Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-10-26

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

All times shown according to UTC.

Time Nick Message
08:10 Gpox joined #bioclipse
08:29 olass joined #bioclipse
08:36 egonw joined #bioclipse
08:36 olass hi egonw
08:41 egonw hi olass
08:51 jonalv joined #bioclipse
08:53 jonalv oh hai
08:53 zarah hello jonalv, you fantastic person you
08:57 mgerlich joined #bioclipse
09:12 sneumann joined #bioclipse
09:20 * jonalv is trying to grokk the JmolEditor and suddenly remembers why he didn't like trying to do that
09:21 jonalv :/
09:33 olass jonalv: egonw implemented MCSS in CDKManager
09:33 jonalv olass: sounds good (what does MCSS stand for?)
09:34 olass Maximum common substructure
09:34 jonalv the jmol manager throws "this method should not be called exceptions"
09:34 olass bad, but who is better suited to fix that than you?
09:36 sneumann hi there, more user feedback / questions from Halle...
09:36 egonw sneumann: please do file it in the bug tracker too...
09:36 egonw I rather not see that precious feedback lost
09:36 sneumann (only if you tell me it is a bug)
09:36 egonw we do not get overly much
09:36 egonw well, the bug tracker is a bad name
09:37 sneumann So I tried BC 2.0.x, because 2.1.x does not have a 64 bit build.
09:37 egonw it's for feature requests too
09:37 egonw sneumann++
09:37 sneumann Weill 2.2 have 64bit ?
09:37 egonw olass: did you hear that :)
09:37 egonw sneumann: yes
09:37 sneumann Ack.
09:37 egonw we had trouble getting 2.1.1 exported
09:37 egonw but that I think we fixed now
09:37 egonw the 2.2 RC1 should have 64 bit again
09:37 olass sneumann: hopefully will be a 2.2RC2 tomorrow
09:37 egonw RC2 ?
09:38 sneumann I have a molecule, and I use BC to modify it x times, and I want to save all that in an SDF
09:38 sneumann Problem: I can read SDF, but I can't add a molecule to it,
09:38 sneumann not with "New" nor with dragndrop
09:38 sneumann Did I miss something, or is that a feature request ?
09:39 egonw good feature request
09:39 sneumann Ack.
09:39 egonw I think we'll drag-n-drop into the SDF editor
09:39 Gpox @pz 393
09:39 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=393
09:40 egonw oh... fika starts here...
09:40 egonw there is a work around
09:40 * sneumann is listening ...
09:40 egonw you can save each file in a tmp folder
09:41 egonw there is a 'New SD File' wizard that takes one or more files
09:41 egonw but that is rather clumsy
09:41 egonw sneumann: check 393 Gpox just posted
09:41 egonw been open for a while
09:41 sneumann Yes, looks good.
09:41 egonw olass, Gpox: we also need a 'add' button for the mol table editor
09:41 sneumann Never mind, I don't *need* it, I can get away with individual files.
09:42 egonw which will add an entry to the SD file, and then allows editing like it already does...
09:42 egonw ok, fika now...
09:42 egonw feels really swedish
09:42 olass sneumann: please file bugs... we love that...
09:42 egonw haven't started really working yet, but still time for fika :)
09:42 olass good suggestions btw
09:42 jonalv bugs++
09:42 egonw featureRequesta++
09:42 egonw bbl
09:44 sneumann My most recent report is @pz 1677
09:49 masak joined #bioclipse
09:50 Gpox I think that should be bug #1677
09:50 Gpox @ping
09:50 zarah Gpox: pong
09:51 Gpox bug 1677
09:51 Gpox @pz 1677 this works at least
09:51 zarah Gpox: Zarro boogs found.
09:52 masak not anymore...
09:52 Gpox :(
09:52 masak now it only matches on just the number.
09:52 masak @pz 1677
09:52 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1677
09:52 Gpox Is there a way to add a comment?
09:53 jonalv egonw: ping
09:53 jonalv olass: ping
09:53 olass pong
09:53 masak Gpox: you mean like this? '@pz 1677 # IM IN UR SEARCH MAKIN A COMMENT'
09:54 jonalv olass: Has someone updated Jmol lately?
