Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-02-17

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All times shown according to UTC.

Time Nick Message
01:33 CIA-55 bioclipse: egonw * r8854 /bioclipse2/trunk/cdk-externals​/trunk/org.openscience.cdk.io/ (2 files in 2 dirs): Updated to fix reading of MDL molfiles with no coordinates (fixes #495)
01:33 CIA-55 bioclipse: gilleain * r8855 /bioclipse2/trunk/cdk-externals/trunk/org.op​enscience.cdk.render/src/org/openscience/cdk​/renderer/selection/RectangleSelection.java: What is wrong with intermediate variables?
01:33 zarah bug #495 | http://tinyurl.com/bq966z
01:36 CIA-55 bioclipse: ospjuth * r8856 /bioclipse2/trunk/plugins/ne​t.bioclipse.data.sampledata/ (data/SMILES/ data/SMILES/moleculesNoHeader.smi plugin.xml): Added large SMILES file to sample data.
01:41 CIA-55 bioclipse: gilleain * r8857 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintWidget.java: Using RingGenerator rather than BasicBondGenerator.
07:37 Gpoks joined #bioclipse
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08:06 egonw joined #bioclipse
08:06 egonw moin
08:08 sneumann hi there
08:14 masak joined #bioclipse
08:29 CIA-55 bioclipse: egonw * r8858 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: Compile fix for a recent commit that change the var name
08:35 CIA-55 bioclipse: goglepox * r8859 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/icons/jcp/ (25 files): Converted jcp icons and added color
08:35 CIA-55 bioclipse: goglepox * r8860 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.jchempaint/src/net/bioclipse/cdk/jchem​paint/handlers/ChangeModuleHandler.java: Changes to support AlterBondOrderModule
08:35 CIA-55 bioclipse: goglepox * r8861 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml:
08:35 CIA-55 bioclipse: Changed toolbar to conform with the one from JCP application see bug #454
08:35 CIA-55 bioclipse: Edit modules is also the same to facilitate functionality.
08:35 zarah bug #454 | http://tinyurl.com/bj4nul
08:36 CIA-55 bioclipse: goglepox * r8862 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: changed from renderer2DModel to rendererModel fixing compile error from previous renameing.
08:36 CIA-55 bioclipse: goglepox * r8863 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml:
08:36 CIA-55 bioclipse: Removed 'Atom Action' and 'Add Hexagon'
08:36 CIA-55 bioclipse: as they where there to check the contextmenu
08:38 egonw Gpox:++
08:39 egonw @pz property cdkmolecule
08:39 zarah [381] Missing property source for CDK... http://tinyurl.com/by8jlg
08:39 zarah Entire list at http://tinyurl.com/d7ymgh
08:39 Gpox egonw: Had you done any work on the CDKMolecule PropertySource?
08:39 egonw no
08:39 egonw are you here today?
08:39 Gpox yes
08:40 egonw can you come over?
08:40 Gpox ok
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09:00 edrin hi
09:05 masak hi
09:09 maclean joined #bioclipse
09:41 jonalv joined #bioclipse
09:41 jonalv oh hai
09:42 egonw hi all
09:43 maclean hi
09:44 masak egonw: which of you two are coming to Yukikos today?
09:45 egonw arvid is, I am not
09:45 egonw I brought lasagna
09:45 masak oki.
09:48 masak egonw: tell Gpox we booked a table for 11:30.
09:48 masak oh, he's here now.
09:49 CIA-55 bioclipse: egonw * r8864 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.business/src/net/bioclipse/cdk/domain/ (CDKMolecule.java CDKMoleculePropertySource.java): Implemented a IPropertySource
09:51 maclean egonw : I can't work out why c1ccccc1 isn't working from the 'Create New Smiles Resource'
09:51 CIA-55 bioclipse: egonw * r8865 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: Default to the CDKMolecule, if nothing is selected... however, fails, because 'model' is never set... (see bug #517)
09:51 zarah bug #517 | http://tinyurl.com/aq5emv
09:51 egonw maclean: ack... I'll have a look at it and see if I can find irregularities...
09:52 maclean take a look at the bug report, as I give some clues
09:53 maclean also, a successful benzene has single bonds in the outline, while the broken one has aromatic bonds ?!
09:54 egonw they are single as the CDK does not have a UNDEFINED bond type :(
09:55 egonw did I mention already that SMILES is a rather nasty format?
