From j-osborne at northwestern.edu Fri Mar 3 14:37:44 2006 From: j-osborne at northwestern.edu (John Osborne) Date: Fri Mar 3 15:05:56 2006 Subject: [Biojava-dev] Moving to Java 1.5 Message-ID: <44089B08.5080500@northwestern.edu> I know we discussed this last October and as I remember it the plan was to move to 1.5 in the new year... I have just been switching over some ontology code from 1.4 that I would like to move to 1.5 (and eventually submit to biojava)- what are people's thoughts on this now? I am developing on a Mac and with the release of 1.5 for the Mac I think that ought to persuade a lot more people to move over. -John From mark.schreiber at novartis.com Sun Mar 5 20:19:55 2006 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Sun Mar 5 20:21:47 2006 Subject: [Biojava-dev] Moving to Java 1.5 Message-ID: I'm happy with a move to 1.5. The main problems have been the appropriate JDKs for Mac and Compaq Alpha. If they are no longer problems then I think we should consider the move. - Mark John Osborne Sent by: biojava-dev-bounces@portal.open-bio.org 03/04/2006 03:37 AM To: biojava-dev@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] Moving to Java 1.5 I know we discussed this last October and as I remember it the plan was to move to 1.5 in the new year... I have just been switching over some ontology code from 1.4 that I would like to move to 1.5 (and eventually submit to biojava)- what are people's thoughts on this now? I am developing on a Mac and with the release of 1.5 for the Mac I think that ought to persuade a lot more people to move over. -John _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From smh1008 at cam.ac.uk Mon Mar 6 02:50:28 2006 From: smh1008 at cam.ac.uk (David Huen) Date: Mon Mar 6 03:08:08 2006 Subject: [Biojava-dev] Moving to Java 1.5 In-Reply-To: References: Message-ID: On Mar 6 2006, mark.schreiber@novartis.com wrote: >I'm happy with a move to 1.5. > >The main problems have been the appropriate JDKs for Mac and Compaq Alpha. >If they are no longer problems then I think we should consider the move. > I think the Mac JDK for 1.5 requires migration to OS-X 1.5 too. Regards, David From m.fortner at sbcglobal.net Mon Mar 6 08:36:05 2006 From: m.fortner at sbcglobal.net (Mark Fortner) Date: Mon Mar 6 08:38:03 2006 Subject: [Biojava-dev] Moving to Java 1.5 In-Reply-To: <44089B08.5080500@northwestern.edu> References: <44089B08.5080500@northwestern.edu> Message-ID: <440C3AC5.1070109@sbcglobal.net> It might be worth testing things out with RetroWeaver (http://retroweaver.sf.net) as a stopgap measure. It's supposed to allow you to develop in 1.5 and deploy 1.4 compatible binaries. I haven't tried it myself, but I've heard good things about it. It might also be worth testing on a Mactel box. HTH, Mark John Osborne wrote: > I know we discussed this last October and as I remember it the plan > was to move to 1.5 in the new year... > > I have just been switching over some ontology code from 1.4 that I > would like to move to 1.5 (and eventually submit to biojava)- what are > people's thoughts on this now? I am developing on a Mac and with the > release of 1.5 for the Mac I think that ought to persuade a lot more > people to move over. > > -John > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > From sylvain.foisy at bioneq.qc.ca Mon Mar 6 10:03:42 2006 From: sylvain.foisy at bioneq.qc.ca (Sylvain Foisy) Date: Mon Mar 6 10:54:37 2006 Subject: [Biojava-dev] Moving to Java 1.5 In-Reply-To: <44089B08.5080500@northwestern.edu> Message-ID: Hi, The big problem on the Mac is that although X.4 has the Java JRE 1.5, the SDK is still officially stuck at JDK 1.4. JDK 1.5 is still in Developer's Preview mode. Just an observation Sylvain On 3/3/06 2:37 PM, "[NAME]" <[ADDRESS]> wrote: > I know we discussed this last October and as I remember it the plan was > to move to 1.5 in the new year... > > I have just been switching over some ontology code from 1.4 that I > would like to move to 1.5 (and eventually submit to biojava)- what are > people's thoughts on this now? I am developing on a Mac and with the > release of 1.5 for the Mac I think that ought to persuade a lot more > people to move over. > > -John > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > ================================================================== Sylvain Foisy, Ph. D. Directeur - operations / Project Manager BioneQ - Reseau quebecois de bio-informatique U. de Montreal / Genome-Quebec Adresse postale: Departement de biochimie Pavillon principal 2900, boul. ?douard-Montpetit Montr?al (Qu?bec) H3T 1J4 Tel: (514) 343-6111 x.2545 Fax: (514) 343-7759 Courriel: sylvain.foisy@bioneq.qc.ca ================================================================== From mmccormi at fhcrc.org Mon Mar 6 13:05:29 2006 From: mmccormi at fhcrc.org (Michael McCormick) Date: Mon Mar 6 13:15:43 2006 Subject: [Biojava-dev] Moving to Java 1.5 In-Reply-To: References: Message-ID: Hi, I would not call this a big problem, it just means that the user has to download it themselves, rather than using the Mac update tool. The link for the JDK is here: http://developer.apple.com/java/download/ I have been using this since last year and it works fine. Mike On Mar 6, 2006, at 7:03 AM, Sylvain Foisy wrote: Hi, The big problem on the Mac is that although X.4 has the Java JRE 1.5, the SDK is still officially stuck at JDK 1.4. JDK 1.5 is still in Developer's Preview mode. Just an observation Sylvain On 3/3/06 2:37 PM, "[NAME]" <[ADDRESS]> wrote: > I know we discussed this last October and as I remember it the plan > was > to move to 1.5 in the new year... > > I have just been switching over some ontology code from 1.4 that I > would like to move to 1.5 (and eventually submit to biojava)- what are > people's thoughts on this now? I am developing on a Mac and with the > release of 1.5 for the Mac I think that ought to persuade a lot more > people to move over. > > -John > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > ================================================================== Sylvain Foisy, Ph. D. Directeur - operations / Project Manager BioneQ - Reseau quebecois de bio-informatique U. de Montreal / Genome-Quebec Adresse postale: Departement de biochimie Pavillon principal 2900, boul. ?douard-Montpetit Montr?al (Qu?bec) H3T 1J4 Tel: (514) 343-6111 x.2545 Fax: (514) 343-7759 Courriel: sylvain.foisy@bioneq.qc.ca ================================================================== _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From sylvain.foisy at bioneq.qc.ca Mon Mar 6 13:35:22 2006 From: sylvain.foisy at bioneq.qc.ca (Sylvain Foisy) Date: Mon Mar 6 14:17:56 2006 Subject: [Biojava-dev] Moving to Java 1.5 In-Reply-To: Message-ID: Hi, Well, I know that ;-). But the fact that JDK 1.5 on Mac OS X is still in flux could create some potential problems for some users. Therefore, better be on the safe side. Best regards Sylvain On 3/6/06 1:05 PM, "[NAME]" <[ADDRESS]> wrote: > Hi, > > I would not call this a big problem, it just means that the user has > to download it themselves, rather than using the Mac update tool. The > link for the JDK is here: http://developer.apple.com/java/download/ I > have been using this since last year and it works fine. ================================================================== Sylvain Foisy, Ph. D. Directeur - operations / Project Manager BioneQ - Reseau quebecois de bio-informatique U. de Montreal / Genome-Quebec Adresse postale: Departement de biochimie Pavillon principal 2900, boul. ?douard-Montpetit Montr?al (Qu?bec) H3T 1J4 Tel: (514) 343-6111 x.2545 Fax: (514) 343-7759 Courriel: sylvain.foisy@bioneq.qc.ca ================================================================== From mmccormi at fhcrc.org Mon Mar 6 14:46:45 2006 From: mmccormi at fhcrc.org (Michael McCormick) Date: Mon Mar 6 14:41:49 2006 Subject: [Biojava-dev] Moving to Java 1.5 In-Reply-To: References: Message-ID: <85BDABF0-AB6D-43E4-A47E-87C3E31C32DB@fhcrc.org> Hi, I'm sorry, that might have come out as harsh and that wasn't my intention. :-) I was just trying to point out that people using Java on other OSs have to download it themselves, so I don't think it is a stretch for mac users to do the same. JDK 1.6 is already in alpha and targeted for a fall release. https://mustang.dev.java.net Mike On Mar 6, 2006, at 10:35 AM, Sylvain Foisy wrote: Hi, Well, I know that ;-). But the fact that JDK 1.5 on Mac OS X is still in flux could create some potential problems for some users. Therefore, better be on the safe side. Best regards Sylvain On 3/6/06 1:05 PM, "[NAME]" <[ADDRESS]> wrote: > Hi, > > I would not call this a big problem, it just means that the user has > to download it themselves, rather than using the Mac update tool. The > link for the JDK is here: http://developer.apple.com/java/download/ I > have been using this since last year and it works fine. ================================================================== Sylvain Foisy, Ph. D. Directeur - operations / Project Manager BioneQ - Reseau quebecois de bio-informatique U. de Montreal / Genome-Quebec Adresse postale: Departement de biochimie Pavillon principal 2900, boul. ?douard-Montpetit Montr?al (Qu?bec) H3T 1J4 Tel: (514) 343-6111 x.2545 Fax: (514) 343-7759 Courriel: sylvain.foisy@bioneq.qc.ca ================================================================== _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From j-osborne at northwestern.edu Mon Mar 6 14:30:03 2006 From: j-osborne at northwestern.edu (John Osborne) Date: Mon Mar 6 14:45:58 2006 Subject: [Biojava-dev] Moving to Java 1.5 In-Reply-To: References: Message-ID: <440C8DBB.4070607@northwestern.edu> Michael McCormick wrote: > Hi, > > I would not call this a big problem, it just means that the user has > to download it themselves, rather than using the Mac update tool. The > link for the JDK is here: http://developer.apple.com/java/download/ I > have been using this since last year and it works fine. > I've been using the same version on 10.4 without incident too. Lots of comments, but no one seems to be strongly opposed to switching over... Do any Mac people *definitely* oppose a switchover? -John > Mike > > > On Mar 6, 2006, at 7:03 AM, Sylvain Foisy wrote: > > Hi, > > The big problem on the Mac is that although X.4 has the Java JRE 1.5, the > SDK is still officially stuck at JDK 1.4. JDK 1.5 is still in Developer's > Preview mode. > > Just an observation > > Sylvain > > On 3/3/06 2:37 PM, "[NAME]" <[ADDRESS]> wrote: > >> I know we discussed this last October and as I remember it the plan was >> to move to 1.5 in the new year... >> >> I have just been switching over some ontology code from 1.4 that I >> would like to move to 1.5 (and eventually submit to biojava)- what are >> people's thoughts on this now? I am developing on a Mac and with the >> release of 1.5 for the Mac I think that ought to persuade a lot more >> people to move over. >> >> -John >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev@biojava.org >> http://biojava.org/mailman/listinfo/biojava-dev >> > > ================================================================== > Sylvain Foisy, Ph. D. > Directeur - operations / Project Manager > BioneQ - Reseau quebecois de bio-informatique > U. de Montreal / Genome-Quebec > > Adresse postale: > > Departement de biochimie > Pavillon principal > 2900, boul. ?douard-Montpetit > Montr?al (Qu?bec) H3T 1J4 > > Tel: (514) 343-6111 x.2545 > Fax: (514) 343-7759 > Courriel: sylvain.foisy@bioneq.qc.ca > ================================================================== > > > > _______________________________________________ > 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 sylvain.foisy at bioneq.qc.ca Mon Mar 6 14:53:33 2006 From: sylvain.foisy at bioneq.qc.ca (Sylvain Foisy) Date: Mon Mar 6 14:47:51 2006 Subject: [Biojava-dev] Moving to Java 1.5 In-Reply-To: <85BDABF0-AB6D-43E4-A47E-87C3E31C32DB@fhcrc.org> Message-ID: Hi, No harm done :-) !! You are quite right that as Mac users, we are spoiled. But while other can d/l a non-beta JDK, we are still stuck with beta grade software. I do play with JDK 1.5 and do some stuff but for production-grade code, we stick with JDK 1.4.2. Can't wait for Mustang. Should bring lots of improvement for desktop-type apps in addition to server-side uses. Best regards On 3/6/06 2:46 PM, "[NAME]" <[ADDRESS]> wrote: > Hi, > > I'm sorry, that might have come out as harsh and that wasn't my > intention. :-) I was just trying to point out that people using Java > on other OSs have to download it themselves, so I don't think it is a > stretch for mac users to do the same. JDK 1.6 is already in alpha and > targeted for a fall release. https://mustang.dev.java.net > > Mike > > > On Mar 6, 2006, at 10:35 AM, Sylvain Foisy wrote: > > Hi, > > Well, I know that ;-). But the fact that JDK 1.5 on Mac OS X is still in > flux could create some potential problems for some users. Therefore, > better > be on the safe side. > > Best regards > > Sylvain > > On 3/6/06 1:05 PM, "[NAME]" <[ADDRESS]> wrote: > >> Hi, >> >> I would not call this a big problem, it just means that the user has >> to download it themselves, rather than using the Mac update tool. The >> link for the JDK is here: http://developer.apple.com/java/download/ I >> have been using this since last year and it works fine. > > ================================================================== > Sylvain Foisy, Ph. D. > Directeur - operations / Project Manager > BioneQ - Reseau quebecois de bio-informatique > U. de Montreal / Genome-Quebec > > Adresse postale: > > Departement de biochimie > Pavillon principal > 2900, boul. ?douard-Montpetit > Montr?al (Qu?bec) H3T 1J4 > > Tel: (514) 343-6111 x.2545 > Fax: (514) 343-7759 > Courriel: sylvain.foisy@bioneq.qc.ca > ================================================================== > > > > _______________________________________________ > 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 > ================================================================== Sylvain Foisy, Ph. D. Directeur - operations / Project Manager BioneQ - Reseau quebecois de bio-informatique U. de Montreal / Genome-Quebec Adresse postale: Departement de biochimie Pavillon principal 2900, boul. ?douard-Montpetit Montr?al (Qu?bec) H3T 1J4 Tel: (514) 343-6111 x.2545 Fax: (514) 343-7759 Courriel: sylvain.foisy@bioneq.qc.ca ================================================================== From heuermh at acm.org Mon Mar 6 15:09:20 2006 From: heuermh at acm.org (Michael Heuer) Date: Mon Mar 6 15:18:49 2006 Subject: [Biojava-dev] Moving to Java 1.5 In-Reply-To: <440C8DBB.4070607@northwestern.edu> Message-ID: John Osborne wrote: > Lots of comments, but no one seems to be strongly opposed to switching > over... Do any Mac people *definitely* oppose a switchover? How about we hold off on including java 1.5 features in the codebase until after biojava version 1.5 is released? > http://biojava.open-bio.org/wiki/BioJava:1.5ReleasePlan That way, if you really want to see java 1.5 features in biojava, you'll be more likely to help get biojava version 1.5 out the door. :) michael From j-osborne at northwestern.edu Mon Mar 6 15:37:43 2006 From: j-osborne at northwestern.edu (John Osborne) Date: Mon Mar 6 15:32:41 2006 Subject: [Biojava-dev] Moving to Java 1.5 In-Reply-To: References: Message-ID: <440C9D97.4020304@northwestern.edu> What's the plan/status for 1.5 anyway? I couldn't see anything on the webpage, does anybody have a link? Is the biojava 1.5 the biojavax stuff? -John Michael Heuer wrote: > John Osborne wrote: > > >> Lots of comments, but no one seems to be strongly opposed to switching >> over... Do any Mac people *definitely* oppose a switchover? >> > > How about we hold off on including java 1.5 features in the codebase until > after biojava version 1.5 is released? > > >> http://biojava.open-bio.org/wiki/BioJava:1.5ReleasePlan >> > > That way, if you really want to see java 1.5 features in biojava, you'll > be more likely to help get biojava version 1.5 out the door. :) > > michael > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > > > From mark.schreiber at novartis.com Mon Mar 6 20:19:08 2006 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Mon Mar 6 20:20:58 2006 Subject: [Biojava-dev] Moving to Java 1.5 Message-ID: Hi - The plan and status are here http://biojava.open-bio.org/wiki/BioJava:1.5ReleasePlan unfortunately most of the core developers are tres busy right now... Any volunteers to take on some of these tasks? Mostly it's bug fixes and biojavax stuff. There has also been lots of development in the structure package. - Mark John Osborne Sent by: biojava-dev-bounces@portal.open-bio.org 03/07/2006 04:37 AM To: Michael Heuer cc: biojava-dev@portal.open-bio.org, (bcc: Mark Schreiber/GP/Novartis) Subject: Re: [Biojava-dev] Moving to Java 1.5 What's the plan/status for 1.5 anyway? I couldn't see anything on the webpage, does anybody have a link? Is the biojava 1.5 the biojavax stuff? -John Michael Heuer wrote: > John Osborne wrote: > > >> Lots of comments, but no one seems to be strongly opposed to switching >> over... Do any Mac people *definitely* oppose a switchover? >> > > How about we hold off on including java 1.5 features in the codebase until > after biojava version 1.5 is released? > > >> http://biojava.open-bio.org/wiki/BioJava:1.5ReleasePlan >> > > That way, if you really want to see java 1.5 features in biojava, you'll > be more likely to help get biojava version 1.5 out the door. :) > > michael > > _______________________________________________ > 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 dag at sonsorol.org Fri Mar 10 14:17:25 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Fri Mar 10 14:16:40 2006 Subject: [Biojava-dev] hey biojava developers ... Message-ID: <14D0D49F-EDE7-42A1-ADB0-1AACE9EA3739@sonsorol.org> Hey folks, This is a heads up on two things: (1) I'm going to have to move the biojava mailing lists to our new server hardware this weekend. All your list settings, subscribers etc. will all be preserved along with the full archives. The main difference is that your list will be hosted at a new server URL: "lists.open-bio.org" where we are concentrating all OBF hosted mailing lists. There will be forwarding rules and aliases left behind on the "old" server so nobody gets lost in the transition. (2) The server hosting biojava.org is going to lose its internet connection (our hosting at Wyeth is going away soon) so we also need to start thinkng about how and when to move your website to the new server. This should be pretty easy for me to do but I'd like to do it in cooperation with the existing website person who can doublecheck that everything gets migrated and remains working. Can someone contact me directly so we can work together? Basically moving the developers and CVS is to the new hardware before we lose our existing net connection is going to be so much work that I'm really trying to speed up the process of moving websites and mailing lists which are much easier to handle by myself. Regards, Chris OBF From dag at sonsorol.org Sat Mar 11 14:22:01 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Sat, 11 Mar 2006 14:22:01 -0500 Subject: [Biojava-dev] quick update on the biojava mailing lists Message-ID: Hi folks, biojava-l at biojava.org and biojava-dev at biojava.org have been moved onto our new OBF server hardware in the new datacenter. Until we can bring your website onto that machine as well your lists are hosted on the machine "lists.open-bio.org" I've got aliases on the old server that will forward list mail from biojava.org -> lists.open-bio.org and I've updated the main page on your website with the new URL. Regards, Chris OBF From dag at sonsorol.org Tue Mar 14 09:41:34 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Tue, 14 Mar 2006 09:41:34 -0500 Subject: [Biojava-dev] help test the new open-bio anonymous source code server Message-ID: Hi folks, Apologies for the cross-post. I need some help testing out a new open- bio server The new server is http://code.open-bio.org and it has been purpose built to replace our existing anonymous CVS server (cvs.open-bio.org, etc. etc.) In addition to anonymous CVS, this new system also offers anonymous rsync mirrors of all our source code. For security reasons (the anonymous CVS pserver protocol is considered insecure) we run these anon access methods on a locked down machine that only has a read only copy of the codebase. The webserver page (except for the viewcvs CGI) actually redirects to a wiki entry on a different server so we don' have to maintain a website on the new box. The anonymous access repository is currently updated every 30 minutes from the main developer system. Things I need help with: - check out http://code.open-bio.org -- does the documentation make sense? Can it be made better? If so, change it! (it is a wiki after all...) - please experiment with anonymous CVS, confirm that you can check out code - experiment with rsync! this is a new feature for us that we could not offer on the old server (due to upstream port ACLs on a core router) - provide feedback on the "speed" and bandwidth of the anoncvs server, does it seem reasonable? Let me know what you'll think. The reason for this move is that one of our core hosting facilities (datacenter at Wyeth Research) is no longer going to be useable by us as they are changing their WAN links in such a way that our servers will not be able to directly access the internet. We are in the process of moving *every* open-bio.org service onto new hardware located in a different datacenter. Our mailing lists have already been migrated, websites are moving as well. Expect some big changes once we tackle the task of moving all the developers and the writable CVS repositories to the new datacenter - that will happen probably within the next 2 weeks. Regards, Chris Dagdigian OBF From mark.schreiber at novartis.com Thu Mar 16 21:52:52 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Fri, 17 Mar 2006 10:52:52 +0800 Subject: [Biojava-dev] Away Message-ID: Hello - I'm going to be travelling a lot in the next 5 weeks and may only have patchy access to email and no access to CVS or my development machines. Therefore I won't be able to offer much in the way of technical support. Hopefully Richard and Michael will be able to deal with any major issues that crop up. Best regards, - Mark Mark Schreiber Research Investigator (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 richard.holland at ebi.ac.uk Mon Mar 20 12:13:19 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Mon, 20 Mar 2006 17:13:19 +0000 Subject: [Biojava-dev] Dynamic features and sequences in BJX Message-ID: <1142874799.3906.41.camel@texas.ebi.ac.uk> Hi there. I've managed to do some testing and bugfixing and I think you'll find that dynamically-loaded features and sequence portions should now work. This means that when using FeatureFilter objects to load features, you only get the features you want loaded as they are (mostly) filtered at database level, and that these features will not drag the entire sequence out of the db until you query their symbols, and even then you'll only get the portion you request. If you do wish to work with the features and edit the underlying sequence or load it permanently, then you need to use fullyLoadRichSequence() in BioSQLRichSequenceDB. It's in CVS now. Hope it works for you all. Enjoy! cheers, Richard -- Richard Holland European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK Tel: +44-(0)1223-494416 --------------- From richard.holland at ebi.ac.uk Wed Mar 22 05:07:16 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Wed, 22 Mar 2006 10:07:16 +0000 Subject: [Biojava-dev] Extra method in GenbankRichSequenceDB removed Message-ID: <1143022037.3899.7.camel@texas.ebi.ac.uk> Hi all. Someone added a method: public RichSequence getRichSequence(String id, Namespace nsp) throws BioException, IllegalIDException; to org.biojavax.bio.seq.db.ncbi.GenbankRichSequenceDB so that the following is possible: db.getRichSequence(id,nsp); This is actually unnecessary as the same effect can be achieved by calling: db.setNamespace(nsp); db.getRichSequence(id); Any objections if I remove the extra method? cheers, Richard -- Richard Holland European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK Tel: +44-(0)1223-494416 --------------- From Yan.Bai at UTSouthwestern.edu Wed Mar 22 11:34:32 2006 From: Yan.Bai at UTSouthwestern.edu (Yan Bai) Date: Wed, 22 Mar 2006 10:34:32 -0600 Subject: [Biojava-dev] SeqIOTools method not found Message-ID: I am new in this mailing list, I've download biojava package, pretty sure CLASSPATH was set up right. I typed the example given on the tutorial (Trace2Seq.java), got compiler error as below. In biojava source code, I couldn't find the method named as "writeFasta" in SeqIOTools with "Sequence" as the 2nd parameter, neither did I find any methods with 'Sequence' as the 2nd parameter, but they all show up on API. I am in the first step of trying Biojava, and this is frustrating. Apprecate if someone will help me out. ------------------------------------- Trace2Seq.java:18: cannot find symbol symbol : method writeFasta(java.io.PrintStream,org.biojava.bio.seq.Sequence) location: class org.biojava.bio.seq.io.SeqIOTools SeqIOTools.writeFasta(System.out, seq); ^ 1 error -------------------------------------- From richard.holland at ebi.ac.uk Wed Mar 22 12:21:25 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Wed, 22 Mar 2006 17:21:25 +0000 Subject: [Biojava-dev] SeqIOTools method not found In-Reply-To: References: Message-ID: <1143048086.3899.45.camel@texas.ebi.ac.uk> Very odd. Only thing I can think of is that you don't have the correct version of BioJava and instead have some older version where this method didn't exist yet. How did you download it? (if possible, send us the URL of the link you clicked to download it) Make sure you're using at least the 1.4 binary distribution available from the biojava.org website, or if you're using CVS then checkout the module biojava-live for the latest stuff. cheers, Richard On Wed, 2006-03-22 at 10:34 -0600, Yan Bai wrote: > I am new in this mailing list, > I've download biojava package, pretty sure CLASSPATH was set up right. I typed the example given on the tutorial (Trace2Seq.java), got compiler error as below. In biojava source code, I couldn't find the method named as "writeFasta" in SeqIOTools with "Sequence" as the 2nd parameter, neither did I find any methods with 'Sequence' as the 2nd parameter, but they all show up on API. > I am in the first step of trying Biojava, and this is frustrating. Apprecate if someone will help me out. > ------------------------------------- > Trace2Seq.java:18: cannot find symbol > symbol : method writeFasta(java.io.PrintStream,org.biojava.bio.seq.Sequence) > location: class org.biojava.bio.seq.io.SeqIOTools > SeqIOTools.writeFasta(System.out, seq); > ^ > 1 error > -------------------------------------- > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK Tel: +44-(0)1223-494416 --------------- From ady at sanger.ac.uk Wed Mar 22 12:31:25 2006 From: ady at sanger.ac.uk (Andy Yates) Date: Wed, 22 Mar 2006 17:31:25 +0000 Subject: [Biojava-dev] SeqIOTools method not found In-Reply-To: References: Message-ID: <442189ED.9070505@sanger.ac.uk> Hi. A quick look on the latest Biojava API shows that there is a method like this & this is also in the current src tree that I downloaded from biojava just now: http://www.biojava.org/docs/api14/org/biojava/bio/seq/io/SeqIOTools.html#writeFasta(java.io.OutputStream,%20org.biojava.bio.seq.Sequence) My suggestions would be to check your classpath and check your imports in your class file. You should have: import org.biojava.bio.seq.io.SeqIOTools; At the top of the class file. Make sure it is after the package declaration and before the class definition. Cheers, Andy Yates Yan Bai wrote: > I am new in this mailing list, > I've download biojava package, pretty sure CLASSPATH was set up right. I typed the example given on the tutorial (Trace2Seq.java), got compiler error as below. In biojava source code, I couldn't find the method named as "writeFasta" in SeqIOTools with "Sequence" as the 2nd parameter, neither did I find any methods with 'Sequence' as the 2nd parameter, but they all show up on API. > I am in the first step of trying Biojava, and this is frustrating. Apprecate if someone will help me out. > ------------------------------------- > Trace2Seq.java:18: cannot find symbol > symbol : method writeFasta(java.io.PrintStream,org.biojava.bio.seq.Sequence) > location: class org.biojava.bio.seq.io.SeqIOTools > SeqIOTools.writeFasta(System.out, seq); > ^ > 1 error > -------------------------------------- > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev From Yan.Bai at UTSouthwestern.edu Wed Mar 22 13:44:40 2006 From: Yan.Bai at UTSouthwestern.edu (Yan Bai) Date: Wed, 22 Mar 2006 12:44:40 -0600 Subject: [Biojava-dev] SeqIOTools method not found Message-ID: Yeah, I found out that I have a wrong version of biojava.jar, downloaded 1.4 and it works great. Thank you very much. Yan >>> Richard Holland 03/22/06 11:21 AM >>> Very odd. Only thing I can think of is that you don't have the correct version of BioJava and instead have some older version where this method didn't exist yet. How did you download it? (if possible, send us the URL of the link you clicked to download it) Make sure you're using at least the 1.4 binary distribution available from the biojava.org website, or if you're using CVS then checkout the module biojava-live for the latest stuff. cheers, Richard On Wed, 2006-03-22 at 10:34 -0600, Yan Bai wrote: > I am new in this mailing list, > I've download biojava package, pretty sure CLASSPATH was set up right. I typed the example given on the tutorial (Trace2Seq.java), got compiler error as below. In biojava source code, I couldn't find the method named as "writeFasta" in SeqIOTools with "Sequence" as the 2nd parameter, neither did I find any methods with 'Sequence' as the 2nd parameter, but they all show up on API. > I am in the first step of trying Biojava, and this is frustrating. Apprecate if someone will help me out. > ------------------------------------- > Trace2Seq.java:18: cannot find symbol > symbol : method writeFasta(java.io.PrintStream,org.biojava.bio.seq.Sequence) > location: class org.biojava.bio.seq.io.SeqIOTools > SeqIOTools.writeFasta(System.out, seq); > ^ > 1 error > -------------------------------------- > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK Tel: +44-(0)1223-494416 --------------- _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev From Yan.Bai at UTSouthwestern.edu Wed Mar 22 16:05:06 2006 From: Yan.Bai at UTSouthwestern.edu (Yan Bai) Date: Wed, 22 Mar 2006 15:05:06 -0600 Subject: [Biojava-dev] ABI file parser Message-ID: Thank you all for helping me out. Another question is about the ABI file parser, located in the package org.biojava.bio.program.ABIFParser. Comments of this file indicate that it parses files from 377 DNA sequencer, while our sequence files are generated by 3730 XL, are there any mismatches between these two formats? Is there a parser specific for 3730? I couldn't find anything describe the 3730 XL format like the one Clark Tibbett wrote. Thanks for any inputs. Yan >>> "Dickson S. Guedes" 03/22/06 2:01 PM >>> Hi Yan, Download BioJava - http://biojava.org/wiki/BioJava:Download Getting Started - http://biojava.org/wiki/BioJava:GetStarted Look at the sites above to get information about correct installation of Biojava framework. []s -- Dickson S. Guedes /* * UNISUL - Universidade do Sul de Santa Catarina * ATI - Assessoria de Tecnologia da Informa??o * (0xx48) 621-3200 - http://www.unisul.br * * "Quis custodiet ipsos custodes?" */ Yan Bai wrotes: > I am new in this mailing list, > I've download biojava package, pretty sure CLASSPATH was set up right. I typed the example given on the tutorial (Trace2Seq.java), got compiler error as below. In biojava source code, I couldn't find the method named as "writeFasta" in SeqIOTools with "Sequence" as the 2nd parameter, neither did I find any methods with 'Sequence' as the 2nd parameter, but they all show up on API. > I am in the first step of trying Biojava, and this is frustrating. Apprecate if someone will help me out. > ------------------------------------- > Trace2Seq.java:18: cannot find symbol > symbol : method writeFasta(java.io.PrintStream,org.biojava.bio.seq.Sequence) > location: class org.biojava.bio.seq.io.SeqIOTools > SeqIOTools.writeFasta(System.out, seq); > ^ > 1 error > -------------------------------------- From russ at kepler-eng.com Wed Mar 22 16:25:11 2006 From: russ at kepler-eng.com (Russ Kepler) Date: Wed, 22 Mar 2006 14:25:11 -0700 Subject: [Biojava-dev] ABI file parser In-Reply-To: References: Message-ID: <200603221425.12183.russ@kepler-eng.com> On Wednesday 22 March 2006 02:05 pm, Yan Bai wrote: > Another question is about the ABI file parser, located in the package > org.biojava.bio.program.ABIFParser. Comments of this file indicate that it > parses files from 377 DNA sequencer, while our sequence files are generated > by 3730 XL, are there any mismatches between these two formats? Is there a > parser specific for 3730? I couldn't find anything describe the 3730 XL > format like the one Clark Tibbett wrote. The differences that I can really are the addition of the quality calls and (maybe) caller name. I'm sure that there are others, but since I wasn't looking for them I never really noticed their absence. I've got a parser that keeps the quality call values if you need it. From guedes at unisul.br Wed Mar 22 15:01:15 2006 From: guedes at unisul.br (Dickson S. Guedes) Date: Wed, 22 Mar 2006 17:01:15 -0300 Subject: [Biojava-dev] SeqIOTools method not found In-Reply-To: References: Message-ID: <4421AD0B.8030606@unisul.br> Hi Yan, Download BioJava - http://biojava.org/wiki/BioJava:Download Getting Started - http://biojava.org/wiki/BioJava:GetStarted Look at the sites above to get information about correct installation of Biojava framework. []s -- Dickson S. Guedes /* * UNISUL - Universidade do Sul de Santa Catarina * ATI - Assessoria de Tecnologia da Informa??o * (0xx48) 621-3200 - http://www.unisul.br * * "Quis custodiet ipsos custodes?" */ Yan Bai wrotes: > I am new in this mailing list, > I've download biojava package, pretty sure CLASSPATH was set up right. I typed the example given on the tutorial (Trace2Seq.java), got compiler error as below. In biojava source code, I couldn't find the method named as "writeFasta" in SeqIOTools with "Sequence" as the 2nd parameter, neither did I find any methods with 'Sequence' as the 2nd parameter, but they all show up on API. > I am in the first step of trying Biojava, and this is frustrating. Apprecate if someone will help me out. > ------------------------------------- > Trace2Seq.java:18: cannot find symbol > symbol : method writeFasta(java.io.PrintStream,org.biojava.bio.seq.Sequence) > location: class org.biojava.bio.seq.io.SeqIOTools > SeqIOTools.writeFasta(System.out, seq); > ^ > 1 error > -------------------------------------- From heuermh at acm.org Wed Mar 22 16:19:58 2006 From: heuermh at acm.org (Michael Heuer) Date: Wed, 22 Mar 2006 16:19:58 -0500 (EST) Subject: [Biojava-dev] Dynamic features and sequences in BJX In-Reply-To: <1142874799.3906.41.camel@texas.ebi.ac.uk> Message-ID: Richard Holland wrote: > I've managed to do some testing and bugfixing and I think you'll find > that dynamically-loaded features and sequence portions should now work. > > This means that when using FeatureFilter objects to load features, you > only get the features you want loaded as they are (mostly) filtered at > database level, and that these features will not drag the entire > sequence out of the db until you query their symbols, and even then > you'll only get the portion you request. If you do wish to work with the > features and edit the underlying sequence or load it permanently, then > you need to use fullyLoadRichSequence() in BioSQLRichSequenceDB. So if I pull out a sequence and iterate over its features, as long as I don't call any of the SymbolList methods on it or on any of the features, the symbols will never be populated from the database? Very cool. michael From richard.holland at ebi.ac.uk Thu Mar 23 04:22:01 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Thu, 23 Mar 2006 09:22:01 +0000 Subject: [Biojava-dev] Dynamic features and sequences in BJX In-Reply-To: References: Message-ID: <1143105721.3899.47.camel@texas.ebi.ac.uk> Yes. And in addition, if you do reference its symbols, then only the part you reference will be loaded. cheers, Richard On Wed, 2006-03-22 at 16:19 -0500, Michael Heuer wrote: > Richard Holland wrote: > > > I've managed to do some testing and bugfixing and I think you'll find > > that dynamically-loaded features and sequence portions should now work. > > > > This means that when using FeatureFilter objects to load features, you > > only get the features you want loaded as they are (mostly) filtered at > > database level, and that these features will not drag the entire > > sequence out of the db until you query their symbols, and even then > > you'll only get the portion you request. If you do wish to work with the > > features and edit the underlying sequence or load it permanently, then > > you need to use fullyLoadRichSequence() in BioSQLRichSequenceDB. > > So if I pull out a sequence and iterate over its features, as long as I > don't call any of the SymbolList methods on it or on any of the features, > the symbols will never be populated from the database? > > Very cool. > > michael > -- Richard Holland European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK Tel: +44-(0)1223-494416 --------------- From richard.holland at ebi.ac.uk Thu Mar 23 04:30:03 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Thu, 23 Mar 2006 09:30:03 +0000 Subject: [Biojava-dev] ABI file parser In-Reply-To: <200603221425.12183.russ@kepler-eng.com> References: <200603221425.12183.russ@kepler-eng.com> Message-ID: <1143106203.3899.54.camel@texas.ebi.ac.uk> I've used the BioJava ABI parser to parse 3730 ABI files without any problems, and it successfully reads both base calls and quality scores. You should use the ABIFChromatogram method getBaseCalls() to return an alignment of two sequences - the first sequence is the sequence data, the second is a sequence made up of Integer scores. cheers, Richard On Wed, 2006-03-22 at 14:25 -0700, Russ Kepler wrote: > On Wednesday 22 March 2006 02:05 pm, Yan Bai wrote: > > > Another question is about the ABI file parser, located in the package > > org.biojava.bio.program.ABIFParser. Comments of this file indicate that it > > parses files from 377 DNA sequencer, while our sequence files are generated > > by 3730 XL, are there any mismatches between these two formats? Is there a > > parser specific for 3730? I couldn't find anything describe the 3730 XL > > format like the one Clark Tibbett wrote. > > The differences that I can really are the addition of the quality calls and > (maybe) caller name. I'm sure that there are others, but since I wasn't > looking for them I never really noticed their absence. I've got a parser > that keeps the quality call values if you need it. > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK Tel: +44-(0)1223-494416 --------------- From a.maule at cs.ucl.ac.uk Thu Mar 23 07:50:35 2006 From: a.maule at cs.ucl.ac.uk (Andy Maule) Date: Thu, 23 Mar 2006 12:50:35 -0000 Subject: [Biojava-dev] BioJava code repository Message-ID: <001601c64e78$628fc870$630d1080@cs.ucl.ac.uk> Hi, I'm looking for java applications that use Ensembl for a research project. In particular I'm interested in seeing how applications have been changed in response to changes in the schema of Ensembl. So I need to look at the source code repositories, and I've been looking at the biojava CVS. For those who are interested the project involves predicting the impact of database schema changes on applications. I'm going to use the change history of the Ensembl schema to find an interesting schema change(s) that will affect the application. I'm then going to run a tool over the application to see if I can effectivley predict what needs to be changed. I'm then going to compare the predicted changes with the actual changes, to see if my analysis was correct. I'd be more than happy to explain the project further if anyone would like to know more. As far as I can see Biojava is still