From king.jordan at biology.gatech.edu Tue Aug 14 13:44:23 2007 From: king.jordan at biology.gatech.edu (King Jordan) Date: Tue, 14 Aug 2007 13:44:23 -0400 Subject: [Biojava-l] Chromatogram viewer Message-ID: <002e01c7de9a$c0451070$c642cf82@ad.gatech.edu> I would like to be able to display a specific sub-range of a chromatogram. For instance, I may have and abi or scf file with 1,000 bp and I would like to display only positions 200-400. Is there some way to modify the abi or scf file with biojava to accomplish this? Thanks in advance, King ----------------------- I. King Jordan Associate Professor School of Biology Georgia Institute of Technology 310 Ferst Drive Atlanta, GA 30332-0230 404-385-2224 http://esbg.gatech.edu From russ at kepler-eng.com Tue Aug 14 17:20:59 2007 From: russ at kepler-eng.com (Russ Kepler) Date: Tue, 14 Aug 2007 15:20:59 -0600 Subject: [Biojava-l] Chromatogram viewer In-Reply-To: <002e01c7de9a$c0451070$c642cf82@ad.gatech.edu> References: <002e01c7de9a$c0451070$c642cf82@ad.gatech.edu> Message-ID: <200708141521.00254.russ@kepler-eng.com> On Tuesday 14 August 2007 11:44:23 King Jordan wrote: > I would like to be able to display a specific sub-range of a chromatogram. > For instance, I may have and abi or scf file with 1,000 bp and I would like > to display only positions 200-400. Is there some way to modify the abi or > scf file with biojava to accomplish this? It would be easier to simple use the standard TraceRenderer in a panel that limits the displayed range to the positions desired in the SequenceRenderContext that's passed to the renderers. I don't have an example handy but could hack something up if it'd help. From krisveni at gmail.com Tue Aug 14 18:54:57 2007 From: krisveni at gmail.com (Veni Kunche) Date: Tue, 14 Aug 2007 17:54:57 -0500 Subject: [Biojava-l] I would like to volunteer for BioJava Message-ID: <4648a92c0708141554y4eb396b1ne8a6bafb8e6a3990@mail.gmail.com> Hi everyone, I hope to start grad school in Fall '08 to do M.S. in Bioinformatics. I would like to volunteer at BioJava to gain experience related to Bioinformatics. Below is a brief review of my skills and experience. Please let me know if I may contribute in some way. Thank you! Education: University of Wisconsin ? Madison Bachelors in Computer Science, December 2003 Technical Skills: - Languages: JAVA, C, C++, C#, Visual Basic, Visual C++, MATLAB - Web Design/Programming: Apache, HTML, JavaScript, PHP, MySQL, AJAX - Web Services: XML/XSLT, RDF/XML, SOAP, VoiceXML - Developmental Tools: Eclipse, Visual Studio .NET, XMLSPY, BeVocal Caf?, TellMe Studio, ESRI ArcWeb Services, Google Maps API - Certification(s): Sun Certified Programmer for the Java 2 Platform SE 5.0 Experience: US Geological Survey: Web Developer/Database Administrator (9/06-Present) - Implementing Bulletin's Live, a JAVA application which lets users view pesticide restrictions in a certain county. Pesticide enforcement officials can aslo log onto the site and record their findings. UW Madison, Coon Research Group: Volunteer Programmer (7/07 ? Present) - Developing a MATLAB application that analyzes Mass Spectrometry data to remove noise Phone2Car: Application Developer (02/05 ? 12/05) - Developed a VoiceXML based automated ride-sharing prototype CUNA MUTUAL: Business Systems Developer (Intern) (03/04 ? 11/05) - Main developer for three connectivity solutions to download financial information (XML docs) from Loanliner.com to data processor's host system (XML, XSLT, VB6, SOAP) - Developed a parser to transport TransUnion Credit Report data into a host system using XSLT and JavaScript - Implemented a .Net wrapper for CUNA's calcEngine ResponsComm: Web Developer (11/04 ? 11/05) - Developed several Mambo components Open Collaborative Leadership Organization: Web Developer / Associate Director of IT / Volunteer (01/03 ? 