From ap3 at sanger.ac.uk Wed May 5 05:04:46 2004 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Wed May 5 05:08:53 2004 Subject: [Biojava-l] Biojava goes 3D Message-ID: <4098AE2E.40904@sanger.ac.uk> Hi everybody! I am working at the Sanger Centre to extend the DAS protocol toward protein structures. Biojava so far did not contain many tools for protein structure bioinformatics, so I am trying to commit a few things... Biojava now contains a PDB file parser and a few classes to represent three dimensional biological objects like protein structures, or DNA structures. See: org.biojava.bio.structure This is some example code: Q: How can I parse a PDB file ? import org.biojava.bio.structure.*; import org.biojava.bio.structure.io.*; public class simplePDB { public static void main(String args[]){ String filename = "path/to/pdbfile.ent" ; PDBFileReader pdbreader = new PDBFileReader(); try{ Structure struc = pdbreader.getStructure(filename); System.out.println(struc); } catch (Exception e){ e.printStackTrace(); } } } Regards, Andreas -- -------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK From td2 at sanger.ac.uk Wed May 5 05:38:26 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Wed May 5 05:42:23 2004 Subject: [Biojava-l] Website updates Message-ID: Hi... After four years of only minor changes to the main biojava.org website, we've finally decided to make a break. The first stage of the website improvements is now complete: there's a totally new style for all the main pages, based on the biopython.org stylesheet, and I've fixed some of the more out-of-date parts of the text. There are more changes due in the next few weeks -- for instance, it would be good to add a page with some high-level information about the BioJava design. All suggestions are welcome (especially if accompanied by some text :-). Note: you might have to click "refresh" in your browser to see the new-style pages. Thomas. From td2 at sanger.ac.uk Wed May 5 05:53:31 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Wed May 5 05:57:28 2004 Subject: [Biojava-l] Website updates In-Reply-To: References: Message-ID: <111F1D8A-9E7A-11D8-9372-000A95C8B056@sanger.ac.uk> Just a couple of extra points... The "participants" page is currently looking rather sparse -- anyone who's contributed to biojava (major features / documentation / patches / complaints / whatever) is welcome to a slot here -- just send me a short bio and I'll add it to the page. I'd also like to add some kind of "BioJava application directory", but this is only really worthwhile if there's a significant number of entries. If you've written something with Biojava and want to tell the world about it, please sent me a link. Thanks! Thomas. On 5 May 2004, at 10:38, Thomas Down wrote: > Hi... > > After four years of only minor changes to the main biojava.org > website, we've finally decided to make a break. The first stage of > the website improvements is now complete: there's a totally new style > for all the main pages, based on the biopython.org stylesheet, and > I've fixed some of the more out-of-date parts of the text. > > There are more changes due in the next few weeks -- for instance, it > would be good to add a page with some high-level information about the > BioJava design. All suggestions are welcome (especially if > accompanied by some text :-). > > Note: you might have to click "refresh" in your browser to see the > new-style pages. > > Thomas. > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > From verhoeff2 at gis.a-star.edu.sg Wed May 5 06:01:25 2004 From: verhoeff2 at gis.a-star.edu.sg (VERHOEF Frans) Date: Wed May 5 06:08:36 2004 Subject: [Biojava-l] Website updates Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D560B077B@BIONIC.biopolis.one-north.com> Nice job! The website looks remarkably clean and fresh. Frans From mark.schreiber at group.novartis.com Wed May 5 21:44:19 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Wed May 5 21:48:26 2004 Subject: [Biojava-l] Alignment/ Alphabet issues (was biojava v2 alpha1 release) Message-ID: Hi John - if you get source from BioJava live or a recent snapshot it should be able to handle gap counting in Alignments via DistributionTools various distributions form alignment methods. It is done through a very dodgey hack that hopefully is not needed in BJ2 (or is at least formalized so anyone can do it). Gaps are not too well handled in BJ1. They sort of are and are not part of the alphabet. I am also working on a generalized wrapper to allow soft masking of an alphabet as well as a SymbolTokenization that understands how to deal with it. Should be done soon if there is interest but it would be better handled at a more core level if possible in BJ2. On the subject of LGPL v GPL, having worked in companies for a while making biojava GPL would render it unusable for industry. Even if I write something that will never be shrinkwrapped and sold no legal team will ever allow me to use biojava if it means anything I write has to be GPL. We may choose to make it GPL but we don't want to be forced to. Regards, Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 "Osborne, John" Sent by: biojava-dev-bounces@portal.open-bio.org 05/06/2004 03:50 AM To: "Matthew Pocock" cc: biojava-dev@biojava.org Subject: RE: [Biojava-dev] biojava v2 alpha1 release I think lGPL is fine, although I would be happier with the more "viral" GPL but until I contribute some source I'll try to keep my mouth shut. :) I'm just curious though, is anybody out there actually distributing biojava as part of commerical *commodity* software? I'm not talking one of a kind projects that use biojava, but shrinked wrapped software where source code protection really matters. Speaking of which, is there a javadoc or download area for bjv2? (haven't installed subversion) I've been waiting ages to contribute, but most of the stuff I would put in is multiple alignment analysis stuff, which is a bit of a mess in bjv1 (gap character issues, alignment handling code split across packages, etc...) Maybe bjv2 is the trick. -John -----Original Message----- From: biojava-dev-bounces@portal.open-bio.org [mailto:biojava-dev-bounces@portal.open-bio.org] On Behalf Of Matthew Pocock Sent: Wednesday, May 05, 2004 12:58 PM To: biojava-dev@biojava.org Subject: [Biojava-dev] biojava v2 alpha1 release Hi, I have just committed the alpha1 release of biojava 2 (code-named medusa) to svn. To compile & run BJV2, you will need a 1.5 java sdk, SVN (1.0 or newer) and a reasonably up-to-date ANT. I'm releasing this revision under lGPL. I am happy to move to another open-source license if people feel it would be helpfull. GPL and OSL appear to be no good - to viral. BSD and friends are no good - too easy to split/pilfer. I'm reading through licences on http://www.opensource.org/licenses/ in the vain hope of finding something suitable. All bugs/questions either direct to me or to biojava-dev. Matthew ---- Getting bjv2: the complete thing http://www.derkholm.net/svn/repos/bjv2 development version http://www.derkholm.net/svn/repos/bjv2/trunk alpha1 release http://www.derkholm.net/svn/repos/bjv2/branches/medusa ---- Things I want in the license: 1) "we" own the code - a 3rd party can't take it, change the formatting and stop us using it 2) "you" can incorporate the library into your app. this requries you to: acknowledge that you use us & what license you use us under provide access to the source - presumably as a link to our repository 3) if "you" have modified "our" source and then distribute the modification you must: notify the user that you've done this make the source of the modifications available under this license allow the modifications to be rolled back into the main copy of the code (we may chose not to though) 4) "you" can use example code without tainting your apps with our license 5) none of this lGPL linking rubbish - what's that all about anyway? 