Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-05-12

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All times shown according to UTC.

Time Nick Message
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07:37 egonw_ hi shk3
07:37 egonw_ where are you?
07:38 shk3 in the office
07:38 egonw ah...
07:38 egonw we are meting at 9:30, right?
07:39 shk3 yes
07:41 egonw has gilleain arrived already too?
07:42 jonalv joined #bioclipse
07:46 jonalv out of 208 new world order tests 18 errors and 2 failures now. egonw++
07:47 egonw many fails were do to unit tests being run twice
07:47 egonw giving 'File already exists!' exceptions
07:47 jonalv aha
07:48 egonw two more unit tests are failing becuase of the following problem:
07:48 jonalv so the ones that are left are going to be worse?
07:48 egonw the method in the CDKManager throws a BioclipseException
07:48 egonw which the unit tests make sure happens
07:48 rojasm joined #bioclipse
07:48 egonw with @Test(expected=BioclipseException.class)
07:48 egonw but
07:48 egonw the NWO proxy code wraps that in a RuntimeException
07:49 egonw no clue how to resolve that one
07:50 jonalv egonw: BioclipseException is checked and I sort of hate checked exceptions so yea I might have wrapped it in a RuntimeException. Should we change that?
07:50 egonw dunno
07:51 egonw you're the NWO designer
07:51 egonw now you have the use case
07:51 jonalv egonw: the cdkmanager is your area. You are the boss in this question. What would you like to see? :)
07:51 egonw I don't mind throwing some other exception
07:51 egonw when you decide what exception can be thrown under what conditions
07:52 jonalv egonw: if you ask me any exception is okey to throw anytime but checked exceptions must be caought and that sucks...
07:59 egonw so, what do you require manager methods to do?
07:59 egonw clearly, not throw BioclipseException
08:00 egonw should they use RuntimeExceptions?
08:00 jonalv egonw: there is nothing wrong with them throwing Biocliseexception
08:00 jonalv egonw: I want them to do that
08:00 jonalv egonw: why do you think that I don't want them throwing Bioclispeexception?
08:00 egonw ok, so the unit test is wrong?
08:01 jonalv egonw: no probably not.
08:01 jonalv I don't know
08:01 egonw well, please make up your mind
08:01 jonalv for JavaScript it doesn't matter I think
08:01 jonalv for java it is probably important that it actually throws a BioclipseExceptin
08:01 jonalv I will see if I can do that at all
08:02 jonalv I am not sure...
08:03 edrin joined #bioclipse
08:06 jonalv egonw: I am trying to rethrow that BiocliseException now instead...
08:11 maclean joined #bioclipse
08:12 jonalv egonw: okey that was ugly but now two more tests pass. I hope this was sort of what we wanted. BioclipseExcpetion really get's special treatment now though...
08:13 egonw well, that's why it is a BioclipseException, not?
08:13 jonalv egonw, olass: I am beginnign to think that maybe BioclipseException should be the only checked exception thrown by managers...
08:14 egonw was that not already the idea??
08:14 jonalv egonw: I guess... but don't come and expect Eclipse core excetions from the methods next...
08:14 jonalv egonw: the idea? oh no not really
08:15 jonalv egonw: That might be a better solution though
08:17 jonalv egonw: I guess I should do a rebase?
08:17 egonw yes, please do
08:22 CIA-40 bioclipse: miguelrojasch * r10240 /bioclipse2/trunk/_playground_/net.bioclipse.mede​a/src/net/bioclipse/plugins/medea/core/reaction/ (6 files): Updated Iterations object with chemObjects. Updated Qsar definitions
08:25 CIA-40 bioclipse: miguelrojasch * r10241 /bioclipse2/trunk/_playground_/net.bio​clipse.medea/src/net/bioclipse/medea/ (. Activator.java): Add Activator for medea
08:26 CIA-40 bioclipse: miguelrojasch * r10242 /bioclipse2/trunk/_playground_/net.bioclipse​.medea/src/net/bioclipse/plugins/medea/core/ (2 files in 2 dirs): More updated.
08:30 jonalv egonw: I ahve a feeling that I am maily merging you changes now...