02/05) - Designed and developed an non-profit knowledge-management system (PHP/MySQL) serving such organizations as the United Nations, Lt. Gov. Barbara Lawton, and the U.S. Congressional Foresight Seminars - Provided technical support to the UW-Madison Collaborative Leadership Course which included installing and maintaining PHP based wiki's and Mambo's (CMS) to serve as eDemocracy communities From ayates at ebi.ac.uk Wed Aug 15 04:33:10 2007 From: ayates at ebi.ac.uk (Andy Yates) Date: Wed, 15 Aug 2007 09:33:10 +0100 Subject: [Biojava-l] Chromatogram viewer In-Reply-To: <002e01c7de9a$c0451070$c642cf82@ad.gatech.edu> References: <002e01c7de9a$c0451070$c642cf82@ad.gatech.edu> Message-ID: <46C2BA46.6000304@ebi.ac.uk> If you are working with processed traces i.e. ones which are normalized to an intensity of around 1,000 & have very little background noise then it is possible to look at the chromatogram's method getBaseCalls(). This gives you a base call & the offset in the trace it occurs at. Then it's a case of editing the ChromatogramGraphic Option. The ones you need are TO_TRACE_SAMPLE and FROM_TRACE_SAMPLE. So in practice it would look something like this (I haven't compiled this so it may not work but you can get the gist of it). Chromatogram c = getChromatogramFromSomewhere(); ChromatogramGraphic cg = new ChromatogramGraphic(c); Integer from = new Integer(getScanFromBase(c, 200)); Integer to = new Integer(getScanFromBase(c, 400)); cg.setOption(ChromatogramGraphic.Option.FROM_TRACE_SAMPLE, from); cg.setOption(ChromatogramGraphic.Option.TO_TRACE_SAMPLE, to); //Then do the drawing public int getScanFromBase(Chromatogram c, int base) { Alingment align = c.getBaseCalls(); Symbol baseCall = align.symbolAt(Chromatogram.OFFSETS, base); int offset = ((IntegerSymbol)baseCall).intValue(); return offset; } Hope that helps Andy Yates King Jordan wrote: > I would like to be able to display a specific sub-range of a chromatogram. > For instance, I may have and abi or scf file with 1,000 bp and I would like > to display only positions 200-400. Is there some way to modify the abi or > scf file with biojava to accomplish this? > > Thanks in advance, > King > > ----------------------- > I. King Jordan > Associate Professor > School of Biology > Georgia Institute of Technology > 310 Ferst Drive > Atlanta, GA 30332-0230 > 404-385-2224 > http://esbg.gatech.edu > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l From koen.bruynseels at cropdesign.com Wed Aug 15 06:12:39 2007 From: koen.bruynseels at cropdesign.com (koen.bruynseels at cropdesign.com) Date: Wed, 15 Aug 2007 12:12:39 +0200 Subject: [Biojava-l] Koen Bruynseels is out of the office. Message-ID: I will be out of the office starting 04/08/2007 and will not return until 19/08/2007. I will respond to your message when I return. From holland at ebi.ac.uk Wed Aug 15 11:43:59 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Wed, 15 Aug 2007 16:43:59 +0100 Subject: [Biojava-l] I would like to volunteer for BioJava In-Reply-To: <4648a92c0708141554y4eb396b1ne8a6bafb8e6a3990@mail.gmail.com> References: <4648a92c0708141554y4eb396b1ne8a6bafb8e6a3990@mail.gmail.com> Message-ID: <46C31F3F.6010808@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 That's great that you'd like to volunteer. We're still working on a roadplan for the future and have no defined list of things to do (other than docs and unit tests for all the existing code, which if you want to contribute to you would be most welcome to do so!). In the meantime, we welcome any contributions in any area that you feel has room for improvement. For instance, a particular class that you use regularly may not be very efficient, or it might not provide all the features you might like. Or, a particular functionality might be missing altogether from BioJava (e.g. microarray analysis). Currently most of our development is happening in phylogenetics, so if there is an alternative field