using the schema for version 10 as shown in org.ensembl.db.sql.SQLDatabaseAdaptor10. This is only from the CVS repository though. Someone on the Ensembl mailing list pointed me to http://www.derkholm.net/svn/repos and the dazzle project. Could anyone fill me in on whether this repository is the latest version, and is there someway I could access via subversion directly? Also where can I now get information about Dazzle? Thanks Andy Maule From richard.holland at ebi.ac.uk Thu Mar 23 09:33:23 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Thu, 23 Mar 2006 14:33:23 +0000 Subject: [Biojava-dev] BioJava code repository In-Reply-To: <001601c64e78$628fc870$630d1080@cs.ucl.ac.uk> References: <001601c64e78$628fc870$630d1080@cs.ucl.ac.uk> Message-ID: <1143124403.3899.78.camel@texas.ebi.ac.uk> The derkholm.net Subversion repository is the current version of biojava-ensembl, which is a separate project from the main biojava found in the open-bio.org CVS servers. Biojava-ensembl is maintained by Thomas Down and as far as I know is up-to-date to Ensembl version 37. To use the Subversion repository directly you just point the command- line Subversion client at the same URL as the one you typed into your web browser. Dazzle was also written by Thomas Down but I'm not sure if he still maintains it. Best to ask him directly. cheers, Richard On Thu, 2006-03-23 at 12:50 +0000, Andy Maule wrote: > Hi, > > I'm looking for java applications that use Ensembl for a research project. > In particular I'm interested in seeing how applications have been changed in > response to changes in the schema of Ensembl. So I need to look at the > source code repositories, and I've been looking at the biojava CVS. > > For those who are interested the project involves predicting the impact of > database schema changes on applications. I'm going to use the change history > of the Ensembl schema to find an interesting schema change(s) that will > affect the application. I'm then going to run a tool over the application to > see if I can effectivley predict what needs to be changed. I'm then going to > compare the predicted changes with the actual changes, to see if my analysis > was correct. I'd be more than happy to explain the project further if anyone > would like to know more. > > As far as I can see Biojava is still using the schema for version 10 as > shown in org.ensembl.db.sql.SQLDatabaseAdaptor10. This is only from the CVS > repository though. > > Someone on the Ensembl mailing list pointed me to > http://www.derkholm.net/svn/repos and the dazzle project. Could anyone fill > me in on whether this repository is the latest version, and is there someway > I could access via subversion directly? > > Also where can I now get information about Dazzle? > > Thanks > > Andy Maule > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK Tel: +44-(0)1223-494416 --------------- From a.maule at cs.ucl.ac.uk Thu Mar 23 09:38:59 2006 From: a.maule at cs.ucl.ac.uk (Andy Maule) Date: Thu, 23 Mar 2006 14:38:59 -0000 Subject: [Biojava-dev] BioJava code repository In-Reply-To: <1143124403.3899.78.camel@texas.ebi.ac.uk> Message-ID: <001501c64e87$88c6a8b0$630d1080@cs.ucl.ac.uk> Thanks Richard, That clears things up a bit. I'll look through the SVN repository, and see what I can find. Andy -----Original Message----- From: Richard Holland [mailto:richard.holland at ebi.ac.uk] Sent: 23 March 2006 14:33 To: Andy Maule Cc: biojava-dev Subject: Re: [Biojava-dev] BioJava code repository The derkholm.net Subversion repository is the current version of biojava-ensembl, which is a separate project from the main biojava found in the open-bio.org CVS servers. Biojava-ensembl is maintained by Thomas Down and as far as I know is up-to-date to Ensembl version 37. To use the Subversion repository directly you just point the command- line Subversion client at the same URL as the one you typed into your web browser. Dazzle was also written by Thomas Down but I'm not sure if he still maintains it. Best to ask him directly. cheers, Richard On Thu, 2006-03-23 at 12:50 +0000, Andy Maule wrote: > Hi, > > I'm looking for java applications that use Ensembl for a research > project. In particular I'm interested in seeing how applications have > been changed in response to changes in the schema of Ensembl. So I > need to look at the source code repositories, and I've been looking at > the biojava CVS. > > For those who are interested the project involves predicting the > impact of database schema changes on applications. I'm going to use > the change history of the Ensembl schema to find an interesting schema > change(s) that will affect the application. I'm then going to run a > tool over the application to see if I can effectivley predict what > needs to be changed. I'm then going to compare the predicted changes > with the actual changes, to see if my analysis was correct. I'd be > more than happy to explain the project further if anyone would like to > know more. > > As far as I can see Biojava is still using the schema for version 10 > as shown in org.ensembl.db.sql.SQLDatabaseAdaptor10. This is only from > the CVS repository though. > > Someone on the Ensembl mailing list pointed me to > http://www.derkholm.net/svn/repos and the dazzle project. Could anyone > fill me in on whether this repository is the latest version, and is > there someway I could access via subversion directly? > > Also where can I now get information about Dazzle? > > Thanks > > Andy Maule > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK Tel: +44-(0)1223-494416 --------------- From a.maule at cs.ucl.ac.uk Thu Mar 23 09:48:35 2006 From: a.maule at cs.ucl.ac.uk (Andy Maule) Date: Thu, 23 Mar 2006 14:48:35 -0000 Subject: [Biojava-dev] BioJava code repository In-Reply-To: Message-ID: <000701c64e88$e63e5000$630d1080@cs.ucl.ac.uk> Thanks Sylvain, That agrees with the last message I got from Richard Holland, it clears up the confusion. Andy -----Original Message----- From: Sylvain Foisy [mailto:sylvain.foisy at bioneq.qc.ca] Sent: 23 March 2006 14:44 To: Andy Maule Cc: biojava-dev at lists.open-bio.org Subject: Re: [Biojava-dev] BioJava code repository Hi, The Ensembl access libraries found in CVS are way old. Thomas Down, the original creator, has put together a new version that can be accessed through svn at the following location: http://www.derkholm.net/svn/repos/biojava-ensembl/trunk It works with current Ensembl schemas and I know that Thomas still does development on it. Hope this helps Best regards Sylvain On 3/23/06 7:50 AM, "[NAME]" <[ADDRESS]> wrote: > Hi, > > I'm looking for java applications that use Ensembl for a research > project. In particular I'm interested in seeing how applications have > been changed in response to changes in the schema of Ensembl. So I > need to look at the source code repositories, and I've been looking at > the biojava CVS. > > For those who are interested the project involves predicting the > impact of database schema changes on applications. I'm going to use > the change history of the Ensembl schema to find an interesting schema > change(s) that will affect the application. I'm then going to run a > tool over the application to see if I can effectivley predict what > needs to be changed. I'm then going to compare the predicted changes > with the actual changes, to see if my analysis was correct. I'd be > more than happy to explain the project further if anyone would like to > know more. > > As far as I can see Biojava is still using the schema for version 10 > as shown in org.ensembl.db.sql.SQLDatabaseAdaptor10. This is only from > the CVS repository though. > > Someone on the Ensembl mailing list pointed me to > http://www.derkholm.net/svn/repos and the dazzle project. Could anyone > fill me in on whether this repository is the latest version, and is > there someway I could access via subversion directly? > > Also where can I now get information about Dazzle? > > Thanks > > Andy Maule > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > ================================================================== Sylvain Foisy, Ph. D. Directeur - operations / Project Manager BioneQ - Reseau quebecois de bio-informatique U. de Montreal / Genome-Quebec Adresse postale: Departement de biochimie Pavillon principal 2900, boul. ?douard-Montpetit Montr?al (Qu?bec) H3T 1J4 Tel: (514) 343-6111 x.2545 Fax: (514) 343-7759 Courriel: sylvain.foisy at bioneq.qc.ca ================================================================== From sylvain.foisy at bioneq.qc.ca Thu Mar 23 09:43:46 2006 From: sylvain.foisy at bioneq.qc.ca (Sylvain Foisy) Date: Thu, 23 Mar 2006 09:43:46 -0500 Subject: [Biojava-dev] BioJava code repository In-Reply-To: <001601c64e78$628fc870$630d1080@cs.ucl.ac.uk> Message-ID: Hi, The Ensembl access libraries found in CVS are way old. Thomas Down, the original creator, has put together a new version that can be accessed through svn at the following location: http://www.derkholm.net/svn/repos/biojava-ensembl/trunk It works with current Ensembl schemas and I know that Thomas still does development on it. Hope this helps Best regards Sylvain On 3/23/06 7:50 AM, "[NAME]" <[ADDRESS]> wrote: > Hi, > > I'm looking for java applications that use Ensembl for a research project. > In particular I'm interested in seeing how applications have been changed in > response to changes in the schema of Ensembl. So I need to look at the > source code repositories, and I've been looking at the biojava CVS. > > For those who are interested the project involves predicting the impact of > database schema changes on applications. I'm going to use the change history > of the Ensembl schema to find an interesting schema change(s) that will > affect the application. I'm then going to run a tool over the application to > see if I can effectivley predict what needs to be changed. I'm then going to > compare the predicted changes with the actual changes, to see if my analysis > was correct. I'd be more than happy to explain the project further if anyone > would like to know more. > > As far as I can see Biojava is still using the schema for version 10 as > shown in org.ensembl.db.sql.SQLDatabaseAdaptor10. This is only from the CVS > repository though. > > Someone on the Ensembl mailing list pointed me to > http://www.derkholm.net/svn/repos and the dazzle project. Could anyone fill > me in on whether this repository is the latest version, and is there someway > I could access via subversion directly? > > Also where can I now get information about Dazzle? > > Thanks > > Andy Maule > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > ================================================================== Sylvain Foisy, Ph. D. Directeur - operations / Project Manager BioneQ - Reseau quebecois de bio-informatique U. de Montreal / Genome-Quebec Adresse postale: Departement de biochimie Pavillon principal 2900, boul. ?douard-Montpetit Montr?al (Qu?bec) H3T 1J4 Tel: (514) 343-6111 x.2545 Fax: (514) 343-7759 Courriel: sylvain.foisy at bioneq.qc.ca ================================================================== From a.maule at cs.ucl.ac.uk Mon Mar 20 11:04:01 2006 From: a.maule at cs.ucl.ac.uk (Andy Maule) Date: Mon, 20 Mar 2006 16:04:01 -0000 Subject: [Biojava-dev] Biojava Ensembl version Message-ID: <002401c64c37$f149b690$f2421080@cs.ucl.ac.uk> Hi, What version of the Ensembl schema does the latest Biojava use? I'm looking for java applications that use Ensembl for a research project. In particular I'm interested in seeing how applications have been changed in response to changes in the schema of Ensembl. As far as I can see Biojava is still using the schema for version 10 as shown in org.ensembl.db.sql.SQLDatabaseAdaptor10. Is this the latest version used? Thanks Andy Maule From smh1008 at cam.ac.uk Mon Mar 27 13:30:44 2006 From: smh1008 at cam.ac.uk (David Huen) Date: 27 Mar 2006 19:30:44 +0100 Subject: [Biojava-dev] Biojava Ensembl version In-Reply-To: <002401c64c37$f149b690$f2421080@cs.ucl.ac.uk> References: <002401c64c37$f149b690$f2421080@cs.ucl.ac.uk> Message-ID: On Mar 27 2006, Andy Maule wrote: I would suggest contacting Thomas Down about the Ensembl-Biojava bridge. Regards, David Huen >Hi, > >What version of the Ensembl schema does the latest Biojava use? > > I'm looking for java applications that use Ensembl for a research > project. In particular I'm interested in seeing how applications have > been changed in response to changes in the schema of Ensembl. As far as I > can see Biojava is still using the schema for version 10 as shown in > org.ensembl.db.sql.SQLDatabaseAdaptor10. Is this the latest version used? > >Thanks > >Andy Maule > > >_______________________________________________ >biojava-dev mailing list >biojava-dev at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/biojava-dev > From dag at sonsorol.org Mon Mar 27 17:13:54 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Mon, 27 Mar 2006 17:13:54 -0500 Subject: [Biojava-dev] syntax highlighting extension added to your wiki Message-ID: <0C30FEA4-41EB-4114-A3C5-4886CF4518D0@sonsorol.org> Hey folks, Following a suggestion from Mark Schreiber I've installed the Geshi syntax highlighting PHP library into your biojava.org wiki. This extension makes it easier (if you wish) to have code snippets color coded for clarity and readability. You can see examples of the extension in action here: http://biojava.org/wiki/User:Chrisdag To start using it, just change your code blocks to use "" instead of the current "
" within the wiki.

