Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-05-07

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All times shown according to UTC.

Time Nick Message
05:13 egonw joined #bioclipse
05:30 rojasm joined #bioclipse
06:06 rojasm joined #bioclipse
06:18 malick joined #bioclipse
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07:37 de_maas joined #bioclipse
07:45 olas joined #bioclipse
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08:00 masak joined #bioclipse
08:01 CIA-45 bioclipse: ospjuth * r5569 /bioclipse2/trunk/plugins/net.bioclip​se.biomart/src/net/bioclipse/biomart/ (4 files in 2 dirs): Updated getAdapter() methods to use super impl.
08:01 CIA-45 bioclipse: ospjuth * r5570 /bioclipse2/trunk/plugins/net.bioclip​se.biojava.business/src/net/bioclipse​/biojava/domain/BiojavaSequence.java: Updated getAdapter() methods to use super impl.
08:02 CIA-45 bioclipse: ospjuth * r5571 /bioclipse2/trunk/plugins/net.bioclipse.bi​omoby/src/net/bioclipse/biomoby/services/ (4 files): Updated getAdapter() methods to use super impl.
08:09 egonw joined #bioclipse
08:10 * olas is afk for 30 mins
08:38 edrin joined #bioclipse
08:38 edrin hi
08:47 egonw hi edrin
08:47 edrin hi egonw
08:48 edrin no progress in protocol yet, had no time
08:48 egonw ack
09:09 olas hi edrin, hi egonw
09:09 egonw hi olas
09:11 CIA-45 bioclipse: ospjuth * r5572 /bioclipse2/trunk/plugins/n​et.bioclipse.cdk.business/ (3 files in 2 dirs): Updated getAdapter() methods to use super impl.
09:13 CIA-45 bioclipse: ospjuth * r5573 /bioclipse2/trunk/plugins/net.bioclipse.​cdk10.jchempaint/src/net/bioclipse/cdk10​/jchempaint/outline/CDKChemObject.java: Updated getAdapter() methods to use super impl.
09:14 CIA-45 bioclipse: ospjuth * r5574 /bioclipse2/trunk/plugins/net.bioclipse.core/ (9 files in 3 dirs): Added default impl of PropertySource and getAdapter() from BioObject.
09:14 CIA-45 bioclipse: ospjuth * r5575 /bioclipse2/trunk/plugins/net.bioclipse.​core.tests/net.bioclipse.recording/net/b​ioclipse/core/domain/BioListTest.java: Removed unnecessary adapter.
09:18 CIA-45 bioclipse: ospjuth * r5576 /bioclipse2/trunk/plugins/net.bioclipse.j​mol/src/net/bioclipse/jmol/views/outline/ (5 files): Updated getAdapter() methods to use super impl.
09:19 CIA-45 bioclipse: ospjuth * r5577 /bioclipse2/trunk/plugins/net.bioclipse.core​/src/net/bioclipse/core/domain/BioList.java: Updated getAdapter() methods to use super impl.
09:19 CIA-45 bioclipse: ospjuth * r5578 /bioclipse2/trunk/plugins/net.bioclipse​.core.tests/net.bioclipse.recording/net​/bioclipse/recording/RecordTest.java: Removed unnecessary adapter.
09:21 CIA-45 bioclipse: ospjuth * r5579 /bioclipse2/trunk/plugins/ (11 files in 3 dirs): Removed unnecessary getAdapter().
09:23 CIA-45 bioclipse: ospjuth * r5580 /bioclipse2/trunk/plugins/net.bioclipse.serv​ices/src/net/bioclipse/services/views/model/ (5 files): Updated getAdapter() methods to use super impl.
10:21 egonw_ joined #bioclipse
11:12 jonalv hi egonw have you seen masaks mail? What do we think? :)
11:15 CIA-45 bioclipse: jonalv * r5581 /bioclipse2/trunk/plugins/​net.bioclipse.structuredb/ (4 files in 4 dirs):
11:15 CIA-45 bioclipse: exports iBatis stuff (maybe we should have a iBatis plugin?)