you are interested in it would be good to get something going in parallel to expand the project's horizons. Feel free to post ideas and/or code to the biojava-l mailing list, where you'll get pretty good feedback as to what people out there who are using BioJava really want. Thanks again for volunteering. It's much appreciated. cheers, Richard Veni Kunche wrote: > Hi everyone, > > I hope to start grad school in Fall '08 to do M.S. in Bioinformatics. I > would like to volunteer at BioJava to gain experience related to > Bioinformatics. > > Below is a brief review of my skills and experience. Please let me know if I > may contribute in some way. Thank you! > > Education: > University of Wisconsin ? Madison > Bachelors in Computer Science, December 2003 > > Technical Skills: > - Languages: JAVA, C, C++, C#, Visual Basic, Visual C++, MATLAB > - Web Design/Programming: Apache, HTML, JavaScript, PHP, MySQL, AJAX > - Web Services: XML/XSLT, RDF/XML, SOAP, VoiceXML > - Developmental Tools: Eclipse, Visual Studio .NET, XMLSPY, BeVocal Caf?, > TellMe Studio, ESRI ArcWeb Services, Google Maps API > - Certification(s): Sun Certified Programmer for the Java 2 Platform SE 5.0 > > Experience: > US Geological Survey: Web Developer/Database Administrator (9/06-Present) > - Implementing Bulletin's Live, a JAVA application which lets users view > pesticide restrictions in a certain county. Pesticide enforcement officials > can aslo log onto the site and record their findings. > > UW Madison, Coon Research Group: Volunteer Programmer (7/07 ? Present) > - Developing a MATLAB application that analyzes Mass Spectrometry data to > remove noise > > Phone2Car: Application Developer (02/05 ? 12/05) > - Developed a VoiceXML based automated ride-sharing prototype > > CUNA MUTUAL: Business Systems Developer (Intern) (03/04 ? 11/05) > - Main developer for three connectivity solutions to download financial > information (XML docs) from Loanliner.com to data processor's host system > (XML, XSLT, VB6, SOAP) > - Developed a parser to transport TransUnion Credit Report data into a host > system using XSLT and JavaScript > - Implemented a .Net wrapper for CUNA's calcEngine > > ResponsComm: Web Developer (11/04 ? 11/05) > - Developed several Mambo components > > Open Collaborative Leadership Organization: Web Developer / Associate > Director of IT / Volunteer (01/03 ? 02/05) > - Designed and developed an non-profit knowledge-management system > (PHP/MySQL) serving such organizations as the United Nations, Lt. Gov. > Barbara Lawton, and the U.S. Congressional Foresight Seminars > - Provided technical support to the UW-Madison Collaborative Leadership > Course which included installing and maintaining PHP based wiki's and > Mambo's (CMS) to serve as eDemocracy communities > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGwx8/4C5LeMEKA/QRAl69AJ4g71YsFiCqFvYE4nbPGhqMifliZwCfcOfp NGs0nYKbTQiQ/ap5p0yauTw= =MmKB -----END PGP SIGNATURE----- From daniel.rohrbach at web.de Thu Aug 16 19:13:44 2007 From: daniel.rohrbach at web.de (Daniel Rohrbach) Date: Fri, 17 Aug 2007 01:13:44 +0200 Subject: [Biojava-l] construction of profile HMM from Multiple sequence alignment Message-ID: <1707061361@web.de> Hallo, Please, excuse me for possible mistakes because i'm relatively new here. My Question is: Is there any way in Biojava to construct a profile HMM from a multiple sequence alignment? Are algorithms implemented like it is described in the "Biological sequence analysis" book? Thank you for possible answers. _____________________________________________________________________ Der WEB.DE SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! http://smartsurfer.web.de/?mc=100071&distributionid=000000000066 From aulia at students.itb.ac.id Mon Aug 20 03:23:22 2007 From: aulia at students.itb.ac.id (Aulia Rahma Amin) Date: Mon, 20 Aug 2007 14:23:22 +0700 (WIT) Subject: [Biojava-l] construction of profile HMM from Multiple sequence alignment In-Reply-To: <1707061361@web.de> References: <1707061361@web.de> Message-ID: <2692.167.205.35.31.1187594602.squirrel@students.itb.ac.id> Hello, I cannot find a method in biojava to construct a profile HMM correctly from a multiple sequence alignment. So I construct a method to do it using my self made heuristic. I dont know if my heuristics is correct enough because I haven't read "Biological sequence analysis" book yet. -- Aulia Rahma Amin Informatics Bandung Institute of Technology Indonesia > Hallo, > > Please, excuse me for possible mistakes because i'm relatively new here. > > My Question is: Is there any way in Biojava to construct a profile HMM > from a multiple sequence alignment? Are algorithms implemented like it is > described in the "Biological sequence analysis" book? > > > Thank you for possible answers. > _____________________________________________________________________ From yp_riverol at yahoo.com Wed Aug 22 21:28:02 2007 From: yp_riverol at yahoo.com (yasset perez riverol) Date: Wed, 22 Aug 2007 20:28:02 -0500 (CDT) Subject: [Biojava-l] Problem With Isoelectric point Message-ID: <148362.17797.qm@web37914.mail.mud.yahoo.com> Hi, I have a problem when I execute the Isoelectrc Point calculation for this peptides: ALLIDLPV FDIYAGTPV SVLLMSAEI PTGDTTGYLANPEEV I all the case I receive this error : Error, the peptide probably contains only positive or negative charges. Well I try to calculate the isoelectric Point for all the peptides with de Expasy Calculator and I obtained: ALLIDLPV: Theoretical pI: 3.80 Molecular weight (average): 853.07 FDIYAGTPV: Theoretical pI: 3.80 Molecular weight (average): 982.10 SVLLMSAEI: Theoretical pI: 4.00 Molecular weight (average): 962.17 PTGDTTGYLANPEEV: Theoretical pI: 3.57 Molecular weight (average): 1563.64 My code is this: OBioSeq = ProteinTools.createProtein(Sequence); IsoelectricPointCalc OBioIsoc = new IsoelectricPointCalc(); double dIsoelec = 0.0; dIsoelec = OBioIsoc.getPI(OBioSeq,true,true); Thanks in advance Center of Molecular Biology. Havana University Cuba. __________________________________________________ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ?gratis! Reg?strate ya - http://correo.espanol.yahoo.com/ From gwaldon at geneinfinity.org Thu Aug 23 13:57:19 2007 From: gwaldon at geneinfinity.org (george waldon) Date: Thu, 23 Aug 2007 10:57:19 -0700 Subject: [Biojava-l] Problem With Isoelectric point Message-ID: <20070823175719.39780.qmail@mmm1924.dulles19-verio.com> Yasset, Your are right; you should always get a pI value when both peptide ends are free. It probably comes from the binary search; I'll have a look into this. Thanks for reporting this, George -----Original Message----- From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of yasset perez riverol Sent: Wednesday, August 22, 2007 6:28 PM To: biojava-l at lists.open-bio.org Subject: [Biojava-l] Problem With Isoelectric point Hi, I have a problem when I execute the Isoelectrc Point calculation for this peptides: ALLIDLPV FDIYAGTPV SVLLMSAEI PTGDTTGYLANPEEV I all the case I receive this error : Error, the peptide probably contains only positive or negative charges. Well I try to calculate the isoelectric Point for all the peptides with de Expasy Calculator and I obtained: ALLIDLPV: Theoretical pI: 3.80 Molecular weight (average): 853.07 FDIYAGTPV: Theoretical pI: 3.80 Molecular weight (average): 982.10 SVLLMSAEI: Theoretical pI: 4.00 Molecular weight (average): 962.17 PTGDTTGYLANPEEV: Theoretical pI: 3.57 Molecular weight (average): 1563.64 My code is this: OBioSeq = ProteinTools.createProtein(Sequence); IsoelectricPointCalc OBioIsoc = new IsoelectricPointCalc(); double dIsoelec = 0.0; dIsoelec = OBioIsoc.getPI(OBioSeq,true,true); Thanks in advance Center of Molecular Biology. Havana University