From mark.schreiber at group.novartis.com Wed Feb 2 04:00:19 2005 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Wed Feb 2 03:56:15 2005 Subject: [Biojava-l] nightly builds Message-ID: Hello - Is there a plan to reinstate the nightly builds? Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From blum+ at cs.cmu.edu Wed Feb 2 12:59:26 2005 From: blum+ at cs.cmu.edu (Tal Blum) Date: Wed Feb 2 12:55:18 2005 Subject: [Biojava-l] Using pairwiseDP Message-ID: <420114FE.6030908@cs.cmu.edu> Hi, I am trying to use BioJava for doing alignment between two sequences. I tried to use the pairwiseDP class, but it is not clear to me how to construct a MarkovModel for it. The problem, I think, is specifying the emission distributions for pair symbols with gaps. How can you create a pairDistribution with with a gap as an element of the distribution for use in the pairwiseDP? If anyone can refer me to example that uses pairwiseDP I would be grateful. Another question I have is why is there no BaumWelch algorithm for MarkovModels with two heads? Many thanks, Tal Blum From rchoudari at yahoo.com Wed Feb 9 23:56:54 2005 From: rchoudari at yahoo.com (Ravi Choudari) Date: Wed Feb 9 23:52:19 2005 Subject: [Biojava-l] In-Reply-To: Message-ID: <20050210045654.62245.qmail@web51705.mail.yahoo.com> Hi, I am trying to write a ABIF File format parser (reader cum writer). If anybody have the detaild or parser. please help me... Ravi __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From facemann at yahoo.com Thu Feb 10 14:15:49 2005 From: facemann at yahoo.com (Andy Hammer) Date: Thu Feb 10 14:12:04 2005 Subject: [Biojava-l] location of biojava.jar on a linux system Message-ID: <20050210191549.72470.qmail@web31007.mail.mud.yahoo.com> Hello all. I had some apps I wrote with biojava that I wanted to run on a linux system. I do not have root privliges and wondered where I could put biojava.jar to make my application run. The name of the app is MotifSearch.jar. I have tried putting bytecode.jar, xerces.jar and biojava.jar in the local directory and running >java -classpath . -jar MotifSearch.jar but I still get the error: Exception in thread "main" java.lang.NoClassDefFoundError: org/biojava/bio/BioException Any ideas? Thanks Andy __________________________________ Do you Yahoo!? Yahoo! Mail - You care about security. So do we. http://promotions.yahoo.com/new_mail From smh1008 at cus.cam.ac.uk Thu Feb 10 14:53:32 2005 From: smh1008 at cus.cam.ac.uk (David Huen) Date: Thu Feb 10 14:49:01 2005 Subject: [Biojava-l] location of biojava.jar on a linux system In-Reply-To: <20050210191549.72470.qmail@web31007.mail.mud.yahoo.com> References: <20050210191549.72470.qmail@web31007.mail.mud.yahoo.com> Message-ID: <200502101953.33007.smh1008@cus.cam.ac.uk> On Thursday 10 Feb 2005 19:15, Andy Hammer wrote: > Hello all. If you are running the app as a jar, you appear to need to define an env var CLASSPATH that has the jars required. I've never had much joy with defining the classpath on the command line itself but that might just be incompetence on my part. > > I had some apps I wrote with biojava that I wanted to > run on a linux system. I do not have root privliges > and wondered where I could put biojava.jar to make my > application run. The name of the app is > MotifSearch.jar. I have tried putting bytecode.jar, > xerces.jar and biojava.jar in the local directory and > running > > >java -classpath . -jar MotifSearch.jar > > but I still get the error: > Exception in thread "main" > java.lang.NoClassDefFoundError: > org/biojava/bio/BioException > > Any ideas? > Thanks > > Andy > > > > > __________________________________ > Do you Yahoo!? > Yahoo! Mail - You care about security. So do we. > http://promotions.yahoo.com/new_mail > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l -- David Huen, Ph.D. Email: smh1008@cus.cam.ac.uk Dept. of Genetics Fax : +44 1223 333992 University of Cambridge