Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-08-13

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All times shown according to UTC.

Time Nick Message
05:46 Gpox joined #bioclipse
07:44 egonw joined #bioclipse
08:05 jonalv joined #bioclipse
08:05 jonalv moin
08:05 zarah hi jonalv
08:06 shk3 joined #bioclipse
08:13 maclean joined #bioclipse
08:16 CIA-49 bioclipse: jonalv * r6574 /bioclipse2/trunk/plugins/net.bioclipse.qsar/: added bin to svn:ignore
08:22 maclean Hmmm. "import sun.text.CompactShortArray.Iterator;" in net.bioclipse.cdk10.jchempaint.o​utline.StructureContentProvider
08:24 maclean (Causes an error, I should say).
08:32 jonalv I thought I removed that
08:32 jonalv maybe that was at some other place
08:32 jonalv (perhaps someone has found a new favourite iterator class) :)
08:32 maclean Hope not :)
08:33 jonalv but you have latest revision?
08:34 maclean updated about 10 mins ago.
08:34 jonalv okey
08:34 maclean r6551
08:35 jonalv hm I have 6573
08:35 maclean oh. ah. justasec.
08:36 jonalv hm I see that row in my version too
08:36 jonalv curious thing is that I obviiously have that class on my classpacth so I don't get an error
08:36 jonalv although I am pretty sure I got error before...
08:36 jonalv at som other place :)
08:37 egonw btw, never use sun.*
08:37 jonalv but the import is not used so just remove it
08:37 egonw it's not fixed APIs, nor functionality...
08:37 egonw can/will behave differently with each JVM
08:37 maclean Ok. Weird that I have a different version, though...
08:37 jonalv what system you on?
08:38 jonalv I think I had that problem on Ubuntu and I probably fixed without commiting. d'oh///
08:38 maclean XP.
08:38 jonalv ah I am on mac and the author is too. Probably just a miss with autocomplete...
08:39 maclean I could try it out on my mac, too 'spose.
08:39 jonalv just remove the import. it's not used :)
08:41 maclean Oh I know. It was just the update I was concerned about. n/m.
08:41 jonalv zarah: tell masak Please don't import sun.text.CompactShortArray.Iterator and hardcode java.util.Iterator in the code. Better to import java.util.Iterator from the beginning. :)
08:41 zarah Consider it noted.
08:42 jonalv what update would that be?
08:44 maclean well, you said you had r6573, while I only have r6551.
08:47 jonalv yea update man :)
09:14 gilleain joined #bioclipse
09:27 maclean joined #bioclipse
09:29 CIA-49 bioclipse: gilleain * r6575 /bioclipse2/trunk/plugins/net.bioclipse.jmol/src​/net/bioclipse/jmol/actions/ExportHandler.java: Export an image from JMol as a .png file
09:36 egonw joined #bioclipse
10:38 olas joined #bioclipse
10:38 olas hi
10:38 zarah hi olas
10:38 zarah olas: You have new messages. Write '@messages' to read them.
10:38 olas @msg
10:38 zarah olas: egonw said a paper on BioJava has appeared: http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed​&Cmd=ShowDetailView&TermToSearch=18689808
10:38 olas egonw: yea, saw that
10:39 olas @tell edrin please ping me, I have some questions about setting up ejabberd here
10:39 zarah Consider it noted.
10:41 maclean pfft. "...packages for manipulating sequences and 3D structures". 3D structures? not noticably.
10:44 egonw blog about your critique :)
10:45 maclean Ha!
10:45 egonw if you link to the DOI http://dx.doi.org/DOI
10:45 egonw then Chemical blogspace will recognize that you have something to say about that paper
10:45 maclean Oh, that's cool.
11:02 thomas_ku joined #bioclipse
11:37 egonw @tell olas using ZINC8 directly now... only 2.1% differences...
11:37 zarah Consider it noted.
11:52 olas @msg
11:52 zarah olas: egonw said using ZINC8 directly now... only 2.1% differences...