11:15 CIA-45 bioclipse: Fixed path/url problems. Eclipse classloader obviously works a bit different...
11:55 rojasm joined #bioclipse
12:14 jonalv joined #bioclipse
12:14 CIA-45 bioclipse: ospjuth * r5582 /bioclipse2/trunk/plugins/net.bio​clipse.core/META-INF/MANIFEST.MF: Export props package.
12:18 egonw jonalv: breifly...
12:18 egonw what was it about again?
12:22 jonalv egonw, tabs...
12:23 egonw rigth...
12:23 egonw yes, go ahead
12:23 egonw sounds fine
12:23 egonw must I install those template thingies?
12:23 * jonalv guess so...
12:23 masak egonw: do you have any opinion about the tab mail?
12:24 masak or should I just go ahead and replace all tab chars?
12:25 egonw [14:23] <egonw> yes, go ahead
12:25 egonw masak: do I really need to install those templates?
12:25 masak egonw: no
12:26 masak but I would like you to change the tab policy
12:26 masak as laid out in the mail
12:26 egonw right
12:27 masak goodie
12:27 egonw thoughts about setting up a svn postcommit script to scan for tabs too?
12:27 masak that might be a nice idea
12:27 masak maybe a precommit one that rejects files with tabs?
12:28 masak because mid-line tabs might need manual intervention anyway
12:28 masak (tabs are evil, mid-line tabs doubly so)
12:28 egonw masak: yes
12:31 * olas likes tabs
12:32 * olas use tabs a lot
12:32 * olas is afraid all his commits will be rejected
12:33 masak olas: have you read my mail?
12:35 egonw yeah, we have to put a stop to olas commits...
12:35 jonalv lol
12:35 egonw he just keeps committing those horrofying tabs
12:35 egonw he just goes on and on and on ...
12:36 * olas has installed masaks files now
12:36 * olas is scared
12:37 olas damn
12:37 olas too afraid to code :-)
12:37 masak :)
12:37 masak don't panic
12:37 masak I'm watching over you, as usual
12:38 olas *phew*
12:38 * masak adopts his God pose
12:38 olas Masak implements Creator ?
12:38 masak conform, humans!
12:38 masak olas: also, Masak is a singleton
12:52 olas egonw: http://bioclipse.blogspot.com/2008/05​/jchempaint-with-highligting-in.html
12:53 olas egonw: how do I go about coloring individual atoms in different colors?
12:53 olas That is very important!
12:53 egonw mom
12:53 olas also: how finished is the JCP integration in Bioclipse2?
12:53 egonw we're still talking JCP based on cdk-1.0.x, right?
12:53 * olas is on mac and cannot test the actual editing part
12:53 olas yes
12:54 egonw olas: it's still broken
12:54 egonw haven't finished it yet...
12:54 EskilA joined #bioclipse
12:54 egonw there is a problem with getting the data model updated...
12:54 olas please please...
12:54 egonw have to track down why that fails...
12:54 egonw yes, I know...
12:54 egonw no time, no time... :(
12:54 olas :-(
12:55 egonw looks nice
12:55 egonw ok, here's a request
12:55 egonw can we have filters for the Outline?
12:55 olas we could have
12:55 egonw so that we can filter the tree for C atoms?
12:55 olas sure
12:55 olas what for?
12:55 * egonw mumbles... 'have to keep him busy, so that he doens't ask about JCP all the time ... '
12:55 olas :-)
12:56 masak egonw: good plan
12:56 olas only display C atoms? What for?
12:56 egonw masak: I like the TAB things... that will keep him busy :)
12:56 egonw olas: no, any arbitrary filtering...
12:56 egonw never mind
12:56 * olas is not THAT busy...
12:56 masak egonw: exactly
12:56 egonw not really important...
12:56 egonw olas: oh, you;re not busy yet...
12:56 egonw in that case...