Phone: +44 1223 333982/766748 Cambridge, CB2 3UH U.K. From rahul at genebrew.com Thu Feb 10 15:17:34 2005 From: rahul at genebrew.com (Rahul Karnik) Date: Thu Feb 10 15:15:58 2005 Subject: [Biojava-l] location of biojava.jar on a linux system In-Reply-To: <20050210191549.72470.qmail@web31007.mail.mud.yahoo.com> References: <20050210191549.72470.qmail@web31007.mail.mud.yahoo.com> Message-ID: <12915.165.89.84.88.1108066654.squirrel@www.genebrew.com> >>java -classpath . -jar MotifSearch.jar "-cp ." only works with unzipped jar files. In your case, I would use: java -cp xerces.jar:biojava.jar: -jar MotifSearch.jar Hope that helps, Rahul From facemann at yahoo.com Fri Feb 11 14:02:02 2005 From: facemann at yahoo.com (Andy Hammer) Date: Fri Feb 11 13:57:27 2005 Subject: [Biojava-l] location of biojava.jar on a linux system Message-ID: <20050211190202.27945.qmail@web31001.mail.mud.yahoo.com> I think I am on the same page as everyone here. But I still get: >java -cp xerces.jar:biojava.jar -jar MotifSearch.jar Exception in thread "main" java.lang.NoClassDefFoundError: org/biojava/bio/BioException More info: ahammer@marchingmen2:~/ext> pwd /uufs/inscc.utah.edu/common/home/ahammer/ext ahammer@marchingmen2:~/ext> ahammer@marchingmen2:~/ext> echo $CLASSPATH .:/uufs/inscc.utah.edu/common/home/ahammer/ext/ ahammer@marchingmen2:~/ext> ahammer@marchingmen2:~/ext> ls -l total 4772 -rw-r--r-- 1 ahammer gestelan 2674782 2003-10-15 10:37 biojava.jar -rw-r--r-- 1 ahammer gestelan 93463 2003-10-07 17:59 bytecode.jar -rw-r--r-- 1 ahammer gestelan 30117 2003-10-07 17:59 commons-cli.jar -rw-r--r-- 1 ahammer gestelan 145563 2003-10-15 10:04 grammars.jar -rw-r--r-- 1 ahammer gestelan 46056 2003-10-07 17:59 htmlparser.jar -rw-r--r-- 1 ahammer gestelan 50962 2005-02-10 11:38 MotifSearch.jar -rw-r--r-- 1 ahammer gestelan 1808885 2005-02-11 11:55 xerces.jar ahammer@marchingmen2:~/ext> I don't understard why this doesn't work. It works fine on a windows box. It makes me think it wouldn't work even if I had access to the jre/ext directory. Andy __________________________________ Do you Yahoo!? Yahoo! Mail - Easier than ever with enhanced search. Learn more. http://info.mail.yahoo.com/mail_250 From adionne at warnex.ca Fri Feb 11 14:18:12 2005 From: adionne at warnex.ca (Alexandre Dionne-Laporte) Date: Fri Feb 11 14:14:32 2005 Subject: [Biojava-l] location of biojava.jar on a linux system In-Reply-To: <20050211190202.27945.qmail@web31001.mail.mud.yahoo.com> References: <20050211190202.27945.qmail@web31001.mail.mud.yahoo.com> Message-ID: <1108149492.26566.23.camel@thorgal.bioinfo> include the full path of the biojava archive in the definition of your classpath: #java -cp /uufs/inscc.utah.edu/common/home/ahammer/ext/xerces.jar:/uufs/inscc.utah.edu/common/home/ahammer/ext/biojava.jar -jar MotifSearch.jar Alex. On Fri, 2005-02-11 at 14:02, Andy Hammer wrote: > I think I am on the same page as everyone here. > But I still get: > >java -cp xerces.jar:biojava.jar -jar MotifSearch.jar > Exception in thread "main" > java.lang.NoClassDefFoundError: > org/biojava/bio/BioException > > More info: > ahammer@marchingmen2:~/ext> pwd > /uufs/inscc.utah.edu/common/home/ahammer/ext > ahammer@marchingmen2:~/ext> > ahammer@marchingmen2:~/ext> echo $CLASSPATH > .:/uufs/inscc.utah.edu/common/home/ahammer/ext/ > ahammer@marchingmen2:~/ext> > ahammer@marchingmen2:~/ext> ls -l > total 4772 > -rw-r--r-- 1 ahammer gestelan 2674782 2003-10-15 > 10:37 biojava.jar > -rw-r--r-- 1 ahammer gestelan 93463 2003-10-07 > 17:59 bytecode.jar > -rw-r--r-- 1 ahammer gestelan 30117 2003-10-07 > 17:59 commons-cli.jar > -rw-r--r-- 1 ahammer gestelan 145563 2003-10-15 > 10:04 grammars.jar > -rw-r--r-- 1 ahammer gestelan 46056 2003-10-07 > 17:59 htmlparser.jar > -rw-r--r-- 1 ahammer gestelan 50962 2005-02-10 > 11:38 MotifSearch.jar > -rw-r--r-- 1 ahammer gestelan 1808885 2005-02-11 > 11:55 xerces.jar > ahammer@marchingmen2:~/ext> > > I