6) "we" are not liable for anything - we don't claim the code is fit for any purpose and if it craps out, you pay the consequences _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From max_dipl at web.de Thu May 6 11:13:17 2004 From: max_dipl at web.de (Maximilian Haeussler) Date: Thu May 6 11:16:59 2004 Subject: [Biojava-l] SequencePoster <-> SequencePanel Message-ID: <409A560D.1000107@web.de> Hi everyone, still searching for something similar to SequencePanel that does not throw exceptions in a JScrollPane...while doing this, I stumbled upon SequencePoster. Hum...the javadoc for both looks very very similar, if not identical... can someone give me a hint on the difference between SequencePanel and SequencePoster? This question sounds rather stupid, but doing a diff on both didn't really help, and I don't really know where to search. And in the demos-dir, there are EmblViewer and BeadDemo but they look really pretty similar... Thanks Max From matthew_pocock at yahoo.co.uk Thu May 6 12:59:56 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Thu May 6 13:04:02 2004 Subject: [Biojava-l] SequencePoster <-> SequencePanel In-Reply-To: <409A560D.1000107@web.de> References: <409A560D.1000107@web.de> Message-ID: <409A6F0C.3030105@yahoo.co.uk> SequencePoster is going to die before the next release. SequencePoster lets you split the display accross multiple lines of display - wrapparround genomes. This functionality can be created using multiple SequencePannel instances, with less complicated code. Maximilian Haeussler wrote: > Hi everyone, > still searching for something similar to SequencePanel that does not > throw exceptions in a JScrollPane...while doing this, I stumbled upon > SequencePoster. Hum...the javadoc for both looks very very similar, if > not identical... can someone give me a hint on the difference between > SequencePanel and SequencePoster? > This question sounds rather stupid, but doing a diff on both didn't > really help, and I don't really know where to search. And in the > demos-dir, there are EmblViewer and BeadDemo but they look really > pretty similar... > > Thanks > Max > > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > From kalle.naslund at genpat.uu.se Fri May 7 08:44:24 2004 From: kalle.naslund at genpat.uu.se (=?ISO-8859-1?Q?Kalle_N=E4slund?=) Date: Fri May 7 08:44:57 2004 Subject: [Biojava-l] SequencePoster <-> SequencePanel In-Reply-To: <409A560D.1000107@web.de> References: <409A560D.1000107@web.de> Message-ID: <409B84A8.5010609@genpat.uu.se> Maximilian Haeussler wrote: > Hi everyone, > still searching for something similar to SequencePanel that does not > throw exceptions in a JScrollPane...while doing this, I stumbled upon > SequencePoster. Hum...the javadoc for both looks very very similar, if > not identical... can someone give me a hint on the difference between > SequencePanel and SequencePoster? > This question sounds rather stupid, but doing a diff on both didn't > really help, and I don't really know where to search. And in the > demos-dir, there are EmblViewer and BeadDemo but they look really > pretty similar... > > Thanks > Max > > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l Its highly probable that i have nailed down the reason you are seeing lots of IndexOutOfBoundsException being thrown. SequencePanel. The actual output will most likely look something like this. java.lang.IndexOutOfBoundsException: max must exceed min: min=1, max=-18 at org.biojava.bio.symbol.RangeLocation.(RangeLocation.java:61) at org.biojava.bio.gui.sequence.GUITools.getVisibleRange(GUITools.java:36) at org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer.paint(FeatureBlockSequenceRenderer.java:216) at org.biojava.bio.gui.sequence.SequenceRendererWrapper.paint(SequenceRendererWrapper.java:160) I have a fix for this problem ( developed with help from Matthew ). BUT, it seems like the fix might cause some rendering issues. Atleast that was my initial thougt, untill a few hours ago, when i checked out a fresh sourceetree and tried out the demo applications, and it seems the current sourcetree has the same rendering issus as my fixed version. The rendering issues i am talking about is that some of the demos render LOTS of empty space behind the sequences. From a quick look it looks like it first renders the sequence, and then an equaly large empty part, behind the sequence. I see this behaviour with the following demo applications seqviewer.BeadDemo seqviewer.EmblViewer2 What these two things share, is that they both use SequencePanel. What i would like, if that anyone can just take a quick look at the BeadDemo and EmblViewer2 demos, and just check that they see the same rendering problem as i see, so i am 100% its not a bug i have introduced somehow. If thats the case, i would feel comfortable in commiting the changes that will fix the Exception throwing. And i can then try to find out why the SequencePanel renders lots of blank space. regards Kalle From verhoeff2 at gis.a-star.edu.sg Thu May 6 22:25:15 2004 From: verhoeff2 at gis.a-star.edu.sg (VERHOEF Frans) Date: Fri May 7 11:58:34 2004 Subject: [Biojava-l] Locations in centiMorgans Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D560B047B@BIONIC.biopolis.one-north.com> Hi everyone, I have a bunch of SNPs of which I do have their chromosomal location. I do however need their location in centiMorgans. Currently I am fetching for every gene two known nearby centiMorgan locations (using NCBI's genome viewer) and interpolate to derive the centiMorgan location for every SNP inside the gene, using a small script I wrote. This method is a bit time consuming and needs to be automated in the near future. Does anyone of you have any idea of how to go about this? Is there a way to fit biojava in? Thanks, Frans Verhoef Bioinformatics Specialist Genome Institute of Singapore 60 Biopolis Street, #02-01 Genome, Singapore 138672 Tel: +65 6478 8000 DID: +65 6478 8060 HP: +65 9848 4325 Email: verhoeff2@gis.a-star.edu.sg ------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. ------------------------------- From bcpowell at email.unc.edu Mon May 10 15:12:53 2004 From: bcpowell at email.unc.edu (Bradford Powell) Date: Mon May 10 15:17:28 2004 Subject: [Biojava-l] Why is FramedFeature.Template.readingFrame static? Message-ID: Hi, I'm not sure if I am missing something here, but I'm confused as to why the field readingFrame in FramedFeature.Template is declared static. None of the fields (that I've looked at) in similar *Feature.Template classes are static. I would think it might cause problems with multi-threaded apps if every FramedFeature.Template has the same reading frame. -- Bradford Powell From td2 at sanger.ac.uk Mon May 10 15:44:17 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Mon May 10 15:48:04 2004 Subject: [Biojava-l] Why is FramedFeature.Template.readingFrame static? In-Reply-To: References: Message-ID: <6C5DC95C-A2BA-11D8-BD29-000A95C8B056@sanger.ac.uk> On 10 May 2004, at 20:12, Bradford Powell wrote: > Hi, > > I'm not sure if I am missing something here, but I'm confused as to why > the field readingFrame in FramedFeature.Template is declared static. > None > of the fields (that I've looked at) in similar *Feature.Template > classes > are static. I would think it might cause problems with multi-threaded > apps if every FramedFeature.Template has the same reading frame. That's a bug, plain and simple. I've fixed it now in CVS (should be fixed in tommorow's autobuild). Thanks for spotting it, Thomas. From dag at sonsorol.org Mon May 10 20:25:26 2004 From: dag at sonsorol.org (Chris Dagdigian) Date: Mon May 10 20:32:36 2004 Subject: [Biojava-l] {off topic} Apple is giving away 5 workgroup sized clusters in a program for bioinformatics researchers Message-ID: <40A01D76.3010502@sonsorol.org> Hi folks, Apologies for the semi off topic posting but I think it may be appropriate because I know lots of people doing really clever informatics stuff tend to be on the open-bio.org mailing lists. I want to make sure many of the small group, individuals and DIY types hear about this as they can probably benefit the most from a influx of hardware. In short, Apple just announced a program to give away 5 fully provisioned mini-clusters (4 Xserve G5 nodes) in a judged process specifically aimed at bioinformatics types. Awards are announced on 29 June 2004. The URL is here: http://www.apple.com/science/clusteraward/ Regards, Chris From td2 at sanger.ac.uk Tue May 11 04:08:17 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Tue May 11 04:12:04 2004 Subject: [Biojava-l] Why is FramedFeature.Template.readingFrame static? In-Reply-To: <6C5DC95C-A2BA-11D8-BD29-000A95C8B056@sanger.ac.uk> References: <6C5DC95C-A2BA-11D8-BD29-000A95C8B056@sanger.ac.uk> Message-ID: <5BFBF468-A322-11D8-BD29-000A95C8B056@sanger.ac.uk> On 10 May 2004, at 20:44, Thomas Down wrote: > > On 10 May 2004, at 20:12, Bradford Powell wrote: > >> Hi, >> >> I'm not sure if I am missing something here, but I'm confused as to >> why >> the field readingFrame in FramedFeature.Template is declared static. >> None >> of the fields (that I've looked at) in similar *Feature.Template >> classes >> are static. I would think it might cause problems with multi-threaded >> apps if every FramedFeature.Template has the same reading frame. > > That's a bug, plain and simple. I've fixed it now in CVS (should be > fixed in tommorow's autobuild). Actually I didn't quite fix it (hence the build failure last night). A couple of classes which used FramedFeature.Template were assuming the field was static and accessing it as such. The resulting code was pretty nonsensical, so I can only assume it was generated by some kind of automatic cleanup heuristics in an IDE. It really is fixed now... Thomas. From max_dipl at web.de Tue May 11 09:38:20 2004 From: max_dipl at web.de (Maximilian Haeussler) Date: Tue May 11 09:42:09 2004 Subject: [Biojava-l] Highlight Features when clicked? newbie Message-ID: <40A0D74C.6090902@web.de> Hi everyone, is there a simple way to highlight a feature when it is clicked? Just like in most programs with a gui, word or whatever, I want to draw something a around a selected feature, a black rectangle for instance when the user clicks on it. I suppose this is a pretty common problem for everyone using the gui-classes. I'm playing around with a FeatureFilter.ByFeature in conjunction with a RectangularBeadRenderer but this can't be way that the authors of the gui classes had imagined when they wrote them. (As features are not graphical objects in Biojava, I can't send them messages directly.) So I have to draw the rectangle directly onto the graphics, right? But how could I find out the coordinates of the feature's edges?? Is there some mechanism in those javadocs ( I've come to hate them pretty much :-) that I've overlooked? Thanks Max From dag at sonsorol.org Tue May 11 10:01:20 2004 From: dag at sonsorol.org (Chris Dagdigian) Date: Tue May 11 10:05:20 2004 Subject: [Biojava-l] testing a new Open-Bio website and mail list archive search Message-ID: <40A0DCB0.1050207@sonsorol.org> Hello Everyone, A fantastic volunteer (Kyle Jensen) has been steathily working on a problem for us that has long been a major issue for us -- website searching and indexing. We've tried various solutions and ht://dig implementations in the past and nothing really worked well. Kyle has been setting up a search indexing system based on the code from www.swish-e.org and so far it looks very very promising. We have 2 main indexed search sites: This page is a search index for all of the open-bio hosted websites: http://search.open-bio.org/cgi-bin/obf-search.cgi This page is just for searching mailing list archives: http://search.open-bio.org/cgi-bin/mail-search.cgi Please give the pages a whirl and let me know what you think. Thanks again Kyle! -Chris open-bio.org admin team From matthew_pocock at yahoo.co.uk Tue May 11 10:54:55 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Tue May 11 10:58:57 2004 Subject: [Biojava-l] Highlight Features when clicked? newbie In-Reply-To: <40A0D74C.6090902@web.de> References: <40A0D74C.6090902@web.de> Message-ID: <40A0E93F.6040401@yahoo.co.uk> Hi, One solution is to have 2 top-level renderers. One is painted 'behind' the other, and highlights a range. The one in front is your normal renderer. Wire the events so that selecting a feature sets the highlighting range on the 'behind' renderer. If you check out the das client code from cvs (it's in a different cvs module to biojava-live), you should be able to find some example code for this. Matthew Maximilian Haeussler wrote: > Hi everyone, > > is there a simple way to highlight a feature when it is clicked? Just > like in most programs with a gui, word or whatever, I want to draw > something a around a selected feature, a black rectangle for instance > when the user clicks on it. I suppose this is a pretty common problem > for everyone using the gui-classes. > I'm playing around with a FeatureFilter.ByFeature in conjunction with > a RectangularBeadRenderer but this can't be way that the authors of > the gui classes had imagined when they wrote them. (As features are > not graphical objects in Biojava, I can't send them messages directly.) > > So I have to draw the rectangle directly onto the graphics, right? But > how could I find out the coordinates of the feature's edges?? Is there > some mechanism in those javadocs ( I've come to hate them pretty much > :-) that I've overlooked? > > Thanks > Max > > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > From kalle.naslund at genpat.uu.se Wed May 12 05:56:03 2004 From: kalle.naslund at genpat.uu.se (=?ISO-8859-1?Q?Kalle_N=E4slund?