTER "[filter string];BIOMOLECULE n"
07:19 CIA-30 jmol: #
07:21 CIA-30 jmol: hansonr * r9331 /trunk/Jmol/src/org/jmol/adapter​/readers/cifpdb/PdbReader.java: (log message trimmed)
07:21 CIA-30 jmol: version=11.5.32
07:21 CIA-30 jmol: # new feature: load [file info] FILTER "[filter string]"
07:21 CIA-30 jmol: # new feature: load [file info] FILTER "BIOMOLECULE n"
07:21 CIA-30 jmol: # new feature: load [file info] FILTER "BIOMOLECULE n;APPLY SYMMETRY"
07:21 CIA-30 jmol: # new feature: load [file info] FILTER "[filter string];BIOMOLECULE n"
07:21 CIA-30 jmol: #
07:22 CIA-30 bioclipse: egonw * r5501 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10.jchempaint/src/net/bio​clipse/cdk10/jchempaint/ui/editor/ (4 files): Copied in some code snippets from BC1; now about to merge JCPEditor bits...
07:32 rojasm joined #cdk
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07:50 CIA-30 bioclipse: egonw * r5502 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10.jchempaint/src/net/bio​clipse/cdk10/jchempaint/ui/editor/ (4 files): OK, this should show up a JCP editor... not tested.. actually, I don't think the data->editor link is set up yet
08:07 CIA-30 bioclipse: egonw * r5503 /bioclipse2/trunk/plugins/net.bioclipse.cdk10/: Fixed this externals
08:11 CIA-30 bioclipse: egonw * r5504 /bioclipse2/trunk/plugins/net.bioclipse.cdk/: Fixed this externals
08:15 CIA-30 bioclipse: ospjuth * r5505 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10/META-INF/MANIFEST.MF: Added jars to manifest.
08:22 CIA-30 jmol: hansonr * r9332 /trunk/Jmol/src/org/jmol/ (6 files in 4 dirs):
08:22 CIA-30 jmol: 11.5.32 VERSION -- load FILTER
08:22 CIA-30 jmol: # application only: command undo disabled automatically if saving takes more than one second
08:22 CIA-30 jmol: # flag is "set undo TRUE/FALSE"
08:22 CIA-30 jmol: #
08:22 CIA-30 bioclipse: ospjuth * r5506 /bioclipse2/trunk/plugins/net.bioclipse.cdk10/ (META-INF/MANIFEST.MF build.properties): Exported vecmath but still does not work.
08:22 CIA-30 jmol: hansonr * r9333 /trunk/Jmol/src/org/openscienc​e/jmol/app/ScriptWindow.java:
08:22 CIA-30 jmol: 11.5.32 VERSION -- load FILTER
08:22 CIA-30 jmol: # application only: command undo disabled automatically if saving takes more than one second
08:22 CIA-30 jmol: # flag is "set undo TRUE/FALSE"
08:22 CIA-30 jmol: #
08:31 CIA-30 bioclipse: jonalv * r5507 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10/.classpath: updated classpath. jchempaint compiles for me after this
08:31 CIA-30 bioclipse: ospjuth * r5508 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.jchempaint/src/net/bioclipse/cdk​10/jchempaint/ui/editor/JCPPage.java: Added file accessing, placed FIXME for egonw to continue parsing stream into JCPModel.
08:41 CIA-30 bioclipse: egonw * r5509 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10/META-INF/MANIFEST.MF: Export the root CDK java package too
08:56 egonw joined #cdk
09:01 CIA-30 bioclipse: egonw * r5510 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.jchempaint/src/net/bioclipse/cdk​10/jchempaint/ui/editor/JCPPage.java: Basic JCP online; not sure it even edits yet, but display works: http://chem-bla-ics.blogspot.com/200​8/04/jchempaint-for-bioclipse2.html
09:04 CIA-30 bioclipse: ospjuth * r5511 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.ui/src/net/bioclipse/cdk/ui/editors/sdf/ (4 files): The SDFEditor now displays the parsed SDF file as SMILES. Will continue to update using StructureWidget.
09:12 CIA-30 bioclipse: jonalv * r5512 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/src​/net/bioclipse/cdk/ui/editors/sdf/SDFEditor.java: Stay within the 80 cols marginal
09:15 thomas_ku joined #cdk
09:15 thomas_ku moin
09:22 malick joined #cdk
09:33 CIA-30 bioclipse: egonw * r5513 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.jchempaint/src/net/bioclipse/cdk​10/jchempaint/ui/editor/JCPPage.java: Some cleanup, and implementation of other methods (by C/P from BC1 code)
09:33 CIA-30 bioclipse: egonw * r5514 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.jchempaint/src/net/bioclipse/cdk​10/jchempaint/ui/editor/JCPPage.java: Fixed copyright information
09:33 CIA-30 bioclipse: egonw * r5515 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.jchempaint/src/net/bioclipse/cdk​10/jchempaint/ui/editor/JCPPage.java: Fixed half screen mode of JCP tab
09:35 CIA-30 bioclipse: jonalv * r5516 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): Wrote failing test for createMoleculeIterator in cdk manager
10:19 steinbeck joined #cdk
11:34 jpansanel moin
11:40 CIA-30 bioclipse: ospjuth * r5517 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.ui/src/net/bioclipse/cdk/ui/editors/sdf/ (7 files): The SDFEditor now displays the structure inline the table. Really fast with the SWT.VIRTUAL option set! Double-click an SDFile to test.