Regards,
Chris
open-bio.org



From guedes at unisul.br  Mon Mar 27 17:43:39 2006
From: guedes at unisul.br (Dickson S. Guedes)
Date: Mon, 27 Mar 2006 19:43:39 -0300
Subject: [Biojava-dev] syntax highlighting extension added to your wiki
In-Reply-To: <0C30FEA4-41EB-4114-A3C5-4886CF4518D0@sonsorol.org>
References: <0C30FEA4-41EB-4114-A3C5-4886CF4518D0@sonsorol.org>
Message-ID: <44286A9B.1080105@unisul.br>

Thanks Chris,

I'am going to update CookBook with the new feature! ;)

[]s
-- 
Dickson S. Guedes
/*
  * UNISUL - Universidade do Sul de Santa Catarina
  * ATI - Assessoria de Tecnologia da Informa??o
  * Tubar?o - SC / Brasil
  * (0xx48) 621-3200 - http://www.unisul.br
  *
  *    "Quis custodiet ipsos custodes?"
  */


Chris Dagdigian escreveu:
> Hey folks,
> 
> Following a suggestion from Mark Schreiber I've installed the Geshi  
> syntax highlighting PHP library into your biojava.org wiki.
> 
> This extension makes it easier (if you wish) to have code snippets  
> color coded for clarity and readability.
> 
> You can see examples of the extension in action here:
> 
> http://biojava.org/wiki/User:Chrisdag
> 
> To start using it, just change your code blocks to use " java>" instead of the current "
" within the wiki.
> 
> Regards,
> Chris
> open-bio.org
> 
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

From darin.london at duke.edu  Tue Mar 28 09:42:45 2006
From: darin.london at duke.edu (Darin London)
Date: Tue, 28 Mar 2006 09:42:45 -0500
Subject: [Biojava-dev] Announcing BOSC 2006
Message-ID: <44294B65.4050207@duke.edu>

MEETING ANNOUNCEMENT & CALL FOR SPEAKERS

The 7th annual Bioinformatics Open Source Conference (BOSC 2006) is
organized by the
not-for-profit Open Bioinformatics Foundation. The meeting will take place
Aug 4,5th in Fortaleza, Brasil, and is one of several Special Interest
Group (SIG) meetings occurring in conjunction with the 14th
International Conference
on Intelligent Systems for Molecular Biology.  Please consult The Official
BOSC 2006 Website at

http://www.open-bio.org/wiki/BOSC_2006

for details and information. 

In addition, a BOSC weblog has been setup to make it easier to
desiminate all BOSC
related announcements:

http://wiki.open-bio.org/boscblog/

And if you have an ICAL compatible Calendar, there is an EventDB calendar
set up with all BOSC related deadlines.

http://eventful.com/groups/G0-001-000014747-0

More information about ISMB can be found at the Official
ISMB 2006 Website:

http://ismb2006.cbi.cnptia.embrapa.br/


Thank You, and we look forward to seeing you all,
The BOSC Organizing Committee.

From j-osborne at northwestern.edu  Tue Mar 28 12:42:46 2006
From: j-osborne at northwestern.edu (John Osborne)
Date: Tue, 28 Mar 2006 11:42:46 -0600
Subject: [Biojava-dev] Ontology.Impl
Message-ID: <44297596.3010902@northwestern.edu>

Can anybody tell me why this is a final class? I am trying to convert 
some code to biojava and I thought it would be handy to subclass the 
ontology class implementation until I realized it was final. Is this an 
effort to enforce composition? I'm not an expert OO programmer so maybe 
somebody can enlighten me...

 -John


From a.maule at cs.ucl.ac.uk  Wed Mar 29 12:12:33 2006
From: a.maule at cs.ucl.ac.uk (Andy Maule)
Date: Wed, 29 Mar 2006 18:12:33 +0100
Subject: [Biojava-dev] TranscriptAdaptor34
Message-ID: <002901c65353$f8439f10$630d1080@cs.ucl.ac.uk>

Hi,

I'm looking through the source code repository at
org.biojava.bio.seq.db.ensembl.core20.TranscriptAdaptor34.java

The the 'source' column was added to the 'gene' table in Ensembl in version
31. However this column was only added to the TranscriptAdaptor for version
34. 

Was this an oversight, or was this intentional?

Sorry for asking such a specific question :-) It is very interesting to me
to know for the analysis I'm doing.

The person who committed the changes was Thomas.

Thanks

Andy Maule


From dag at sonsorol.org  Sat Mar 11 19:22:01 2006
From: dag at sonsorol.org (Chris Dagdigian)
Date: Sat, 11 Mar 2006 14:22:01 -0500
Subject: [Biojava-dev] quick update on the biojava mailing lists
Message-ID: 


Hi folks,

biojava-l at biojava.org and biojava-dev at biojava.org have been moved  
onto our new OBF server hardware in the new datacenter. Until we can  
bring your website onto that machine as well your lists are hosted on  
the machine "lists.open-bio.org"

I've got aliases on the old server that will forward list mail from  
biojava.org -> lists.open-bio.org and I've updated the main page on  
your website with the new URL.

Regards,
Chris
OBF




From dag at sonsorol.org  Tue Mar 14 14:41:34 2006
From: dag at sonsorol.org (Chris Dagdigian)
Date: Tue, 14 Mar 2006 09:41:34 -0500
Subject: [Biojava-dev] help test the new open-bio anonymous source code
	server
Message-ID: 


Hi folks,

Apologies for the cross-post. I need some help testing out a new open- 
bio server

The new server is http://code.open-bio.org and it has been purpose  
built to replace our existing anonymous CVS server (cvs.open-bio.org,  
etc. etc.)

In addition to anonymous CVS, this new system also offers anonymous  
rsync mirrors of all our source code.

For security reasons (the anonymous CVS pserver protocol is  
considered insecure) we run these anon access methods on a locked  
down machine that only has a read only copy of the codebase. The  
webserver page (except for the viewcvs CGI) actually redirects to a  
wiki entry on a different server so we don' have to maintain a  
website on the new box.

The anonymous access repository is currently updated every 30 minutes  
from the main developer system.

Things I need help with:

  - check out http://code.open-bio.org -- does the documentation make  
sense? Can it be made better? If so, change it! (it is a wiki after  
all...)

  - please experiment with anonymous CVS, confirm that you can check  
out code

  - experiment with rsync! this is a new feature for us that we could  
not offer on the old server (due to upstream port ACLs on a core router)

  - provide feedback on the "speed" and bandwidth of the anoncvs  
server, does it seem reasonable?

Let me know what you'll think. The reason for this move is that one  
of our core hosting facilities (datacenter at Wyeth Research) is no  
longer going to be useable by us as they are changing their WAN links  
in such a way that our servers will not be able to directly access  
the internet. We are in the process of moving *every* open-bio.org  
service onto new hardware located in a different datacenter.

Our mailing lists have already been migrated, websites are moving as  
well. Expect some big changes once we tackle the task of moving all  
the developers and the writable CVS repositories to the new  
datacenter - that will happen probably within the next 2 weeks.

Regards,
Chris Dagdigian
OBF




From mark.schreiber at novartis.com  Fri Mar 17 02:52:52 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Fri, 17 Mar 2006 10:52:52 +0800
Subject: [Biojava-dev] Away
Message-ID: 

Hello -

I'm going to be travelling a lot in the next 5 weeks and may only have 
patchy access to email and no access to CVS or my development machines. 
Therefore I won't be able to offer much in the way of technical support. 

Hopefully Richard and Michael will be able to deal with any major issues 
that crop up.

Best regards,

- Mark

Mark Schreiber
Research Investigator (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 richard.holland at ebi.ac.uk  Mon Mar 20 17:13:19 2006
From: richard.holland at ebi.ac.uk (Richard Holland)
Date: Mon, 20 Mar 2006 17:13:19 +0000
Subject: [Biojava-dev] Dynamic features and sequences in BJX
Message-ID: <1142874799.3906.41.camel@texas.ebi.ac.uk>

Hi there.

I've managed to do some testing and bugfixing and I think you'll find
that dynamically-loaded features and sequence portions should now work.

This means that when using FeatureFilter objects to load features, you
only get the features you want loaded as they are (mostly) filtered at
database level, and that these features will not drag the entire
sequence out of the db until you query their symbols, and even then
you'll only get the portion you request. If you do wish to work with the
features and edit the underlying sequence or load it permanently, then
you need to use fullyLoadRichSequence() in BioSQLRichSequenceDB.