08:30 jonalv egonw:  on the other hadn I am guessing you are quite busy so I will try and do this...
08:31 * egonw is getting ready for setting up a few more bc2 plugins
08:31 jonalv egonw: New World Order from the start? Cool?
08:32 masak joined #bioclipse
08:39 maclean joined #bioclipse
08:41 jonalv egonw: did you remove roundtrip tests from AstractCDKManagerPluginTest?
08:42 egonw roundtrip tests?
08:42 egonw I did not remove anything, actually
08:42 jonalv egonw: sdf and cml
08:42 jonalv egonw: you must have
08:42 egonw how so?
08:42 shk3 joined #bioclipse
08:42 jonalv egonw: I am trying to merge this...
08:43 jonalv egonw: it seems there is a MockMolecule instead..
08:43 egonw jonalv: which commit are you talking about?
08:44 jonalv egonw: I don't really know. How can I tell?
08:44 egonw git annotate ?
08:44 jonalv 42352 is the only number I see and it does not make sence..
08:45 jonalv egonw: I am running opendiff..
08:45 egonw oh...
08:45 egonw in that case ...
08:45 egonw hahaha :)
08:45 egonw seriously... no clue what method/class/you are refering too
08:45 jonalv egonw: git annotate does not exist..
08:45 egonw git blame ?
08:46 jonalv egonw: seriously merging other peoples chagnes suck
08:46 egonw yes, it does
08:47 jonalv egonw: well those roundrtip tests are not in my latest test run so you must have reomved them. Now they are going!
08:47 egonw which is why patches need to be clean
08:47 CIA-40 bioclipse: goglepox * r10243 /bioclipse2/trunk/plugins/ (5 files in 4 dirs): Added copyright and moved to net.bc.inchi.ui
08:47 egonw and why whitespace and good commit messages is so important
08:48 shk3_ joined #bioclipse
09:03 egonw joined #bioclipse
09:09 jonalv uhm who is working on cdk.loadReadctions?
09:11 egonw stefan/miguel
09:11 egonw is it giving trouble?
09:12 egonw he's sitting next to me...
09:12 egonw so, just relay messages here...
09:13 jonalv egonw: could you ask him if there is a test for it?
09:13 jonalv egonw: merging cdkmanager is steadily becoming more and more impossible...
09:14 shk3_ hi
09:14 zarah hello shk3_, you fantastic person you
09:14 shk3_ problems with reaction loading?
09:15 jonalv shk3_: well with merging, but I guess it's as things shoudl be
09:16 shk3_ conflicts, you mean?
09:16 shk3_ there are unit tests for the methods in net.bc.cdk.business.test
09:16 shk3_ as long as these work, it should be fine, generally speaking
09:17 jonalv plugin or "standard"?
09:17 shk3_ standard
09:18 jonalv shk3_: okry, need to start looking at those as well.
09:19 jonalv egonw: Do you think we should move everything into  plugintests?
09:19 egonw please explain
09:21 jonalv should all manager method tests be as pluign tests and the "normal" tests only do things like chcking anotations and such?
09:22 egonw yes, I think all tests need to become plugin tests
09:22 egonw the system runs pretty fast
09:24 jonalv I am beginning to think that we should merge this into trunk and then solve all problems as they pop up. But then again, probably a bad idea...
09:25 egonw that's what this rebasing is equivalent to
09:26 jonalv it'st just that people keep adding more code that is wrong that we have to change all the time..
09:27 jonalv zarah: tell olass please keep you code within 80 cols even if it is in JUnit test code...
09:27 zarah Consider it noted.
09:28 CIA-40 bioclipse: egonw * r10244 /bioclipse2/trunk/_playground_​/org.openscience.cdk.qsarweka/ (34 files in 13 dirs): Added CDK-Weka plugin (GPL-licensed)
09:34 jonalv zarah: tell olass please keep your code within 80 cols
09:34 zarah Consider it noted.
09:38 jonalv zarah: tell shk3_ please keep your code within 80 cols
09:38 zarah Consider it noted.
09:42 jonalv egonw: inchi seems to need to depend on cdk.business but that introduces a cycle. This sort of feels familiar. Where you working on this?
