Camelia, the Perl 6 bug

IRC log for #cdk, 2008-08-26

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All times shown according to UTC.

Time Nick Message
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08:20 jpansanel moin
08:20 zarah hi jpansanel
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12:04 CIA-35 cdk: thomaskuhn * r12085 /cdk-taverna/trunk/src/main/java/org/o​penscience/cdk/applications/taverna/da​tabase/pgchem/GetMoleculesFromDB.java: Update the java doc and remove a try catch block
12:06 CIA-35 cdk: thomaskuhn * r12086 /cdk-taverna/trunk/src/main/java/org/openscien​ce/cdk/applications/taverna/io/XMLFileIO.java: Remove unused code
12:09 CIA-35 cdk: thomaskuhn * r12087 /cdk-taverna/trunk/src/main/java/org/openscie​nce/cdk/applications/taverna/qsar/model/ART2A​Classificator/ART2AClassificatorWorker.java: Add an option to choose the folder name to store the result files
12:12 CIA-35 cdk: thomaskuhn * r12088 /cdk-taverna/trunk/src/main/java/org/openscience/c​dk/applications/taverna/qsar/model/ART2AClassifica​tor/tools/CompareART2AClassificationResults.java: Add an option to choose the folder name to store the result files
12:14 maclean joined #cdk
12:14 CIA-35 cdk: thomaskuhn * r12089 /cdk-taverna/trunk/src/main/java/org/opensci​ence/cdk/applications/taverna/qsar/model/ART​2AClassificator/tools/action/CompareART2ACla​ssificationResultsChooseFolderAction.java: Add a file chooser to choose the folder to store the result of the classification
12:15 egonw maclean: shall we organize our meeting on monday?
12:16 egonw and shk3 too
12:16 egonw I think Jim is coming too...
12:17 maclean sure. sorry, was in the office, but moving furniture.
12:17 maclean So, who are you meeting on monday?
12:18 CIA-35 cdk: thomaskuhn * r12090 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/​qsar/model/ART2AClassificator/tools/ (3 files in 2 dirs): Add a new worker and the corresponding actions. This worker creates an pdf file from a given ART2A classification
12:22 egonw maclean: you I hope
12:22 egonw and stefan and Jim
12:22 CIA-35 cdk: thomaskuhn * r12091 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/​qsar/model/ART2AClassificator/tools/ (2 files in 2 dirs): Add a new worker and the corresponding actions. This worker extracts the molecule id's from a selected cluster or class from an ART2A classification result
12:22 egonw anyone else who wants to talk about CDK/Bioclipse too
12:23 egonw but, I'd very much spend an hour or so to chat with you about teh Bioclipse SENECA plugin
12:23 maclean Sure, that would be good. In the morning, then?
12:23 maclean When do you arrive?
12:23 egonw not sure
12:23 egonw will come from London
12:23 egonw going to the blogging event on Sat
12:24 egonw never went to the EBI from that direction...
12:24 maclean Well, there are trains from KGX.
12:24 egonw right
12:24 egonw but then I need a cab
12:24 maclean Takes 45 mins for the good one.
12:24 egonw which I hate
12:24 maclean Or, you could take the ebi bus...
12:24 egonw but that's the best solutoin?
12:24 egonw ok, one going from the south side?
12:24 egonw used the Camb one in the past
12:25 maclean http://www.ebi.ac.uk/Information/Travel/bus.html
12:26 CIA-35 cdk: thomaskuhn * r12092 /cdk-taverna/trunk/src/main/java/org/openscie​nce/cdk/applications/taverna/qsar/model/weka/ (SimpleKMeansWorker.java action/SimpleKMeansWorkerAction.java): Add a new worker and the corresponding actions. This worker uses the WEKE simple Kmeans cluster algorithm to create clustering. This will remove later the "old" implementation of the simpleKmeans cluster worker.
12:26 maclean Hills road stop, at 8:35. Means getting the 7:15 train, though...
12:27 CIA-35 cdk: thomaskuhn * r12093 /cdk-taverna/trunk/src/main/java/org/openscie​nce/cdk/applications/taverna/qsar/model/weka/ (EMClusterWorker.java action/EMClusterWorkerAction.java): Add a new worker and the corresponding actions. This worker uses the WEKE EM cluster algorithm to create clustering. This will remove later the "old" implementation of the EM cluster worker.
12:27 maclean Also : http://www.livedepartureboards.co.​uk/ldb/sumdep.aspx?T=KGX&S=CBG
12:27 egonw bus 7 miught be an option...
12:27 egonw going from Great Chesterford
12:28 egonw OK, thanx for these links...
12:28 maclean n/p
12:28 egonw ok, so around 9/9.30 seems possible...
12:28 egonw don't Sun will be late, so early up should not be a problem
12:28 maclean sounds good.
12:29 egonw I have a plane that evening from stansted
12:29 egonw so the earlier I arrive the more time we have
12:29 maclean That's true.