Cuba. __________________________________________________ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ?gratis! Reg?strate ya - http://correo.espanol.yahoo.com/ _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From gwaldon at geneinfinity.org Thu Aug 23 16:31:11 2007 From: gwaldon at geneinfinity.org (george waldon) Date: Thu, 23 Aug 2007 13:31:11 -0700 Subject: [Biojava-l] Problem With Isoelectric point Message-ID: <20070823203111.26626.qmail@mmm1924.dulles19-verio.com> This is now fixed in the trunk. You'll have to make your own build of biojava.jar from the CVS tree to get correct(ed) pI values. George -----Original Message----- From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of yasset perez riverol Sent: Wednesday, August 22, 2007 6:28 PM To: biojava-l at lists.open-bio.org Subject: [Biojava-l] Problem With Isoelectric point Hi, I have a problem when I execute the Isoelectrc Point calculation for this peptides: ALLIDLPV FDIYAGTPV SVLLMSAEI PTGDTTGYLANPEEV I all the case I receive this error : Error, the peptide probably contains only positive or negative charges. Well I try to calculate the isoelectric Point for all the peptides with de Expasy Calculator and I obtained: ALLIDLPV: Theoretical pI: 3.80 Molecular weight (average): 853.07 FDIYAGTPV: Theoretical pI: 3.80 Molecular weight (average): 982.10 SVLLMSAEI: Theoretical pI: 4.00 Molecular weight (average): 962.17 PTGDTTGYLANPEEV: Theoretical pI: 3.57 Molecular weight (average): 1563.64 My code is this: OBioSeq = ProteinTools.createProtein(Sequence); IsoelectricPointCalc OBioIsoc = new IsoelectricPointCalc(); double dIsoelec = 0.0; dIsoelec = OBioIsoc.getPI(OBioSeq,true,true); Thanks in advance Center of Molecular Biology. Havana University Cuba. __________________________________________________ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ?gratis! Reg?strate ya - http://correo.espanol.yahoo.com/ _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From abhi232 at cc.gatech.edu Sun Aug 26 03:04:31 2007 From: abhi232 at cc.gatech.edu (abhi232 at cc.gatech.edu) Date: Sun, 26 Aug 2007 03:04:31 -0400 (EDT) Subject: [Biojava-l] Applet Creation Questions Message-ID: <50890.74.232.148.95.1188111871.squirrel@webmail.cc.gatech.edu> hi all, I dont know whether this question has been asked before or not.If asked please direct me to the link. I am currently trying to create an applet for viewing and modifying a chromatogram.I have an ab1 file of which i am creating a chromatogram and after that using the chromatogramgraphic class i am drawing it onto to the graphics context.I am creating a uffered image out of the chromatogramGraphic class object which i create. My issues with this are: 1: the chromatogram does not spread out evenly as in the image that i get is very compact whereas i want a well spread out image.I have tried almost all the chromatogramgraphic.option class variables but it does not change anything. 2:How do i display the corresponding base calls associated with the particular colours. Thanks a lot for the help. Abhinav From holland at ebi.ac.uk Tue Aug 28 04:21:08 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Tue, 28 Aug 2007 09:21:08 +0100 Subject: [Biojava-l] Applet Creation Questions In-Reply-To: <50890.74.232.148.95.1188111871.squirrel@webmail.cc.gatech.edu> References: <50890.74.232.148.95.1188111871.squirrel@webmail.cc.gatech.edu> Message-ID: <46D3DAF4.6070303@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I don't think the chromatogram class allows for spacing to be changed or base calls to be added. If you would like to add these features that would be great, or alternatively you can copy the class and make your own modified local copy. We need to be careful with the graphics/GUI portion of BioJava - each person has their own individual taste as to how things should appear, making a generic solution very hard to create. Any changes must also