11:52 olas nice!
11:53 olas egonw: looks VERY promising
11:53 egonw yes, it is
11:53 olas what are the diffs?
11:53 egonw I think a good deal of the 2.1% is actually misunderstanding on my side of N.am
11:53 egonw this refers to amide nitrogens
11:53 egonw but apparently this includes not just amides as we know from proteins
11:53 egonw but also the thioamides
11:54 egonw so, not just O=C-N, but also S=C-N
11:54 * olas is not good at chemistry
11:54 egonw maclean: as a protein scientist... does that make sense to use?
11:54 egonw it's about Sybyl atom types, so force field stuff...
11:54 olas @seen edrin
11:54 zarah edrin was last seen 2008-08-12T17:49:19 in #bioclipse saying 'hi egonw'
11:55 * olas will be back in 15 mins
12:01 maclean Oops. Sorry, forgot to set away status.
12:01 maclean I don't know if there are SCN groups in biomolecules.
12:02 maclean In some ligand, perhaps.
12:02 egonw yeah, in ligands for sure
12:02 egonw there are drugs using that group
12:02 egonw but never seen that called 'amide' before
12:03 maclean 'Thioamide' is a kind of old-fashioned name, I think.
12:03 egonw :)
12:04 egonw yeah, chemoinformatics is rather old
12:04 egonw lots of backward compatability involved :(
12:04 maclean ha.
12:04 egonw and backwards means 'deal with specs that have never been specified'
12:05 maclean Reverse-engineering specifications is never too fun.
12:05 egonw ha... and typically forbidden too
12:05 egonw not start about licensing mess that thenhappens
12:05 egonw no, reverse-engineering is not an option
12:06 egonw additionally... which impl to work on?
12:06 maclean Indeed.
12:13 CIA-49 bioclipse: gilleain * r6576 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/net​/bioclipse/ui/contenttypes/CmlFileDescriber.java: Fix for CML files that have nested molecule tags (polymers, for example). It now keeps track of the 'depth' in the document tree, and only counts the top level molecules, not the children.
12:59 olas @tell edrin I got ejabberd set up and can connect to it. Need jars to be able to test
12:59 zarah Consider it noted.
13:03 egonw olas++
13:10 egonw (4-benzhydrylpiperazin-1-yl​)carbonyl-fluoro-BLAHdione
13:11 egonw brilliant name :)
13:24 EskilA joined #bioclipse
13:38 CIA-49 bioclipse: biocoder * r6577 /bioclipse2/trunk/plugins/net.bioclipse.cha​rt/src/net/bioclipse/chart/ChartUtils.java: Added bar plot method
13:41 CIA-49 bioclipse: biocoder * r6578 /bioclipse2/trunk/plugins/net.bioc​lipse.chart/META-INF/MANIFEST.MF: Updated libraries
14:25 jonalv how does the BLAH group look?
14:25 maclean It's very generic.
14:37 jonalv okey
15:06 CIA-49 bioclipse: shk3 * r6579 /bioclipse2/trunk/plugins/net.bioclipse.cd​k10.jchempaint/src/net/bioclipse/cdk10/jch​empaint/ui/editor/AbstractJCPEditor.java: added save as (bug #2037392)
16:27 olas @tell shk3 do not close bugs that you have not submitted. Comment that you have fixed the bug, reassign to the person who submitted, and ask him/her to verify and close it.
16:27 zarah Consider it noted.
16:29 jonalv shk3: did you add things to the MockIFile?
16:29 jonalv shk3: I am considering moving it to net.bioclipse.core.tests
16:37 olas @seen shk3
16:37 zarah shk3 was last seen 2008-08-13T15:08:27 in #cdk saying 'definitly'
16:55 edrin joined #bioclipse
16:56 shk3 jonalv:
16:56 zarah shk3: You have new messages. Write '@messages' to read them.