09:54 masak Gpox: doesn't work presently, but I can easily make it work, if you want...
09:54 jonalv olass: we have a contextmenu in jmol now
09:54 jonalv olass: and it can bring up a seperate console window
09:54 olass I think I saw a jmol update by egonw not long ago
09:54 Gpox yeah it would be nice
09:54 * jonalv wonders if all those jmol features are compatible with Bioclipse...
09:55 masak Gpox: oki. stand by for a commit.
10:09 jonalv olass: do you have any ideas on that jmol append?
10:09 olass no
10:10 olass search jmol docs
10:10 jonalv olass: I have tried to just append another mol file to your content String and just reloaded it but it doesn't seem to do it
10:10 jonalv olass: do I ahve to do something more fancy when reloading?
10:10 olass jonalv: never tried it
10:10 olass search jmol docs
10:11 olass but I think you need to do two calls
10:11 olass 1. load first mol
10:11 jonalv olass: but I am looking at your code
10:11 olass 2. append second mol
10:11 olass my code?
10:11 olass ?
10:11 jonalv olass: yea the jmoleditor
10:11 olass ?
10:11 * olass has never written append
10:12 olass jmoleditor is not my code
10:12 jonalv olass: no I am trying to add append to your code
10:12 olass many people has edited it
10:12 jonalv olass: not?
10:12 olass many people has edited it
10:12 olass have
10:12 jonalv olass: the copyright notics says it's yours...
10:12 jonalv so I thought it was yours...
10:13 jonalv + it has huge blocks of outcommented code and that is usually found in your code so it looks like you wrote it..
10:13 olass jonalv: file a bug then
10:13 olass and search jmol dos for append
10:13 olass docs
10:14 jonalv olass: I guess  Icould but I wanted to lookinto this now and thougth maybe you ahd some inputs since you wrote it...
10:14 olass sorry, no
10:14 jonalv olass: I wonder if we should just create an sdf file and open that?
10:14 olass better ask egonw, he is a jmol contributor
10:14 olass jonalv: no
10:14 olass we need superimposition
10:15 jonalv olass: but isn't that the same thing?
10:15 olass no
10:15 olass SDF opens in multiple models
10:15 olass not visible at the same time
10:15 jonalv but you can show multiple models simultanesouly can't you?
10:15 olass how?
10:16 olass jonalv: if you can, just do it.
10:16 olass I am happy in whatever way you solve the problem :)
10:17 olass hmm, youc ould be right
10:17 jonalv olass: our jmol editor already does that if you open an sdf file and select two models in the outline
10:17 jonalv it's vey ugly though...
10:17 olass jonalv: feel free to try
10:17 olass you don't need to ask
10:17 jonalv olass: but jmol is a mess and I don't want to add to it
10:17 olass jonalv: ask on the jmol list then
10:18 olass bbl
10:18 jonalv cya
10:21 samuell joined #bioclipse
10:25 * egonw is back from a long fika
10:25 egonw had to explain rightwing extramism to my son
10:25 jonalv egonw: regarding openining mulitple mols in jmol. How do we want to do that?
10:26 jonalv egonw: you know jmol...
10:26 egonw I suggest jmol.append()
10:26 egonw which takes an IFile
10:26 jonalv egonw: yes and what does that method do?
10:26 egonw and translates it into a jmol.run() with the absolute path
10:26 egonw and "load append" as script
10:26 jonalv egonw: "load apend" as script?
10:26 jonalv egonw: will this be the same as openining an sdf?
10:26 egonw and I suggest DnD would do the same
10:27 egonw no
10:27 egonw well, depends on what you meab
10:27 egonw load append will not replace what is already loaded
10:27 egonw loading a SD file replaces what was loaded...
10:27 jonalv egonw: our latest version of jmol comes with a context menu with lot's of strane actions btw, did you check that they are compatible with bioclipse?
10:28 egonw mmm...
10:28 egonw no, did not
10:28 jonalv egonw: but our jmoleditor has a content String. IF we do like you sugeest that String won't be updated with the jmol content
10:28 egonw crap
10:28 egonw file a bug report :(
10:28 egonw jonalv: was just thinking about that
10:29 egonw I guess jmol.append() should indeed trigger creation a new unsaved file
10:29 jonalv the whole jmol thing in Bioclispe feels more and more like an ugly hack
10:29 jonalv egonw: but the jmol editor does not support save, does it?
10:29 egonw indeed
10:30 egonw because we do not have IJmolMolecule yet
10:30 * jonalv feels dirty all over after just looking at the jmol stuff
10:35 jonalv egonw: can jmol handle cml?
10:35 egonw yes
10:39 jonalv egonw. Gpox: How do I do a load append using an IFile witout runnign into problems with Virtual files?
10:40 egonw jonalv: what 'load append' are you thinking about?
10:40 egonw I was thinking about the Jmol script 'load append'
10:40 jonalv egonw: yea me too
10:40 egonw ok :)
10:41 jonalv but it takes a path right
10:41 jonalv and if we are trying to append a virtual file -> trouble
10:41 jonalv I only see trouble right now...
10:44 jonalv Gpox, olass: Virtual is scheduled for removal right? What's the ETA for that and will we have some other solution with real tempo files instead?
10:44 olass schedule is 2.4 probably
10:45 olass proposed is a simlar function which is file-based
10:45 jonalv how do I do toOSString in a Virtual secure way? IS there a wiki pge?
10:46 olass jonalv: what do you want to achieve?
10:46 olass it is kept in memory, so you can never get a path to it
10:46 jonalv olass: run the jmol script "load append <path to file to append>"
10:46 olass impossible with virtual
10:46 Gpox you cant
10:46 olass serialize to a temp file if you like
10:46 jonalv olass: so what do we do then?
10:46 olass File.createTempFile()
10:47 olass I usually do that
10:47 olass works like a charm
10:47 jonalv is there a wikipage on this? Are there helpmethods somewhere?
10:47 olass ?
10:47 olass this is a Java function
10:47 olass http://java.sun.com/j2se/1.5.0/docs/​api/java/io/File.html#createTempFile(java.lang.String,%20java.lang.String)
10:47 zarah olass's link is also http://tinyurl.com/4662p
10:48 jonalv olass: When you guys keep wanting to return fro ma job I get forced to write loong explanations on the wiki. Now I want the same in all fairness :)
10:48 olass jonalv: the link above is not enough?
10:48 jonalv olass: where do I put this tempfile?
10:49 jonalv it ends up in the temp folder?
10:49 jonalv hm
10:49 olass Java puts it for you
10:49 jonalv intresting
10:49 jonalv but how do I create one of these thingies startign from an IFIle?
10:50 egonw copy inputstream from IFile into outputstream of temp file
10:52 jonalv hm
10:52 jonalv okey
10:52 * jonalv thinks maybe we should have a method that does this...
10:54 jonalv egonw: do you know by heart how to do that?
10:55 * jonalv mumbles something about how nasty file handling is in java
10:55 Gpox http://ostermiller.org/convert_ja​va_outputstream_inputstream.html
10:55 zarah Gpox's link is also http://tinyurl.com/ygzyksg
10:56 jonalv Gpox: hm isn't it the other way aroudn I want to do?
10:56 egonw yeah, it's suprising this is not part of the Java library itself
10:56 * jonalv is confused now
10:56 egonw I keep writing custom implementations myself
11:17 egonw samuell: ping
11:17 samuell png
11:17 samuell pong
11:17 egonw do you skype?
11:17 samuell Yep: samuel_lampa
11:17 egonw ok, hang on...
11:20 jonalv hm okey I fixed jmol load append but the outline is not getting updated... :(
12:23 egonw jonalv++
12:56 egonw olass: can I calculate QSAR descriptors from the command line with the QSAR feature?
12:56 olass yes
12:56 egonw demo script?
12:57 olass yes
12:57 egonw gist or myexperiment.org ?
12:57 olass gist
12:57 egonw manager:qsar tagged?
12:58 olass ?
12:58 egonw :)
12:58 egonw do you have a number of the gist?
12:58 egonw or how do I find it?