12:57 * olas is not too busy to request JCP
12:57 jonalv olas: You are not busy? Maybe you could give me a hand then? ;)
12:57 * olas is too busy for most other things
12:58 olas egonw: seriously, about JCP, we desperately need it by end of May
12:58 olas if that is not possible you must tell me asap
12:58 olas need to cancel a lot of stuff then
12:58 egonw oi...
12:58 olas and about the individual coloring of atoms, how do I go about that?
12:59 masak if I can be of any help with that JCP thing...
12:59 masak just let me know
12:59 masak I'm busy too, but it sounds like fun
12:59 egonw masak: yes you could be helpful...
12:59 egonw right now... I ran into this problem...
12:59 egonw if you start the editor...
12:59 egonw you can change edit mode...
12:59 olas masak is on mac
12:59 egonw right click on an atom
12:59 egonw oh crap...
12:59 masak sorry...
12:59 egonw stupid Macs
13:00 masak indeed
13:00 olas stupid JCP
13:00 egonw for using default Java libraries??
13:00 masak is that the problem?
13:00 olas is that the problem?
13:00 olas :-)
13:00 egonw yes, the Mac JVM has a few AWT bugs
13:00 masak oh
13:00 olas how does Jmol solve it?
13:00 olas because thay do
13:00 egonw only use Image
13:01 egonw or something like that...
13:01 egonw actually...
13:01 egonw Miguel Howard did file a bug report on something
13:01 egonw which he in the end had to work around
13:01 egonw but don't think that bug got fixed by Apple ever
13:01 olas can you find out how he worked around it?
13:02 olas it's still the hardest bug of Bioclipse
13:02 olas (and the award is still a box of toffifee)
13:02 olas egonw: still there?
13:03 egonw yes... making an API change in the CDK
13:03 olas olas (3:02:03 PM): and about the individual coloring of atoms, how do I go about that?
13:03 egonw to fix a limitation
13:03 egonw olas: right
13:03 olas you said it was possible
13:03 olas please get me started
13:03 egonw olas: so how did you color the atoms in the screenshot in the blog?
13:03 olas that's just highlighting
13:03 olas I need individual coloring
13:03 olas in different colors
13:04 egonw ok
13:05 egonw user setColorHash
13:05 egonw use setColorHash
13:06 olas hmm
13:06 olas on the renderer?
13:06 egonw use Renderer2DModel.setColorHash
13:06 olas will look at that
13:14 egonw olas: I have no idea how that is used...
13:15 egonw oh... that's for the background color :(
13:15 olas who might know?
13:15 egonw stefan
13:15 egonw ok... do this:
13:15 egonw write a custom AtomColorer
13:15 olas but it IS possible to color individual atoms?
13:15 egonw yes, sure
13:15 olas what is an AtomColorer
13:15 olas any article on that?
13:15 olas junit test?
13:15 egonw no, don't think so...
13:15 egonw :)
13:15 olas or existing AtomColorer?
13:15 egonw yes
13:16 olas that sounds interesting
13:16 egonw cdk.renderer.color
13:16 egonw CDKAtomColors is the default
13:16 olas I can write an AtomColorer that will color atoms by my algorithm?
13:16 egonw right
13:16 olas cool, that's just what I need
13:16 olas renderer2D.setColorer(myOwnColoere)
13:16 egonw then just Renderer2DModel.setAtomColorer(yourColorer)
13:16 egonw :)
13:19 de_maas left #bioclipse
13:31 olas joined #bioclipse
13:31 * olas computer crahed horribly bad
13:31 olas crashed
13:32 olas but hey, it's a Mac
13:32 egonw no...?!??! it's a Mac... not windows!
13:32 * olas was suspecting that comment from egonw
13:32 masak egonw: trust me. they crash too.
13:32 olas too often..
13:32 olas seems to be memory problems on most accasions
13:32 olas I have too much memory :-)
13:33 CIA-45 bioclipse: ospjuth * r5583 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.jche​mpaint/src/net/bioclipse/cdk10/jchempaint/outline/ (CDKChemObject.java ChemObjectPropertySource.java): Added PropertySources for CDKChemObjects.
13:35 egonw hehehe
13:35 olas hmm, egonw: problem
13:35 olas again
13:35 egonw sure, what's up?
