Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-05-07

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All times shown according to UTC.

Time Nick Message
06:44 Gpox joined #bioclipse
06:44 Gpoks joined #bioclipse
06:50 Gpox joined #bioclipse
07:18 edrin joined #bioclipse
07:24 egonw joined #bioclipse
07:25 egonw moin
07:25 zarah ni hao egonw
07:58 jonalv joined #bioclipse
07:59 jonalv o/
08:19 edrin joined #bioclipse
08:42 shk3 hi all
08:42 zarah hi shk3
08:42 shk3 for me, showing the help in bc no longer works
08:42 shk3 does it work for you
08:42 shk3 ?
08:46 egonw mom
09:10 olass joined #bioclipse
09:10 masak joined #bioclipse
09:15 jonalv egonw: rebased
09:15 egonw jonalv++
09:27 masak rebase++
09:27 edrin hi olass
09:28 jonalv :( //found a bug in my method for finding the method to invoke.
09:30 CIA-40 bioclipse: shk3 * r10107 /bioclipse2/trunk/plugins/net​.bioclipse.chemoinformatics/ (2 files in 2 dirs): extended cheat sheet for tanimoto
09:30 olass jonalv: catch 22?
09:30 jonalv olass: ah no not really, different methods :)
09:31 olass *puh*
09:32 egonw olass: ping
09:32 egonw I'll cc lars on the bug report
09:32 olass do that
09:33 olass I'll CC you on my email to Lars
09:38 CIA-40 bioclipse: goglepox * r10108 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint/src/net/bioclipse/cdk/jch​empaint/editor/SWTMouseEventRelay.java:
09:38 CIA-40 bioclipse: Changed parameter to mouseWheelMoved...(
09:38 CIA-40 bioclipse: to 0
09:38 CIA-40 bioclipse: goglepox * r10109 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​jchempaint/src/net/bioclipse/cdk/jchempaint/ (2 files in 2 dirs):
09:38 CIA-40 bioclipse: Chaged to untyped events and added doit = false
09:38 CIA-40 bioclipse: Resolves bug #1022
09:38 zarah bug #1022 | http://tinyurl.com/djuyq6
09:43 CIA-40 bioclipse: goglepox * r10110 /bioclipse2/trunk/cdk-externals/trunk/o​rg.openscience.cdk.control/src/org/open​science/cdk/controller/ZoomModule.java:
09:43 CIA-40 bioclipse: Activated zoom to cursor
09:43 CIA-40 bioclipse: Fixes bug #770
09:43 zarah bug #770 | http://tinyurl.com/ctwfkj
09:43 egonw Gpox++
09:48 CIA-40 bioclipse: shk3 * r10111 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/ (6 files in 5 dirs): Added tanimoto ui elements
09:53 CIA-40 bioclipse: shk3 * r10112 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/src​/net/bioclipse/cdk/ui/wizards/TanimotoWizard.java: createSDF method has been renamed
10:24 egonw shk3: the help works for me
10:24 egonw (sorry for the delayed answer)
10:24 egonw that's the downside of parallel computing
10:28 egonw olass: ping
10:28 shk3 ok
10:28 egonw cannot run the linux download, I'm running 64 bit
10:28 shk3 then it must be my eclipse configuration
10:33 egonw perhaps...
10:34 egonw maybe I am trying something different...
10:34 egonw I tried the Help menu
10:34 egonw for the core feature only
10:34 egonw and hit the second item...
10:34 egonw the one below 'Welcome'...
10:36 shk3 that's what I am doing
10:36 shk3 and I get a
10:36 shk3 java.lang.NoClassDefFoundError: org/eclipse/equinox/http/jetty/JettyConfigurator
10:36 egonw mmm...
10:37 shk3 but it looks like and seems to be an eclipse config problem
10:37 egonw that sounds like a missing plugin
10:37 egonw right
10:37 shk3 another question
10:37 shk3 on the welcome screen,
10:37 shk3 the buttons/icons are in two lines for me
10:38 shk3 if I hover over on in the first line
10:38 shk3 (overview/first steps)
10:38 egonw yes, same here
10:38 shk3 the text is behind the icons in secons row
10:38 egonw is a eclipse/linux thing
10:38 egonw anoying indeed
10:38 egonw please file a bug report
10:38 shk3 ah, linux only
10:38 shk3 ?
10:38 egonw not sure about win
10:38 egonw but OS/X is fine
10:39 shk3 ah
10:39 egonw please file that report, assign to Ola and cc me
10:41 shk3 done
10:43 egonw thanx
11:26 egonw olass: ping
11:26 olass egonw: pong
11:26 egonw olass: should the CDKMOlecule use the CDKManager?
11:26 egonw or must not?
11:26 egonw or ...
11:26 olass hmm
11:26 olass why not?
11:27 olass jonalv, comment?
11:27 egonw getFingerprint is not using it
11:27 egonw toString is
11:27 olass getFingerprint is not in cdkmanager ;)
11:27 olass I think they should use CDKManager
11:27 egonw mmm... damn
11:27 olass I see no reason not to...
11:27 egonw inchi stuff is in the inchi manager of course
11:27 jonalv olass: what are we talking about?
11:27 olass yup
11:27 olass this adds a dep
11:27 olass I can live with that
11:28 egonw no, circular deps
11:28 olass hmm
11:28 olass you need an adapter then
11:28 olass Gpox is the master of Adapters
11:28 * olass knows only very little
11:28 egonw mmm...
11:28 egonw inchi did not really depend on cdk.business
11:29 egonw unclean dep list
11:30 CIA-40 bioclipse: egonw * r10113 /bioclipse2/trunk/plugins/net.bioclips​e.inchi.business/META-INF/MANIFEST.MF: Removed non-existing dependency
11:39 egonw Gpox: ping
11:39 egonw Gpox: can you help me with an adapter thingy
11:39 Gpox sure
11:40 egonw here?
11:43 olass egonw: regarding r10113; How can you remove something which is non-existing?
11:51 egonw magic
11:52 egonw sorry, bad commit message
12:12 jonalv olass: do you have a minute_
12:13 olass in tel
12:14 egonw olass: please fix 1025
12:14 egonw I need that fixed for my current work
12:14 egonw (it's easy)
12:18 jonalv Nooo I can haz no Virtual project
12:24 CIA-40 bioclipse: carl_masak * r10114 /bioclipse2/trunk/plugins/net.bioclips​e.scripting.ui/src/net/bioclipse/scrip​ting/ui/business/GuiActionAdvice.java: [GuiActionAdvice] removed unused import
12:31 * masak discovers js.delay(seconds)
12:31 masak I don't think it's in the right place.
12:31 masak it has nothing whatsoever to do with Javascript or the Javascript console.
12:32 egonw wait before running the rest of the javascript ?
12:32 masak all it does is lock up Bioclipse for the specified number of seconds.
12:32 masak its implementation is one-threaded Java.
12:32 masak other threads can still continue running their Javascript scripts while delay() is running.
12:32 masak it's a sham.
12:36 egonw can you fix it?
12:36 masak maybe we should just move it to ui.
12:36 masak since that's what we're locking up.
12:37 egonw :)
12:37 egonw no, don't think that was Ola's idea of the method
12:37 egonw he uses it in the JChemPaint drawing script
12:38 masak I know. I read the commit in which he added it.
12:38 masak I'm just saying it's not a js-specific manager method.
12:39 masak the js namespace is for doing things with the Javascript console.
12:39 egonw so, do you know how to make it what Ola wanted it to do and make it treadsafe?
12:39 masak egonw: threadsafe delay? :)
12:40 masak well, I don't know...
12:40 masak making it an async gui action would be sufficient, I think.
12:40 * jonalv might have some ideas. What's the problem masak? :)
12:40 masak but that whole area is sort of awaiting the New New New World Order, so...
12:41 * jonalv loves to have ideas and to see other people implement them ;)
12:41 masak my point wasn't that it locks up the system. I don't much care about that.
12:41 masak my point was that it doesn't belong in the js namespace.
12:42 jonalv masak: what do you mean by "locks up the system"?
12:42 masak jonalv: it uses the main thread to do Thread.delay()
12:43 jonalv masak: the gui thread?
12:43 masak hm, don't know which thread...
