Camelia, the Perl 6 bug

IRC log for #cdk, 2008-03-14

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
00:42 dleidert joined #cdk
03:11 CIA-11 jmol: hansonr * r9111 /branches/bob-deleteatoms/Jmol/src/org/jmol/ (26 files in 7 dirs):
03:11 CIA-11 jmol: bob-deleteatoms branch
03:11 CIA-11 jmol: # new feature: zap {atom expression} # zaps models associated with given atoms.
03:11 CIA-11 jmol: # use "show models" to see what models are present, then zap them with their
03:11 CIA-11 jmol: # file.model number:
03:11 CIA-11 jmol: # zap 1.1,2.1
03:11 CIA-11 jmol: # partial implementation -- still needs work on shapespecial
06:23 thomas_ku joined #cdk
06:23 CIA-11 joined #cdk
06:58 jbrefort joined #cdk
07:39 tjeerd joined #cdk
07:43 rojasm joined #cdk
07:51 egonw joined #cdk
08:14 thomas_ku moin
08:56 jonalv joined #cdk
09:47 egonw bbl
11:01 carsten joined #cdk
11:29 CIA-11 jmol: hansonr * r9112 /branches/bob-deleteatoms/Jmol/src/org/jmol/ (10 files in 3 dirs): (log message trimmed)
11:29 CIA-11 jmol: bob-deleteatoms branch
11:29 CIA-11 jmol: untested additional work on deleting atoms, including
11:29 CIA-11 jmol: -- consideration of trajectories
11:29 CIA-11 jmol: -- consideration of data frames
11:29 CIA-11 jmol: -- draw, isosurface, molecular orbitals
11:29 CIA-11 jmol: -- NOT lcaoCartoon
12:54 egonw joined #cdk
12:56 rojasm hi egonw
12:56 egonw hi rojasm
12:56 rojasm sorry a lot of questions :(
12:57 rojasm The Convertor for cdk object to CML ist not able to put in the same file two different elements, isn't it?
12:57 rojasm like list of reactions and list of molecules
12:57 egonw there can be only one root element
12:57 rojasm :(
12:57 rojasm ok.
12:58 egonw use the <cml> as root
12:58 rojasm Because it makes difficult to put ref
12:59 rojasm ok I see
13:00 tjeerd anyone here (bad) experience(s) with the readW and Wolf RAW->mzXML converters?
13:00 rojasm not :(
13:01 tjeerd was just giving it a try yesterday, but converting RAW MS to mzXML doesn't even work, program gave an error, sent an e-mail to the author
13:02 rojasm I can understand very good! the raw files are changing every time depending from the company
13:03 tjeerd the machine itself is not that old I thought, last year of two years ago? and used the latest release of the tools
13:03 rojasm Differents version with his software don't convert approprieate either
13:03 tjeerd seems to yes
13:04 egonw welcome to the world of file formats :)
13:04 rojasm I don't know exactly how is working readW
13:05 tjeerd I also came along a Java-library which can read netCDF
13:05 tjeerd but it would be an extra step (RAW->NetCDF->mzXML/CMLSpect)
13:06 rojasm I think each company has its own convert RAW>NetCDF
13:06 tjeerd yes
13:07 rojasm But for Thermo for example the NetCDF doesn't contain all information from the RAW
13:07 tjeerd so not a good alternative, losing information
13:07 rojasm I think more strategy
13:08 rojasm you have to use allways his software :(
13:08 tjeerd ofcourse, make it difficult as company for everybody out there
13:09 rojasm I was trying a paar of mounths to extract all the information. And I was combaning different format. NetCDF and TXT
13:10 rojasm but dons't give  xcms this conversion?
13:10 tjeerd xcms can read the CDF files nicely
13:10 rojasm ok!
13:11 tjeerd but in practice - if I understand correctly - then CDF files already have lost some information when they were converted from RAW
13:12 rojasm for the case of spectral trees yes!
13:15 rojasm egonw: you meant CMLcml as a root?
13:16 rojasm or CMLElement?
13:16 egonw rojasm: yes
13:57 rojas1 joined #cdk
14:06 jpansanel moin
14:20 tjeerd nice
14:21 tjeerd came along http://ncrr.pnl.gov/software/X2XML.stm
14:21 tjeerd the bad: it requires .net
14:28 egonw you could try mono
14:28 tjeerd tried it
14:28 tjeerd first Wine and then installed mono for Windows