13:35 olas the AtomColorer works only on IAtom
13:36 olas what if I want the color to depend on a calculation on all molecules?
13:36 olas all atoms I mean
13:36 egonw how do you mean?
13:36 olas so let's say, I color one atom red, and the neighbouring will be pink
13:36 egonw yeah, that's exact what it does
13:36 olas ??
13:36 egonw oh...
13:37 egonw you mean color as function to some other atom?
13:37 olas yes
13:37 egonw you mean color as function of a distance to some other atom?
13:37 olas that's just an example
13:37 olas color atoms based on a calculation on the molecule
13:37 egonw well, you need to have the AtomColorer create new colors...
13:37 olas but I just get an IAtom as input
13:38 olas how can I get the molecule?
13:38 egonw MyCustomAtomColorer.newColors​BasedOnDistanceTo(IMolecule, IAtom centralAtom)
13:38 olas I mean, the other atoms and bonds in the molecule
13:38 egonw you can't
13:38 olas but how too hook that into JCP?
13:38 olas but I must!
13:39 egonw do it from the class which recieved to call to color atoms...
13:39 egonw if you ensure that that is in a bioclispe class
13:39 egonw e.g. in the MDLEditorPage tihngy
13:39 olas what do you mean?
13:39 olas how can I do that?
13:39 * olas is confused
13:40 * egonw notices that Olas memory has not recovered from the reboot yet
13:40 olas hmm
13:40 olas can Atoms have properties?
13:40 egonw yes
13:40 olas :-)
13:40 olas then I can set a custom property
13:40 egonw IAtom.setProperty(Object, Object)
13:40 olas and color by it
13:40 egonw sure
13:40 egonw yes
13:40 olas that would be ok with me I suppose
13:41 egonw yes, that would be fine
13:41 olas good
13:55 jonalv okey people, I have compile error on cdk again
13:55 jonalv It sais I am missing kxml2-2.3.0.jar
13:55 egonw :)
13:55 egonw yeah... I did say:
13:55 olas update
13:55 olas I added it yesterday
13:55 egonw [15:03] <egonw> yes... making an API change in the CDK
13:55 olas oh
13:55 egonw minor ones...
13:56 egonw just global replace IChemObjectReader -> ISimpleChemObjectReader
13:56 jonalv okey, ETA?
13:56 egonw done
13:56 egonw ETA: -5 mins
13:56 masak that's fast!
13:56 egonw -8 actually
13:56 masak wow!
13:56 jonalv so why am I haviong problems?
13:56 egonw ah...
13:57 egonw jonalv: that ETA
13:57 egonw jonalv: please just do that global replace...
13:57 jonalv huh?
13:57 egonw right click on net.bioclipse.cdk in the navigator
13:57 egonw then go to Search menu -> File...
13:57 egonw then as Search cdk.io.IChemObjectReader
13:58 egonw hit the Replace button
13:58 egonw and replace it with cdk.io.ISimpleChemObjectReader
13:58 egonw my ETA is 30 minutes...
13:58 egonw (need to reboot Eclipse for that)
13:59 * jonalv istryibng that
13:59 jonalv *is trying
13:59 jonalv egonw, you saking that it takes you 30 minutes to reboot eclipse?
14:06 CIA-45 bioclipse: jonalv * r5584 /bioclipse2/trunk/plugins/ (6 files in 4 dirs): Followed egonw's instructions and replaced all cdk.io.IChemObjectReader with cdk.io.ISimpleChemObjectReader. It seemed to have bettered things. (No idea why...)
14:06 egonw jonalv: I renamed the interface
14:06 egonw that's all
14:07 jonalv hm hm do I need to do it in cdk10 too?
14:07 egonw no
14:07 jonalv I don't have commit bit to cdk...
14:12 egonw do you need that?
14:17 CIA-45 bioclipse: ospjuth * r5585 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10.jchempaint/src/net/bio​clipse/cdk10/jchempaint/ui/editor/ (5 files): Created interface IJCPBasedEditor for multiple editors based on JCP. Also addded options to set AtomColorer on editor DrawingPanel.