don't understard why this doesn't work. It works > fine on a windows box. It makes me think it wouldn't > work even if I had access to the jre/ext directory. > > Andy > > > > __________________________________ > Do you Yahoo!? > Yahoo! Mail - Easier than ever with enhanced search. Learn more. > http://info.mail.yahoo.com/mail_250 > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l From heuermh at acm.org Fri Feb 11 14:30:16 2005 From: heuermh at acm.org (Michael Heuer) Date: Fri Feb 11 15:15:08 2005 Subject: [Biojava-l] location of biojava.jar on a linux system In-Reply-To: <1108149492.26566.23.camel@thorgal.bioinfo> Message-ID: Hello Alex, Combining the java command line arguments -cp and -jar will not work as you expect -- the -jar argument overrides the CLASSPATH. "When you use this option, the JAR file is the source of all user classes, and other user class path settings are ignored." > http://java.sun.com/j2se/1.5.0/docs/tooldocs/solaris/java.html#options michael On Fri, 11 Feb 2005, Alexandre Dionne-Laporte wrote: > include the full path of the biojava archive in the definition of your > classpath: > > #java -cp > /uufs/inscc.utah.edu/common/home/ahammer/ext/xerces.jar:/uufs/inscc.utah.edu/common/home/ahammer/ext/biojava.jar -jar MotifSearch.jar > > Alex. > > On Fri, 2005-02-11 at 14:02, Andy Hammer wrote: > > I think I am on the same page as everyone here. > > But I still get: > > >java -cp xerces.jar:biojava.jar -jar MotifSearch.jar > > Exception in thread "main" > > java.lang.NoClassDefFoundError: > > org/biojava/bio/BioException > > > > More info: > > ahammer@marchingmen2:~/ext> pwd > > /uufs/inscc.utah.edu/common/home/ahammer/ext > > ahammer@marchingmen2:~/ext> > > ahammer@marchingmen2:~/ext> echo $CLASSPATH > > .:/uufs/inscc.utah.edu/common/home/ahammer/ext/ > > ahammer@marchingmen2:~/ext> > > ahammer@marchingmen2:~/ext> ls -l > > total 4772 > > -rw-r--r-- 1 ahammer gestelan 2674782 2003-10-15 > > 10:37 biojava.jar > > -rw-r--r-- 1 ahammer gestelan 93463 2003-10-07 > > 17:59 bytecode.jar > > -rw-r--r-- 1 ahammer gestelan 30117 2003-10-07 > > 17:59 commons-cli.jar > > -rw-r--r-- 1 ahammer gestelan 145563 2003-10-15 > > 10:04 grammars.jar > > -rw-r--r-- 1 ahammer gestelan 46056 2003-10-07 > > 17:59 htmlparser.jar > > -rw-r--r-- 1 ahammer gestelan 50962 2005-02-10 > > 11:38 MotifSearch.jar > > -rw-r--r-- 1 ahammer gestelan 1808885 2005-02-11 > > 11:55 xerces.jar > > ahammer@marchingmen2:~/ext> > > > > I don't understard why this doesn't work. It works > > fine on a windows box. It makes me think it wouldn't > > work even if I had access to the jre/ext directory. > > > > Andy > > > > > > > > __________________________________ > > Do you Yahoo!? > > Yahoo! Mail - Easier than ever with enhanced search. Learn more. > > http://info.mail.yahoo.com/mail_250 > > _______________________________________________ > > Biojava-l mailing list - Biojava-l@biojava.org > > http://biojava.org/mailman/listinfo/biojava-l > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > From adionne at warnex.ca Fri Feb 11 16:43:03 2005 From: adionne at warnex.ca (Alexandre Dionne-Laporte) Date: Fri Feb 11 16:37:43 2005 Subject: [Biojava-l] location of biojava.jar on a linux system In-Reply-To: References: Message-ID: <1108158183.26566.37.camel@thorgal.bioinfo> The obvious choice then is to redefine the classpath in the manifest file or have a ant script to create the jar (biojava is in the lib directory) : hmmmm... does this help or what ? Al. On Fri, 2005-02-11 at 14:30, Michael Heuer wrote: > Hello Alex, > > Combining the java command line arguments -cp and -jar will not work as > you expect -- the -jar argument overrides the CLASSPATH. > > "When you use this option, the JAR file is the source of all user > classes, and other user class path settings are ignored." > > > http://java.sun.com/j2se/1.5.0/docs/tooldocs/solaris/java.html#options > > michael > > > On