12:43 masak the one you get when you don't switch threads anywhere.
12:43 jonalv I would think it did it to whatever thread happends to call it...
12:46 masak aye.
13:04 CIA-40 bioclipse: ospjuth * r10115 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business/src/net/bioclipse/cdk/d​omain/CDKMoleculeSelectionHelper.java: Added license/copyright. Solves 1025.
13:05 olass masak: we were discussiong the right place for it
13:05 * olass has been in tel for some time
13:06 olass we placed it in js since found no better place
13:09 CIA-40 bioclipse: ospjuth * r10116 /bioclipse2/trunk/features/net.bio​clipse.xws4j_feature/feature.xml: Unpack xws4j upon installation.
13:19 egonw olass: can you please send me a screenshot of what the welcome page looks like on your machine?
13:19 egonw then I'll blog on planet eclipse about this...
13:19 egonw and ask if someone there knows a solution...
13:21 shk3 joined #bioclipse
13:31 egonw olass: how can I convert an IFile into an IMolecule withouth knowing about CDKMnaager?
13:31 egonw e.g. using Jmol readers?
13:32 olass no idea...
13:32 egonw though not refering to any specific IMolecule impl
13:32 olass jonalv?
13:32 jonalv joined #bioclipse
13:35 egonw jonalv: can you drop by for a sec?
13:35 jonalv yes \o/
13:43 jonalv egonw: those tests where more or less already ordered that way so whenever you want to start fiddling with cdkmanagerpluginstests give me a ping
13:48 CIA-40 bioclipse: ospjuth * r10117 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (6 files in 3 dirs): Link to XMPP cheat sheet from welcome page.
13:57 CIA-40 bioclipse: ospjuth * r10118 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (META-INF/MANIFEST.MF about.mappings bioclipse.product): Updated for version 090506 in product.
13:58 CIA-40 bioclipse: carl_masak * r10119 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java:
13:58 CIA-40 bioclipse: [ScriptingConsoleView] don't exec empty commands
13:58 CIA-40 bioclipse: Before, a '> ' sign was printed and the command was executed, even when
13:58 CIA-40 bioclipse: empty. Now, we bail out early instead.
13:59 CIA-40 bioclipse: carl_masak * r10120 /bioclipse2/trunk/plugins/ (4 files in 3 dirs):
13:59 CIA-40 bioclipse: [ScriptingConsoleView] factored out code into method
13:59 CIA-40 bioclipse: The new method, 'carryOutCommand', prints the command to the console and
13:59 CIA-40 bioclipse: executes it. It is thus a wrapper for 'executeCommand'. It's private, but
13:59 CIA-40 bioclipse: there's a public 'carryOutCommandAndWait' that also waits for the script
13:59 CIA-40 bioclipse: execution to finish before returning control.
13:59 CIA-40 bioclipse: Fixes #941.
13:59 zarah bug #941 | http://tinyurl.com/d78kuh
14:00 olass masak++
14:01 olass good work
14:03 masak olass: did it work? I didn't test it. :)
14:03 olass haha
14:03 * olass is used to masak code working
14:03 olass and... I haven't closed the bug yet
14:04 * masak is rife with expectation
14:04 olass sorry, but cannot test right now :(
14:04 olass later today hopefully
14:04 masak I haven't stricken out the bug from the list yet either.
14:04 masak olass: no rush.
14:06 egonw jonalv: ping
14:07 egonw I'm ready for NWO stuff
14:13 shk3 Is there a way to create an ICDKMolecule from a cdk atomcontainer/molecule?
14:13 shk3 should be common, but I can't find it
14:14 egonw new CDKMOlecule(IAtomContainer) ?
14:17 shk3 hm
14:17 shk3 why is this via constructor
14:17 olass should be like that
14:17 shk3 whereas there are methods like
14:17 olass shk3: we do not expose CDK internals (like IAtomContainer) in the bioclispe scripting API
14:18 olass or at least try not to
14:18 shk3 cdkmanager.create(IMolecule)
14:18 shk3 ok
14:18 shk3 anyway
14:19 CIA-40 bioclipse: ospjuth * r10121 /bioclipse2/trunk/plugins/net.bioclipse.ds/: Initial import.