09:42 egonw update please
09:42 jonalv egonw: I have rebased...
09:42 egonw nb.inchi depended on cdk.business in the past, but no more
09:43 jonalv egonw: yea it doesn't for me. But it seems to be neeeded...
09:43 egonw run clean classpath?
09:44 jonalv there is some code using stuff from cdk.business still so I think we need to fix that
09:44 jonalv egonw: oh maybe this is because I choose the wrong one when I was merging
09:44 egonw what stuff?
09:44 egonw possibly
09:44 jonalv if (molecule instanceof CDKMolecule) {
09:44 jonalv IAtomContainer container = ((CDKMolecule)molecule).getAtomContainer();
09:45 egonw right, that is old stuff
09:45 jonalv AAAAAAAAAAAAAHHHHHHHHHHHHHHHHHHHHHHHHHHHH
09:45 egonw check the current code
09:45 jonalv I GIVE UP!
09:46 shk3__ joined #bioclipse
09:46 jonalv egonw: yes there other coe used adapter. I spent an eternity trying to figure out which one to choose and I of cousrse picked the wrong one
09:46 egonw :)
09:46 egonw next time... ask the author
09:46 jonalv egonw: you will have to merge this. I obviously don't know enough about it
09:47 * jonalv is gonna push his rebased master and leave the branch merge to egonw
09:47 jonalv half a day lost... *yey*
09:47 jonalv :(
09:50 jonalv egonw: I have pushed the master you will have to do the reabse when you have the time...
09:51 egonw ack
09:51 egonw not before tonite
09:51 egonw likely tomorrow
09:55 CIA-40 bioclipse: egonw * r10245 /bioclipse2/trunk/_playground_/org.opensc​ience.cdk.qsarweka/META-INF/MANIFEST.MF: Added missing deps
10:01 jonalv egonw: I wonder if I should stay away from that branch until then...
10:01 egonw yes, would make sense
10:12 CIA-40 bioclipse: egonw * r10246 /bioclipse2/trunk/_playgro​und_/net.sourceforge.weka/ (14 files in 7 dirs): Added bundle with Weka 3.4.6 (GPL-licensed)
10:13 CIA-40 bioclipse: egonw * r10247 /bioclipse2/trunk/_playground_/org.opensc​ience.cdk.qsarweka/META-INF/MANIFEST.MF: Added dependency on the Weka lib
10:15 rojasm joined #bioclipse
10:53 CIA-40 bioclipse: miguelrojasch * r10248 /bioclipse2/trunk/_playgroun​d_/net.bioclipse.medea.test/ (4 files in 3 dirs): Added molecule for prediction test
11:18 olass joined #bioclipse
11:20 egonw hi olass
11:20 olass hi egonw
11:20 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
11:20 olass @msg
11:20 zarah olass: 3 d 20 h 43 m 51 s ago, jonalv said why does not cdk.getNoMolecules work with an IFile?
11:20 zarah olass: 1 h 52 m 32 s ago, jonalv said please keep you code within 80 cols even if it is in JUnit test code...
11:20 zarah olass: 1 h 46 m 9 s ago, jonalv said please keep your code within 80 cols
11:21 olass zarah: tell jonalv thanks for the reminder
11:21 zarah Consider it noted.
11:21 jonalv zarah: just tell me...
11:21 zarah jonalv: 8 s ago, olass said thanks for the reminder
11:21 olass jonalv: it probably should...
11:21 jonalv olass: yes
11:22 olass (cdk.getNoMolecules work with an IFile)
11:22 olass my guess is that I needed it at the time and forgot to make it general
11:24 jonalv olass: net.bioclipse.ds and medea are that LCs stuff?
11:24 olass not medea
11:24 jonalv olass: what's medea then? :)
11:24 maclean medea is the mass-spectrum stuff
11:24 Gpox is that getNumberOfMolecules or is it return no molecuels?
11:25 jonalv maclean: aha
11:25 maclean :) I read it as the second one, too
11:25 egonw Medea is the PhD thesis of Miguel
11:25 jonalv egonw: oh so it's what you are working on now?