It's in CVS now. Hope it works for you all. Enjoy!

cheers,
Richard

-- 
Richard Holland
European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, UK
Tel: +44-(0)1223-494416
---------------



From richard.holland at ebi.ac.uk  Wed Mar 22 10:07:16 2006
From: richard.holland at ebi.ac.uk (Richard Holland)
Date: Wed, 22 Mar 2006 10:07:16 +0000
Subject: [Biojava-dev] Extra method in GenbankRichSequenceDB removed
Message-ID: <1143022037.3899.7.camel@texas.ebi.ac.uk>

Hi all.

Someone added a method:

public RichSequence getRichSequence(String id, Namespace nsp) throws
BioException, IllegalIDException;

to org.biojavax.bio.seq.db.ncbi.GenbankRichSequenceDB so that the
following is possible:

db.getRichSequence(id,nsp);

This is actually unnecessary as the same effect can be achieved by
calling:

db.setNamespace(nsp);
db.getRichSequence(id);

Any objections if I remove the extra method?

cheers,
Richard

-- 
Richard Holland
European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, UK
Tel: +44-(0)1223-494416
---------------



From Yan.Bai at UTSouthwestern.edu  Wed Mar 22 16:34:32 2006
From: Yan.Bai at UTSouthwestern.edu (Yan Bai)
Date: Wed, 22 Mar 2006 10:34:32 -0600
Subject: [Biojava-dev] SeqIOTools method not found
Message-ID: 

I am new in this mailing list,  
I've download biojava package, pretty sure CLASSPATH was set up right. I typed the example given on the tutorial (Trace2Seq.java), got compiler error as below. In biojava source code, I couldn't find the method named as "writeFasta" in SeqIOTools with "Sequence" as the 2nd parameter, neither did I find any methods with 'Sequence' as the 2nd parameter, but they all show up on API. 
I am in the first step of trying Biojava, and this is frustrating. Apprecate if someone will help me out. 
-------------------------------------
Trace2Seq.java:18: cannot find symbol
symbol  : method writeFasta(java.io.PrintStream,org.biojava.bio.seq.Sequence)
location: class org.biojava.bio.seq.io.SeqIOTools
      SeqIOTools.writeFasta(System.out, seq);
                ^
1 error
--------------------------------------




From richard.holland at ebi.ac.uk  Wed Mar 22 17:21:25 2006
From: richard.holland at ebi.ac.uk (Richard Holland)
Date: Wed, 22 Mar 2006 17:21:25 +0000
Subject: [Biojava-dev] SeqIOTools method not found
In-Reply-To: 
References: 
Message-ID: <1143048086.3899.45.camel@texas.ebi.ac.uk>

Very odd. Only thing I can think of is that you don't have the correct
version of BioJava and instead have some older version where this method
didn't exist yet.

How did you download it? (if possible, send us the URL of the link you
clicked to download it)

Make sure you're using at least the 1.4 binary distribution available
from the biojava.org website, or if you're using CVS then checkout the
module biojava-live for the latest stuff.

cheers,
Richard

On Wed, 2006-03-22 at 10:34 -0600, Yan Bai wrote:
> I am new in this mailing list,  
> I've download biojava package, pretty sure CLASSPATH was set up right. I typed the example given on the tutorial (Trace2Seq.java), got compiler error as below. In biojava source code, I couldn't find the method named as "writeFasta" in SeqIOTools with "Sequence" as the 2nd parameter, neither did I find any methods with 'Sequence' as the 2nd parameter, but they all show up on API. 
> I am in the first step of trying Biojava, and this is frustrating. Apprecate if someone will help me out. 
> -------------------------------------
> Trace2Seq.java:18: cannot find symbol
> symbol  : method writeFasta(java.io.PrintStream,org.biojava.bio.seq.Sequence)
> location: class org.biojava.bio.seq.io.SeqIOTools
>       SeqIOTools.writeFasta(System.out, seq);
>                 ^
> 1 error
> --------------------------------------
> 
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
-- 
Richard Holland
European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, UK
Tel: +44-(0)1223-494416
---------------



From ady at sanger.ac.uk  Wed Mar 22 17:31:25 2006
From: ady at sanger.ac.uk (Andy Yates)
Date: Wed, 22 Mar 2006 17:31:25 +0000
Subject: [Biojava-dev] SeqIOTools method not found
In-Reply-To: 
References: 
Message-ID: <442189ED.9070505@sanger.ac.uk>

Hi.

A quick look on the latest Biojava API shows that there is a method like 
this & this is also in the current src tree that I downloaded from 
biojava just now:

http://www.biojava.org/docs/api14/org/biojava/bio/seq/io/SeqIOTools.html#writeFasta(java.io.OutputStream,%20org.biojava.bio.seq.Sequence)

My suggestions would be to check your classpath and check your imports 
in your class file. You should have:

import org.biojava.bio.seq.io.SeqIOTools;

At the top of the class file. Make sure it is after the package 
declaration and before the class definition.

Cheers,

Andy Yates

Yan Bai wrote:
> I am new in this mailing list,  
> I've download biojava package, pretty sure CLASSPATH was set up right. I typed the example given on the tutorial (Trace2Seq.java), got compiler error as below. In biojava source code, I couldn't find the method named as "writeFasta" in SeqIOTools with "Sequence" as the 2nd parameter, neither did I find any methods with 'Sequence' as the 2nd parameter, but they all show up on API. 
> I am in the first step of trying Biojava, and this is frustrating. Apprecate if someone will help me out. 
> -------------------------------------
> Trace2Seq.java:18: cannot find symbol
> symbol  : method writeFasta(java.io.PrintStream,org.biojava.bio.seq.Sequence)
> location: class org.biojava.bio.seq.io.SeqIOTools
>       SeqIOTools.writeFasta(System.out, seq);
>                 ^
> 1 error
> --------------------------------------
> 
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev


From Yan.Bai at UTSouthwestern.edu  Wed Mar 22 18:44:40 2006
From: Yan.Bai at UTSouthwestern.edu (Yan Bai)
Date: Wed, 22 Mar 2006 12:44:40 -0600
Subject: [Biojava-dev] SeqIOTools method not found
Message-ID: 

Yeah, I found out that I have a wrong version of biojava.jar, downloaded 1.4 and it works great.
Thank you very much.

Yan

>>> Richard Holland  03/22/06 11:21 AM >>>
Very odd. Only thing I can think of is that you don't have the correct
version of BioJava and instead have some older version where this method
didn't exist yet.

How did you download it? (if possible, send us the URL of the link you
clicked to download it)

Make sure you're using at least the 1.4 binary distribution available
from the biojava.org website, or if you're using CVS then checkout the
module biojava-live for the latest stuff.

cheers,
Richard

On Wed, 2006-03-22 at 10:34 -0600, Yan Bai wrote:
> I am new in this mailing list,  
> I've download biojava package, pretty sure CLASSPATH was set up right. I typed the example given on the tutorial (Trace2Seq.java), got compiler error as below. In biojava source code, I couldn't find the method named as "writeFasta" in SeqIOTools with "Sequence" as the 2nd parameter, neither did I find any methods with 'Sequence' as the 2nd parameter, but they all show up on API. 
> I am in the first step of trying Biojava, and this is frustrating. Apprecate if someone will help me out. 
> -------------------------------------
> Trace2Seq.java:18: cannot find symbol
> symbol  : method writeFasta(java.io.PrintStream,org.biojava.bio.seq.Sequence)
> location: class org.biojava.bio.seq.io.SeqIOTools
>       SeqIOTools.writeFasta(System.out, seq);
>                 ^
> 1 error
> --------------------------------------
> 
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
-- 
Richard Holland
European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, UK
Tel: +44-(0)1223-494416
---------------

_______________________________________________
biojava-dev mailing list
biojava-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-dev




From Yan.Bai at UTSouthwestern.edu  Wed Mar 22 21:05:06 2006
From: Yan.Bai at UTSouthwestern.edu (Yan Bai)
Date: Wed, 22 Mar 2006 15:05:06 -0600
Subject: [Biojava-dev] ABI file parser
Message-ID: 

Thank you all for helping me out.

Another question is about the ABI file parser, located in the package  org.biojava.bio.program.ABIFParser. Comments of this file indicate that it parses files from 377 DNA sequencer, while our sequence files are generated by 3730 XL,  are there any mismatches between these two formats? Is there a parser specific for 3730? I couldn't find anything describe the 3730 XL format like the one Clark Tibbett wrote.  

Thanks for any inputs.

Yan 

>>> "Dickson S. Guedes"  03/22/06 2:01 PM >>>


Hi Yan,

Download BioJava
- http://biojava.org/wiki/BioJava:Download

Getting Started
- http://biojava.org/wiki/BioJava:GetStarted

Look at the sites above to get information about correct installation of 
Biojava framework.

[]s
-- 
Dickson S. Guedes
/*
  * UNISUL - Universidade do Sul de Santa Catarina
  * ATI - Assessoria de Tecnologia da Informa??o
  * (0xx48) 621-3200 - http://www.unisul.br
  *
  *    "Quis custodiet ipsos custodes?"
  */

Yan Bai wrotes:
 > I am new in this mailing list,
 > I've download biojava package, pretty sure CLASSPATH was set up 
right. I typed the example given on the tutorial (Trace2Seq.java), got 
compiler error as below. In biojava source code, I couldn't find the 
method named as "writeFasta" in SeqIOTools with "Sequence" as the 2nd 
parameter, neither did I find any methods with 'Sequence' as the 2nd 
parameter, but they all show up on API.
 > I am in the first step of trying Biojava, and this is frustrating. 
Apprecate if someone will help me out.
 > -------------------------------------
 > Trace2Seq.java:18: cannot find symbol
 > symbol  : method 
writeFasta(java.io.PrintStream,org.biojava.bio.seq.Sequence)
 > location: class org.biojava.bio.seq.io.SeqIOTools
 >       SeqIOTools.writeFasta(System.out, seq);
 >                 ^
 > 1 error
 > --------------------------------------






From russ at kepler-eng.com  Wed Mar 22 21:25:11 2006
From: russ at kepler-eng.com (Russ Kepler)
Date: Wed, 22 Mar 2006 14:25:11 -0700
Subject: [Biojava-dev] ABI file parser
In-Reply-To: 
References: 
Message-ID: <200603221425.12183.russ@kepler-eng.com>

On Wednesday 22 March 2006 02:05 pm, Yan Bai wrote:

> Another question is about the ABI file parser, located in the package 
> org.biojava.bio.program.ABIFParser. Comments of this file indicate that it
> parses files from 377 DNA sequencer, while our sequence files are generated
> by 3730 XL,  are there any mismatches between these two formats? Is there a
> parser specific for 3730? I couldn't find anything describe the 3730 XL
> format like the one Clark Tibbett wrote.

The differences that I can really are the addition of the quality calls and 
(maybe) caller name.  I'm sure that there are others, but since I wasn't 
looking for them I never really noticed their absence.  I've got a parser 
that keeps the quality call values if you need it.


From guedes at unisul.br  Wed Mar 22 20:01:15 2006
From: guedes at unisul.br (Dickson S. Guedes)
Date: Wed, 22 Mar 2006 17:01:15 -0300
Subject: [Biojava-dev] SeqIOTools method not found
In-Reply-To: 
References: 
Message-ID: <4421AD0B.8030606@unisul.br>



Hi Yan,

Download BioJava
- http://biojava.org/wiki/BioJava:Download

Getting Started
- http://biojava.org/wiki/BioJava:GetStarted

Look at the sites above to get information about correct installation of 
Biojava framework.