14:23 CIA-40 bioclipse: ospjuth * r10122 /bioclipse2/trunk/plugins/net.bioclipse.ds/ (54 files in 15 dirs): Some components for bioclipse decision support, see http://wiki.bioclipse.net/index.ph​p?title=Bioclipse_Decision_Support.
14:23 masak ds?
14:23 zarah CIA-40's link is also http://tinyurl.com/cko8t2
14:23 masak ah.
14:24 CIA-40 bioclipse: ospjuth * r10123 /bioclipse2/trunk/plugins/net.bi​oclipse.ds/src/net/bioclipse/ds/ (16 files in 6 dirs): Some components for bioclipse decision support, see http://wiki.bioclipse.net/index.ph​p?title=Bioclipse_Decision_Support.
14:24 zarah CIA-40's link is also http://tinyurl.com/cko8t2
14:29 CIA-40 bioclipse: ospjuth * r10124 /bioclipse2/trunk/features/​net.bioclipse.ds_feature/: Initial import.
14:32 CIA-40 bioclipse: ospjuth * r10125 /bioclipse2/trunk/features​/net.bioclipse.ds_feature/ (.project build.properties feature.xml): Feature for bioclipse decision support, see http://wiki.bioclipse.net/index.ph​p?title=Bioclipse_Decision_Support.
14:32 zarah CIA-40's link is also http://tinyurl.com/cko8t2
14:32 CIA-40 bioclipse: ospjuth * r10126 /bioclipse2/trunk/plugins/​net.bioclipse.ds.signsig/: Initial import.
14:33 CIA-40 bioclipse: ospjuth * r10127 /bioclipse2/trunk/plugins/net​.bioclipse.ds.signsig.bursi/: Initial import.
14:33 CIA-40 bioclipse: ospjuth * r10128 /bioclipse2/trunk/plugins/​net.bioclipse.ds.smarts/: Initial import.
14:34 CIA-40 bioclipse: ospjuth * r10129 /bioclipse2/trunk/plugins/net​.bioclipse.ds.smarts.bursi/: Initial import.
14:35 CIA-40 bioclipse: ospjuth * r10130 /bioclipse2/trunk/plugins/net.bioclipse.ds.tests/: Initial import.
14:35 CIA-40 bioclipse: ospjuth * r10131 /bioclipse2/trunk/plugins/n​et.bioclipse.ds.dblookup/: Initial import.
14:36 CIA-40 bioclipse: ospjuth * r10132 /bioclipse2/trunk/plugins/net.​bioclipse.ds.dblookup.bursi/: Initial import.
14:40 CIA-40 bioclipse: ospjuth * r10133 /bioclipse2/trunk/plugins/ (107 files in 62 dirs): Som stubs for bioclipse decision support, see http://wiki.bioclipse.net/index.ph​p?title=Bioclipse_Decision_Support.
14:40 zarah CIA-40's link is also http://tinyurl.com/cko8t2
14:41 CIA-40 bioclipse: ospjuth * r10134 /bioclipse2/trunk/features/net.b​ioclipse.ds_feature/feature.xml: Updated feature with all ds plugins.
14:42 shk3 btw, I can no longer expand sdf files in the navigator.
14:42 shk3 is that intended?
14:42 olass yes
14:42 olass removed completely
14:42 olass did not work
14:42 olass and was confusing
14:43 * olass is going to the box
14:43 shk3 hm
14:57 olass hmm
14:57 olass uhm?
14:58 masak uh...
14:58 olass huh?
15:02 masak "huh?"?
15:03 olass äh..
15:17 jonalv okey...
15:18 olass egonw: question
15:18 olass why does the getMDLMolfileString not accept an IMolecule?
15:19 olass I think we should always expose IMolecule outwards...
15:19 olass egonw: you agree?
15:19 olass can I fix it?
15:19 olass (or will you)?
15:19 olass egonw: around?
15:20 jonalv olass: could we have a freeze of the cdkmanager? :)
15:21 olass right
15:21 olass wish we could...
15:22 * jonalv mentally prepares for lot of merge sessions the comming time
15:22 olass jonalv++ //take a deeeeep breath
15:25 egonw olass: yes, please go ahead
15:25 egonw but I will review your patch!