16:57 shk3 added the setconent
16:57 shk3 plus an exists flag
16:57 shk3 @messages
16:57 zarah shk3: olas said do not close bugs that you have not submitted. Comment that you have fixed the bug, reassign to the person who submitted, and ask him/her to verify and close it.
16:57 jonalv okey, did olas say that you copied the class into net.bioclipse.cdk10?
16:58 jonalv I am gonna move it to net.bioclipse.core.tests and then everyone who needs it can depend on that plugin...
17:00 shk3 i didn't copy that
17:01 shk3 no test in net.bc.cdk10
17:01 jonalv sry net.bc.cdk10.tests
17:02 shk3 neither
17:02 jonalv okey good
17:02 shk3 test is only cdk.business.test
17:02 jonalv aha
17:02 shk3 btw, question
17:03 shk3 it looks like the swt/jfaces save as dialog has nothing like a filter
17:03 shk3 for suggesting file types
17:03 shk3 is that true?
17:03 jonalv no idea
17:03 shk3 looks like
17:03 shk3 if you do save as in eclipse,
17:03 shk3 it's not there as well
17:03 shk3 pretty bad
17:04 shk3 without that, the save as is pretty much useless
17:04 jonalv yea, you should ask the people on #eclipse
17:04 shk3 well, you can check and tell the user
17:04 jonalv they should know
17:04 shk3 but that's not good
17:04 shk3 true
17:04 shk3 they should
17:12 CIA-49 bioclipse: jonalv * r6580 /bioclipse2/trunk/plugins/net.bioclipse.tests/: Initial import.
17:14 CIA-49 bioclipse: jonalv * r6581 /bioclipse2/trunk/plugins/net.bioclipse.tests/ (14 files in 7 dirs): Initial import of plugin containing test suites for all tests in Bioclipse. (If you don't know what to do run them and start fixing broken things... :)
17:23 CIA-49 bioclipse: jonalv * r6582 /bioclipse2/trunk/plugins/net.biocl​ipse.cdk.business/src/net/bioclipse​/cdk/domain/CDKAdapterFactory.java: Work in progress on AdapterFactory for cdk molecules
17:25 CIA-49 bioclipse: jonalv * r6583 /bioclipse2/trunk/plugins/net.bioclipse.core​/src/net/bioclipse/core/BioclipseStore.java: Work in progress on a model store for parsed Models
17:28 CIA-49 bioclipse: jonalv * r6584 /bioclipse2/trunk/plugins/ (9 files in 7 dirs): Moved MockIFile from cdk.business.test to core.test. Also a higly unfinished BioclipseStoreTest along in this commit...
17:34 olas hi edrin
17:34 olas got a minute?
17:34 edrin yes
17:34 zarah edrin: You have new messages. Write '@messages' to read them.
17:34 edrin @message
17:34 zarah edrin: olas said please ping me, I have some questions about setting up ejabberd here
17:34 zarah edrin: olas said I got ejabberd set up and can connect to it. Need jars to be able to test
17:34 olas oh
17:34 edrin ah
17:35 olas could you send me some?
17:35 olas jars?
17:35 olas need to leave in 5 mins now
17:35 olas will you be online tomorrow?
17:35 * jonalv is leaving now, hafe fun!
17:35 olas I might need some more help regarding setup
17:36 olas edrin?
17:38 olas ok, have to leave now
17:38 olas bye
17:38 olas left #bioclipse
17:52 edrin zarah: tell olas I will be available tomorrow but I can't tell you a certain time, i am sorry. I am currently very occupied with diagnostics stuff. But I started working on the source again and merged client and component in one lib to decrease redundancy of source
17:52 zarah Consider it noted.
18:03 thomas_ku joined #bioclipse
19:09 edrin left #bioclipse
21:54 CIA-49 bioclipse: edrin_t * r6585 /xws/trunk/xws-coffee-machine-sample/ (3 files in 2 dirs):
21:56 edrin joined #bioclipse

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