09:57 CIA-55 bioclipse: goglepox * r8866 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java:
09:57 CIA-55 bioclipse: JChemPaintEditor now uses setInput instead of setAtomContainer
09:57 CIA-55 bioclipse: to pass the model to the editor widget. fixes bug #517
09:57 zarah bug #517 | http://tinyurl.com/aq5emv
09:57 egonw Gpox++
09:57 egonw very quick :)
09:58 egonw Gpox: btw... please fix this too:
09:58 egonw implicit hydrogen labels for carbons should only be left or right
09:59 egonw it's only non-carbons where below and above is used
09:59 egonw should be an easy fix
09:59 egonw shall I file it?
10:00 Gpox well it is in CDK
10:01 egonw jcp-prim, right?
10:01 egonw shall give it a go?
10:01 maclean GeometryTools.getBestAlignmentForLabelXY
10:02 egonw OK, I'll look at it...
10:02 maclean returns an int : left (-1), right(1), up(2), down(-2)
10:03 egonw yes, so we need a special variant for just left and right
10:03 egonw wondering how the old JCP did that...
10:03 Gpox there is getBestAlignmentForLabel, just need a check in BasicAtomGenerator on which to use
10:06 CIA-55 bioclipse: goglepox * r8867 /bioclipse2/trunk/cdk-externals/trunk/org.ope​nscience.cdk.render/src/org/openscience/cdk/r​enderer/generators/BasicAtomGenerator.java: Only render implicit hydrogen in Y if not carbon
10:07 egonw tack!
10:15 masak @lunch
10:27 egonw Gpox make sure to apply patches also to jcp-prim
10:33 CIA-55 bioclipse: gilleain * r8868 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint.view/src/net/bioclipse/​cdk/jchempaint/view/SWTRenderer.java: Scaled wedges.
10:47 CIA-55 bioclipse: gilleain * r8869 /bioclipse2/trunk/ (16 files in 8 dirs):
10:47 CIA-55 bioclipse: - Changed name of ISelection to avoid eclipse naming conflicts.
10:47 CIA-55 bioclipse: - The ControllerHub now does the selection, and calls the event handler when done.
10:47 CIA-55 bioclipse: - Removed/altered constructors in the two selection modules.
10:51 CIA-55 bioclipse: gilleain * r8870 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml: Ah the perils of xml config files...
10:53 julio joined #bioclipse
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10:56 julio joined #bioclipse
10:58 egonw maclean: ping
10:58 maclean pong
10:59 egonw I think it might be isAromaticRing
10:59 egonw ringIsAromatic()
10:59 egonw which is stupid...
10:59 egonw if the ring atoms are not aromatic
10:59 egonw only then check to see if the bonds are aromatic too
10:59 egonw hahaha
10:59 egonw funny, isn't it :)
10:59 maclean yesss.
10:59 maclean I don't follow, though
11:00 maclean is it a rendering problem, then?
11:00 egonw well... there is no comment, so not sure what the code is supposed to do...
11:00 egonw no
11:00 egonw that method says the benzene is not aromatic
11:00 egonw which it is...
11:00 egonw well, sort of...
11:00 egonw the thing is...
11:00 maclean lets not get into that argument again! :)
11:00 egonw I'm not sure what the algo is supposed to do:
11:01 maclean what class is this?
11:01 egonw 1. isArom if atoms AND bonds are aromatic
11:01 egonw RingGenerator
11:01 egonw or,
11:01 egonw 2. isArom if atoms OR bonds are aromatic
11:01 maclean so it IS a rendering problem (generation == rendering...)
11:02 egonw oh... in that way...
11:02 maclean right, I see the method
11:02 egonw yes
11:02 maclean that was Niels Out's code, I think.
11:02 egonw sure :)
11:02 egonw since he was not a chemist...
11:02 maclean Or, inherited, anyway
11:02 egonw it is like mine...
11:02 maclean (honest :)
11:03 egonw so, what would be reasonable...
11:03 egonw AND or OR ...
11:03 egonw I think OR...
11:03 maclean yes, I suppose
11:04 maclean but it does seem reasonable to assume AND - since atoms can't be aromatic unless their bonds are, no?
11:04 egonw true
11:04 egonw so, maybe just test bonds?
11:04 egonw and not atoms
11:05 maclean sure, okay - if you're happy with that.
11:05 maclean oh, no wait.
11:05 maclean wtf is this method doing?
11:05 * maclean belatedly sees
11:05 egonw what is in SVN is broken anyway...
11:06 egonw like I said...
11:06 egonw that code does:
11:06 egonw if not all atoms are aromatic, test if all bonds are also aromatic...
11:06 egonw yeah, right
11:07 maclean if any of the atoms are set as not aromatic, test to see if ALL the bonds are aromatic
11:07 maclean so, catching the case that one of the atoms is unset, I suppose
11:09 maclean but, also - this doesn't really adress the root problem, that you can get different molecules for c1ccccc1 if you go through CML.
11:09 egonw um, the default is to *not* show aromaticity...
11:10 egonw did you check that?
11:10 maclean do you mean that the RendererModel.shoudlShowAromaticity() should return false by default?
11:10 maclean it does
11:11 egonw no, true by default
11:11 egonw does it?
11:11 egonw mm...
11:11 egonw not picked up by the pref page, which uses a new RendererModel()...
11:11 egonw will check
11:11 egonw anyway...
11:11 egonw inner arom ring is now working again
11:11 egonw will commit
11:11 maclean ok
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11:13 CIA-55 bioclipse: egonw * r8871 /bioclipse2/trunk/cdk-externals/trunk/org.o​penscience.cdk.render/src/org/openscience/c​dk/renderer/generators/RingGenerator.java: Reset the isAromatic var when checking the bonds
11:14 maclean riight. I see.
11:48 CIA-55 bioclipse: gilleain * r8872 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​jchempaint/src/net/bioclipse/cdk/jchempaint/ (5 files in 2 dirs): Added bond length to JCP preferences. Changes to FIVE files, to add one parameter!!
11:50 egonw :)
11:50 stain 2009-02-17 11:48:08 [0x0-0x31031].net.sf.taverna.workbench[766] ERROR 2009-02-17 11:48:08,538 Error finding class org.openscience.cdk.applications.ta​verna.scuflworkers.cdk.CDKScavenger ACL=loader{org.openscience.cdk.appli​cations.taverna:cdk-taverna:0.5.1.0} from 15937105
11:50 stain 2009-02-17 11:48:08 [0x0-0x31031].net.sf.taverna.workbench[766] java.lang.UnsupportedClassVersionError: Bad version number in .class file
11:50 stain do I need Java 6 to use CDK-Taverna..?
11:52 maclean ye
11:52 maclean +s
11:53 maclean and taverna 1.7, not T2.
11:53 CIA-55 bioclipse: goglepox * r8873 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​jchempaint/src/net/bioclipse/cdk/jchempaint/ (6 files in 2 dirs): Removed duplicate of CDKChemObject and ChemObjectPropertySource bug #518
11:53 zarah bug #518 | http://tinyurl.com/bdhzsl
11:53 CIA-55 bioclipse: goglepox * r8874 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Removed tabs and fixed indentation
11:55 stain why could it not be compiled for Java 5.. :'(
11:55 egonw what could not?
11:57 stain the plugin
11:58 stain (there's no Java 6 for my mac)
11:59 egonw my plugin?
12:00 egonw if so, please paste error message...
12:00 egonw then I'll fix it immediately
12:00 stain :)
12:00 stain I pasted it above
12:00 stain java.lang.UnsupportedClassVersionError: Bad version number in .class file for org.openscience.cdk.applications.ta​verna.scuflworkers.cdk.CDKScavenger
12:01 egonw ah, sorry...
12:01 egonw that scrolled off screen before I saw it...
12:01 egonw CDK-Taverna...
12:02 egonw you tried installing it from the update site?
12:02 maclean Dr Kuhn said that it uses java6-specific code, so I don't think that it could be done for java5
12:02 egonw will need to ping Thomas then to recompile with J5 ...
12:02 egonw ah. ic...
12:02 maclean (at least, that's what he said last year)
12:02 egonw Dr Kuhn... heheheh
12:02 egonw have not checked much of his code recently... I should...
12:13 masak egonw: just out of curiosity: why shouldn't 'get' methods be recorded?
12:14 egonw should they?
12:14 egonw maybe they should...
12:14 egonw had an internal conflict about it...
12:14 egonw these get methods will get called really a lot...
12:14 egonw being used in GUI stuff...
12:14 masak ok.
12:14 masak aye.