=) Date: Wed May 12 06:00:14 2004 Subject: [Biojava-l] SequencePoster <-> SequencePanel In-Reply-To: <409A560D.1000107@web.de> References: <409A560D.1000107@web.de> Message-ID: <40A1F4B3.7090003@genpat.uu.se> Maximilian Haeussler wrote: > Hi everyone, > still searching for something similar to SequencePanel that does not > throw exceptions in a JScrollPane...while doing this, I stumbled upon > SequencePoster. Hum...the javadoc for both looks very very similar, if > not identical... can someone give me a hint on the difference between > SequencePanel and SequencePoster? > This question sounds rather stupid, but doing a diff on both didn't > really help, and I don't really know where to search. And in the > demos-dir, there are EmblViewer and BeadDemo but they look really > pretty similar... Could you please try out the code in CVS, and see if it helps, hopefully you wont see any more IndexOutOfBoundsExceptions. mvh Kalle From td2 at sanger.ac.uk Thu May 13 16:53:35 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Thu May 13 16:57:18 2004 Subject: [Biojava-l] Dazzle 1.01 Message-ID: <99D2EB58-A51F-11D8-B592-000A95C8B056@sanger.ac.uk> Hi, I've just released a new version of Dazzle modular DAS server. It's available from the usual place: http://www.biojava.org/dazzle/ The main change since version 1.00 is the addition of a new plugin which allows Dazzle annotation servers to be set up backed by SQL databases in the LDAS format. Instructions for using LdasDataSource can be found at the bottom of the deployment guide. The plugin API is unchanged since 1.00 Thomas. From d.naki at cox.net Thu May 13 17:07:38 2004 From: d.naki at cox.net (Don Naki) Date: Thu May 13 21:06:08 2004 Subject: [Biojava-l] SimpleGappedSymbolList from a String Message-ID: <008901c4392e$528b8290$6901a8c0@DNAKIXPLT> Hi all, I have a couple of 'novice' questions... I can't seem to figure out how to create a SimpleGappedSymbolList from a String. I want to parse "-AQSD--VP-" and create a SimpleGappedSymbolList from it. ProteinTools has methods to return a SymbolList, Sequence, and GappedSequence from a String, but not a GappedSymbolList. I understand GappedSequence extends GappedSymbolList, but I want just the GappedSymbolList. Alternatively, is there a way to get a GappedSymbolList from a GappedSequence? A second question is that ProteinTools.createGappedProteinSequence("-AQSD--VP-").seqString() results in the String "XAQSD--VPX". The first and last '-' characters are now represented by 'X'. Is this a special kind of gap symbol? If so, how can I distinguish between '-' and 'X' Symbols? Thanks in advance, Don From Adam_Tracy at affymetrix.com Thu May 13 20:59:25 2004 From: Adam_Tracy at affymetrix.com (Tracy, Adam) Date: Thu May 13 21:11:31 2004 Subject: [Biojava-l] accessing the HSP alignment using biojava Message-ID: <53386E0C47E7D41194BB0002B325C997F96B90@NTEX60> hello, and thank you for your contribution to biojava - i'm following the example of how to parse blast alignments outlined on your website here: http://www.biojava.org/docs/bj_in_anger/ExtractSearchInformation.htm now, i'm curious to access the consensus string that describes the relationship between the subject and the query, for instance the middle row below: Query: 276 QSFQRVQGFKKMVDRWRNSHTRCMWQMTLSQRRNLYATLRMQDTMGQELALANKQLLMVR 455 +SFQ+ G KK VDRWRNSHT C+WQM L QRRN YATLRMQDTM QELALA KQLLMVR Sbjct: 120 ESFQKAMGLKKTVDRWRNSHTHCLWQMALGQRRNPYATLRMQDTMVQELALAKKQLLMVR 179 in the code snippet below, i can get the two sequence fragments from the seqString() method called on the SymbolList items contained within the SubHit's Alignment, but not the consensus string. is there a protocol defined in the API that might help me with this? for (Iterator k = result.getHits().iterator(); k.hasNext(); ) { SeqSimilaritySearchHit hit = (SeqSimilaritySearchHit) k.next(); for (Iterator alignments = hit.getSubHits().iterator(); alignments.hasNext();) { SeqSimilaritySearchSubHit sh = (SeqSimilaritySearchSubHit) alignments.next(); Alignment al = sh.getAlignment(); for (Iterator syms = al.symbolListIterator(); syms.hasNext();) { SymbolList sl = (SymbolList) syms.next(); sl.seqString(); } } } thank you for your time! ant -------- Adam Tracy | Staff Software Engineer | CIS Software Operations AFFYMETRIX, INC. | 6550 Vallejo St. Suite 100 | Emeryville, CA 94608 | Tel: 510-428-8536 From matthew_pocock at yahoo.co.uk Fri May 14 06:21:55 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Fri May 14 06:25:50 2004 Subject: [Biojava-l] Re: [Biojava-dev] Feature at position 0 In-Reply-To: <000601c43850$459e5500$a52c5289@nt.cmmt.ubc.ca> References: <000601c43850$459e5500$a52c5289@nt.cmmt.ubc.ca> Message-ID: <40A49DC3.4020605@yahoo.co.uk> I think for the sake of useability, we could either relax the location constraint to allow point locations at 0, or in the sp parser, re-write these as <1 - what do people think? Matthew Tao Xu wrote: >Hi there, > >I am trying to use SeqIOTools.readSwissport() to process a SwissProt flat file. An Exception is thrown whenever a feature at position 0 is encountered. The user manual from UniProt/SwissProt says that a feature at position 0 means the initiator methionine was cleaved off. >This happens quite often ( at least a few persent of the SwissProt records has this line "FT INIT_MET 0 0". I googled and found your message. Is there a solution to this problem now? Thanks a lot for your help. > >Regards, > >Tao > >On Wednesday 15 Oct 2003 2:11 pm, Mark Southern wrote: > > >>This is a real world example. >> >>Swissprot ID KAP3_RAT (AC P12369) is an example of a sequence with a >>feature entry at sequence location 0: >> >>FT INIT_MET 0 0 BY SIMILARITY. >> >> >>This raises an IllegalArgumentException when the sequence is read in via >>SeqIOTools.fileToBiojava (see below). >> >>I don't know how oftem this would come up but its definitely a situation >>that isn't handled at the moment. Thoughts anyone? >> >> >> >Hmm, this one could be a problem - our coordinate system starts from one. >What do they mean by position 0? A cleaved methionine that's gone alreadY? > >Maybe our code ought to have the option to skip these silently? > >Regards, >David Huen > > > >------------------------------------------------------------------------ > >_______________________________________________ >biojava-dev mailing list >biojava-dev@biojava.org >http://biojava.org/mailman/listinfo/biojava-dev > > From matthew_pocock at yahoo.co.uk Fri May 14 06:25:16 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Fri May 14 06:29:07 2004 Subject: [Biojava-l] SimpleGappedSymbolList from a String In-Reply-To: <008901c4392e$528b8290$6901a8c0@DNAKIXPLT> References: <008901c4392e$528b8290$6901a8c0@DNAKIXPLT> Message-ID: <40A49E8C.2090207@yahoo.co.uk> Don Naki wrote: >Hi all, >I have a couple of 'novice' questions... > >I can't seem to figure out how to create a SimpleGappedSymbolList from a String. I want to parse "-AQSD--VP-" and create a SimpleGappedSymbolList from it. >ProteinTools has methods to return a SymbolList, Sequence, and GappedSequence from a String, but not a GappedSymbolList. I understand GappedSequence extends GappedSymbolList, but I want just the GappedSymbolList. Alternatively, is there a way to get a GappedSymbolList from a GappedSequence? > > We could add a uitlity method to do this. Why do you /have/ to have a GappedSymbolList that is not a GappedSequence? Is there a specific memory constraint? >A second question is that ProteinTools.createGappedProteinSequence("-AQSD--VP-").seqString() results in the String "XAQSD--VPX". The first and last '-' characters are now represented by 'X'. Is this a special kind of gap symbol? If so, how can I distinguish between '-' and 'X' Symbols? > > This is a tokenization bug - the leading/trailing gaps are not being recognised by the tokenizer, and then replaced by X. It's probably in CharacterTokenization - needs a special-case for AlphabetManager.getGapSymbol() - could someone look a this? >Thanks in