12:58 olass try 'help qsar'
12:58 olass from memory: qsar.calculate(mol, descid);
12:59 egonw ok, thanx
12:59 olass not sure if there are good gists for this
12:59 olass try the cheatsheet
12:59 egonw is there a way of interacting with QSARML resources via script?
12:59 egonw will chekc the help
13:00 egonw of the manager
13:09 * jonalv restarts this shitmachine
13:12 olass egonw: with QSARML - no
13:12 olass too complex
13:12 olass in the future - maybe
13:12 olass but needs a lot of work
13:14 egonw yes, I can imagine... was just wondering :)
14:21 * egonw is looking for the matrix editor...
14:21 egonw what feature it is in...
14:22 egonw there is no such feature...
14:22 egonw :(
14:34 olass egonw: the plugin is in the QSAR feature
14:34 egonw damn
14:35 egonw is it?
14:35 olass there has been no need for a matrix feature until now
14:35 egonw I have a bioclipse.statistics
14:35 olass oh... I could be wrong
14:35 egonw http://github.com/egonw/bioclipse.statistics
14:35 zarah egonw's link is also http://tinyurl.com/yzj4q9n
14:35 olass ?
14:35 olass that is a repo
14:35 olass not a feature
14:35 olass repo != feature
14:36 egonw ah, indeed
14:36 egonw OK, about finished setting up a statistics feature
14:36 olass ok
14:36 olass sounds good
14:36 egonw trying to figure out why the matrix editor does not show up for .csv files...
14:39 * olass is struggling with content types for KAlign...
14:47 egonw olass: I like permission to move net.bioclipse.chart into bioclipse.statistics
14:47 egonw net.bioclipse.statistics is critically depending on it
14:49 olass where is it now?
14:50 egonw damn... sorry, I thouht it was in bioclipse.qsar
14:50 egonw mom
14:50 egonw I don't know
14:50 * egonw is searching
14:51 egonw umm... never mind
14:51 * egonw is still suffering from lack of focus...
14:51 egonw it's where it should be
14:51 egonw sorry
14:51 egonw will shut up again
14:53 edrin joined #bioclipse
15:04 edrin hi
15:04 zarah hello edrin, you fantastic person you
15:04 egonw argh... bioclipse is not booting...
15:04 egonw "Scoped incremental build before launch" ??
15:05 egonw but everything was build... ?!?!
15:14 egonw rebooted eclipse
15:14 egonw at least it does something now when 'scoped incremental build' ...
15:17 egonw ok, winter has started...
15:17 egonw it's 16:17 here, and getting dark outside :(
15:20 edrin egonw:
15:20 egonw hej edrin
15:20 edrin hi
15:20 zarah hello edrin, you fantastic person you
15:20 edrin do you think it is possible to go here http://de.wikipedia.org/wiki/Kiruna by car from Uppsala in March
15:20 zarah edrin's link is also http://tinyurl.com/yz3unwp
15:39 egonw joined #bioclipse
15:49 masak joined #bioclipse
15:51 egonw olass: https://gist.github.com/84b5bf389fafa029aa59
15:56 edrin masak: do you speak ada ?
15:56 masak edrin: not as such, no. do you have some Ada code there?
15:56 edrin http://en.wikipedia.org/wiki/A​da_%28programming_language%29
15:56 zarah edrin's link is also http://tinyurl.com/uqjq3
15:56 edrin its like pascal
15:57 masak I know what it is.
15:57 masak I just haven't used it.
15:57 masak I wouldn't describe it as "like Pascal" :)
15:57 masak it's very strong on static checking on different kinds.
15:58 masak it shares a few features with Perl 6, actually.
16:00 olass egonw++
16:01 masak joined #bioclipse
16:04 CIA-51 bioclipse.cheminformatics: Egon Willighagen 2.2.x * r0978cc8 / (2 files): Added a method to calculate a tanimoto matrix (using the CDK fingerprint) for a list of molecules - http://bit.ly/YrO9O
16:04 masak sorry, I'm having hardware problems. I dropped out momentarily.
16:04 masak edrin: what made you think of Ada all of a sudden?
16:04 edrin i wanted to port an algo to java, but the original prog is written in Ada...
16:05 masak cool!
16:05 edrin ic you like these kind of thing ;)
16:06 masak of course! exotic code, who doesn't like that?