11:26 egonw yes
11:26 egonw medea is quite nice
11:26 egonw and linked to the seneca work done here
11:26 egonw structure elcuidation
11:26 egonw but now first going for lunch
11:26 egonw will explain more later
11:26 jonalv oki
11:26 egonw there should be a medea wiki page in wiki.bioclipse
11:26 egonw bbl
11:51 jonalv this computer need a restart
12:08 egonw joined #bioclipse
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12:10 maclean joined #bioclipse
12:11 egonw back
12:12 shk3 joined #bioclipse
12:14 egonw maclean: http://wiki.bioclipse.net/ind​ex.php?title=Reaction_plugin
12:14 zarah egonw's link is also http://tinyurl.com/6r6hab
12:17 shk3_ joined #bioclipse
12:20 rojasm joined #bioclipse
12:27 egonw jonalv: rebase on master about finished
12:28 jonalv egonw: cool
12:30 CIA-40 bioclipse: shk3 * r10249 /bioclipse2/trunk/plugins/net.bioclipse.reaction/ (11 files in 10 dirs): reaction editor roughly working
12:32 egonw jonalv: cleaning up some code with compile errors now for the NWO...
12:32 egonw that is
12:32 egonw new code, that got added by the mergning
12:33 CIA-40 bioclipse: shk3 * r10250 /bioclipse2/trunk/plugins/net.bioclips​e.reaction/src/net/bioclipse/reaction/ (61 files in 9 dirs): reaction editor roughly working
12:39 egonw jonalv: NewWorldOrder2 branch set up on pele
12:40 jonalv egonw++
12:55 jonalv egonw: did we loose the AllNewWorldOrderManagerPluginTest in this rebase?
13:00 egonw I still seem to have ti
13:00 egonw I still seem to have it
13:01 jonalv I am probably not checking it out in the correct way...
13:04 CIA-40 bioclipse: miguelrojasch * r10251 /bioclipse2/trunk/_playgro​und_/net.bioclipse.medea/ (10 files in 5 dirs): The last update
13:05 jonalv rojasm: uhm do you mean the latest? :)
13:10 CIA-40 bioclipse: goglepox * r10252 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): Added adapting ability for adapting to JChemPaintEditor
13:10 CIA-40 bioclipse: goglepox * r10253 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​jchempaint/src/net/bioclipse/cdk/jchempaint/ (3 files in 2 dirs):
13:10 CIA-40 bioclipse: Changed to make use of adapting to JCPEdiotr
13:10 CIA-40 bioclipse: This also makes it work with MultiPageMoleculesEditor too
13:13 egonw Gpox: what is it used for, IEditor.getAdapter() ?
13:14 Gpox to get a JChemPaintEdtior from both JChemPaintEdtior and MultiPageMoleculesEditor, it makes the toolbar in 2d structure view work
13:14 egonw ah, ok... makes sense
13:15 shk3__ joined #bioclipse
13:24 jonalv egonw++
13:24 Gpox joined #bioclipse
13:24 egonw jonalv: what did I do now?!?
13:25 jonalv egonw: so many cdkmanagerplugins tests are passing :)
13:25 masak egonw++
13:25 jonalv egonw: maybe we are actually ready to merge into trunk soon? :)
13:25 masak \o/
13:25 egonw oh goodies...
13:25 egonw jonalv: what's the score?
13:25 egonw I had not run them yet
13:26 egonw I have not run them yet
13:26 jonalv 212 tests, 14 errors 2 failures
13:27 jonalv (that's all the NewWorldOrder tests)
13:28 egonw and just CDKManager?
13:30 jonalv 152 tests 2 errors and 2 failures
13:35 CIA-40 bioclipse: shk3 * r10254 /bioclipse2/trunk/plugins/net.bioclipse.re​action/src/net/bioclipse/reaction/editor/ (ReactionEditor.java ReactionMultiPageEditor.java): working on save
13:36 olass jonalv++ //things seem to be progressing very well!
13:36 * olass has a busy day today :(
13:36 masak olass-- # Java-style comments
13:37 olass uhm
13:37 olass @slap masak
13:37 * zarah jabs masak with a C pointer
13:37 olass ?