[]s
-- 
Dickson S. Guedes
/*
  * UNISUL - Universidade do Sul de Santa Catarina
  * ATI - Assessoria de Tecnologia da Informa??o
  * (0xx48) 621-3200 - http://www.unisul.br
  *
  *    "Quis custodiet ipsos custodes?"
  */

Yan Bai wrotes:
 > I am new in this mailing list,
 > I've download biojava package, pretty sure CLASSPATH was set up 
right. I typed the example given on the tutorial (Trace2Seq.java), got 
compiler error as below. In biojava source code, I couldn't find the 
method named as "writeFasta" in SeqIOTools with "Sequence" as the 2nd 
parameter, neither did I find any methods with 'Sequence' as the 2nd 
parameter, but they all show up on API.
 > I am in the first step of trying Biojava, and this is frustrating. 
Apprecate if someone will help me out.
 > -------------------------------------
 > Trace2Seq.java:18: cannot find symbol
 > symbol  : method 
writeFasta(java.io.PrintStream,org.biojava.bio.seq.Sequence)
 > location: class org.biojava.bio.seq.io.SeqIOTools
 >       SeqIOTools.writeFasta(System.out, seq);
 >                 ^
 > 1 error
 > --------------------------------------




From heuermh at acm.org  Wed Mar 22 21:19:58 2006
From: heuermh at acm.org (Michael Heuer)
Date: Wed, 22 Mar 2006 16:19:58 -0500 (EST)
Subject: [Biojava-dev] Dynamic features and sequences in BJX
In-Reply-To: <1142874799.3906.41.camel@texas.ebi.ac.uk>
Message-ID: 

Richard Holland wrote:

> I've managed to do some testing and bugfixing and I think you'll find
> that dynamically-loaded features and sequence portions should now work.
>
> This means that when using FeatureFilter objects to load features, you
> only get the features you want loaded as they are (mostly) filtered at
> database level, and that these features will not drag the entire
> sequence out of the db until you query their symbols, and even then
> you'll only get the portion you request. If you do wish to work with the
> features and edit the underlying sequence or load it permanently, then
> you need to use fullyLoadRichSequence() in BioSQLRichSequenceDB.

So if I pull out a sequence and iterate over its features, as long as I
don't call any of the SymbolList methods on it or on any of the features,
the symbols will never be populated from the database?

Very cool.

   michael



From richard.holland at ebi.ac.uk  Thu Mar 23 09:22:01 2006
From: richard.holland at ebi.ac.uk (Richard Holland)
Date: Thu, 23 Mar 2006 09:22:01 +0000
Subject: [Biojava-dev] Dynamic features and sequences in BJX
In-Reply-To: 
References: 
Message-ID: <1143105721.3899.47.camel@texas.ebi.ac.uk>

Yes.

And in addition, if you do reference its symbols, then only the part you
reference will be loaded.

cheers,
Richard

On Wed, 2006-03-22 at 16:19 -0500, Michael Heuer wrote:
> Richard Holland wrote:
> 
> > I've managed to do some testing and bugfixing and I think you'll find
> > that dynamically-loaded features and sequence portions should now work.
> >
> > This means that when using FeatureFilter objects to load features, you
> > only get the features you want loaded as they are (mostly) filtered at
> > database level, and that these features will not drag the entire
> > sequence out of the db until you query their symbols, and even then
> > you'll only get the portion you request. If you do wish to work with the
> > features and edit the underlying sequence or load it permanently, then
> > you need to use fullyLoadRichSequence() in BioSQLRichSequenceDB.
> 
> So if I pull out a sequence and iterate over its features, as long as I
> don't call any of the SymbolList methods on it or on any of the features,
> the symbols will never be populated from the database?
> 
> Very cool.
> 
>    michael
> 
-- 
Richard Holland
European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, UK
Tel: +44-(0)1223-494416
---------------



From richard.holland at ebi.ac.uk  Thu Mar 23 09:30:03 2006
From: richard.holland at ebi.ac.uk (Richard Holland)
Date: Thu, 23 Mar 2006 09:30:03 +0000
Subject: [Biojava-dev] ABI file parser
In-Reply-To: <200603221425.12183.russ@kepler-eng.com>
References: 
	<200603221425.12183.russ@kepler-eng.com>
Message-ID: <1143106203.3899.54.camel@texas.ebi.ac.uk>

I've used the BioJava ABI parser to parse 3730 ABI files without any
problems, and it successfully reads both base calls and quality scores.

You should use the ABIFChromatogram method getBaseCalls() to return an
alignment of two sequences - the first sequence is the sequence data,
the second is a sequence made up of Integer scores.

cheers,
Richard

On Wed, 2006-03-22 at 14:25 -0700, Russ Kepler wrote:
> On Wednesday 22 March 2006 02:05 pm, Yan Bai wrote:
> 
> > Another question is about the ABI file parser, located in the package 
> > org.biojava.bio.program.ABIFParser. Comments of this file indicate that it
> > parses files from 377 DNA sequencer, while our sequence files are generated
> > by 3730 XL,  are there any mismatches between these two formats? Is there a
> > parser specific for 3730? I couldn't find anything describe the 3730 XL
> > format like the one Clark Tibbett wrote.
> 
> The differences that I can really are the addition of the quality calls and 
> (maybe) caller name.  I'm sure that there are others, but since I wasn't 
> looking for them I never really noticed their absence.  I've got a parser 
> that keeps the quality call values if you need it.
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
-- 
Richard Holland
European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, UK
Tel: +44-(0)1223-494416
---------------



From a.maule at cs.ucl.ac.uk  Thu Mar 23 12:50:35 2006
From: a.maule at cs.ucl.ac.uk (Andy Maule)
Date: Thu, 23 Mar 2006 12:50:35 -0000
Subject: [Biojava-dev] BioJava code repository
Message-ID: <001601c64e78$628fc870$630d1080@cs.ucl.ac.uk>

Hi,

I'm looking for java applications that use Ensembl for a research project.
In particular I'm interested in seeing how applications have been changed in
response to changes in the schema of Ensembl. So I need to look at the
source code repositories, and I've been looking at the biojava CVS. 

For those who are interested the project involves predicting the impact of
database schema changes on applications. I'm going to use the change history
of the Ensembl schema to find an interesting schema change(s) that will
affect the application. I'm then going to run a tool over the application to
see if I can effectivley predict what needs to be changed. I'm then going to
compare the predicted changes with the actual changes, to see if my analysis
was correct. I'd be more than happy to explain the project further if anyone
would like to know more.

As far as I can see Biojava is still using the schema for version 10 as
shown in org.ensembl.db.sql.SQLDatabaseAdaptor10. This is only from the CVS
repository though.

Someone on the Ensembl mailing list pointed me to
http://www.derkholm.net/svn/repos and the dazzle project. Could anyone fill
me in on whether this repository is the latest version, and is there someway
I could access via subversion directly?

Also where can I now get information about Dazzle?

Thanks

Andy Maule




From richard.holland at ebi.ac.uk  Thu Mar 23 14:33:23 2006
From: richard.holland at ebi.ac.uk (Richard Holland)
Date: Thu, 23 Mar 2006 14:33:23 +0000
Subject: [Biojava-dev] BioJava code repository
In-Reply-To: <001601c64e78$628fc870$630d1080@cs.ucl.ac.uk>
References: <001601c64e78$628fc870$630d1080@cs.ucl.ac.uk>
Message-ID: <1143124403.3899.78.camel@texas.ebi.ac.uk>

The derkholm.net Subversion repository is the current version of
biojava-ensembl, which is a separate project from the main biojava found
in the open-bio.org CVS servers. Biojava-ensembl is maintained by Thomas
Down  and as far as I know is up-to-date to
Ensembl version 37.

To use the Subversion repository directly you just point the command-
line Subversion client at the same URL as the one you typed into your
web browser.

Dazzle was also written by Thomas Down but I'm not sure if he still
maintains it. Best to ask him directly.

cheers,
Richard

On Thu, 2006-03-23 at 12:50 +0000, Andy Maule wrote:
> Hi,
> 
> I'm looking for java applications that use Ensembl for a research project.
> In particular I'm interested in seeing how applications have been changed in
> response to changes in the schema of Ensembl. So I need to look at the
> source code repositories, and I've been looking at the biojava CVS. 
> 
> For those who are interested the project involves predicting the impact of
> database schema changes on applications. I'm going to use the change history
> of the Ensembl schema to find an interesting schema change(s) that will
> affect the application. I'm then going to run a tool over the application to
> see if I can effectivley predict what needs to be changed. I'm then going to
> compare the predicted changes with the actual changes, to see if my analysis
> was correct. I'd be more than happy to explain the project further if anyone
> would like to know more.
> 
> As far as I can see Biojava is still using the schema for version 10 as
> shown in org.ensembl.db.sql.SQLDatabaseAdaptor10. This is only from the CVS
> repository though.
> 
> Someone on the Ensembl mailing list pointed me to
> http://www.derkholm.net/svn/repos and the dazzle project. Could anyone fill
> me in on whether this repository is the latest version, and is there someway
> I could access via subversion directly?
> 
> Also where can I now get information about Dazzle?
> 
> Thanks
> 
> Andy Maule
> 
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
-- 
Richard Holland
European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, UK
Tel: +44-(0)1223-494416
---------------



From a.maule at cs.ucl.ac.uk  Thu Mar 23 14:38:59 2006
From: a.maule at cs.ucl.ac.uk (Andy Maule)
Date: Thu, 23 Mar 2006 14:38:59 -0000
Subject: [Biojava-dev] BioJava code repository
In-Reply-To: <1143124403.3899.78.camel@texas.ebi.ac.uk>
Message-ID: <001501c64e87$88c6a8b0$630d1080@cs.ucl.ac.uk>

Thanks Richard,

That clears things up a bit. I'll look through the SVN repository, and see
what I can find.

Andy

-----Original Message-----
From: Richard Holland [mailto:richard.holland at ebi.ac.uk] 
Sent: 23 March 2006 14:33
To: Andy Maule
Cc: biojava-dev
Subject: Re: [Biojava-dev] BioJava code repository


The derkholm.net Subversion repository is the current version of
biojava-ensembl, which is a separate project from the main biojava found in
the open-bio.org CVS servers. Biojava-ensembl is maintained by Thomas Down
 and as far as I know is up-to-date to Ensembl
version 37.

To use the Subversion repository directly you just point the command- line
Subversion client at the same URL as the one you typed into your web
browser.

Dazzle was also written by Thomas Down but I'm not sure if he still
maintains it. Best to ask him directly.

cheers,
Richard

On Thu, 2006-03-23 at 12:50 +0000, Andy Maule wrote:
> Hi,
> 
> I'm looking for java applications that use Ensembl for a research 
> project. In particular I'm interested in seeing how applications have 
> been changed in response to changes in the schema of Ensembl. So I 
> need to look at the source code repositories, and I've been looking at 
> the biojava CVS.
> 
> For those who are interested the project involves predicting the 
> impact of database schema changes on applications. I'm going to use 
> the change history of the Ensembl schema to find an interesting schema 
> change(s) that will affect the application. I'm then going to run a 
> tool over the application to see if I can effectivley predict what 
> needs to be changed. I'm then going to compare the predicted changes 
> with the actual changes, to see if my analysis was correct. I'd be 
> more than happy to explain the project further if anyone would like to 
> know more.
> 
> As far as I can see Biojava is still using the schema for version 10 
> as shown in org.ensembl.db.sql.SQLDatabaseAdaptor10. This is only from 
> the CVS repository though.
> 
> Someone on the Ensembl mailing list pointed me to 
> http://www.derkholm.net/svn/repos and the dazzle project. Could anyone 
> fill me in on whether this repository is the latest version, and is 
> there someway I could access via subversion directly?
> 
> Also where can I now get information about Dazzle?
> 
> Thanks
> 
> Andy Maule
> 
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org 
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
-- 
Richard Holland
European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, UK
Tel: +44-(0)1223-494416
---------------




From a.maule at cs.ucl.ac.uk  Thu Mar 23 14:48:35 2006
From: a.maule at cs.ucl.ac.uk (Andy Maule)
Date: Thu, 23 Mar 2006 14:48:35 -0000
Subject: [Biojava-dev] BioJava code repository
In-Reply-To: 
Message-ID: <000701c64e88$e63e5000$630d1080@cs.ucl.ac.uk>

Thanks Sylvain,

That agrees with the last message I got from Richard Holland, it clears up
the confusion.