preserve the existing behaviour as default. The classes provided in these areas are therefore to be treated more as demonstrations of capability rather than complete solutions. cheers, Richard abhi232 at cc.gatech.edu wrote: > hi all, > I dont know whether this question has been asked before or not.If asked > please direct me to the link. > I am currently trying to create an applet for viewing and modifying a > chromatogram.I have an ab1 file of which i am creating a chromatogram and > after that using the chromatogramgraphic class i am drawing it onto to the > graphics context.I am creating a uffered image out of the > chromatogramGraphic class object which i create. > My issues with this are: > 1: the chromatogram does not spread out evenly as in the image that i get > is very compact whereas i want a well spread out image.I have tried almost > all the chromatogramgraphic.option class variables but it does not change > anything. > 2:How do i display the corresponding base calls associated with the > particular colours. > > Thanks a lot for the help. > Abhinav > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFG09r04C5LeMEKA/QRAnV5AKCI+/r97uOrRKlA7RTjltHvnVntYQCfUxCj fCrKGO0b6HTEydH+5e/UJ60= =qecU -----END PGP SIGNATURE----- From daniel.rohrbach at web.de Tue Aug 28 09:36:25 2007 From: daniel.rohrbach at web.de (Daniel Rohrbach) Date: Tue, 28 Aug 2007 15:36:25 +0200 Subject: [Biojava-l] problems with the profilehmm demo Message-ID: <1726503210@web.de> Hi all, i'm trying to run the "How do I make a ProfileHMM" example but it doesn't want to work. I copied the code to my program and when I start it I get the following exceptions: Exception in thread "main" java.lang.IndexOutOfBoundsException: Can't find symbol for index 0 at org.biojava.bio.symbol.LinearAlphabetIndex.symbolForIndex(LinearAlphabetIndex.java:106) at org.biojava.bio.dist.SimpleDistribution$Trainer.trainImpl(SimpleDistribution.java:332) at org.biojava.bio.dist.SimpleDistribution$Trainer.train(SimpleDistribution.java:306) at org.biojava.bio.dist.SimpleDistributionTrainerContext.train(SimpleDistributionTrainerContext.java:126) at biojavatests.HMMTest.main(HMMTest.java:71) The error occurs at mt.train(). It seems that there was no, wrong or empty alphabet set for the trainer that shall be used. here the link to the examplepage: http://biojava.org/wiki/BioJava:CookBook:DP:HMM any help on this topic? Thanks in advance __________________________________________________________________________ Erweitern Sie FreeMail zu einem noch leistungsst?rkeren E-Mail-Postfach! Mehr Infos unter http://produkte.web.de/club/?mc=021131 From markjschreiber at gmail.com Tue Aug 28 10:28:13 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Tue, 28 Aug 2007 22:28:13 +0800 Subject: [Biojava-l] problems with the profilehmm demo In-Reply-To: <1726503210@web.de> References: <1726503210@web.de> Message-ID: <93b45ca50708280728o669d99b5s82fdab744525563c@mail.gmail.com> Hi - This is a bug that has been submitted to bugzilla. Strangely it was not an issue in the pre-releases of biojava. I was kind of hoping someone else would fix it but I guess I will have to find time to take a look. - Mark On 8/28/07, Daniel Rohrbach wrote: > Hi all, > > i'm trying to run the "How do I make a ProfileHMM" example but it doesn't want to work. I copied the code to my program and when I start it I get the following exceptions: > > Exception in thread "main" java.lang.IndexOutOfBoundsException: Can't find symbol for index 0 > at org.biojava.bio.symbol.LinearAlphabetIndex.symbolForIndex(LinearAlphabetIndex.java:106) > at org.biojava.bio.dist.SimpleDistribution$Trainer.trainImpl(SimpleDistribution.java:332) > at org.biojava.bio.dist.SimpleDistribution$Trainer.train(SimpleDistribution.java:306) > at org.biojava.bio.dist.SimpleDistributionTrainerContext.train(SimpleDistributionTrainerContext.java:126) > at