13:37 egonw masak-- // for being a Perl nazi
13:37 masak ouch, that's sharp!
13:37 masak :)
13:37 jonalv egonw++, olass++ //we are doing Java here
13:38 * masak wisely abstains from removing karma from jonalv
13:43 steinbeck joined #bioclipse
13:44 egonw ha, there he is!
13:44 egonw welcome, 3G user
13:47 CIA-40 bioclipse: miguelrojasch * r10255 /bioclipse2/trunk/_playground_/net.bioclipse​.medea/src/net/bioclipse/plugins/medea/core/ (5 files in 4 dirs): Commit the probability functionality
13:50 CIA-40 bioclipse: shk3 * r10256 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: added methods to paint reactions
13:59 steinbeck_ joined #bioclipse
14:02 egonw joined #bioclipse
14:03 olass egonw: ping
14:04 olass egonw: We would like to merge the NWO on thursday into SVN
14:04 olass if you can be at BMC by then
14:04 olass we really need your help with this
14:04 olass damn
14:04 * olass will email
14:06 egonw joined #bioclipse
14:09 egonw joined #bioclipse
14:09 CIA-40 bioclipse: shk3 * r10257 /bioclipse2/trunk/plugins/net.biocli​pse.seneca/src/net/bioclipse/seneca/ (5 files in 5 dirs): number of steps is set in interface
14:10 shk3_ joined #bioclipse
14:14 shk3__ joined #bioclipse
14:15 * jonalv wonders whether wtgcs internet connection is especially unstable today...
14:16 egonw stefan is having trouble with the wireless
14:16 egonw mine seems to be ok
14:16 egonw or am I dropping out all the time too?
14:16 jonalv egonw: you are comming and going...
14:16 masak nuh huh.
14:16 egonw ah, ic
14:20 CIA-40 bioclipse: shk3 * r10258 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: added methods to paint reactions
14:24 CIA-40 bioclipse: shk3 * r10259 /bioclipse2/trunk/plugins/net.bioclipse.seneca/​src/net/bioclipse/seneca/editor/JudgePage.java: proper file names given when dropping
14:26 CIA-40 bioclipse: egonw * r10260 /bioclipse2/trunk/features/n​et.bioclipse.medea_feature/ (. .project build.properties feature.xml): Added a MEDEA feature
14:28 CIA-40 bioclipse: egonw * r10261 /bioclipse2/trunk/ (10 files in 6 dirs): Added a medea manager for the JS console
14:45 CIA-40 bioclipse: miguelrojasch * r10262 /bioclipse2/trunk/_playground_/net.bioclipse​.medea.test/src/testFiles/30460-92-5-2d.mol: added new molecule 30460-92-5-2d.mol
14:45 masak wow, Java++
14:46 egonw huh? que?
14:46 CIA-40 bioclipse: shk3 * r10263 /bioclipse2/trunk/plugins/net.bioclipse.seneca/​src/net/bioclipse/seneca/editor/JudgePage.java: save before judge page has been shown does no longer corrups sjs file
14:46 masak egonw: I just got a 'variable x might not have been initialized'
14:46 olass egonw: jcp does not compile
14:46 olass something with reactions
14:46 masak which alerted me to a misparenthisation.
14:46 olass did we not agree that reactions in post 2.0?
14:47 olass net.bc.cdk.jcp does not compile
14:47 olass ChemModelManipulator.newChemModel( reaction );
14:47 olass not applicable
14:47 shk3__ please update
14:47 olass shk3__: I have
14:47 egonw 10258
14:48 olass of cdk plugins?
14:48 egonw that or newer is supposed to fix an earlier break
14:48 egonw no, commit of bioclipse svn
14:48 olass or bioclipse?
14:48 olass org.openscience or net.bioclipse plugins?
14:48 shk3__ net.bc.cdk.jchempaint
14:48 shk3__ plugin
14:48 olass ok
14:48 egonw I don't have compile errors here, btw
14:49 olass should the reaction stuff not be in a branch?
14:49 olass since we agreed it is 2.1?