advance, >Don > > Matthew From td2 at sanger.ac.uk Fri May 14 06:36:24 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Fri May 14 06:40:06 2004 Subject: [Biojava-l] Re: [Biojava-dev] Feature at position 0 In-Reply-To: <40A49DC3.4020605@yahoo.co.uk> References: <000601c43850$459e5500$a52c5289@nt.cmmt.ubc.ca> <40A49DC3.4020605@yahoo.co.uk> Message-ID: <8C5F6372-A592-11D8-8F19-000A95C8B056@sanger.ac.uk> On 14 May 2004, at 11:21, Matthew Pocock wrote: > I think for the sake of useability, we could either relax the location > constraint to allow point locations at 0, or in the sp parser, > re-write these as <1 - what do people think? Ugh. I'm not sure "<1" will appeal to people who are into round-tripping. I think my (slightly) favoured option would be to remove the location constraints on Features completely. I know this is pretty horrible, but off-sequence locations do seem to be things people use. I'd definitely vote against special-casing locations at position 0 -- that just feels like a slippery slope. What happens when people want to model larger leader-peptides in this way? If we're going to allow off-sequence locations at all we should bite the bullet and allow them without restriction. *sigh* Thomas From bcpowell at email.unc.edu Fri May 14 09:42:29 2004 From: bcpowell at email.unc.edu (Bradford Powell) Date: Fri May 14 09:46:41 2004 Subject: CircularLocations (was Re: [Biojava-l] Re: [Biojava-dev] Feature at position 0) In-Reply-To: <8C5F6372-A592-11D8-8F19-000A95C8B056@sanger.ac.uk> Message-ID: On Fri, 14 May 2004, Thomas Down wrote: > > On 14 May 2004, at 11:21, Matthew Pocock wrote: > > > I think for the sake of useability, we could either relax the location > > constraint to allow point locations at 0, or in the sp parser, > > re-write these as <1 - what do people think? > > Ugh. > > I'm not sure "<1" will appeal to people who are into round-tripping. > > I think my (slightly) favoured option would be to remove the location > constraints on Features completely. I know this is pretty horrible, > but off-sequence locations do seem to be things people use. > This brings up another issue that I have been thinking about recently. I'm not really comfortable with how circular sequences and circular locations are handled in biojava. For those who aren't familiar, CircularLocations are mapped as CompoundLocations. I would prefer for features on a circular sequence (a CircularView of a sequence) to have coordinates that are outside of the sequence coordinates. Usually I use the convention that the larger coordinate is within 1..length. This makes it easy to check for features that overlap the origin (their min values are <= 0). While I'm thinking of it, there are a couple of bugs I've seen in CircularView: 1-- If subList or subString are called with start and end values that should produce a list longer than the original sequence, things don't happen as I would expect. Suppose you have a sequence 'seq': CircularView cv = new CircularView(seq); SymbolList subL = cv.subList(1, seq.length() + 3) subL.length() has the value 3 instead of seq.length()+3 (i.e. it holds just the first three symbols of seq because the start and stop coordinates are immediately translated to be within 1..length() upon entry to subList(). I can see two ways to resolve this-- one would be to check to see if start-stop > length() and add appropriate numbers of copies of the source symbolList to the sublist as seen above. The other way would be to use a WrappedSymbolListView (this is what I have done for my purposes, code available if people think this would be a good idea). 2-- I almost hesitate to report this "bug" because I like to use negative coordinates in locations on circular sequences-- createFeature() in CircularView throws an exception if getMax() > length() but not if getMin() <= 0. I guess it is a bug one way or the other because it is inconsistant. Since the topic of removing location constraints for features came up, I would say that it would at least make sense to remove the restrictions for circular sequences. Whew, that message was longer than I thought it would be. -- Bradford Powell From taoxu at bioinformatics.ubc.ca Fri May 14 13:33:07 2004 From: taoxu at bioinformatics.ubc.ca (Tao Xu) Date: Fri May 14 13:37:35 2004 Subject: [Biojava-l] Re: [Biojava-dev] Feature at position 0 Message-ID: <34ce131723.3172334ce1@cmmt.ubc.ca> I have noticed that the in the nightly build, no Exception is thrown. I guess it just simply ignored the features at position 0, as David suggested. I tend to like the idea of relax the location constraint. Another approach might be create a RelaxLocation class. Regards, Tao ----- Original Message ----- From: Matthew Pocock Date: Friday, May 14, 2004 3:21 am Subject: Re: [Biojava-dev] Feature at position 0 > I think for the sake of useability, we could either relax the > location > constraint to allow point locations at 0, or in the sp parser, re- > write > these as <1 - what do people think? > > Matthew > > Tao Xu wrote: > > >Hi there, > > > >I am trying to use SeqIOTools.readSwissport() to process a > SwissProt flat file. An Exception is thrown whenever a feature at > position 0 is encountered. The user manual from UniProt/SwissProt > says that a feature at position 0 means the initiator methionine > was cleaved off. > >This happens quite often ( at least a few persent of the > SwissProt records has this line "FT INIT_MET 0 0". I > googled and found your message. Is there a solution to this > problem now? Thanks a lot for your help. > > > >Regards, > > > >Tao > > > >On Wednesday 15 Oct 2003 2:11 pm, Mark Southern wrote: > > > > > >>This is a real world example. > >> > >>Swissprot ID KAP3_RAT (AC P12369) is an example of a sequence > with a > >>feature entry at sequence location 0: > >> > >>FT INIT_MET 0 0 BY SIMILARITY. > >> > >> > >>This raises an IllegalArgumentException when the sequence is > read in via > >>SeqIOTools.fileToBiojava (see below). > >> > >>I don't know how oftem this would come up but its definitely a > situation>>that isn't handled at the moment. Thoughts anyone? > >> > >> > >> > >Hmm, this one could be a problem - our coordinate system starts > from one. > >What do they mean by position 0? A cleaved methionine that's > gone alreadY? > > > >Maybe our code ought to have the option to skip these silently? > > > >Regards, > >David Huen > > > > > > > >------------------------------------------------------------------ > ------ > > > >_______________________________________________ > >biojava-dev mailing list > >biojava-dev@biojava.org > >http://biojava.org/mailman/listinfo/biojava-dev > > > > > > From Adam_Tracy at affymetrix.com Fri May 14 13:59:26 2004 From: Adam_Tracy at affymetrix.com (Tracy, Adam) Date: Fri May 14 14:11:31 2004 Subject: [Biojava-l] Extending the default SAX handlers Message-ID: <53386E0C47E7D41194BB0002B325C997F96B96@NTEX60> hello - I'm working with the SAX based BLAST parsing kit here, and have run into a problem that seems to have been noted by some other posts, namely that the "MatchConsensus" fragment of the HSP's is not kept in the SeqSimilaritySearchSubHit item after parsing. I need that. After perusing the framework, I came across AlignmentStAXHanlder, and extended it with another call to addHandler() in the creator method for another private inner class that I added to the class, much in the same pattern as how it was adding