12:15 * masak has mixed feelings about recording
12:15 masak it's great and all, but ultimately it doesn't work.
12:15 masak I know, I helped write it.
12:16 maclean :(
12:16 masak maclean: your commit messages are too silly! :)
12:16 maclean such as?
12:17 masak "Ah the perils of xml config files..."
12:17 maclean yes, well, you know
12:17 masak "What is wrong with intermediate variables?"
12:17 maclean That's just good sense
12:17 masak :)
12:18 maclean It's an improvement on "Minor changes", though.
12:18 egonw Or "Fixed bug #XXXX"
12:19 maclean No that's very useful, surely?
12:19 masak I'm not complaining, just noting that the comments are slightly silly.
12:19 egonw I'd rather have a Dept of Silly Commits, than a Dept of Uninformative Commits
12:20 maclean Oh, egonw : I see that there is core.Preferences and jface.preferences.IPreferencesStore
12:20 masak egonw: aye.
12:20 egonw maclean: use the first
12:20 masak "Commit messages are more useful the shorter they are. Provide the reasons for your commit and then stop. Don't document your code in commit messages. Don't talk directly to other developers via commit messages. Try to maximize the utility for the next person who looks at your commit message through the narrow lens of some svn utility."
12:20 egonw the latter is depreacted
12:20 maclean oh
12:20 maclean really?
12:20 maclean :(
12:20 maclean so how do I store Colors?
12:20 egonw ColorEditorField
12:21 maclean nope
12:21 maclean you can't store the color in the Preferences object
12:21 maclean there is this PreferenceConverter that takes a IPreferenceStore
12:22 egonw oh...
12:22 egonw RGB with int sliders then?
12:22 maclean guess so
12:22 maclean are you sure that PreferenceStore is deprecated?
12:23 egonw that's what my book said
12:23 egonw "Making Enterprise quality Plugins"
12:23 maclean hmmm. maybe I'm looking at old docs then
12:30 CIA-55 bioclipse: goglepox * r8875 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/outline/StructureContentProvider.java: Refactored out the creation of CDKChemObjects into separate methods
12:31 CIA-55 bioclipse: goglepox * r8876 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: Change so selection provides CDKChemObjects
12:36 CIA-55 bioclipse: goglepox * r8877 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui.sdfeditor/plugin.xml: Renamed SDFEditor to MoleculeTableEditor
12:48 CIA-55 bioclipse: goglepox * r8878 /bioclipse2/trunk/plugins/net.bioc​lipse.seneca/META-INF/MANIFEST.MF: Added net.bioclipse.cdk.jchempaint.view to dependencies to fix compile error
13:30 CIA-55 bioclipse: carl_masak * r8879 /bioclipse2/trunk/plugins/ (3 files in 2 dirs):
13:30 CIA-55 bioclipse: hid explicit output of 'Undefined' value (fixes #511)
13:30 CIA-55 bioclipse: * a regexp now matches on the string "org.mozilla.javascript.Undefined@" in
13:30 CIA-55 bioclipse:  the beginnings of return strings, and supresses such return strings
13:30 CIA-55 bioclipse: * would be better to filter on type, but not sure that info is available to
13:30 CIA-55 bioclipse:  the Java level
13:30 CIA-55 bioclipse: * also fixed complaint about font change in the bug ticket
13:30 zarah bug #511 | http://tinyurl.com/ba8uc5
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13:36 steinbeck Hi everyone
13:37 maclean hi
13:37 egonw hi steinbeck
13:37 steinbeck egonw: which Eclipse version are you running?
13:37 egonw 3.4.1
13:38 steinbeck ack - thanks
13:38 steinbeck Ubuntu package manager has 3.2.2
13:38 steinbeck Is that a large drawback?
13:39 egonw yes
13:39 egonw that will not work
13:40 egonw you need to grab a version from eclipse.org
13:40 egonw that will not work <- with BC2 that is
13:40 egonw for CDK it should be fine
13:47 steinbeck ack
13:47 steinbeck thanks
13:51 CIA-55 bioclipse: gilleain * r8880 /bioclipse2/trunk/cdk-externals/trunk/org​.openscience.cdk.render/src/org/openscien​ce/cdk/renderer/RenderingParameters.java: Default bond color was not set by default.
13:57 egonw maclean++
13:57 maclean setting the colors is turning out to be a big headache :(
13:58 egonw mmm...