14:49 * olass don't want things half-working in 2.0
14:49 olass or at least a separate plugin?
14:49 olass egonw: what is your opinion?
14:49 shk3__ well, I need to use the jcp widget
14:50 egonw I think all functionality that could use this functionality is in separate plugins
14:50 shk3__ that can't be a separate plugin
14:50 olass shk3__: if you add another plugin you can still take advantage of other plugins
14:50 egonw so, users should not be able to just randomly run into it
14:50 olass egonw: good
14:50 olass no published methods
14:50 * olass is happy about that
14:51 jonalv a branch sounds like a genreally good idea...
14:51 egonw thanx god we will move to git in just two weeks
14:51 olass svn supports branches
14:52 jonalv olass: no
14:52 egonw it supports to concept
14:52 egonw not the use
14:52 * olass hates branches in svn
14:52 jonalv olass: or well it doesn't disallow it. IT jsut doesn't really help you...
14:53 CIA-40 bioclipse: shk3 * r10264 /bioclipse2/trunk/plugins/net.bioclipse​.data.seneca/data/example2/example.sjs: adopted example to number of steps ui
14:55 CIA-40 bioclipse: miguelrojasch * r10265 /bioclipse2/trunk/_playground_/net.bioclipse.medea​.test/src/net/bioclipse/medea/test/MedeaTest.java: updating the path of file-test 30460-92-5-2d.mol
14:55 wins joined #bioclipse
14:58 jonalv hi wins
14:58 wins hi
14:59 zarah oh hai wins
14:59 jonalv masak-- for refusing to fix bug: 1038 :(
14:59 wins another bot?
14:59 maclean zarah is, yes
14:59 masak you're a smart girl, zarah.
14:59 zarah masak: So they keep telling me. Over.
15:00 masak jonalv: I didn't look, but I think I know which ticket that is.
15:00 masak jonalv: (you lazy sod.)
15:01 maclean plz, what is tabless.xml?
15:01 maclean something to do with formatting, from the bug report
15:02 masak maclean: it's a file with settings, primarily for removing tabs as the default in files.
15:02 jonalv maclean: it's the Eclipse setting file masak++ made for us to use so that we would don't use any tabs-- any longer. However masak-- set the standard tab size to 2 so when people indent one step it get's indented 2 steps only. The CDK manager class is full of t step indentations... :(
15:03 masak maclean: i.e. the tab key no longer corresponds to the tab char.
15:03 jonalv instead it correpsnds to 2 spaces...
15:03 masak I happen to like 2-step indent.
15:03 maclean ah, the bit I didn't know was that it was the eclipse config
15:03 masak it's not my fault people don't look when they code.
15:03 maclean I find 2-step too short.
15:03 masak me too, for indentation.
15:04 masak but for other kinds of adjustments, it's handy.
15:04 jonalv masak: I think they might look but think: "Oh are we doing 2 step indenation? =Well I am using the file I was suposed to do so I guess we must be..."
15:05 steinbeck_ C=C1C(=O)CC2CC1C2(C)(C)
15:05 egonw steinbeck_: thanx
15:05 steinbeck_ Welcome
15:05 CIA-40 bioclipse: miguelrojasch * r10266 /bioclipse2/trunk/_playground_/net.bioclipse​.medea/src/net/bioclipse/plugins/medea/core/ (Fragmenter.java reaction/ExtractorSetQsarsRSI.java): control for nulls
15:05 jonalv @gg C=C1C(=O)CC2CC1C2(C)(C)
15:06 zarah jonalv: http://www.chemaxon.com/forum/ftopic2432.html
15:06 maclean "Geometry option fails for (bastard) Claus Benzol" :D
15:06 egonw juk
15:06 egonw evil
15:06 egonw oops
15:06 egonw being logged
15:06 egonw no, chemaxon is not evil
15:06 egonw just proprietary
15:06 egonw good software, free for academics
15:06 egonw java too
15:10 shk3_ joined #bioclipse
15:10 masak jonalv: a fair point. please fix the file, then.
15:11 jonalv masak: huh
15:11 jonalv ?