14:18 CIA-45 bioclipse: ospjuth * r5586 /bioclipse2/trunk/plugins/net.bioclipse.cdk1​0.jchempaint/src/net/bioclipse/cdk10/jchempa​int/outline/StructureContentProvider.java: Made constructor public.
14:21 CIA-45 bioclipse: ospjuth * r5587 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10.jchempaint/src/net/bio​clipse/cdk10/jchempaint/ui/editor/ (IJCPBasedEditor.java JCPMultiPageEditorContributor.java): Updates in interface required by ActionContributor.
14:25 CIA-45 bioclipse: ospjuth * r5588 /bioclipse2/trunk/plugins/net.bioclipse.cdk​10.jchempaint/src/net/bioclipse/cdk10/jchem​paint/ui/editor/JChemPaintPopupMenu.java: Changed to interface IJCPBasedEditor instead of gardcoded to MDLMolfileEditor.
14:25 egonw jonalv: another small API change coming up in trunk/
14:26 olas does it have with getting JCP to work in Bioclipse? :-)
14:26 egonw yeah, sure :)
14:26 egonw whatever you like ...
14:26 egonw hahahaha
14:27 egonw seriously...
14:27 egonw there is a nice Bioclipse spin off...
14:27 egonw this is all for reading PubChem search results
14:27 olas I like it
14:27 olas nice
14:27 olas we should add that
14:27 egonw yes
14:27 olas I will assist if you like
14:27 egonw jonalv: are you up to that?
14:27 olas but JCP is of course more urgent...
14:28 egonw importing 11M compounds from PubChem into BC2?
14:28 olas why not?
14:28 olas it's a big file, but whateve
14:28 olas will be even better with MySQL
14:29 olas egonw: can I color the background of an atom?
14:29 olas not just the text?
14:29 egonw yes
14:29 olas how?
14:29 egonw that's what that HashMap was for
14:29 olas AtomBackgroundColorer?
14:29 egonw [15:06] <egonw> use Renderer2DModel.setColorHash
14:29 olas hmm ok
14:29 egonw inconsistent... yes, I know
14:29 olas maybe that's what I want then...
14:32 * egonw is about to process a 256MB PubChem search result file with the CDK...
14:33 egonw here goes...
14:33 egonw Processed 2000
14:33 egonw 3k
14:33 egonw 4k
14:33 egonw quite fast :)
14:33 egonw 5k
14:34 egonw 6k
14:34 egonw ah... NullPointerException
14:34 egonw :)
14:36 egonw about 4ms per molecule
14:36 * egonw is pleased
14:36 egonw ummm... per substance
14:50 * jonalv is back. egonw, what was that about?
14:50 egonw [16:32] * egonw is about to process a 256MB PubChem search result file with the CDK...
14:50 egonw performance
14:50 jonalv <egonw> jonalv: are you up to that?
14:50 egonw ah... can your structuredb deal with PubChem's 11M compounds?
14:51 * jonalv has no idea. I can't even get it to run in Bioclipse
14:52 jonalv class not found excetion related to logging :(
14:52 * jonalv HATES logging. It's just problems!
14:52 masak indeed.
14:53 masak in my days, we printed to the raster printer, and we were happy
14:54 jonalv cdk is not compiling again...
14:55 jonalv egonw, could you assist?
14:55 egonw sure
14:55 * egonw just boots a second Eclipse
14:59 * egonw has some patches in git uncommited to svn
15:10 CIA-45 bioclipse: egonw * r5589 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10.jchempaint/src/net/bio​clipse/cdk10/jchempaint/ui/editor/ (3 files): Attempting to get JCP going
15:11 egonw jonalv: ok, got git-svn in sync again...
