Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-06-03

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All times shown according to UTC.

Time Nick Message
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07:04 slyrus egonw: I'll try the new bioclipse target thing in the morning
07:06 egonw slyrus: ack
07:12 egonw annzi: ping
07:13 annzi yes
07:13 egonw can you make a demo MoSS data set?
07:13 egonw or have one? a small one?
07:14 CIA-69 bioclipse.moss: Egon Willighagen master * r9ebd002 / plugins/net.bioclipse.moss/plugin.xml : Defined content types for MoSS input and output files - http://bit.ly/du2AAO
07:14 CIA-69 bioclipse.moss: Egon Willighagen master * rce86e6c / (13 files in 6 dirs): Added template data plugin for example MoSS files - http://bit.ly/9LcBdf
07:15 annzi egonw: I have the ones you get from downloading moss
07:15 annzi there are a few
07:15 egonw what is the license of those?
07:16 egonw Gpox: ping
07:16 Gpox pong
07:16 egonw Gpox: meanwhile... can you give me some tipse about this:
07:16 egonw Gpox: say, I want to set up a mol table editor for a file, looking like a SMILES file, but different format
07:16 annzi egonw: http://www.borgelt.net/moss.html you find three examples on top of the page
07:16 zarah annzi's link is also http://tinyurl.com/ye7vrkn
07:17 egonw Gpox: say, a MoSS input or MoSS output file?
07:18 Gpox IMoleculesEditorInput, I don't remeber how hardcoded it is that the fist column is the structure
07:19 egonw Gpox: ack, thanx for the pointer
07:19 Gpox if they are small there is one for lists the same as smiles are using
07:20 Gpox IMoleculesEditorModel is the interface
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07:59 CIA-69 bioclipse.moss: Egon Willighagen master * re39b379 / plugins/net.bioclipse.data.mo​ss/data/MoSS/small.mossinput : Some small demo data: find the acid - http://bit.ly/bw6seY
07:59 CIA-69 bioclipse.moss: Egon Willighagen master * r57e4e83 / (2 files): Added ouput with default MoSS settings - http://bit.ly/bCLv0n
08:07 CIA-69 bioclipse.moss: Egon Willighagen master * r034ff74 / plugins/net.bioclipse.moss/src/net/b​ioclipse/moss/wizards/InputPage.java : Use the new file types - http://bit.ly/8Z2PKz
08:10 egonw Gpox: technical question about popup menus...
08:10 egonw Gpox: anzzi's code is using the EP org.eclipse.ui.popupMenus
08:11 egonw can that be replaced with org.eclipse.ui.menus
08:11 egonw using
08:11 egonw <menuContribution
08:11 egonw locationURI="popup:
08:11 egonw ..."> ?
08:11 annzi egonw: popup menues will be removed later
08:11 Gpox yes
08:11 egonw annzi: ah, ok
08:11 annzi It now opens via new
08:12 egonw also the Run MoSS action?
08:12 annzi but i'm lazy when working, i want to open it fast
08:12 egonw now that there are content types, we can show it just for .mossinput files
08:13 annzi not sure about the moss action
08:13 annzi but probably yes
08:13 egonw ok, then I'll go ahead
08:13 egonw tie it, it should not be much work
08:14 egonw Gpox: one last thing...
08:14 egonw the attribute locationURI ... does that really point somewhere?
08:14 egonw ah, no... this looks nice, but too much work for now... :(
08:14 egonw Gpox: nvm
08:18 annzi egonw: I have a git question. I want to update my moss branch and accidentally removed your last commit:( it is unstaged now. Is there a way to redo that commit without messing things up? What happens if I commit it again?
08:18 annzi *git is hard*
08:18 egonw git reset origin/master ?
08:19 egonw or first: git checkout .
08:23 annzi egonw: thank you!! I did git checkout . and then fetched again :)
08:23 egonw good
08:34 egonw annzi: about to commit something?
08:34 egonw I have on last commit, I think
08:34 annzi egonw: no
08:34 annzi go ahead
08:37 CIA-69 bioclipse.moss: Egon Willighagen master * r2333fb7 / plugins/net.bioclipse.moss/plugin.xml : Restrict the popup action to .mossinput files - http://bit.ly/9U7zxm
09:18 egonw @seen jonalv
09:18 zarah jonalv was last seen 18 h 21 m 22 s ago in #bioclipse saying 'egonw: right, and then what do I do?'