12:29 CIA-35 cdk: thomaskuhn * r12094 /cdk-taverna/trunk/src/main/java/org/openscie​nce/cdk/applications/taverna/qsar/model/weka/ (3 files in 2 dirs): Add a new worker and the corresponding actions. This worker extracts the results of the classification from WEKA cluster algorithms.
12:29 CIA-35 cdk: thomaskuhn * r12095 /cdk-taverna/trunk/src/main/java/or​g/openscience/cdk/applications/tave​rna/qsar/model/weka/WekaTools.java: Class which provides some basic methods to use the WEKA library.
12:29 maclean I'll book the meeting room for 10ish, then?
12:30 egonw ok
12:30 egonw gives us some time to grab coffee and a brownie
12:31 maclean Sure.
12:33 CIA-35 cdk: thomaskuhn * r12096 /cdk-taverna/trunk/src/main/java/org/opens​cience/cdk/applications/taverna/renderers/ (2 files): add a suppress warning tag
12:34 CIA-35 cdk: thomaskuhn * r12097 /cdk-taverna/trunk/src/main/java/org/openscience​/cdk/applications/taverna/tools/ChartTool.java: Class which provides the possibility to create charts using jfreechart. This is used to show some results in a graphical manner.
12:35 CIA-35 cdk: thomaskuhn * r12098 /cdk-taverna/trunk/src/main/java/org/openscie​nce/cdk/applications/taverna/tools/ConvertFin​gerprintItemListToMathematicaDataMatrix.java: Add a worker which transforms a fingerprint item list to a Mathematica data vector. This vector will be stored within a list of strings.
12:36 CIA-35 cdk: thomaskuhn * r12099 /cdk-taverna/trunk/src/main/resources/ (3 files in 2 dirs): Add the new worker and actions to the config files
12:37 egonw maclean: sent email to Jim
12:38 CIA-35 cdk: thomaskuhn * r12100 /cdk-taverna/trunk/src/test/java/org/opens​cience/cdk/applications/taverna/database/p​gchem/GetSelectedMoleculesFromDBTest.java: Add a junit test for the get selected molecules from db worker
12:39 maclean Got the mail, tack.
12:41 CIA-35 cdk: thomaskuhn * r12101 /cdk-taverna/trunk/src/test/java/org/opensci​ence/cdk/applications/taverna/qsar/model/ART​2AClassificator/ART2AClassificatorTest.java: Add a unit test for testing the serialization
12:42 CIA-35 cdk: thomaskuhn * r12102 /cdk-taverna/trunk/src/test/java/org/op​enscience/cdk/applications/taverna/qsar​/model/ART2AClassificator/tools/GetART2​AClassificationResultAsPDFTest.java: Add a junit test
12:42 CIA-35 cdk: thomaskuhn * r12103 /cdk-taverna/trunk/src/test/java/org/openscience/c​dk/applications/taverna/qsar/model/ART2AClassifica​tor/tools/GetMoleculeIDsForGivenClassesTest.java: Add a junit test
12:42 CIA-35 cdk: thomaskuhn * r12104 /cdk-taverna/trunk/src/test/java/org/op​enscience/cdk/applications/taverna/qsar​/model/weka/EMClusterWorkerTest.java: Add a junit test
12:42 CIA-35 cdk: thomaskuhn * r12105 /cdk-taverna/trunk/src/test/java/org/ope​nscience/cdk/applications/taverna/qsar/m​odel/weka/SimpleKMeansWorkerTest.java: Add a junit test
12:42 CIA-35 cdk: thomaskuhn * r12106 /cdk-taverna/trunk/src/test/java/org/opens​cience/cdk/applications/taverna/qsar/model​/weka/ExtractClusterResultWorkerTest.java: Add a junit test
12:44 egonw thomas_ku: happily hacking? :)
12:44 thomas_ku yeah a bit
12:44 CIA-35 cdk: thomaskuhn * r12108 /cdk-taverna/trunk/src/test/java/org/openscienc​e/cdk/applications/taverna/tools/ConvertFingerp​rintItemListToMathematicaDataVectorTest.java: Add a junit test
12:44 CIA-35 cdk: thomaskuhn * r12107 /cdk-taverna/trunk/src/test/java/org/openscie​nce/cdk/applications/taverna/qsar/model/weka/ (EMClusterWorkerTest.java ExtractClusterResultWorkerTest.java): Updated the java docs
12:44 thomas_ku and commiting old stuff ;-)
12:44 egonw good :)
12:45 egonw btw.. in JavaDoc, the first line must end in a '.'
12:45 egonw like in normal language
12:45 egonw it's used to determine what the one line description of a method/class is
12:45 masak the first sentence.
12:45 thomas_ku ok thanks
12:45 masak it can span several lines.
12:45 egonw masak: yes, indeed
12:45 thomas_ku for the information
12:46 egonw thomas_ku: just to give a multiline example without a period ? :)
12:47 masak if you want several sentences in the one-sentece description, you have to use '.' for '.' :)
12:47 masak or when writing things like "Ph.D."
12:48 egonw ah, nice tip
12:48 egonw that's blogable
12:48 masak heh
12:48 masak it's from Effective Java, I believe
12:48 egonw masak: please post at bioclipse.blogspot.com
12:48 masak egonw: I do, occasionally
12:48 masak but I tend to blog about new features, not general Javadoc advice
12:49 maclean I was writing on a message board recently that stripped all but [[a-z][A-Z].,] which mean't that "don't" came out as "dont". very annoying.
12:49 masak I can recommend the whole Javadoc manual, however. it's great.
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