16:08 edrin maybe i will refer back to you
16:08 masak Ada in itself is not a guarantee of zero-defect code, by the way: http://use.perl.org/~Ovid/journal/37699
16:08 zarah masak's link is also http://tinyurl.com/ygcpg4q
16:16 masak 'Ada is not pretty, it is not friendly, it is not agile, it is not clever. It is tedious, ugly, draconian and *safe*.' :)
16:20 olass ada sounds boring
16:21 edrin indeed
16:25 masak olass: you will want your nuclear reactor and airplane software to be boring and predictable...
16:26 egonw more importantly...
16:26 olass I'm sure I could produce bugs in ada too
16:26 egonw you want mathematics to prove the code is correct
16:26 egonw QED
16:26 egonw I rest my case
16:27 masak olass: yes, but the focus is on catching those bugs at compile time. the whole language is geared towards that.
16:31 olass logical bugs too?
16:31 olass how can the compiler know what I meant doing?
16:31 masak olass: don't be silly.
16:31 olass you see
16:31 masak interesting fact: the 'hello world' program for Java and Ada both require 97 bytes :)
16:32 edrin suggesting that Java is better then Ada
16:32 edrin than even
16:33 masak I'm no believer of an absolute ordering of programming languages according to how good they are.
16:34 masak I'm sure Ada was a big step forward in terms of its strictness in its time.
16:34 edrin masak: eh
16:34 masak I'm also sure it must have been a bitch to implement. :)
16:34 edrin Windows is better than Linux
16:34 edrin *silence*
16:34 edrin ...
16:34 masak edrin: you're probably more knowledgeable there than I am.
16:35 masak I haven't used Windows much.
16:35 masak I know for sure it's not for me, that's all.
16:35 edrin ok
16:35 edrin and is debian better than Ubuntu ?
16:35 masak Ubuntu is a Debian.
16:36 olass lol
16:36 olass edrin gave up
16:36 masak yay! I won the flamewar :)
16:38 edrin1 joined #bioclipse
16:38 edrin1 ok
16:38 edrin1 i better stop
16:40 edrin1 I need a way to connect my Aspergillus with Bio and XMPP
16:41 edrin1 any suggestions how to do this?
16:45 edrin1 hi
16:45 zarah ni hao edrin1
16:46 olass edrin1: what do you need to analyze?
16:46 olass some sequence maybe?
16:46 olass do some BLAST or alignment?
16:46 edrin1 yes
16:46 olass so think of a service you need
16:47 olass abd implement it as XMPP
16:47 edrin1 for example this http://www3.interscience.wiley.com/​cgi-bin/fulltext/119201431/PDFSTART
16:47 zarah edrin1's link is also http://tinyurl.com/ygpf9s6
16:47 edrin1 the code is written in Ada
16:47 edrin1 :/
16:47 edrin1 but its only one example
16:47 olass oh
16:48 olass edrin1: do you have an ada compiler?
16:48 edrin1 to setup a whole analysis "cluster" one would have to port many more algorithms
16:48 olass it's perfect for a service, since ada is not so portable
16:48 edrin1 no, i do not have an Ada compiler
16:49 olass no open source impl?
16:49 edrin1 of course one could tunnel the input/output from XMPP Java service to an ada program... but actually a native java implementation would be interesting :)
16:50 edrin1 olass: yes, its actually "opensource" i think
16:50 edrin1 olass: look here: http://ihg2.helmholtz-muen​chen.de/ihg/mitoprot.html there is an ftp link with source code
16:50 zarah edrin1's link is also http://tinyurl.com/c474bx
16:50 olass edrin1: so set it up
16:50 olass tunneling XMPP into ADA sounds like the way to go
16:51 olass I mean, that's what service are for
16:51 edrin1 actually this would be pragmatic
17:07 * egonw is leaving for dinner
17:08 egonw olass: need more time to comment on your gdoc
17:08 egonw left some comments already...
18:18 edrin1 me gone
18:18 edrin1 left #bioclipse
19:43 samuell joined #bioclipse
22:03 edrin joined #bioclipse
22:08 edrin left #bioclipse

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