it's hitSequence,and subjectSequence fragments: private class MatchConsensusStAXHandler extends StringElementHandlerBase { private SearchContentHandler sch; public void startElement( String nsURI, String localName, String qName, Attributes attrs, DelegationManager dm) throws SAXException { super.startElement(nsURI, localName, qName, attrs, dm); } protected void setStringValue(String s) throws SAXException { sch = ssContext.getSearchContentHandler(); sch.addSubHitProperty("matchConsensus", s); } } Now, when I iterate over the SeqSimilaritySearchSubHit items, I can get at the match consensus, simply by calling sh.getAnnotation().getProperty("matchConsensus"); HOWEVER, I don't want to modify kernel code in order to get this behavior. I've been looking for a way to easily plug in my own extension here, either by subclassing the right class, or registering the above handler somehow, but I cannot seem to get at that without subclassing all the classes above the alignment handler in the data structure hierarchy, and initializing them myself. I believe, if AlignmentStAXHandler.ALIGNMENT_HANDLER_FACTORY was not declared as final, I would probably be able to register my own subclass of AlignmentStAXHandler there, with this extended behavior. But darn, I can't. Thanks in advance for any help. ant -------- Adam Tracy | Staff Software Engineer | CIS Software Operations AFFYMETRIX, INC. | 6550 Vallejo St. Suite 100 | Emeryville, CA 94608 | Tel: 510-428-8536 From d.naki at cox.net Fri May 14 11:37:43 2004 From: d.naki at cox.net (Don Naki) Date: Sun May 16 00:31:52 2004 Subject: [Biojava-l] SimpleGappedSymbolList from a String References: <008901c4392e$528b8290$6901a8c0@DNAKIXPLT> <40A49E8C.2090207@yahoo.co.uk> Message-ID: <003a01c439c9$66b2f370$6501a8c0@DNAKIXPLT> Thanks for the quick reply, I suppose I can use a GappedSequence instead of a GappedSymbolList; it's just that I don't need features and annotations. Thanks for addressing the ProteinTools.createGappedProteinSequence bug. P.S. The web site looks great; very clean. > Don Naki wrote: > > >Hi all, > >I have a couple of 'novice' questions... > > > >I can't seem to figure out how to create a SimpleGappedSymbolList from a String. I want to parse "-AQSD--VP-" and create a SimpleGappedSymbolList from it. > >ProteinTools has methods to return a SymbolList, Sequence, and GappedSequence from a String, but not a GappedSymbolList. I understand GappedSequence extends GappedSymbolList, but I want just the GappedSymbolList. Alternatively, is there a way to get a GappedSymbolList from a GappedSequence? > > > > > We could add a uitlity method to do this. Why do you /have/ to have a > GappedSymbolList that is not a GappedSequence? Is there a specific > memory constraint? > > >A second question is that ProteinTools.createGappedProteinSequence("-AQSD--VP-").seqString() results in the String "XAQSD--VPX". The first and last '-' characters are now represented by 'X'. Is this a special kind of gap symbol? If so, how can I distinguish between '-' and 'X' Symbols? > > > > > This is a tokenization bug - the leading/trailing gaps are not being > recognised by the tokenizer, and then replaced by X. It's probably in > CharacterTokenization - needs a special-case for > AlphabetManager.getGapSymbol() - could someone look a this? > > >Thanks in advance, > >Don > > > > > Matthew From mark.schreiber at group.novartis.com Tue May 18 21:55:56 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Tue May 18 21:59:39 2004 Subject: CircularLocations (was Re: [Biojava-l] Re: [Biojava-dev] Feature at position 0) Message-ID: Hello - As you probably have seen CircularLocations are an Ugly Hack. I can say that cause I wrote them! They have been through many iterations and have some fundamental problems. Point 1 you raise below is more of a difference from what you might expect than a bug. Point 2 is a bug. I'm happy to change both but it might take me a while to get around to it. If you want to have a hack yourself be my guest. Fundametally the seperation of strand and location in the biojava API doesn't suit circular locations very well. Hopefully this is fixed in BJ2 (I haven't checked the API yet). - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 Bradford Powell Sent by: biojava-l-bounces@portal.open-bio.org 05/14/2004 09:42 PM To: biojava-l@biojava.org cc: Subject: CircularLocations (was Re: [Biojava-l] Re: [Biojava-dev] Feature at position 0) On Fri, 14 May 2004, Thomas Down wrote: > > On 14 May 2004, at 11:21, Matthew Pocock wrote: > > > I think for the sake of useability, we could either relax the location > > constraint to allow point locations at 0, or in the sp parser, > > re-write these as <1 - what do people think? > > Ugh. > > I'm not sure "<1" will appeal to people who are into round-tripping. > > I think my (slightly) favoured option would be to remove the location > constraints on Features completely. I know this is pretty horrible, > but off-sequence locations do seem to be things people use. > This brings up another issue that I have been thinking about recently. I'm not really comfortable with how circular sequences and circular locations are handled in biojava. For those who aren't familiar, CircularLocations are mapped as CompoundLocations. I would prefer for features on a circular sequence (a CircularView of a sequence) to have coordinates that are outside of the sequence coordinates. Usually I use the convention that the larger coordinate is within 1..length. This makes it easy to check for features that overlap the origin (their min values are <= 0). While I'm thinking of it, there are a couple of bugs I've seen in CircularView: 1-- If subList or subString are called with start and end values that should produce a list longer than the original sequence, things don't happen as I would expect. Suppose you have a sequence 'seq': CircularView cv = new CircularView(seq); SymbolList subL = cv.subList(1, seq.length() + 3) subL.length() has the value 3 instead of seq.length()+3 (i.e. it holds just the first three symbols of seq because the start and stop coordinates are immediately translated to be within 1..length() upon entry to subList(). I can see two ways to resolve this-- one would be to check to see if start-stop > length() and add appropriate numbers of copies of the source symbolList to the sublist as seen above. The other way would be to use a WrappedSymbolListView (this is what I have done for my purposes, code available if people think this would be a good idea). 2-- I almost hesitate to report this "bug" because I like to use negative coordinates in locations on circular sequences-- createFeature() in CircularView throws an exception if getMax() > length() but not if getMin() <= 0. I guess it is a bug one way or the other because it is inconsistant. Since the topic of removing location constraints for features came up, I would say that it would at least make sense to remove the restrictions for circular sequences. Whew, that message was longer than I thought it would be. -- Bradford Powell _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From p.lord at russet.org.uk Thu May 20 06:06:09 2004 From: p.lord at russet.org.uk (Phillip Lord) Date: Thu May 20 06:13:19 2004 Subject: [Biojava-l] CFP: The Seventh Annual Bio-ontologies Meeting Message-ID: Apologies for those of you who get this more than once. The deadline for submissions is now approaching. The Seventh Annual Bio-ontologies Meeting Call For Submissions ============================================================== Key Information =============== Organisers: Robert Stevens(1), Robin McEntire(2), Phillip Lord(1), and James.A.Butler(2) (1) Dept of Computer Science, University of Manchester (2) GlaxoSmithKline Submission Deadline: 31st May 2004 Contact: bio-ontologies@lists.man.ac.uk Website: http://bio-ontologies.man.ac.uk Location: Glasgow, Scotland. Date: 30th July Main Conference: http://www.iscb.org/ismbeccb2004/ Registration: http://www.iscb.org/ismbeccb2004/reg.html Registration Costs: 80 Academic, 110 Corporate, 60 Student (Prices in UK Pounds. 