13:58 egonw feel free to say, "this is not worth it at this moment... delaying until later..."
13:58 maclean well it needs to be done at some point.
13:59 maclean I'm just thinking that it might be better to store r, g, b int values in the RendererModel.
14:00 egonw sounds good
14:00 maclean rather than having code like v = ((a >> 24) & 0xFF) | ((r >> 24) & 0xFF)...
14:00 egonw indeed
14:01 CIA-55 bioclipse: gilleain * r8881 /bioclipse2/trunk/cdk-externals/trunk/org.ope​nscience.cdk.render/src/org/openscience/cdk/r​enderer/generators/BasicBondGenerator.java: Use the default bond color.
14:02 egonw I am wondering how to do some SQL magic...
14:02 egonw I want to update a table...
14:02 egonw with a where inchi=bla
14:02 egonw but that inchi might actually be missing...
14:02 egonw so, sort of combo of INSERT and UPDATE ...
14:04 maclean eugh. I never get SQL right.
14:05 egonw OK, forgot it...
14:05 egonw I'll just set up a new table
14:06 egonw and adjust the select
14:08 maclean probably best :)
14:19 CIA-55 bioclipse: carl_masak * r8882 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java:
14:19 CIA-55 bioclipse: fixed #497
14:19 CIA-55 bioclipse: De-commented a previously commented-out instruction that is required for the
14:19 CIA-55 bioclipse: line-breaker not to hang. Don't know why it had been commented out.
14:26 egonw masak: see email about 8882
14:26 * masak sees email
14:27 maclean it's not really talking to other devs. more like a statement.
14:27 masak egonw: I _know_ who did it. it was me.
14:27 egonw well... it begs to be commented about...
14:28 masak I just don't know why I did it. I think it just got accidentally committed during some experimentation.
14:28 masak anyway, thanks for the tips about blame/annotate. they might come in handy for someone else.
14:29 masak oh, and 'blame' works in svn as well. as does 'praise'.
14:29 egonw :)
14:30 masak in git, only 'blame' and 'annotate' seem to work.
14:33 egonw so does git annotate
14:37 masak yes, that's what I said. :)
14:41 CIA-55 bioclipse: carl_masak * r8883 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: corrected a few typos
14:57 edrin btw. where is Ola?
14:57 egonw in Camrdige/UK
14:58 edrin oh
14:59 maclean really?
15:06 masak YA RLY
15:09 maclean I was about to say "I haven't seen him!" then realised that Cambridge isn't /that/ small...
15:11 egonw :)
15:11 egonw he's at the UCC, AFAIK
15:19 CIA-55 bioclipse: shk3 * r8884 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/META-INF/MANIFEST.MF: want to reuse the cml namespace constant
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15:50 CIA-55 bioclipse: shk3 * r8885 /bioclipse2/trunk/plugins/net.bioclipse.cml/ (2 files in 2 dirs): the validation is only for *.xml and *.xml files
16:00 julio left #bioclipse
16:03 masak "*.xml and *.xml files"? :)
16:03 masak what's the difference?
16:09 maclean intonation
16:09 masak ah, of course.
16:09 masak it's not how you say it, it's how you SAY it.
16:10 maclean exactly.
16:10 masak steinbeck: come back! I was just kidding!
16:11 maclean :)
16:12 CIA-55 bioclipse: gilleain * r8886 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​jchempaint/src/net/bioclipse/cdk/jchempaint/ (5 files in 2 dirs): Added more preferences to the JCP preference page.
16:13 maclean A serious commit message from a serious dev.
16:13 maclean :-|
16:17 masak maclean++ # for taking commit messages seriously
16:17 maclean tack
16:25 shk3 shall I do a speclipse release for the last beta?
16:26 maclean who are you asking?
16:26 maclean neither ola nor egon are on...
16:26 maclean :)
16:27 shk3 ah
16:27 shk3 well
16:33 masak no-one but us chickens here.
16:34 shk3 I will go ahead
16:39 CIA-55 bioclipse: shk3 * r8887 /bioclipse2/trunk/plugins/net.bioclip​se.nmrshiftdb/src/net/bioclipse/nmrsh​iftdb/wizards/ElucidateWizard.java: want to reuse the cml namespace constant
16:40 CIA-55 bioclipse: shk3 * r8888 /bioclipse2/trunk/plugins/n​et.bioclipse.spectrum/src/ (2 files in 2 dirs): want to reuse the cml namespace constant
16:58 CIA-55 bioclipse: gilleain * r8889 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​jchempaint/src/net/bioclipse/cdk/jchempaint/ (6 files in 3 dirs):
16:58 CIA-55 bioclipse: - Added another preference.