Fri, 11 Feb 2005, Alexandre Dionne-Laporte wrote: > > > include the full path of the biojava archive in the definition of your > > classpath: > > > > #java -cp > > /uufs/inscc.utah.edu/common/home/ahammer/ext/xerces.jar:/uufs/inscc.utah.edu/common/home/ahammer/ext/biojava.jar -jar MotifSearch.jar > > > > Alex. > > > > On Fri, 2005-02-11 at 14:02, Andy Hammer wrote: > > > I think I am on the same page as everyone here. > > > But I still get: > > > >java -cp xerces.jar:biojava.jar -jar MotifSearch.jar > > > Exception in thread "main" > > > java.lang.NoClassDefFoundError: > > > org/biojava/bio/BioException > > > > > > More info: > > > ahammer@marchingmen2:~/ext> pwd > > > /uufs/inscc.utah.edu/common/home/ahammer/ext > > > ahammer@marchingmen2:~/ext> > > > ahammer@marchingmen2:~/ext> echo $CLASSPATH > > > .:/uufs/inscc.utah.edu/common/home/ahammer/ext/ > > > ahammer@marchingmen2:~/ext> > > > ahammer@marchingmen2:~/ext> ls -l > > > total 4772 > > > -rw-r--r-- 1 ahammer gestelan 2674782 2003-10-15 > > > 10:37 biojava.jar > > > -rw-r--r-- 1 ahammer gestelan 93463 2003-10-07 > > > 17:59 bytecode.jar > > > -rw-r--r-- 1 ahammer gestelan 30117 2003-10-07 > > > 17:59 commons-cli.jar > > > -rw-r--r-- 1 ahammer gestelan 145563 2003-10-15 > > > 10:04 grammars.jar > > > -rw-r--r-- 1 ahammer gestelan 46056 2003-10-07 > > > 17:59 htmlparser.jar > > > -rw-r--r-- 1 ahammer gestelan 50962 2005-02-10 > > > 11:38 MotifSearch.jar > > > -rw-r--r-- 1 ahammer gestelan 1808885 2005-02-11 > > > 11:55 xerces.jar > > > ahammer@marchingmen2:~/ext> > > > > > > I don't understard why this doesn't work. It works > > > fine on a windows box. It makes me think it wouldn't > > > work even if I had access to the jre/ext directory. > > > > > > Andy > > > > > > > > > > > > __________________________________ > > > Do you Yahoo!? > > > Yahoo! Mail - Easier than ever with enhanced search. Learn more. > > > http://info.mail.yahoo.com/mail_250 > > > _______________________________________________ > > > Biojava-l mailing list - Biojava-l@biojava.org > > > http://biojava.org/mailman/listinfo/biojava-l > > _______________________________________________ > > Biojava-l mailing list - Biojava-l@biojava.org > > http://biojava.org/mailman/listinfo/biojava-l > > > > From facemann at yahoo.com Fri Feb 11 16:55:46 2005 From: facemann at yahoo.com (Andy Hammer) Date: Fri Feb 11 16:51:06 2005 Subject: [Biojava-l] location of biojava.jar on a linux system Message-ID: <20050211215546.44478.qmail@web31010.mail.mud.yahoo.com> I think I will try to modify the classpath in the manifest file next. Thanks for all the feed back! Andy __________________________________ Do you Yahoo!? Yahoo! Mail - Helps protect you from nasty viruses. http://promotions.yahoo.com/new_mail From dag at sonsorol.org Thu Feb 17 08:50:55 2005 From: dag at sonsorol.org (Chris Dagdigian) Date: Thu Feb 17 08:46:14 2005 Subject: [Biojava-l] Important info for all Open-Bio affiliated developers (people with CVS write access...) Message-ID: <4214A13F.6010006@sonsorol.org> Hi folks, apologies for the large cross-posting. Really short summary: We are going to migrate to newer server hardware over the next few months. If you are an OBF developer (someone who has a login account on "pub" with CVS write permission to one or more repositories) then you'll need to make sure we have your most current email address so we can communicate the transition plan directly without spamming N number of mailing lists. We need updated contact info in order to manage the transition. Details below. Long winded details: Our existing servers (the developer CVS repository and the 2nd system that handles websites & mailing lists) are getting a bit old and more importantly are running older Linux distributions that are long past official support dates and are difficult to update, secure and maintain. We have 2 brand new servers sitting online in a Boston area colocation