Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-01-22

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All times shown according to UTC.

Time Nick Message
07:02 rojasm joined #bioclipse
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07:32 rojasm egon: how is possible that not all konqueror windows are in kde 4.0?
07:38 egonw ubuntu, right?
07:38 egonw run:
07:38 egonw konqueror-kde4
07:38 rojasm yes
07:39 egonw because ubuntu has both konqueror and konqueror-kde4 execs...
07:39 viklund joined #bioclipse
07:39 rojasm ok. But I want as default
07:39 egonw not sure how to do that
07:39 rojasm ok
07:42 egonw ok, going afk for a while for meetings
07:42 egonw bbl
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09:40 CIA-14 bioclipse: carl_masak * r4744 /branches/bioclipse2/core/plugins/net​.bioclipse.scripting/src/net/bioclips​e/scripting/ScriptingException.java:
09:40 CIA-14 bioclipse: [ScriptingException.java]
09:40 CIA-14 bioclipse: * Added a constructor which wraps exceptions.
09:40 CIA-14 bioclipse: * Added a serial version ID.
10:06 CIA-14 bioclipse: carl_masak * r4745 /branches/bioclipse2/core/plugins/n​et.bioclipse.scripting/src/net/bioc​lipse/scripting/JsEnvironment.java:
10:06 CIA-14 bioclipse: [JsEnvironment.java]
10:06 CIA-14 bioclipse: * Nice formatting of ScriptingExceptions
10:22 CIA-14 bioclipse: jonalv * r4746 /branches/bioclipse2/ (6 files in 5 dirs): Removed ScriptingException, now throws IllegalArgumentException instead
10:23 CIA-14 bioclipse: carl_masak * r4747 /branches/bioclipse2/core/plugins/n​et.bioclipse.ui/src/net/bioclipse/u​i/views/ScriptingConsoleView.java:
10:23 CIA-14 bioclipse: [ScriptingConsoleView.java]
10:23 CIA-14 bioclipse: * reinstated commented-out update line
10:23 CIA-14 bioclipse: * here's the problem:
10:23 CIA-14 bioclipse: ** without this line, the view does not scroll down after a command
10:23 CIA-14 bioclipse: ** with this line, the view updates too frequently on X11 systems
10:24 CIA-14 bioclipse: carl_masak * r4748 /branches/bioclipse2/bioinformatics/plugins​/net.bioclipse.biojava.business/src/net/bio​clipse/biojava/domain/BiojavaSequence.java:
10:24 CIA-14 bioclipse: [BiojavaSequence.java]
10:24 CIA-14 bioclipse: * removed unused imports
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10:36 CIA-14 bioclipse: ospjuth * r4749 /branches/bioclipse2/bioinformatics/plugins/n​et.bioclipse.biojava.ui/src/net/bioclipse/bio​java/ui/views/SequenceContentProvider.java: Get BiojavaManager from biojava.business.activator. Solves 1875106.
10:39 CIA-14 bioclipse: jonalv * r4750 /branches/bioclipse2/bioinformatics/plugin​s/net.bioclipse.biojava.business/src/net/b​ioclipse/biojava/business/Activator.java: Changed timeout from 30 secs to 10 secs and now throw IllegalstateException if the biojavamanager can't be found instead of just writing a message to standard out
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10:47 CIA-14 bioclipse: carl_masak * r4751 /branches/bioclipse2/core/plugins/net.bioclipse.u​i/src/net/bioclipse/ui/views/JsConsoleView.java:
10:47 CIA-14 bioclipse: [JsConsoleView.java]
10:47 CIA-14 bioclipse: * fixed exponential-time bug in regular exception
10:59 * jonalv @ lunch
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12:15 CIA-14 bioclipse: ospjuth * r4752 /branches/bioclipse2/core/plugi​ns/net.bioclipse.ui/plugin.xml: Removed deprecated QSAR-nature.
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13:11 egonw olas: what's a 'nature' exactly?