Andy

-----Original Message-----
From: Sylvain Foisy [mailto:sylvain.foisy at bioneq.qc.ca] 
Sent: 23 March 2006 14:44
To: Andy Maule
Cc: biojava-dev at lists.open-bio.org
Subject: Re: [Biojava-dev] BioJava code repository


Hi,

The Ensembl access libraries found in CVS are way old. Thomas Down, the
original creator, has put together a new version that can be accessed
through svn at the following location:

http://www.derkholm.net/svn/repos/biojava-ensembl/trunk

It works with current Ensembl schemas and I know that Thomas still does
development on it.

Hope this helps

Best regards

Sylvain


On 3/23/06 7:50 AM, "[NAME]" <[ADDRESS]> wrote:

> Hi,
> 
> I'm looking for java applications that use Ensembl for a research 
> project. In particular I'm interested in seeing how applications have 
> been changed in response to changes in the schema of Ensembl. So I 
> need to look at the source code repositories, and I've been looking at 
> the biojava CVS.
> 
> For those who are interested the project involves predicting the 
> impact of database schema changes on applications. I'm going to use 
> the change history of the Ensembl schema to find an interesting schema 
> change(s) that will affect the application. I'm then going to run a 
> tool over the application to see if I can effectivley predict what 
> needs to be changed. I'm then going to compare the predicted changes 
> with the actual changes, to see if my analysis was correct. I'd be 
> more than happy to explain the project further if anyone would like to 
> know more.
> 
> As far as I can see Biojava is still using the schema for version 10 
> as shown in org.ensembl.db.sql.SQLDatabaseAdaptor10. This is only from 
> the CVS repository though.
> 
> Someone on the Ensembl mailing list pointed me to 
> http://www.derkholm.net/svn/repos and the dazzle project. Could anyone 
> fill me in on whether this repository is the latest version, and is 
> there someway I could access via subversion directly?
> 
> Also where can I now get information about Dazzle?
> 
> Thanks
> 
> Andy Maule
> 
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org 
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

==================================================================
Sylvain Foisy, Ph. D.
Directeur - operations / Project Manager
BioneQ - Reseau quebecois de bio-informatique
U. de Montreal / Genome-Quebec

Adresse postale:

Departement de biochimie
Pavillon principal
2900, boul. ?douard-Montpetit
Montr?al (Qu?bec) H3T 1J4

Tel: (514) 343-6111 x.2545
Fax: (514) 343-7759
Courriel: sylvain.foisy at bioneq.qc.ca
==================================================================






From sylvain.foisy at bioneq.qc.ca  Thu Mar 23 14:43:46 2006
From: sylvain.foisy at bioneq.qc.ca (Sylvain Foisy)
Date: Thu, 23 Mar 2006 09:43:46 -0500
Subject: [Biojava-dev] BioJava code repository
In-Reply-To: <001601c64e78$628fc870$630d1080@cs.ucl.ac.uk>
Message-ID: 

Hi,

The Ensembl access libraries found in CVS are way old. Thomas Down, the
original creator, has put together a new version that can be accessed
through svn at the following location:

http://www.derkholm.net/svn/repos/biojava-ensembl/trunk

It works with current Ensembl schemas and I know that Thomas still does
development on it.

Hope this helps

Best regards

Sylvain


On 3/23/06 7:50 AM, "[NAME]" <[ADDRESS]> wrote:

> Hi,
> 
> I'm looking for java applications that use Ensembl for a research project.
> In particular I'm interested in seeing how applications have been changed in
> response to changes in the schema of Ensembl. So I need to look at the
> source code repositories, and I've been looking at the biojava CVS.
> 
> For those who are interested the project involves predicting the impact of
> database schema changes on applications. I'm going to use the change history
> of the Ensembl schema to find an interesting schema change(s) that will
> affect the application. I'm then going to run a tool over the application to
> see if I can effectivley predict what needs to be changed. I'm then going to
> compare the predicted changes with the actual changes, to see if my analysis
> was correct. I'd be more than happy to explain the project further if anyone
> would like to know more.
> 
> As far as I can see Biojava is still using the schema for version 10 as
> shown in org.ensembl.db.sql.SQLDatabaseAdaptor10. This is only from the CVS
> repository though.
> 
> Someone on the Ensembl mailing list pointed me to
> http://www.derkholm.net/svn/repos and the dazzle project. Could anyone fill
> me in on whether this repository is the latest version, and is there someway
> I could access via subversion directly?
> 
> Also where can I now get information about Dazzle?
> 
> Thanks
> 
> Andy Maule
> 
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

==================================================================
Sylvain Foisy, Ph. D.
Directeur - operations / Project Manager
BioneQ - Reseau quebecois de bio-informatique
U. de Montreal / Genome-Quebec

Adresse postale:

Departement de biochimie
Pavillon principal
2900, boul. ?douard-Montpetit
Montr?al (Qu?bec) H3T 1J4

Tel: (514) 343-6111 x.2545
Fax: (514) 343-7759
Courriel: sylvain.foisy at bioneq.qc.ca
==================================================================





From a.maule at cs.ucl.ac.uk  Mon Mar 20 16:04:01 2006
From: a.maule at cs.ucl.ac.uk (Andy Maule)
Date: Mon, 20 Mar 2006 16:04:01 -0000
Subject: [Biojava-dev] Biojava Ensembl version
Message-ID: <002401c64c37$f149b690$f2421080@cs.ucl.ac.uk>

Hi,

What version of the Ensembl schema does the latest Biojava use? 

I'm looking for java applications that use Ensembl for a research project.
In particular I'm interested in seeing how applications have been changed in
response to changes in the schema of Ensembl. As far as I can see Biojava is
still using the schema for version 10 as shown in
org.ensembl.db.sql.SQLDatabaseAdaptor10. Is this the latest version used? 

Thanks

Andy Maule




From smh1008 at cam.ac.uk  Mon Mar 27 18:30:44 2006
From: smh1008 at cam.ac.uk (David Huen)
Date: 27 Mar 2006 19:30:44 +0100
Subject: [Biojava-dev] Biojava Ensembl version
In-Reply-To: <002401c64c37$f149b690$f2421080@cs.ucl.ac.uk>
References: <002401c64c37$f149b690$f2421080@cs.ucl.ac.uk>
Message-ID: 

On Mar 27 2006, Andy Maule wrote:

I would suggest contacting Thomas Down about the Ensembl-Biojava bridge.

Regards,
David Huen

>Hi,
>
>What version of the Ensembl schema does the latest Biojava use? 
>
> I'm looking for java applications that use Ensembl for a research 
> project. In particular I'm interested in seeing how applications have 
> been changed in response to changes in the schema of Ensembl. As far as I 
> can see Biojava is still using the schema for version 10 as shown in 
> org.ensembl.db.sql.SQLDatabaseAdaptor10. Is this the latest version used?
>
>Thanks
>
>Andy Maule
>
>
>_______________________________________________
>biojava-dev mailing list
>biojava-dev at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


From dag at sonsorol.org  Mon Mar 27 22:13:54 2006
From: dag at sonsorol.org (Chris Dagdigian)
Date: Mon, 27 Mar 2006 17:13:54 -0500
Subject: [Biojava-dev] syntax highlighting extension added to your wiki
Message-ID: <0C30FEA4-41EB-4114-A3C5-4886CF4518D0@sonsorol.org>


Hey folks,

Following a suggestion from Mark Schreiber I've installed the Geshi  
syntax highlighting PHP library into your biojava.org wiki.

This extension makes it easier (if you wish) to have code snippets  
color coded for clarity and readability.

You can see examples of the extension in action here:

http://biojava.org/wiki/User:Chrisdag

To start using it, just change your code blocks to use "" instead of the current "
" within the wiki.

Regards,
Chris
open-bio.org




From guedes at unisul.br  Mon Mar 27 22:43:39 2006
From: guedes at unisul.br (Dickson S. Guedes)
Date: Mon, 27 Mar 2006 19:43:39 -0300
Subject: [Biojava-dev] syntax highlighting extension added to your wiki
In-Reply-To: <0C30FEA4-41EB-4114-A3C5-4886CF4518D0@sonsorol.org>
References: <0C30FEA4-41EB-4114-A3C5-4886CF4518D0@sonsorol.org>
Message-ID: <44286A9B.1080105@unisul.br>

Thanks Chris,

I'am going to update CookBook with the new feature! ;)

[]s
-- 
Dickson S. Guedes
/*
  * UNISUL - Universidade do Sul de Santa Catarina
  * ATI - Assessoria de Tecnologia da Informa??o
  * Tubar?o - SC / Brasil
  * (0xx48) 621-3200 - http://www.unisul.br
  *
  *    "Quis custodiet ipsos custodes?"
  */


Chris Dagdigian escreveu:
> Hey folks,
> 
> Following a suggestion from Mark Schreiber I've installed the Geshi  
> syntax highlighting PHP library into your biojava.org wiki.
> 
> This extension makes it easier (if you wish) to have code snippets  
> color coded for clarity and readability.
> 
> You can see examples of the extension in action here:
> 
> http://biojava.org/wiki/User:Chrisdag
> 
> To start using it, just change your code blocks to use " java>" instead of the current "
" within the wiki.
> 
> Regards,
> Chris
> open-bio.org
> 
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 


From darin.london at duke.edu  Tue Mar 28 14:42:45 2006
From: darin.london at duke.edu (Darin London)
Date: Tue, 28 Mar 2006 09:42:45 -0500
Subject: [Biojava-dev] Announcing BOSC 2006
Message-ID: <44294B65.4050207@duke.edu>

MEETING ANNOUNCEMENT & CALL FOR SPEAKERS

The 7th annual Bioinformatics Open Source Conference (BOSC 2006) is
organized by the
not-for-profit Open Bioinformatics Foundation. The meeting will take place
Aug 4,5th in Fortaleza, Brasil, and is one of several Special Interest
Group (SIG) meetings occurring in conjunction with the 14th
International Conference
on Intelligent Systems for Molecular Biology.  Please consult The Official
BOSC 2006 Website at

http://www.open-bio.org/wiki/BOSC_2006

for details and information. 

In addition, a BOSC weblog has been setup to make it easier to
desiminate all BOSC
related announcements:

http://wiki.open-bio.org/boscblog/

And if you have an ICAL compatible Calendar, there is an EventDB calendar
set up with all BOSC related deadlines.

http://eventful.com/groups/G0-001-000014747-0

More information about ISMB can be found at the Official
ISMB 2006 Website:

http://ismb2006.cbi.cnptia.embrapa.br/


Thank You, and we look forward to seeing you all,
The BOSC Organizing Committee.


From j-osborne at northwestern.edu  Tue Mar 28 17:42:46 2006
From: j-osborne at northwestern.edu (John Osborne)
Date: Tue, 28 Mar 2006 11:42:46 -0600
Subject: [Biojava-dev] Ontology.Impl
Message-ID: <44297596.3010902@northwestern.edu>

Can anybody tell me why this is a final class? I am trying to convert 
some code to biojava and I thought it would be handy to subclass the 
ontology class implementation until I realized it was final. Is this an 
effort to enforce composition? I'm not an expert OO programmer so maybe 
somebody can enlighten me...

 -John



From a.maule at cs.ucl.ac.uk  Wed Mar 29 17:12:33 2006
From: a.maule at cs.ucl.ac.uk (Andy Maule)
Date: Wed, 29 Mar 2006 18:12:33 +0100
Subject: [Biojava-dev] TranscriptAdaptor34
Message-ID: <002901c65353$f8439f10$630d1080@cs.ucl.ac.uk>

Hi,

I'm looking through the source code repository at
org.biojava.bio.seq.db.ensembl.core20.TranscriptAdaptor34.java

The the 'source' column was added to the 'gene' table in Ensembl in version
31. However this column was only added to the TranscriptAdaptor for version
34. 

Was this an oversight, or was this intentional?

Sorry for asking such a specific question :-) It is very interesting to me
to know for the analysis I'm doing.

The person who committed the changes was Thomas.

Thanks

Andy Maule