11:53 CIA-30 bioclipse: jonalv * r5518 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Wrote some logging in structuredb and it's tests
11:55 egonw joined #cdk
12:04 CIA-30 cdk: miguelrojasch * r10690 /cdk/branches/miguelrojasch-CMLReact/src/main/org/​openscience/cdk/dict/data/reaction-processes.owl: added dependences process reactions with mechanisms in the owl
12:09 steinbeck joined #cdk
12:12 jpansanel moin steinbeck
12:12 steinbeck moin
12:12 CIA-30 bioclipse: jonalv * r5519 /bioclipse2/trunk/plugins/net.bioclipse​.structuredb/src/net/bioclipse/structur​edb/business/StructuredbManager.java:
12:12 CIA-30 bioclipse: minor details
12:12 CIA-30 bioclipse: switched to unsopprtedoperationexception and added a few whitespaces in log message
12:29 steinbeck_ joined #cdk
12:34 egonw joined #cdk
12:45 CIA-30 bioclipse: egonw * r5520 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Added support for reading SDF
12:46 CIA-30 bioclipse: ospjuth * r5521 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.ui/src/net/bioclipse/cdk/ui/editors/sdf/ (4 files): Set init size to 100x100. Display name if exists.
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13:19 carsten joined #cdk
13:26 CIA-30 cdk: thomaskuhn * r10691 /cdk-taverna/trunk/src/main/java/org/openscience​/cdk/applications/taverna/CDKTavernaConfig.java: Add a database id to the config. This is used to store the database id within each cmlchemfile property
13:40 CIA-30 cdk: thomaskuhn * r10693 /cdk-taverna/trunk/src/main/java/org/o​penscience/cdk/applications/taverna/da​tabase/pgchem/GetMoleculesFromDB.java: Worker for getting the molecules back from the database
13:40 CIA-30 cdk: thomaskuhn * r10694 /cdk-taverna/trunk/src/main/java/org/op​enscience/cdk/applications/taverna/data​base/pgchem/InsertMoleculeIntoDB.java: Change the insert molecules into database worker to use the modified dbconnector
13:41 CIA-30 cdk: thomaskuhn * r10695 /cdk-taverna/trunk/src/main/java/org/ope​nscience/cdk/applications/taverna/databa​se/pgchem/InsertQSARResultsIntoDB.java: Add a worker which stores qsar result in a database table
13:42 CIA-30 cdk: thomaskuhn * r10696 /cdk-taverna/trunk/src/main/java/org/open​science/cdk/applications/taverna/database​/pgchem/IterativeGetMoleculeFromDB.java: Add an iterative molecule reader. The default configuration takes each time 100 molecules from the database
13:42 CIA-30 cdk: thomaskuhn * r10697 /cdk-taverna/trunk/src/main/java/org/opens​cience/cdk/applications/taverna/database/p​gchem/IterativeHasNextMoleculeFromDB.java: Add an iterative molecule reader. The default configuration takes each time 100 molecules from the database
13:42 CIA-30 cdk: thomaskuhn * r10698 /cdk-taverna/trunk/src/main/java/org/opens​cience/cdk/applications/taverna/database/p​gchem/IterativeMoleculeFromDBReader.java: Add an iterative molecule reader. The default configuration takes each time 100 molecules from the database
13:44 CIA-30 cdk: thomaskuhn * r10699 /cdk-taverna/trunk/src/main/java/org/ope​nscience/cdk/applications/taverna/databa​se/pgchem/UpdateQSARResultsIntoDB.java: This worker updates qsar results within the database table. This is needed for cases like the adding a "new" qsar calculation results to the qsar result table
13:44 CIA-30 cdk: thomaskuhn * r10700 /cdk-taverna/trunk/src/main/java/org/opensc​ience/cdk/applications/taverna/database/pgc​hem/action/InsertMoleculeIntoDBAction.java: Change the action for the use of the modified dbconnector
13:45 CIA-30 cdk: thomaskuhn * r10701 /cdk-taverna/trunk/src/main/java/org/o​penscience/cdk/applications/taverna/qs​ar/AbstractMolecularDescriptor.java: Same small error handling changes
13:46 CIA-30 cdk: thomaskuhn * r10702 /cdk-taverna/trunk/src/main/java/org/openscience/c​dk/applications/taverna/qsar/VectorGenerator.java: Change the comment and the copyright year
13:52 CIA-30 cdk: thomaskuhn * r10703 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/​qsar/VectorGeneratorForDBInput.java: Add a vector generator which will be used for inserting the QSAR results into the database
13:54 CIA-30 cdk: thomaskuhn * r10704 /cdk-taverna/trunk/src/main/java/org/open​science/cdk/applications/taverna/qsar/des​criptors/molecular/RuleOfFiveFilter.java: Add a try catch block for this worker like it is already within the other QSAR worker
13:55 CIA-30 cdk: thomaskuhn * r10705 /cdk-taverna/trunk/src/main/java/org/openscie​nce/cdk/applications/taverna/scuflworkers/cdk​/CDKLocalWorkerWithDatabaseConnection.java: Add an interface which is used for the database worker to allow the configuration of the database connection
13:55 CIA-30 cdk: thomaskuhn * r10706 /cdk-taverna/trunk/src/main/java/org​/openscience/cdk/applications/tavern​a/tools/ExtractIDFromMolFile.java: Add an origin to this worker. This origin is used as input and will be piped through.
