Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-10-01

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All times shown according to UTC.

Time Nick Message
05:58 thomas_ku joined #bioclipse
06:18 egonw joined #bioclipse
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08:24 olas joined #bioclipse
08:24 olas moin
08:25 olas egonw: everything went well?
08:25 egonw olas: yes, guess so...
08:26 egonw copy/pasted some text from the website, wrote some bits...
08:26 egonw I hope it makes sense
08:26 egonw the competition is not that big
08:30 olas true
08:42 EskilA joined #bioclipse
09:05 masak joined #bioclipse
11:21 EskilA joined #bioclipse
12:08 EskilA joined #bioclipse
12:21 olas joined #bioclipse
12:40 CIA-31 bioclipse: ospjuth * r3879 /trunk/playground/plugins/net.bioclip​se.biomoby/src/net/bioclipse/biomoby/ (4 files in 2 dirs): Working on only showing active services
13:14 CIA-31 bioclipse: biocoder * r3880 /trunk/playground/plugins/net.biocli​pse.chart/src/net/bioclipse/dialogs/ (ChartDialog.java HistogramDialog.java): Created HistogramDialog for setting up histograms
13:16 CIA-31 bioclipse: biocoder * r3881 /trunk/plugins/net.bioclipse.statistics/src/​net/bioclipse/editors/MatrixGridEditor.java: Created actions for the different kinds of plots, factored functionality into methods
13:16 egonw EskilA: you are biocoder, right?
13:16 egonw damn, forgot it already...
13:16 EskilA yeah
13:17 EskilA didn't think about conventions when i choose that name :p
13:17 egonw good to see you are around...
13:17 egonw no worries...
13:17 egonw we havent' been talking enough :)
13:17 EskilA yeah
13:17 egonw OK, get me up to speed with the MatrixGridEditor...
13:17 egonw it does not work with the MatrixResource...
13:17 egonw should it?
13:18 EskilA Well, currently it only parses csv files, so it's very much in a developmental stage right now
13:18 EskilA so that's something we should get it to do eventualy
13:19 egonw are the plot functionalities online?
13:19 EskilA yes, they should be working now
13:19 egonw one can label columns, right?
13:19 EskilA yes
13:19 egonw OK, excellent
13:19 egonw that's all I need at this moment...
13:20 egonw so... what resource gets created from a .csv file?
13:20 EskilA in the files, not inside the editor though
13:20 egonw fine...
13:23 egonw please tell me what type of IBioResource I need to create...
13:23 EskilA the file is parsed into a IMatrixImplementationResource
13:23 egonw so, it *is* using MatrixResource??
13:24 egonw OK, the parse method now splits on whitespace and ',' ...
13:25 EskilA yes
13:25 egonw OK, so why can't I use the GridMatrixEditor use on a QSAR descriptot .jam output file?
13:26 EskilA I don't know, I'm not very knowledgeable about matrix formats etc.
13:26 egonw the file opens fine in my old KTable based editor...
13:26 egonw which means that the resource is fine...
13:27 egonw better put...
13:27 egonw that it must be the way the GridMatrixEditor reads data from the resource...
13:27 egonw OK, that will help me debug things...
13:27 EskilA yes, I think so
13:29 egonw Mmmm... colIds etc should not be stored in the MatrixResource but in the Impl instead...
13:30 egonw also, there are set() methods missing...
13:30 egonw like setColumnName(int) etc
13:30 egonw why getColumnCount() as you already have the matrix size?
13:31 egonw oh, because you its nicer than getSize() -> int[]
13:31 egonw OK, fair...
13:31 EskilA I only wrote insertRow and parseStringIntoMatrix
13:32 egonw yes, I can write quite stupid code
13:32 egonw I am aware of that :)
13:33 olas does the gridMatrixEditor has the extension .jam in its extension point?
13:33 olas sorry, extension in plugin.xml?
13:33 olas or is it just .csv?
13:33 egonw not sure...
13:33 olas that could be one source of error
13:33 egonw the MatrixResource does at least
13:33 olas see the gridMatrixEditor.plugin.xml
13:34 olas but the editor will only open files it has registerd fiule names for
13:34 olas doesn't care what resource it is
13:34 egonw yes, it has
13:34 olas (which is stupid and will be remedied in bioclispe2)
13:37 masak joined #bioclipse
13:37 EskilA yeah
13:40 CIA-31 bioclipse: egonw * r3882 /trunk/plugins/net.bioclipse.cdk.​descriptor/META-INF/MANIFEST.MF: Added two missing dependencies.
13:41 egonw mmm...
13:42 egonw the grid editor works now...