13:12 egonw and what was wrong with the qsar nature?
13:13 olas it was at the wrong place
13:13 egonw ah
13:13 olas a nature is something you add to a project
13:14 olas JAVA-nature is a nature for Java-projects
13:14 egonw it's like a .something file?
13:14 olas QSAR nature is a nature for QSAR-projects
13:14 olas not really
13:14 olas but a nature says that the project is of a certain type
13:14 olas which means you can say:
13:14 olas This functionality is only available in Java projects
13:15 olas etc
13:15 olas The QSAR-nature in net.bioclipse.ui was long since deprecated and replaced
13:15 olas but had forgottoen to remove it
13:15 egonw it's now in net.bioclipse.qsar or so?
13:15 egonw really need to have a look at that...
13:25 olas yes
13:25 olas I am working on it
13:25 olas but have had to do a lot of other stuff in the meantime...
13:31 egonw very recognizable...
14:28 CIA-14 bioclipse: ospjuth * r4753 /branches/bioclipse2/bioinformatics/plug​ins/net.bioclipse.biojava.business.tests​/tests/net/bioclipse/biojava/business/ (BiojavaHelperTest.java BiojavaManagerTest.java): Added some tests for BiojavaHelper
14:29 CIA-14 bioclipse: ospjuth * r4754 /branches/bioclipse2/bioinformatics/p​lugins/net.bioclipse.biojava.business​/src/net/bioclipse/biojava/business/ (BiojavaHelper.java BiojavaManager.java IBiojavaManager.java): Added BiojavaHelper with tools for Biojava. Also extended the manager with functionality.
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14:33 CIA-14 bioclipse: ospjuth * r4755 /branches/bioclipse2/bioinformatics/plugins/net.​bioclipse.biojava.business.tests/tests/net/biocl​ipse/biojava/business/BiojavaManagerTest.java: Some cleanup.
14:34 CIA-14 bioclipse: ospjuth * r4756 /branches/bioclipse2/bioinformatics​/plugins/net.bioclipse.biojava.ui/ (10 files in 3 dirs): Added actions for translation and transctiption.
14:36 masak joined #bioclipse
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15:07 CIA-14 bioclipse: jonalv * r4757 /branches/bioclipse2/bioinformatics/plugins/​net.bioclipse.biojava.business/src/net/biocl​ipse/biojava/business/BiojavaManager.java: Added causing Exception to stack trace
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16:15 CIA-14 bioclipse: jonalv * r4758 /branches/bioclipse2/_playground_/net.​bioclipse.springBasedPrototypePlugin/: Initial import.
16:17 CIA-14 bioclipse: jonalv * r4759 /branches/bioclipse2/_playground_/net.​bioclipse.springBasedPrototypePlugin/ (17 files in 8 dirs): An "empty plugin" to be used as a base for plugins using Spring to contribute with managers. It contains a working ExampleManager
16:30 CIA-14 bioclipse: carl_masak * r4760 /trunk/playground/plugins/net.bioclipse.base2​/src/net/bioclipse/base2/views/TreeView.java:
16:30 CIA-14 bioclipse: [TreeView.java]
16:30 CIA-14 bioclipse: * early attempts at a context menu
16:32 CIA-14 bioclipse: ospjuth * r4761 /branches/bioclipse2/bioinformatics​/plugins/net.bioclipse.biojava.ui/ (8 files in 2 dirs): Added some actions for translation back and forth.
16:32 CIA-14 bioclipse: ospjuth * r4762 /branches/bioclipse2/bioinformatics/plugi​ns/net.bioclipse.biojava.business.tests/ (2 files in 2 dirs): Added tests for new sequence creation.
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16:34 CIA-14 bioclipse: ospjuth * r4763 /branches/bioclipse2/bioinformatics/p​lugins/net.bioclipse.biojava.business​/src/net/bioclipse/biojava/business/ (BiojavaManager.java IBiojavaManager.java): Implemented new sequence construction from plain text, fasta, and name + plain text.
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