13:56 CIA-30 cdk: thomaskuhn * r10707 /cdk-taverna/trunk/src/main/resources/ (2 files in 2 dirs): Add the new worker to the configuration
13:56 CIA-30 cdk: thomaskuhn * r10708 /cdk-taverna/trunk/src/test/java/org/ope​nscience/cdk/applications/taverna/databa​se/pgchem/GetMoleculesFromDBTest.java: Add a new unit test for the new worker
13:57 CIA-30 cdk: thomaskuhn * r10709 /cdk-taverna/trunk/src/test/java/org/ope​nscience/cdk/applications/taverna/databa​se/pgchem/InsertMoleculeIntoDBTest.java: Adapt for the modified dbconnector
13:57 CIA-30 cdk: thomaskuhn * r10710 /cdk-taverna/trunk/src/test/java/org/open​science/cdk/applications/taverna/database​/pgchem/InsertQSARResultsIntoDBTest.java: Add a new unit test for the new worker
13:57 CIA-30 cdk: thomaskuhn * r10711 /cdk-taverna/trunk/src/test/java/org/opensc​ience/cdk/applications/taverna/database/pgc​hem/IterativeMoleculeFromDBReaderTest.java: Add a new unit test for the new worker
13:57 CIA-30 cdk: thomaskuhn * r10712 /cdk-taverna/trunk/src/test/java/org/open​science/cdk/applications/taverna/database​/pgchem/UpdateQSARResultsIntoDBTest.java: Add a new unit test for the new worker
13:58 CIA-30 cdk: thomaskuhn * r10713 /cdk-taverna/trunk/src/test/java/or​g/openscience/cdk/applications/tave​rna/qsar/VectorGenerationTest.java: Update the copyright year
13:58 CIA-30 cdk: thomaskuhn * r10714 /cdk-taverna/trunk/src/test/java/org/o​penscience/cdk/applications/taverna/qs​ar/VectorGeneratorForDBInputTest.java: Add a new unit test for the new worker
14:13 CIA-30 bioclipse: ospjuth * r5522 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/ (4 files in 2 dirs): Read and display properties in SDFileEditor.
14:30 CIA-30 bioclipse: jonalv * r5523 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): Work with trying to get multiple databases to work. No success though. This code mostly consists of cleanups and logging.
14:43 CIA-30 bioclipse: jonalv * r5524 /bioclipse2/trunk/plugins/net.bioclips​e.hsqldb.tests/tests/log4j.properties: added log4j.properties
14:49 CIA-30 cdk: rajarshi * r10715 /cdk/trunk/src/main/org/openscienc​e/cdk/qsar/descriptors/molecular/ (LengthOverBreadthDescriptor.java WHIMDescriptor.java): Made exception messages consistent
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16:55 CIA-30 jmol: nicove * r9334 /trunk/Jmol/ (18 files in 5 dirs): Translation: Hungarian (hu)
17:03 CIA-30 bioclipse: egonw * r5525 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.jchempaint/ (17 files in 3 dirs): Ported more stuff from BC1, no idea what it all does, and still no editing functionality... :(
17:36 rojasm joined #cdk
17:44 rojasm left #cdk
18:08 CIA-30 jmol: nicove * r9335 /branches/v11_4/Jmol/ (15 files in 4 dirs): Translation: Hungarian (hu)
18:19 CIA-30 jmol: hansonr * r9336 /trunk/Jmol/src/org/jmol/ (5 files in 4 dirs): pdb reader fix in association with biomolecules
18:34 CIA-30 bioclipse: egonw * r5526 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10.jchempaint/src/net/bio​clipse/cdk10/jchempaint/ui/editor/ (3 files in 2 dirs): OK, some editing is starting to work... highlighting is working... actions or update of model is not yet working though; also icons are missing
20:00 CIA-30 bioclipse: egonw * r5527 /bioclipse2/trunk/plugins/net.bioclipse.c​dk10.jchempaint/src/net/bioclipse/cdk10/j​chempaint/ui/editor/resources/small-bin/ (42 files): Added missing icons
20:19 CIA-30 bioclipse: ospjuth * r5528 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/src​/net/bioclipse/cdk/ui/editors/sdf/SDFEditor.java: Added a simple progressbar for parsing large SDFiles.

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