13:42 egonw weird...
13:42 egonw but nice :)
13:42 EskilA I'm glad :D
13:42 olas Can you also plot?
13:43 egonw yes, that seems to work too :)
13:43 jonalv w00t
13:43 olas cool
13:43 EskilA yeah, should be working now
13:43 EskilA I'll be happy to hear your feedback
13:43 olas egonw: can we get a screenshot on the wiki for a QSAR analysis?
13:44 egonw olas: sure...
13:45 egonw will first update the QSAR descriptor wizard job to create a .csv file instead of the .jam file (which was artificial anyway)...
13:45 egonw so that column names can be added too...
13:45 egonw that will be a nice demo for Friday :)
13:45 egonw EskilA: cheers! Keep up the good work!
13:47 egonw EskilA: would be nice that the 'Chart Dialog' would detect if only two columns are selected...
13:47 egonw and automatically fill the X-Values and Y-Values drop down boxes
13:48 EskilA_ joined #bioclipse
13:48 egonw [2007-10-01 15:46:02] <egonw> EskilA: cheers! Keep up the good work!
13:48 egonw [2007-10-01 15:47:18] <egonw> EskilA: would be nice that the 'Chart Dialog' would detect if only two columns are selected...
13:48 egonw [2007-10-01 15:47:28] <egonw> and automatically fill the X-Values and Y-Values drop down boxes
13:49 EskilA_ Thank you!
13:49 EskilA_ I'll look into that
13:50 egonw EskilA_: I'm now updating the QSAR descriptor wizard to spit a CSV file with column names...
13:50 egonw question: columns names are the first line, also ',' separated?
14:06 olas left #bioclipse
14:06 olas joined #bioclipse
14:21 egonw olas: got a sec?
14:29 olas sure
14:29 olas egonw: talk to me
14:30 egonw mom...
14:30 olas :-)
14:30 egonw OK
14:30 egonw yes, I got a problem
14:30 olas oh no
14:30 egonw was right in the middle of the debug session...
14:31 egonw instead of a .jam file, I now try to create a .csv file
14:31 egonw both are in the statistics/plugin.xml as associated with MatrixResource...
14:31 egonw but, of course creation of the resource fails...
14:31 egonw now, I tracked it down into BioResourceType...
14:32 egonw in the getFileExtensions()
14:32 egonw which returns an empty String[] array...
14:32 olas no way I can tell this from memory
14:33 egonw :)
14:33 egonw mom
14:33 egonw wait some more...
14:33 * olas is waiting
14:33 jonalv we are all waiting :)
14:33 masak me too!
14:33 egonw oh, actually it does find a matching BioResourceType...
14:33 egonw and even the right one...
14:36 egonw OK, here's the story...
14:36 egonw it fails with a ClassCastException
14:36 egonw on a method call...
14:36 egonw no idea what is going on here...
14:36 olas hmm
14:37 olas can you give me a class and a line no?
14:37 olas and tell me how to reproduce?
14:38 olas maybe in a bug report?
14:38 olas I'll try to assist asap
14:39 olas (maybe even now)
14:39 egonw need to debug some more
14:39 egonw vefore I can give an accuret problem description
14:40 olas I have to leave in 20 mins
14:41 olas but will look at it first thing in the morning otherwise
14:41 egonw ok, thanx
14:45 olas but please file a bug report and assign it to me
14:46 egonw I think I might have found the problem, finally...
14:46 egonw obviously, far away from where the program actually crashes...
14:46 egonw no idea how the Eclipse people manage to do that...
14:46 egonw but OK, fair...
14:47 egonw you can't have everything...
14:47 egonw OK, found the source of the ClassCastException
14:48 egonw I just hate the  runAsyncMessages() lock.tun crap
14:48 egonw tun=run
14:51 egonw OK, found and solved the problem
14:51 egonw thanx guys, for listening :)
14:52 olas great you found the problem
14:58 egonw OK, going to rewrite some stuff...
14:58 * egonw found more stupid code he wrote himself
15:12 olas left #bioclipse
15:38 CIA-31 bioclipse: egonw * r3883 /trunk/plugins/ (5 files in 4 dirs): Added a framework for propagating the column labels
15:41 CIA-31 bioclipse: egonw * r3884 /trunk/plugins/net.bioclipse.statistics/sr​c/net/bioclipse/model/MatrixResource.java: Fixed output: don't put a ',' at the end of the line.
15:42 CIA-31 bioclipse: egonw * r3885 /trunk/plugins/net.bioclipse.descriptor/src/net​/bioclipse/jobs/DescriptorCalculationJob.java: Use proper file extension.
15:44 egonw EskilA_: still around?
15:49 egonw ha, cool :)
15:55 egonw EskilA_: please be around

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