14:29 tjeerd then trying to install the x2xml program, but nothing happens (as half of the windows programs don't work correctly yet under WINE)
14:30 egonw true
14:34 CIA-11 bioclipse: rklancer * r5093 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (META-INF/MANIFEST.MF src/net/bioclipse/ui/Activator.java): quick fix for verbose logging from Spring -- sets threshold to INFO in code. Obvious edit in n.b.ui.Activator.start() will change you change back to DEBUG or whatever you like
14:34 jpansanel tjeerd : you could try to compile your own version of winex
14:37 CIA-11 bioclipse: ospjuth * r5094 /bioclipse2/trunk/plugins/net.bioclipse.services/ (4 files in 3 dirs): Updated Services Extension Point and added several extensions.
14:38 tjeerd but winex is more focussed om directx-support as I understand
14:38 CIA-11 bioclipse: ospjuth * r5095 /bioclipse2/trunk/plugins/net.bioclips​e.services/src/net/bioclipse/services/ (27 files in 6 dirs): Adadpted model and view for new services extension point.
14:38 jpansanel tjeerd : It has also some particuler DLL used by many Win32 software
14:39 jpansanel tjeerd : did you try to install mono on Linux ?
14:41 * egonw is going offline and hit the couch... quite a nasty flu
14:41 egonw bye all
14:41 egonw have a nice weeekend
14:41 tjeerd idem dito
14:42 tjeerd jpansanel: running Fedore with default WINE installation and installed Mono for Windows on it
14:48 jpansanel ok
14:48 tjeerd but perhaps I'll give winex a try, thanks for the tip
14:49 jpansanel tjeerd : I'm cheating
14:49 jpansanel I'm using windows within VirtualBox
14:49 jpansanel (works pretty fine)
14:49 tjeerd yeah, that's also an alternative
14:50 tjeerd I think best solution is to reboot and get rid of the default Windows-policy here (nothing is allowed to be installed)
14:59 CIA-11 bioclipse: rklancer * r5096 /bioclipse2/trunk/plugins/net.bioclipse.​ui/src/net/bioclipse/ui/Activator.java: quick fix to change Spring-OSGI logging level to WARN while retaining DEBUG logging for everything else. Will add file configuration soon so we can stop mucking around changing logging levels in code!
15:02 CIA-11 bioclipse: rklancer * r5097 /bioclipse2/trunk/plugins/net.bioclipse.​ui/src/net/bioclipse/ui/Activator.java: logging again: small edit to use log4j api consistently--allowed me to remove two imports
15:03 CIA-11 bioclipse: ospjuth * r5098 /bioclipse2/trunk/plugins/net.bioclip​se.services/src/net/bioclipse/service​s/views/ServicesLabelProvider.java: Better display of impls
15:06 dleidert joined #cdk
15:11 CIA-11 bioclipse: rklancer * r5099 /bioclipse2/trunk/plugins/net.biocl​ipse.services/META-INF/MANIFEST.MF: Removing extraneous log4j packages from manifest to keep things neat and clear
15:13 CIA-11 bioclipse: rklancer * r5100 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/META-INF/MANIFEST.MF: oops -- should have rolled into 5099 -- removing org.apache.log4j.spi from manifest since I already removed references to it from the code (physician, heal thyself)
15:29 CIA-11 bioclipse: ospjuth * r5101 /bioclipse2/trunk/plugins/net.bioclipse.services/ (8 files in 3 dirs): Documenting the EP and cleanup of model.
17:14 carsten joined #cdk
18:47 CIA-11 jmol: nicove * r9113 /trunk/Jmol-FAH/projects/ (p2167.xyz.gz p3441.xyz.gz p4426.xyz.gz): Folding@Home
21:50 CIA-11 jmol: hansonr * r9114 /trunk/Jmol/src/org/jmol/ (4 files in 2 dirs): version=11.5.16_dev # bug fix: lcaocartoons do not color properly or get restored from state properly
21:53 CIA-11 jmol: hansonr * r9115 /branches/v11_4/Jmol/src/org/jmol/ (4 files in 2 dirs): version=11.4.RC12_dev # bug fix: lcaocartoons do not color properly or get restored from state properly
21:55 CIA-11 jmol: hansonr * r9116 /branches/bob-deleteatoms/Jmol/src/org/jmol/ (4 files in 2 dirs): bob_deleteatoms # bug fix: lcaocartoons do not color properly or get restored from state properly

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary