Camelia, the Perl 6 bug

IRC log for #cdk, 2008-03-12

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All times shown according to UTC.

Time Nick Message
02:10 CIA-18 jmol: hansonr * r9096 /trunk/Jmol/src/org/jmol/adapte​r/readers/more/Mol2Reader.java: version=11.4.RC12_dev # bug fix: mol2 reader cannot read files with single-line comments
02:11 CIA-18 jmol: hansonr * r9097 /branches/v11_4/Jmol/src/org/jmol/ (adapter/readers/more/Mol2Reader.java viewer/Jmol.properties): version=11.4.RC12_dev # bug fix: mol2 reader cannot read files with single-line comments
02:12 CIA-18 jmol: hansonr * r9098 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: version=11.4.RC12_dev # buf fix: mol2 reader cannot read files with single-line comments
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07:24 tjeerd morning
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09:24 thomas_ku moin
09:33 tjeerd morning
09:34 tjeerd anyone experience here with CMLspect?
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10:23 CIA-20 bioclipse: ospjuth * r5084 /bioclipse2/trunk/plugins/net.bioclipse.services/ (26 files in 7 dirs): Adapted ServiceView to read roots from new Extension point for ServiceRoot. A lot of model and schema changes.
10:28 CIA-20 bioclipse: ospjuth * r5085 /bioclipse2/trunk/plugins/net.bioclipse.services/ (10 files in 3 dirs): Adapted all roots for new EP-system and updated labelprovider to use icon in EP.
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14:26 CIA-19 bioclipse: ospjuth * r5087 /bioclipse2/trunk/plugins/n​et.bioclipse.ui/plugin.xml: Added contexts for Bioinformatics and Chemoinformatics.
14:40 egonw tjeerd: I'm currently replying to your question...
14:42 CIA-19 bioclipse: ospjuth * r5088 /bioclipse2/trunk/plugins/n​et.bioclipse.ui/plugin.xml: Cleanup of contexts
14:43 tjeerd egonw: thanks, I've read the newsgroup post from Mark and your reply there, that also already cleared it a bit up
14:43 egonw ok, good :)
14:43 egonw I'm also sending Prof. Lancashire an email now...
14:44 egonw the CMLSpectView code is available from:
14:44 egonw http://jspecview.svn.sourcefo​rge.net/viewvc/jspecview/dev/
14:50 tjeerd that is the JSpecView program I downloaded and have running here (although only from command-line, still not as applet)
14:52 egonw there is an applet version too...
14:52 tjeerd I downloaded the CMLspect.xml file which came as attachment to the paper
14:52 egonw good
14:52 tjeerd yes, but it doesn't seem to work from within my browser though
14:53 egonw with that ArrayIndexOutOfBoundsException?
14:53 egonw oh, sorry... so, the example from his paper is giving that error?
14:53 egonw sorry... fever is not good for thinking abilities
14:54 tjeerd sorry, let me start at the beginning ;)
14:54 tjeerd JSV application (JAR from command-line) with the CMLspect from the paper works perfectly
14:55 tjeerd JSV application with CMLSpect generated by your R-script (mzXML to CMLSpect) gives the ArrayIndexOutOfBoundsException
14:55 egonw ok, yeah, that's how I interpreted it :)
14:56 egonw CMLSpect is still quite flexible...
14:56 egonw so JSV needs to be patches to support the XCMS-output convention we set up...
14:56 tjeerd that's what I guess indeed
14:59 tjeerd but I guess when using CMLSpect it's theoretically possible to convert it to mzXML (via XSLT or something)?
14:59 egonw no, because mzXML does not support the concept of a consensus spectrum
15:01 egonw tjeerd: are you fluent in Java?
15:02 tjeerd quite fluent
15:02 tjeerd (java is so broad...)
15:05 egonw ok, without having looked at the JSV code today...
15:05 egonw there can be two reaons:
15:05 egonw 1. the individual spectra in the CMLSpect created from the XCMS output do not have the peaks yet
15:05 egonw 2. something goes wrong with the hierarchy of elements
15:06 egonw neither of which should be overly difficult to fix in the JSV code, I think
15:10 CIA-19 bioclipse: jonalv * r5089 /bioclipse2/trunk/plugins/net.bioclipse.cdk/ (.classpath META-INF/MANIFEST.MF): removed weka
15:12 CIA-19 bioclipse: ospjuth * r5090 /bioclipse2/trunk/plugins/net.bioclipse.services/ (7 files in 3 dirs): ServiceTypes now appear in ServiceView. Also added support to filter by context.
15:47 CIA-19 jmol: hansonr * r9099 /trunk/Jmol/src/org/jmol/modelset/Atom.java: Atom deletion developer comments
15:51 CIA-19 bioclipse: ospjuth * r5091 /bioclipse2/trunk/plugins/net.bioclipse.se​rvices/src/net/bioclipse/services/model/: Removed old model fro services
15:52 CIA-19 bioclipse: ospjuth * r5092 /bioclipse2/trunk/plugins/net.bioclipse.services/ (16 files in 6 dirs): Fully supports ServiceImplementations now in ServiceView.
15:57 CIA-19 jmol: hansonr * r9100 /trunk/Jmol/src/org/jmol/modelset/Atom.java: Atom deletion developer comments
16:29 jpansanel moin
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19:19 CIA-19 jmol: hansonr * r9101 /branches/v11_4/Jmol/src/org/jmol/ (popup/PopupResourceBundle.java viewer/Jmol.properties): version=11.4.RC12_dev # menu: internationalization of "Monomer" and "Shapely"
19:20 CIA-19 jmol: hansonr * r9102 /trunk/Jmol/src/org/jmol/ (popup/PopupResourceBundle.java viewer/Jmol.properties): version=11.5.16_dev # menu: internationalization of "Monomer" and "Shapely"
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