15:11 egonw eclipse is recompiling
15:12 jonalv oki
15:15 CIA-45 bioclipse: egonw * r5590 /bioclipse2/trunk/plugins/net.bioclipse.cd​k10.jchempaint/src/net/bioclipse/cdk10/jch​empaint/ui/editor/MDLMolfileEditor.java: Fixed compile problem due to bad merge
15:20 * jonalv is updateing
15:20 egonw so am I :)
15:20 egonw git-svn doesn't understand svn:externals :(
15:20 jonalv aha
15:20 jonalv too bad
15:20 egonw yeah... big downside
15:21 jonalv doesn't that make it more or less useless?
15:22 egonw no, because the normal svn stuff works like a charm
15:22 egonw so I can hack on the train, and still do commits
15:22 jonalv okey but how do you solve the svn:externals stuff?
15:22 egonw manually update :)
15:23 jonalv okey I still can't get the svn stuff to compile here
15:23 jonalv *cdk stufff :)
15:24 egonw yeah, hang on...
15:25 * jonalv is nagning on :)
15:25 * jonalv ca'nt sepll
15:25 jonalv dyslectics have all the fnu
15:26 egonw ok, update to:
15:26 CIA-45 bioclipse: egonw * r5591 /bioclipse2/trunk/plugins/net.bioclipse.cdk/ (.classpath META-INF/MANIFEST.MF): Fixed jar change
15:32 jonalv okey a few less compile error now
15:32 jonalv gonna check what's not compiling
15:33 jonalv IChemObjectReader cannot be resolved to a type in CDKManager
15:33 jonalv what was the new name again?
15:34 egonw it's simple: ISimpleChemObjectReader
15:34 jonalv aha
15:34 jonalv okey I am on it
15:34 jonalv The method customizeReading(ISimpleChemObjectReader, IChemFile) is undefined for the type
15:34 jonalv CDKManagerHelper
15:35 jonalv oh never mind
15:37 egonw which plugin is this?
15:37 egonw oh sorry... that red cross slipped my attention
15:38 egonw you will commit those fixes?
15:38 jonalv seems like you already did it :)
15:38 jonalv ?
15:38 jonalv oh not all
15:38 egonw not for CDKManagerHelper
15:38 jonalv yea commit comming
15:39 CIA-45 bioclipse: jonalv * r5593 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java CDKManagerHelper.java):
15:39 CIA-45 bioclipse: s/IChemObjectReader/ISimpleChemObjectReader/
15:39 CIA-45 bioclipse: cdk now compiles
15:46 jonalv so egonw how are things going with jchempaint?
15:48 egonw not
15:48 egonw not working on that right now
15:48 jonalv why not?
15:49 jonalv oh I thought that was your main thing for the moment
15:49 egonw because I am payed to do other things :)
15:49 jonalv aha
15:49 jonalv $work taking time
15:49 jonalv (yea that was perl lingo)
16:50 CIA-45 bioclipse: jonalv * r5594 /bioclipse2/trunk/plugins/​net.bioclipse.structuredb/ (2 files in 2 dirs):
16:50 CIA-45 bioclipse: [Manifest]
16:50 CIA-45 bioclipse: import org.apache.commons.logging from somewhere (need to make some way to ensure there is one to import)
16:50 CIA-45 bioclipse: [StructuredbManager]
16:50 CIA-45 bioclipse: Create a local user and set him as logged in user for the new local database. (need to make way to find all local structuredb instances and somehow start them up when needed (set logggedinUser and so) )
16:52 * jonalv is off, cya!
17:00 * egonw is leaving too
17:00 egonw bye
17:57 rojasm joined #bioclipse
18:03 CIA-45 bioclipse: ospjuth * r5595 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.jchempaint/ (2 files in 2 dirs): Export resources for multiple JCP editors.
18:51 rojasm hi all,
18:51 rojasm I have some errors with the osgi plugins where I can find it?
18:51 rojasm http://www.osgi.org/Download/Release4V41 maybe?
18:52 rojasm or there is some http address?
19:24 egonw joined #bioclipse
21:13 rojas1 joined #bioclipse
22:42 CIA-45 bioclipse: carl_masak * r5596 /bioclipse2/trunk/ (581 files in 150 dirs): replaced tabs with spaces in all files

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