facility and the various OBF sysadmins are starting to think about planning for transitioning services and user accounts. First to move (I suspect) is going to be the pub.open-bio.org system which is the main CVS sourcecode repository for our various projects such as biojava, bioperl, moby, etc. We think the transition will be pretty quick and transparent. It should not be all that hard to migrate the user accounts and copy over the CVS repository tree. We'll be writing scripts to automate the process and can run repeated migration tests before officially switching on the new system. What CVS committers and developers need to do ============================================= 1. SSH login to pub.open-bio.org 2. Run the "chfn" command to edit your user info 3. Make sure a good email address is listed for the Office: or Phone: field. Info about your project and institution would be great as well but is not required. In a week's time I'm going to capture all the email addresses listed and will insert them into a mailing list that we'll use to communicate our plans. This way we can speak to developers directly without cross posting to many mailing lists. Any user account without a full name and working email address will still be migrated but we are going to lockout the password until we hear from the person in question. What OBF Project Leaders need to do ==================================== 1. Login to pub.open-bio.org 2. Check /etc/groups for your project name and examine the users who have write access to your repository -- Email root-l@open-bio.org with the usernames of any inactive members who can safely be deleted. Regards, Chris one of the open-bio admins (root-l@open-bio.org) -- Chris Dagdigian, BioTeam - Independent life science IT & informatics consulting Office: 617-665-6088, Mobile: 617-877-5498, Fax: 425-699-0193 PGP KeyID: 83D4310E iChat/AIM: bioteamdag Web: http://bioteam.net From jwk18 at csufresno.edu Fri Feb 18 05:20:39 2005 From: jwk18 at csufresno.edu (James Kwong) Date: Fri Feb 18 05:16:26 2005 Subject: [Biojava-l] location of biojava.jar on a linux system Message-ID: <4215C177.3090402@csufresno.edu> y0 facemann, On my linux box, this is what I did to my .bash_profile and added these lines in my home acct: export CLASSPATH=.; export CLASSPATH=$CLASSPATH:/home/james/biojava/biojava-live/ant-build/biojava.jar This way, you won't have to type all the parameters each time you want to execute your java app. -- ________________________________________________________________________________ James Kwong "Give a man a fish and you feed him for a day. Teach him how to fish and you feed him for a lifetime." - Lao Tzu From cgarnier at ttz-Bremerhaven.de Fri Feb 18 05:57:17 2005 From: cgarnier at ttz-Bremerhaven.de (BIBIS, Garnier, Christophe) Date: Fri Feb 18 05:52:48 2005 Subject: AW: [Biojava-l] location of biojava.jar on a linux system Message-ID: another solution is to create a shell script file with the executable rights (say application.sh) and write inside something like: #!/bin/sh # --- # run the application # --- # --- Global Environment Variables --- THIS_PATH=`pwd` CLASSPATH=$THIS_PATH CLASSPATH=$CLASSPATH:/bio/tools/biojava/biojava.jar CLASSPATH=$CLASSPATH:/bio/tools/biojava/bytecode-0.92.jar CLASSPATH=$CLASSPATH:/bio/tools/biojava/jakarta-regexp.jar CLASSPATH=$CLASSPATH:/bio/tools/biojava/xerces.jar CLASSPATH=$CLASSPATH:__ANOTHER_JAR_PATH__ CLASSPATH=$CLASSPATH:__ANOTHER_JAR_PATH__ CLASSPATH=$CLASSPATH:__ANOTHER_JAR_PATH__ CLASSPATH=$CLASSPATH:__ANOTHER_JAR_PATH__ CLASSPATH=$CLASSPATH:__ANOTHER_JAR_PATH__ export CLASSPATH PARA="-Xmx758M" java $PARA __THE_CLASS_TO_CALL__ Replace the corresponding paths to your biojava distribution and the __ANOTHER_JAR_PATH__ as needed By the way, the JAVA platforms Eclipse or Netbeans work very fine and take care about such details. christophe -----Urspr?ngliche Nachricht----- Von: James Kwong [mailto:jwk18@csufresno.edu] Gesendet: Freitag, 18. Februar 2005 11:21 An: biojava-l@biojava.org Betreff: Re: [Biojava-l] location of biojava.jar on a linux system y0 facemann, On my linux box, this is what I did to my .bash_profile and added these lines in my home acct: export CLASSPATH=.; export CLASSPATH=$CLASSPATH:/home/james/biojava/biojava-live/ant-build/biojava.jar This way, you won't have to type all the parameters each time you want to execute your java app. -- ____________________________________________________________________________ ____ James Kwong "Give a man a fish and you feed him for a day. Teach him how to fish and you feed him for a lifetime." - Lao Tzu _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From srinandakumar at yahoo.com Wed Feb 23 11:23:11 2005 From: srinandakumar at yahoo.com (Nandakumar Sreedharan) Date: Wed Feb 23 11:19:50 2005 Subject: [Biojava-l] Please help me update my address book on Ringo Message-ID: <20050223162311.9F263599F3@ringotouch1.ringo.com> Hi I'm updating my address book. Please click on the link below and enter your contact info for me: http://ringo.com/i?uid=f1Ba2b_wyYNG8Yxt& I'm using a new, free service where I put in my contact info for you, you put in your contact info for me, and everyone stays up to date automatically. It's surprisingly easy and useful. Thanks for your help. Nandakumar From heuermh at acm.org Thu Feb 24 15:09:13 2005 From: heuermh at acm.org (Michael Heuer) Date: Thu Feb 24 15:57:59 2005 Subject: [Biojava-l] SourceForge StAX version 1.0 finally released Message-ID: SourceForge StAX version 1.0 finally released In the summer of 2001 the package org.biojava.utils.stax was migrated to a project on SourceForge to allow it to have a life of its own outside of biojava. Although some documentation and features were added, a proper release was never made and the project languished in cvs. Stack API for XML (StAX) is an event-based interface for XML parsing, very similar to Simple API for XML (SAX). However, instead of passing parse events for a whole document to a single ContentHandler, sub-trees can easily be delegated to other handlers. StAX also provides an event-based interface for the process of mapping XML ids to java objects. After a bit of refactoring, documentation, and unit testing, a version 1.0 release of the SourceForge StAX has been made and a new web site has been created at > http://stax.sourceforge.net Changes made since the migration from biojava: DelegationManager replaced by StAXContext and StAXDelegationContext Added IdMapper and IdListener, support for mapping XML ids to objects Built-in handlers return value in endTree instead of requiring subclassing Added convenience delegators DispatchForChild and DispatchOnElement Changes made to prepare the sf StAX for release: Created maven build and web site Added simple unit test cases Built-in handlers are reusable Refactored IDMapper --> IdMapper and similar Source code cleanup and documentation Refactored from biojava to net.sf.stax package The 1.0 release has been thoroughly documented and has nearly complete unit test coverage. The javadoc for each class has an example of how to use that class in a handler, and each unit test contains complete examples of handlers for test xml files. Thank yous to StAX developers Matthew Pocock and Thomas Down, and to Mark Schreiber for unintentionally providing the motivation to get a release done. michael From wendy.wong at gmail.com Mon Feb 28 11:10:32 2005 From: wendy.wong at gmail.com (wendy wong) Date: Mon Feb 28 11:05:25 2005 Subject: [Biojava-l] can a Distribution associated with symbols? In-Reply-To: References: Message-ID: Hi all, I am trying to use biojava to construct a HMM and each state emits a column of symbols. I wonder if there is a way to get around it so that Distribution would be associated with a number instead (going from 0 to num_of_symbol^num_of_rows). Thanks, Wendy