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10:18 egonw bugger... the spectrum functionality is seriously broken by the nu.xom, cmlxom Import-Package transition...
10:21 Gpox On the topic of cmlxom, egon could you comment on bug 1975
10:21 Gpox @pz 1975
10:21 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1975
10:22 egonw oh no
10:23 egonw guys, that bug report is really, really bad news
10:23 egonw ABI conflict
10:24 egonw Gpox: I second your solution
10:24 egonw Gpox: we should also file a bug report upstream to CMLXOM to ask them not to use setLevel()
10:25 egonw but adding log4j.jar into the net.bioclipse.org.cmlxom seems the best thing to do right now
10:51 annzi egonw: can you read SMILES?
10:52 egonw you did the pharmbio.org course, not?
10:52 egonw then you should be able to read them too
10:53 annzi no I didn't take the course
10:55 egonw annzi--
10:55 egonw you cannot do everything...
10:55 annzi I couldn't take it, to late to register
10:55 egonw but it would have been a good course...
10:55 annzi indeed
10:55 annzi maybe in the fall
10:56 masak reading SMILES isn't too hard.
10:56 annzi (when it's not to late to register;)
10:56 egonw ui.open(cdk.fromSMILES("CCC"))
11:09 masak annzi: I think by just studying the examples at http://en.wikipedia.org/wiki/Simplifi​ed_molecular_input_line_entry_specifi​cation#Application_on_some_molecules - one can get a pretty decent idea how SMILES works.
11:09 zarah masak's link is also http://tinyurl.com/3348v7
11:09 annzi masak: thank!
11:10 annzi how kind of you
11:10 masak annzi: planning meeting later today?
11:11 annzi masak: of course, when do you prefer?
11:11 masak going home for lunch now. be back in ~1h. sometime then, perhaps?
11:11 egonw joined #bioclipse
11:12 annzi sounds great, going for lunch myself
11:12 masak &
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15:09 egonw Gpox: got a sec?
15:09 Gpox yes
15:09 egonw I'm looking at RendererModel.setExternalSe​lectedPart(IAtomContainer)
15:09 egonw but I don't get the code...
15:09 egonw is that your code?
15:09 * egonw will run git annotate
15:10 egonw ok, nvm
15:10 egonw got it figured out now
16:52 CIA-69 bioclipse.core: Arvid Berg 2.4.x * r6854c41 / (2 files):
16:52 CIA-69 bioclipse.core: Included a pirvate log4j in bundle
16:52 CIA-69 bioclipse.core: Fix for bug 1975 - http://bit.ly/cnPrCN
16:52 zarah bug #1975 | http://tinyurl.com/2vkdhgl
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18:28 CIA-69 org.openscience.cdk: Egon Willighagen bioclipse2.4 * r740d1cd / (537 files in 177 dirs): Uploaded CDK 1.3.5 + Standard InChI patch + CDK-JChemPaint 10 - http://bit.ly/bzgPiR
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18:38 CIA-69 org.openscience.cdk: Arvid Berg bioclipse2.4 * rd7fe08f / (14 files in 14 dirs): Removed net.bioclipse.xom from Require-Bundle - http://bit.ly/bfsjro
18:38 CIA-69 org.openscience.cdk: Arvid Berg bioclipse2.4 * ra01983d / (4 files in 4 dirs): Removed org.xmlcml.xmlxom from Require-Bundle - http://bit.ly/bHdawM
18:38 CIA-69 org.openscience.cdk: Arvid Berg bioclipse2.4 * r2088c56 / (3 files in 3 dirs): Added Import-Package nu.xom - http://bit.ly/9577JX
18:38 CIA-69 org.openscience.cdk: Arvid Berg bioclipse2.4 * r2c425df / (4 files in 4 dirs): Added Import-Package nu.xom and org.xmlcml.cml.* - http://bit.ly/akup2x
18:38 CIA-69 org.openscience.cdk: Egon Willighagen bioclipse2.4 * r70294c9 / (5 files in 5 dirs): Just depend on nu.xom; XOM 1.2 is fine too... can we depend on verion=1.x in some way? - http://bit.ly/bgiIIU
18:41 CIA-69 org.openscience.cdk: Egon Willighagen bioclipse2.4 * r880dbce / (2 files in 2 dirs): Removed qsar.model.data package with only data, no java classes - http://bit.ly/cBzc24
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