17.5% VAT will be added. Coffee and lunch included) General Information =================== The Bio-Ontologies workshop has been in existence since 1998, and now operates as a Special Interest Group at the ISMB Conference. Bio-Ontologies is well established as one of the key meetings for dissemination of the latest information and research on ontologies in the life sciences and has drawn the key researchers in the field. After last year's highly successful theme of "Ontologies and Text Analysis", we will follow with the timely theme of "Ontologies and Bio-Images". Work is currently being done in the area of ontologies of images, especially in the domain of developmental biology and medicine. A prime example of this work is the Bio-Image databank, which makes extensive use of ontologies. Our guest speaker for this year's topic will be Dr. David Shotton, who will talk about the use of ontologies within the BioImage database. New this year ============= This year, Comparative and Functional Genomics will publish selected presentations from the Seventh Annual Bio-Ontologies Workshop. Previously we have published Conference Reviews in CFG. We are very pleased that last year's Workshop had enough substantial, high-quality work to enable such a special issue this year. We do, however, believe that a level of informality is critical to the success of this Workshop, and so we hope the meeting offers a venue for news and views, perhaps less developed, but up to the minute work. All are welcome! Submissions =========== We invite the submission of two A4 page abstracts for presentation along this theme. Suitable topics include, but are not restricted to: The content of bio-images; The technical origins of images Support for image analysis (e.g., change in shape, colour, texture, etc.) We wish, however, not to restrict the topics presented to the theme alone. So, we are also interested in: Shared experiences in using ontology tools, development methodologies, comparing ontologies, and reusing other people's ontologies; Current research in ontology languages and ontology exchange languages; Updates on ontologies in development by members of the life sciences community, including genomics, proteomics and metabolomics; Practical uses of ontologies in research and drug discovery especially pre-competitive ontologies for the industry. Submission details at http://bio-ontologies.man.ac.uk -- Phillip Lord, Phone: +44 (0) 161 275 6139 PostDoctoral Research Associate, Email: p.lord@russet.org.uk Department of Computer Science http://www.russet.org.uk Kilburn Building http://www.cs.man.ac.uk/~phillord University of Manchester Oxford Road Manchester M13 9PL From max_dipl at web.de Thu May 13 09:17:38 2004 From: max_dipl at web.de (Maximilian Haeussler) Date: Thu May 20 09:21:14 2004 Subject: [Biojava-l] SequencePoster <-> SequencePanel References: <409A560D.1000107@web.de> <40A1F4B3.7090003@genpat.uu.se> Message-ID: <40A37572.4000801@web.de> > > >> still searching for something similar to SequencePanel that does not >> throw exceptions in a JScrollPane...while doing this, I stumbled upon >> SequencePoster. Hum...the javadoc for both looks very very similar, >> if not identical... can someone give me a hint on the difference >> between SequencePanel and SequencePoster? >> This question sounds rather stupid, but doing a diff on both didn't >> really help, and I don't really know where to search. And in the >> demos-dir, there are EmblViewer and BeadDemo but they look really >> pretty similar... > > Could you please try out the code in CVS, and see if it helps, > hopefully you wont see any more IndexOutOfBoundsExceptions. (sorry for writing so late, I accidently deleted my hdd) COOL! :-0 Great! Thanks a lot, really! You fixed my biggest problem with these classes !!! [I'm still getting out-of-bounds exceptions though, but not from the SequencePanel anymore, and these were the biggest nuisance...] Max From mark.schreiber at group.novartis.com Fri May 21 01:55:25 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Fri May 21 01:59:08 2004 Subject: [Biojava-l] BioSQL transaction control Message-ID: Hi - I'm going to start using BioSQL fairly intensively soon and I was wondering at what level the biojava bindings to biosql control transactions. Specifically: if I get a reference to a Sequence object from my SequenceDB does that reference lock the underlying entry (entries) in the database or does it just give me a local copy to play with and then release the lock on the DB? Thanks Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From td2 at sanger.ac.uk Fri May 21 04:34:03 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Fri May 21 04:37:43 2004 Subject: [Biojava-l] BioSQL transaction control In-Reply-To: References: Message-ID: <9DAC57C4-AB01-11D8-882F-000A95C8B056@sanger.ac.uk> On 21 May 2004, at 06:55, mark.schreiber@group.novartis.com wrote: > Hi - > > I'm going to start using BioSQL fairly intensively soon and I was > wondering at what level the biojava bindings to biosql control > transactions. Specifically: if I get a reference to a Sequence object > from > my SequenceDB does that reference lock the underlying entry (entries) > in > the database or does it just give me a local copy to play with and then > release the lock on the DB? Neither. The code supports lazy loading, otherwise it would be easy to make it explode on anything remotely resembling a large sequence, so the Sequence objects you get back are dependent on the database. On the other hand, the schema is too complex to realistically consider "locking" a sequence. So you should only really have one BioSQLSequenceDB accessing a database at a given time. If you need multiple applications accessing the database at once, can you put them all in a single appserver so that they can share a single BioSQLSequenceDB? Otherwise, reasonable options are: - Having one server export an object-oriented view of the BioSQLSequenceDB to other application (Corba/SOAP/RMI/whatever). [Aside: it would be really nice to have some kind of client-server view on BioJava. If this was biojava-specific rather than trying to make it an interoperability point (like BioCorba/bsane/etc.) it might actually be usable] - When you need a sequence, lock the database, get the sequence out of BioSQL, copy it into an in-memory object, then release the lock. - Hack the BioSQL code to disable lazy loading. Without knowing a lot more about your applications, I'm not really in a position to say which of these are more appropriate. Thomas. From dmb at mrc-dunn.cam.ac.uk Sat May 22 21:12:13 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Sat May 22 21:01:49 2004 Subject: [Biojava-l] Network visualization and