16:58 CIA-55 bioclipse: - Applies the global properties to newly opened files.
16:59 CIA-55 bioclipse: shk3 * r8890 /bioclipse2/trunk/plugins/ (5 files in 5 dirs): updated version id
17:03 CIA-55 bioclipse: shk3 * r8891 /bioclipse2/trunk/features/net.biocl​ipse.speclipse_feature/feature.xml: updated version id
17:09 CIA-55 bioclipse: shk3 * r8892 /bioclipse2/trunk/net.bioclipse​.speclipse-updatesite/site.xml: updated version id
17:09 egonw joined #bioclipse
17:20 maclean shk3 : I get an Access Restriction on vecmath from the SelectByClickModule
17:20 maclean didn't someone else have that?
17:20 maclean (and do you remember how to resolve it?)
17:21 shk3 in which project?
17:21 shk3 bioclipse?
17:21 shk3 or jcp?
17:22 maclean oh, right yes - specmol
17:23 shk3 works for me
17:23 shk3 just update
17:23 shk3 d
17:30 CIA-55 bioclipse: shk3 * r8893 /bioclipse2/trunk/plugins/net.bioclipse.specmol/ (3 files in 3 dirs): removed execution environment
17:33 CIA-55 bioclipse: shk3 * r8894 /bioclipse2/trunk/plugins/net.biocl​ipse.spectrum/META-INF/MANIFEST.MF: removed execution environment
17:34 CIA-55 bioclipse: shk3 * r8895 /bioclipse2/trunk/plugins/net.biocli​pse.nmrshiftdb/META-INF/MANIFEST.MF: removed execution environment
17:34 CIA-55 bioclipse: shk3 * r8896 /bioclipse2/trunk/plugins/net.bioc​lipse.bibtex/META-INF/MANIFEST.MF: removed execution environment
17:47 egonw maclean: very briefly back
17:47 maclean yes?
17:47 egonw do you it makes sense to have compact mode
17:47 egonw a global param?
17:47 maclean yes
17:47 egonw I started with the bools
17:47 egonw and left it out...
17:47 egonw this means that one cannot distinguish between large and small displays...
17:48 egonw because it is either compact or not
17:49 maclean well who knows what the user wants for preferences
17:49 maclean they can try it out, find that they don't like it, and change it back
17:49 maclean if they don't have it, they can't try it
17:50 egonw sure...
17:50 egonw but unlike bondwith...
17:50 egonw it's more like something you want to have depend on the size of the diagram
17:50 egonw if small, then compact...
17:50 egonw hence the name 'compact' I'd say
17:50 egonw useCompact... that could be a global param again
17:51 egonw I eman... I would never want the JCP editor in compact mode...
17:51 egonw but very likely I would in the SDF editor
17:51 egonw without having to switch option all the time...
17:51 maclean you mightn't - someone else might
17:51 maclean you don't have to switch all the time.
17:51 egonw sure
17:51 egonw that's not the point I want to make
17:51 maclean for small views it HAS to be compact. there is no option
17:52 egonw it is not a param alwaysShowsAsCompact, is it?
17:52 maclean no, its isCompact set globally
17:52 egonw argh...
17:52 egonw no, that's not what I mean...
17:52 egonw later...
17:53 egonw got to go back to dinner
17:53 maclean ok
18:05 maclean left #bioclipse
18:12 CIA-55 bioclipse: shk3 * r8897 /bioclipse2/trunk/plugins/​net.bioclipse.nmrshiftdb/ (META-INF/MANIFEST.MF configextension.xml): the tutorial shows from welcome
18:13 CIA-55 bioclipse: shk3 * r8898 /bioclipse2/trunk/plugins/net.biocl​ipse.spectrum/configextension.xml: the tutorial should show from welcome
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19:16 maclean joined #bioclipse
19:17 maclean egonw: you're probably right - remove it
19:27 maclean_ joined #bioclipse
20:37 CIA-55 bioclipse: gilleain * r8899 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​jchempaint/src/net/bioclipse/cdk/jchempaint/ (5 files in 2 dirs): Removed the isCompact global preference, as it should not be global.
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