15:25 olass *brr*
15:26 olass egonw: lol
15:26 olass params="IMolecule molecule",
15:26 olass methodSummary="Returns a MDL V2000 molfile serialization")
15:26 olass @TestMethods("testGetMDLMolfileString()")
15:26 olass public String getMDLMolfileString(ICDKMolecule molecule);
15:26 olass no need for me to change the params ;)
15:27 egonw oh. sweden has a swine flu case now too
15:27 egonw right
15:27 olass god have mercy
15:28 egonw in stockholm
15:28 egonw trip to USA!
15:28 egonw not mexico
15:28 olass jost wo'nt admit it
15:28 olass won't
15:29 egonw well, they can just ask the FBI/CIA whatever
15:29 egonw and see which planes she took
15:29 CIA-40 bioclipse: ospjuth * r10135 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): Made getMDLString accept IMolecule instead of ICDKMolecule.
15:29 egonw btw, rajarshi fixed your TokenError bug
15:30 egonw patch pending
15:30 egonw going home now
15:30 egonw bye
15:54 CIA-40 bioclipse: ospjuth * r10136 /bioclipse2/trunk/plugins/net.bi​oclipse.ds/src/net/bioclipse/ds/ (5 files in 2 dirs): Added standard some simple test results.
15:55 CIA-40 bioclipse: ospjuth * r10137 /bioclipse2/trunk/plugins/net​.bioclipse.ds.signsig.bursi/ (2 files in 2 dirs): Created a stub for a SignSIcRunner.
16:14 CIA-40 bioclipse: ospjuth * r10138 /bioclipse2/trunk/plugins/net​.bioclipse.ds.signsig.bursi/ (META-INF/MANIFEST.MF build.properties plugin.xml): Added a bogus test implementation for the SignSic stub.
16:14 CIA-40 bioclipse: ospjuth * r10139 /bioclipse2/trunk/plugins/net.bioclips​e.ds.tests/src/net/bioclipse/ds/tests/ (TestBursiSmarts.java TestDSManager.java TestSignSIc.java): Refactored tests to separate classes. Added a simple SignSic test.
16:15 CIA-40 bioclipse: ospjuth * r10140 /bioclipse2/trunk/plugins/net.bioclipse.ds/src/​net/bioclipse/ds/model/SubStructureMatch.java: Added toString() for better debug out.
16:15 CIA-40 bioclipse: ospjuth * r10141 /bioclipse2/trunk/plugins/net.bioclipse.ds/s​rc/net/bioclipse/ds/business/DSManager.java: Better error handling when initializing tests from EP.
17:34 CIA-40 bioclipse: shk3 * r10142 /bioclipse2/trunk/plugins/net.bioclipse.seneca/ (11 files in 5 dirs): integrated gilliean's annealing engine, result display as sdf
17:37 CIA-40 bioclipse: ospjuth * r10143 /bioclipse2/trunk/plugins/net​.bioclipse.ds.signsig.bursi/ (META-INF/MANIFEST.MF build.properties jars/): Added . in runtime classpath.
17:42 CIA-40 bioclipse: shk3 * r10144 /bioclipse2/trunk/plugins/net.bio​clipse.data.seneca/data/example2/ (c13.cml data.cml example.sjs): updated sample files
17:55 CIA-40 bioclipse: shk3 * r10145 /bioclipse2/trunk/plugins/net.biocli​pse.seneca/src/net/bioclipse/seneca/​anneal/AdaptiveAnnealingEngine.java: scores are displayed as higher=better
18:10 egonw joined #bioclipse
18:24 edrin left #bioclipse
19:13 edrin joined #bioclipse
22:12 paulymer_ joined #bioclipse
22:53 CIA-40 bioclipse: gilleain * r10146 /bioclipse2/trunk/plugins/net.biocli​pse.seneca/src/net/bioclipse/seneca/ (6 files in 2 dirs):
22:53 CIA-40 bioclipse: - Smoothed the integration of the adaptive annealer with bioclipse.
22:53 CIA-40 bioclipse: - Extended the engine to be cancellable through the adapter.

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