15:11 egonw steinbeck_:
15:11 egonw mol = cdk.fromSMILES("C=C1C(=O)CC2CC1C2(C)(C)");
15:11 egonw mol = cdk.generate2dCoordinates(mol);
15:11 egonw ui.open(mol);
15:11 jonalv @gg "mister context"
15:11 zarah jonalv: http://digg.com/world_news/If_Americans_K​new_the_Truth_about_Israel_Palestine_wow
15:11 masak jonalv: if you think 4 tab stops is a better standard, and it seems you do, please fix the setting in the file.
15:12 CIA-40 bioclipse: ospjuth * r10267 /bioclipse2/trunk/plugins/se.uu.farmbio.h​ivpred.client/src/net/bioclipse/xmpp/hivp​red/views/HIVPredictionResultView.java: Ensures that '.' is always used as decimal separator when rounding.
15:12 jonalv masak: no you should fix that, you wrote that file
15:12 masak jonalv: I kinda like it at 2.
15:12 egonw spectrum = medea.predictMassSpectrum(mol);
15:12 masak I'm not inclined to fix it.
15:12 egonw steinbeck_: that would be the call
15:12 masak I like it the way it is.
15:12 egonw but gives me a NPE
15:12 masak it suits me.
15:12 jonalv masak: well then perhaps I can assign all bugs about broken indenation to you?
15:13 masak jonalv: don't be silly.
15:13 CIA-40 bioclipse: ospjuth * r10268 /bioclipse2/trunk/plugins/net.bioclipse.qsar.ui/sr​c/net/bioclipse/qsar/ui/builder/QSARBuilder.java: Ensures that '.' is always used as decimal separator when rounding.
15:14 CIA-40 bioclipse: carl_masak * r10269 /bioclipse2/trunk/plugins/net.bioclipse.sc​ripting.ui/src/net/bioclipse/scripting/ui/ (3 files in 2 dirs):
15:14 CIA-40 bioclipse: [TabCompleter] factored out GUI-indep code
15:14 CIA-40 bioclipse: The behaviour can now be properly tested, which will help prevent unfortunate
15:14 CIA-40 bioclipse: regressions.
15:14 jonalv masak: I honestly think you are being silly. What your file you have on your computer is up to you but the one you publish could maybe be a bit more "idiot proof"?
15:14 masak jonalv: I didn't publish it for the 2 spaces, I published it for the spaces.
15:14 CIA-40 bioclipse: carl_masak * r10270 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
15:14 CIA-40 bioclipse: [JsConsoleView] extra space after 'help'
15:14 CIA-40 bioclipse: This way, people can type 'he', tab complete, and have 'elp ' added, so
15:14 CIA-40 bioclipse: that they can keep on typing "arguments" to the help command.
15:15 jonalv masak: I think you published it to fix the indenation problem. Clearly you failed.
15:15 shk3__ joined #bioclipse
15:15 CIA-40 bioclipse: ospjuth * r10271 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (DescriptorsPage.java MoleculesPage.java ResponsesPage.java): Ensures that '.' is always used as decimal separator when rounding.
15:15 masak jonalv: yes, clearly.
15:18 jonalv egonw: could you send me that UU Beamer template you used? :)
15:19 egonw yes
15:19 egonw ping me in 15 minutes
15:20 jonalv zarah: ping me in 15 minutes
15:20 zarah jonalv: ping
15:20 jonalv zarah: no
15:20 zarah jonalv: I see.
15:22 masak jonalv: ooh, that would be nice indeed.
15:28 CIA-40 bioclipse: miguelrojasch * r10272 /bioclipse2/trunk/_playground_/net.bioc​lipse.medea.test/META-INF/MANIFEST.MF: added plugin for extraction xml functionalities
15:38 jonalv egonw: ping
15:38 egonw pong
15:38 egonw oh, right
15:38 egonw ummm... jonalv ping+15
15:38 egonw in the middle of something right now
15:40 maclean type error : types 'person' and type 'int' are not valid for the sum operator.
15:41 maclean wait, no, that's not the right error.
15:41 maclean never mind.
