Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-09-26

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All times shown according to UTC.

Time Nick Message
06:59 egonw joined #bioclipse
07:12 steinbeck joined #bioclipse
07:22 claes_a Is anyone in here into scripting with bc_rhino?
07:23 egonw the wizard (edrin) is not around...
07:23 egonw but have some experience with it...
07:23 egonw moreover, I can point you to example scripts...
07:24 egonw mom, brb
07:24 claes_a Aight. I'll blurt out my question in the meantime :)
07:25 egonw sure
07:26 claes_a Quite simply, I'd like to create a textfile and add it as a BioResource in the Navigator. Preferably allowing the user to choose the name.
07:26 claes_a All of this from the script.
07:26 claes_a (Already spent one afternoon peering through the bioclipse sources to no avail :( )
07:28 claes_a I found some snippets on how to add bioresources, but they did not give full names (i.e. packages) and I'm not familiar with the code tree.
07:28 egonw OK, this is something you need to ask Johanness....
07:29 egonw please email the user mailing list, and address the email to him
07:29 claes_a ok, thanks.
07:49 CIA-31 bioclipse: ospjuth * r3836 /trunk/playground/plugins/net.bioclipse.taverna/: Initial import.
07:50 olas joined #bioclipse
07:50 olas moin
07:51 CIA-31 bioclipse: ospjuth * r3837 /trunk/playground/plugins/net.bioclipse.taverna/ (180 files in 87 dirs): Initial import to be able to run Taverna WF from within Bioclipse. Does not work yet.
08:06 jonalv joined #bioclipse
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09:39 CIA-31 bioclipse: jonalv * r3838 /trunk/playground/plugins/​net.bioclipse.structuredb/ (6 files in 3 dirs): Persisting is starting to work. Delete works for all objects. All objects get's somewhat persisted but not all fields are persisted yet.
09:39 * jonalv lunch
11:07 thomas_ku_ joined #bioclipse
11:34 olas joined #bioclipse
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11:34 olas joined #bioclipse
11:35 olas hi claes_a
11:35 olas nice to see you here :-)
11:37 steinbeck joined #bioclipse
11:38 jonalv hi claes_a any progress?
11:40 EskilA joined #bioclipse
12:20 egonw jonalv, masak: who was working on the GridEditor again?
12:20 egonw what's the state of that?
12:20 egonw when I use it to open a MatrixResource, it shows nothing...
12:53 jonalv egonw, I think EskilA has it under his wings for the moment
12:55 masak egonw: I'm getting ready to look at that new stuff you wanted me to look at
12:55 EskilA how did you open your MatrixResource?
12:55 masak egonw: where was it again?
12:56 egonw EskilA: via the menu option
12:56 egonw masak: net.bioclipse.cdk.ui
12:56 egonw then bla.bla.view or so
12:56 masak egonw: thx
12:57 masak there are a number of improvements that I've been meaning to do to the Structure2DViewer
12:57 masak that I haven't had time for
12:57 EskilA bioresourcenavigator context menu?
12:57 masak the propertioes don't work properly as of now, for example
12:57 masak and jonalv wanted me to factor the table itself out into a separate class so that it could be used in different modules
12:58 egonw EskilA: yes
12:58 egonw masak: a widget, you mean?
12:58 masak egonw: that would be the effect of it, yes
12:59 masak are there separate thing one should do to make a class a widget? I guess there's an Eclipse tutorial about that somewhere...
12:59 EskilA is the file you're trying to open a .csv file?
12:59 egonw masak: yes
13:00 egonw it's called: "Creating Your Own Widgets using SWT"
13:00 egonw it's rather easy
13:00 egonw EskilA: no
13:00 egonw EskilA: it's the output of a QSAR calculation...
13:00 egonw EskilA: that explains the problem, I guess :)
13:00 EskilA I think so
13:00 egonw EskilA: does it do column labels yet?
13:01 egonw EskilA: do you have a demo file?
13:01 masak egonw: thx, found it
13:01 EskilA It's supposed to, some saving bug seems to remove them though
13:01 EskilA from the file that is
13:01 CIA-31 bioclipse: jonalv * r3839 /trunk/playground/plugins/ne​t.bioclipse.structuredb/src/ (sqlMap.xml sqlMapConfig.xml): Introduced more fields in the resultmaps but have not updated them in the select statements. Need to write reusable paramatermaps for the object types to be used in the insert statements.
13:01 EskilA yes, I can send it to you
13:02 olas EskilA: did you not write a wiuki page about it?
13:03 olas If not, could you please do it and explain how the matrix plugin is used?
13:03 EskilA ok
13:03 olas other people than egonw would probably want to know...
13:03 EskilA surely :)
13:05 egonw EskilA: received the offer, but got timed out...
13:05 egonw please add to net.bioclipse.data.test
13:05 EskilA ok
13:05 egonw in playground/
13:07 CIA-31 bioclipse: egonw * r3840 /trunk/playground/plugins/net.bioclipse.​seneca/src/net/bioclipse/plugins/jobs/De​terministicStructureElucidationJob.java: Be a bit more verbose in the Bioclipse console.
13:13 CIA-31 bioclipse: biocoder * r3841 /trunk/playground/plugins/net.bioclipse.dat​a.test/data/testData/GridEditordataset.csv: Added GridEditorDataset.csv as test data for MatrixGridEditor
13:14 egonw thanx
13:15 CIA-31 bioclipse: egonw * r3842 /trunk/playground/plugins/net.biocl​ipse.seneca/src/net/bioclipse/senec​a/judges/WCCNMRShiftDBJudge.java: Fixed extraction of the molecular formula.
13:41 CIA-31 bioclipse: egonw * r3843 /trunk/playground/plugins/net.biocl​ipse.seneca/src/net/bioclipse/senec​a/judges/WCCNMRShiftDBJudge.java: Now really take into account both possibilities.
14:02 steinbeck left #bioclipse
14:13 masak egonw: so, was it your new net.bioclipse.plugins.swt.w​idgets.JChemPaintView.java that you wanted me to take a look at?
14:13 egonw yes
14:13 masak I'm looking at it now
14:14 egonw to make sure it nicely integrates into tables...
14:14 masak ah
14:14 egonw that resizing etc works
14:14 masak any way to see it running in bioclipse?
14:15 steinbeck joined #bioclipse
14:15 masak so, what I said earlier about a table widget could possibly be a table consisting of instances of this widget?
14:29 CIA-31 bioclipse: steinbeck * r3844 /trunk/playground/plugins/net.biocl​ipse.seneca.examples/data/example4/ (. a-pinen-case.sjs data.cml): Added deterministic CASE for alpha-pinene with the NMRShiftDB judge
14:38 CIA-31 bioclipse: biocoder * r3845 /trunk/playground/plugins/net.bioclipse.chart/ (4 files in 4 dirs): Made a dialog for constructing charts. Made a model class for handling axis data.
14:38 CIA-31 bioclipse: egonw * r3846 /trunk/playground/plugins/net.bioc​lipse.seneca/src/net/bioclipse/plu​gins/views/BestStructureView.java: Fixed a NPE when the view is not shown
14:39 CIA-31 bioclipse: biocoder * r3847 /trunk/plugins/net.bioclipse.statistics/src/​net/bioclipse/editors/MatrixGridEditor.java: Working on integrating charting capabilities withj MatrixGridEditor
14:39 EskilA left #bioclipse
14:46 CIA-31 bioclipse: egonw * r3848 /trunk/playground/plugins/net.bioclipse.seneca/ (3 files in 3 dirs): Added a DEPT-based judge (only works with DetGen)
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