biojava? Message-ID: Hey, I like the nice java dynamic force directed layout network viewer that so many people use. Is this a part of biojava? I would like to make a simple graph viewer using this tool (command line). Anybody know how easy it is to plug functionality into this module? Hmm... Perhaps this is bigger than I first thought... http://www.manageability.org/blog/stuff/open-source-graph-network-visualization-in-java/view Perhaps this is taken care of... Cheers, Dan. From mark.schreiber at group.novartis.com Sun May 23 21:09:43 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Sun May 23 21:13:16 2004 Subject: [Biojava-l] BioSQL transaction control Message-ID: Hi Thomas - Probably having a single BioSQLSequenceDB on the central appserver is the way to go as long as everything is synchronized. Ihave to say the client server idea sounds good though. Could possible make a SessionBean that looks like a SequenceDB, let the server sort out all the transaction control! I might play with that idea for a while and see how it works. - Mark Thomas Down Sent by: biojava-l-bounces@portal.open-bio.org 05/21/2004 04:34 PM To: Mark Schreiber/GP/Novartis@PH cc: biojava-l@open-bio.org Subject: Re: [Biojava-l] BioSQL transaction control On 21 May 2004, at 06:55, mark.schreiber@group.novartis.com wrote: > Hi - > > I'm going to start using BioSQL fairly intensively soon and I was > wondering at what level the biojava bindings to biosql control > transactions. Specifically: if I get a reference to a Sequence object > from > my SequenceDB does that reference lock the underlying entry (entries) > in > the database or does it just give me a local copy to play with and then > release the lock on the DB? Neither. The code supports lazy loading, otherwise it would be easy to make it explode on anything remotely resembling a large sequence, so the Sequence objects you get back are dependent on the database. On the other hand, the schema is too complex to realistically consider "locking" a sequence. So you should only really have one BioSQLSequenceDB accessing a database at a given time. If you need multiple applications accessing the database at once, can you put them all in a single appserver so that they can share a single BioSQLSequenceDB? Otherwise, reasonable options are: - Having one server export an object-oriented view of the BioSQLSequenceDB to other application (Corba/SOAP/RMI/whatever). [Aside: it would be really nice to have some kind of client-server view on BioJava. If this was biojava-specific rather than trying to make it an interoperability point (like BioCorba/bsane/etc.) it might actually be usable] - When you need a sequence, lock the database, get the sequence out of BioSQL, copy it into an in-memory object, then release the lock. - Hack the BioSQL code to disable lazy loading. Without knowing a lot more about your applications, I'm not really in a position to say which of these are more appropriate. Thomas. _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From hlapp at gmx.net Mon May 24 00:20:46 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon May 24 00:24:19 2004 Subject: [Biojava-l] Re: [Bioperl-l] testing a new Open-Bio website and mail list archive search In-Reply-To: <40A0DCB0.1050207@sonsorol.org> Message-ID: There's one thing that I noticed at least for searches against the bioperl mailing lists: the first pages of hits is commit messages from bioperl-guts. The guts list should be excluded from the index I think. Seldom will you want to search for a commit message through this interface. -hilmar On Tuesday, May 11, 2004, at 07:01 AM, Chris Dagdigian wrote: > Hello Everyone, > > A fantastic volunteer (Kyle Jensen) has been steathily working on a > problem for us that has long been a major issue for us -- website > searching and indexing. > > We've tried various solutions and ht://dig implementations in the past > and nothing really worked well. > > Kyle has been setting up a search indexing system based on the code > from www.swish-e.org and so far it looks very very promising. > > We have 2 main indexed search sites: > > This page is a search index for all of the open-bio hosted websites: > http://search.open-bio.org/cgi-bin/obf-search.cgi > > This page is just for searching mailing list archives: > http://search.open-bio.org/cgi-bin/mail-search.cgi > > > Please give the pages a whirl and let me know what you think. > > Thanks again Kyle! > > -Chris > open-bio.org admin team > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From elenges at ifrance.com Wed May 26 02:52:42 2004 From: elenges at ifrance.com (elenges) Date: Wed May 26 02:56:33 2004 Subject: [Biojava-l] Blast2HTML parser problem Message-ID: <200405260652.2ad1@th00.idoo.com> Hi, I use the biojava Blast2HTML package but I reached an error when executing a BLAST of m12345 on RefSeq_RNA Mouse. (Alias DB) After the last result is a part like this: Subset of the database(s) listed below Number of letters searched: 2,879,183,620 Number of sequences searched: 59,079 And it seems that the parser is not able to handle this part but only the "normal" part beggining with Database like : Database: RefSeq_mm AliasDB: Mus musculus subset of NCBI Reference Sequences Rel.5+ (23May2004). Formatted 23May2004. Posted date: May 23, 2004 9:41 PM Number of letters in database: 2,724,797 Number of sequences in database: 1306 When I remove the "Subset ..." part it works fine. Is it planned to handle this case or perhaps I don't have the correct version of the BLAST SAX Parser? Many Thanks in advance for your response, elenges _____________________________________________________________________ Un mot doux ? envoyer? Une sortie cin? ? organiser? Faites le en temps r?el avec MSN Messenger! C'est gratuit! http://ifrance.com/_reloc/m ___[ Pub ]____________________________________________________________ Inscrivez-vous gratuitement sur Tandaime, Le site de rencontres ! http://rencontre.rencontres.com/index.php?origine From adionne at warnex.ca Mon May 31 16:48:48 2004 From: adionne at warnex.ca (Alexandre Dionne Laporte) Date: Mon May 31 16:51:54 2004 Subject: [Biojava-l] Biojava uses which BioSQL shema version ? Message-ID: Hi, First of all, here are the softwares I use: 1) Biojava snapshot 'biojava-20040528' 2) latest biosql shema : biosqldb-mysql.sql v. 1.38 3) Some of Bioperl 1.4 and bioperl-db projects I would like to store entries from a Genbank file from the NCBI to the BioSQL schema using biojava. That I can do with the 'load_seqdatabase.pl' script found in bioperl-db without any problem. In a same way, I would like to retreive sequences with the Biojava package and dump it in Genbank file format, as I can do with 'bioentry2flat.pl' script. My question is : Which version of biosqldb should I use with the biojava snapshot ? Thanks, Alexandre D.L. From td2 at sanger.ac.uk Mon May 31 17:53:11 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Mon May 31 18:02:20 2004 Subject: [Biojava-l] BioJava 1.4pre1 Message-ID: Hi, There's now a biojava 1.4pre1 release available for download and testing: http://www.biojava.org/download14.html BioJava 1.4 includes many new features, including regular expressions on SymbolLists and macromolecular structure APIs, plus the usual bug-fixes and performance improvements. There's hopefully going to be a 1.4final release in about a month, so all testing and bug reports are welcome! Thomas.