15:42 CIA-40 bioclipse: shk3 * r10273 /bioclipse2/trunk/plugins/net.​bioclipse.data.reaction/data/ (a_arginine.ms1.cml a_asparagine.ms1.cml): more examples
15:43 CIA-40 bioclipse: shk3 * r10274 /bioclipse2/trunk/plugins/net.bioclipse.re​action/src/net/bioclipse/reaction/editor/ (ReactMolDrawingComposite.java ReactionEditor.java): the jcp displays
15:47 CIA-40 bioclipse: shk3 * r10275 /bioclipse2/trunk/plugins/net.biocli​pse.spectrum/src/net/bioclipse/spect​rum/business/ISpectrumManager.java: better help
15:56 jonalv egonw: ping
15:57 maclean he's still busy, I think
15:57 maclean (he looks busy)
15:57 jonalv :(
16:00 maclean http://gilleain.tumblr.com​/post/106779540/egon-busy
16:00 zarah maclean's link is also http://tinyurl.com/p8vpym
16:00 maclean :)
16:00 maclean (actually , he might not be now...)
16:01 maclean Perhaps some sort of live feed....
16:03 egonw pong
16:03 egonw OK, done for now
16:03 egonw next problem in Medea is less easy fixed
16:04 jonalv egonw: could you send me that UU Beamer template you used? :)
16:04 egonw yes
16:05 egonw http://frederic.haziza.net/beamer/
16:05 zarah egonw's link is also http://tinyurl.com/oz9pw4
16:09 CIA-40 bioclipse: shk3 * r10276 /bioclipse2/trunk/plugins/net.bioclip​se.data.reaction/data/reaction.2.cml: reaction1 and reaction2 were the same
16:14 jonalv egonw: dz
16:14 * jonalv gives up for today
16:16 CIA-40 bioclipse: shk3 * r10277 /bioclipse2/trunk/plugins/net.bioclipse.re​action/src/net/bioclipse/reaction/editor/ (3 files): cleanup
16:27 CIA-40 bioclipse: miguelrojasch * r10278 /bioclipse2/trunk/_playground_/net.bio​clipse.medea/src/net/bioclipse/plugins​/medea/core/CMLSpectrumCreator.java: exchange int to double value for analysis
16:50 steinbeck joined #bioclipse
16:54 CIA-40 bioclipse: shk3 * r10279 /bioclipse2/trunk/plugins/net.biocl​ipse.reaction/src/net/bioclipse/rea​ction/editor/ReactionEditor.java: removed an important line
16:59 edrin left #bioclipse
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17:04 steinbeck__ joined #bioclipse
17:10 shk3_ joined #bioclipse
17:15 shk3__ joined #bioclipse
17:16 CIA-40 bioclipse: miguelrojasch * r10280 /bioclipse2/trunk/_playground_/net.bioc​lipse.medea.test/src/testFiles/foo.cml: cml result
17:20 steinbeck__ http://cdk.pastebin.com/m2b3b2bb
17:20 zarah steinbeck__'s link is also http://tinyurl.com/pnblww
17:30 CIA-40 bioclipse: shk3 * r10281 /bioclipse2/trunk/plugins/net.bioclipse.seneca/ (10 files in 3 dirs): working on judges page
17:43 rojasm left #bioclipse
19:05 wins joined #bioclipse
19:06 CIA-40 bioclipse: ospjuth * r10282 /bioclipse2/trunk/plugins/net.bioclipse.ds.test​s/src/net/bioclipse/ds/tests/TestSignSIc.java: Changed test for new bogus hit name 'HIT 1'.
20:58 CIA-40 bioclipse: ospjuth * r10283 /bioclipse2/trunk/plugins/ (10 files in 6 dirs): Implemented an ISubStructure in cdk.business and adapted all DS plugins to use this for substructure matches. Part of bug 1037 solved.
20:58 zarah bug #1037 | http://tinyurl.com/qechlm
21:01 CIA-40 bioclipse: ospjuth * r10284 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/domain/ISubStructure.java: Added ISubStructure interface to define that an object can provide substructures for e.g. highlighting in JCP.
21:38 egonw joined #bioclipse
21:44 rojasm joined #bioclipse
23:02 rojasm left #bioclipse

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