biojavatests.HMMTest.main(HMMTest.java:71) > > The error occurs at mt.train(). It seems that there was no, wrong or empty alphabet set for the trainer that shall be used. > > here the link to the examplepage: http://biojava.org/wiki/BioJava:CookBook:DP:HMM > any help on this topic? > > Thanks in advance > __________________________________________________________________________ > Erweitern Sie FreeMail zu einem noch leistungsst?rkeren E-Mail-Postfach! > Mehr Infos unter http://produkte.web.de/club/?mc=021131 > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From daniel.rohrbach at web.de Wed Aug 29 09:32:34 2007 From: daniel.rohrbach at web.de (daniel.rohrbach at web.de) Date: Wed, 29 Aug 2007 15:32:34 +0200 Subject: [Biojava-l] problems with the profilehmm demo Message-ID: <1728297875@web.de> Hi all, hi Mark thanks for the fast Answer. I looked at the code and perhaps solved the problem. During initialisation of the ProfileHMM ( bevore method connectModel() is called ) the transWeights are set with SimpleDistributions sd. These sd again are initialized with an empty Alphabet (no symbol). (*) These Distributions keeps an indexer Object which is used during the training process where the exception occurs. because of (*) the number of indexed symbols is 0 (indexer.symbols.length == 0) and the (FiniteAlphabet)indexer.alphaRef.get() has length 0 too. (Indexer is of type LinearAlphabetIndex) When connectModel() is called the Alphabets ( which are the same as indexer.alphaRef ) are filled with some symbols (EmissionState, DotState ...) (**) BUT the indexer.symbols.length will not be changed (***). This causes the following exception: In SimpleDistribution.Trainer.trainImpl is a method called getWeights(). This will return a double list of length indexer.getAlphabet() which is the same of indexer.alphaRef. Because of (**) this will have a length n>0. So that the for loop in this piece of code runs from 0 to n. Here the exception occurs. indexer.symbolForIndex(i) (0<=i -----Urspr?ngliche Nachricht----- > Von: "Mark Schreiber" > Gesendet: 28.08.07 16:28:23 > An: "Daniel Rohrbach" > CC: biojava-l at lists.open-bio.org > Betreff: Re: [Biojava-l] problems with the profilehmm demo > > Hi - > > This is a bug that has been submitted to bugzilla. Strangely it was > not an issue in the pre-releases of biojava. I was kind of hoping > someone else would fix it but I guess I will have to find time to take > a look. > > - Mark > > On 8/28/07, Daniel Rohrbach wrote: > > Hi all, > > > > i'm trying to run the "How do I make a ProfileHMM" example but it doesn't want to work. I copied the code to my program and when I start it I get the following exceptions: > > > > Exception in thread "main" java.lang.IndexOutOfBoundsException: Can't find symbol for index 0 > > at org.biojava.bio.symbol.LinearAlphabetIndex.symbolForIndex(LinearAlphabetIndex.java:106) > > at org.biojava.bio.dist.SimpleDistribution$Trainer.trainImpl(SimpleDistribution.java:332) > > at org.biojava.bio.dist.SimpleDistribution$Trainer.train(SimpleDistribution.java:306) > > at org.biojava.bio.dist.SimpleDistributionTrainerContext.train(SimpleDistributionTrainerContext.java:126) > > at biojavatests.HMMTest.main(HMMTest.java:71) > > > > The error occurs at mt.train(). It seems that there was no, wrong or empty alphabet set for the trainer that shall be used. > > > > here the link to the examplepage: http://biojava.org/wiki/BioJava:CookBook:DP:HMM > > any help on this topic? > > > > Thanks in advance > > __________________________________________________________________________ > > Erweitern Sie FreeMail zu einem noch leistungsst?rkeren E-Mail-Postfach! > > Mehr Infos unter http://produkte.web.de/club/?mc=021131 > > > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > _______________________________________________________________________ Jetzt neu! Sch?tzen Sie Ihren PC mit McAfee und WEB.DE. 3 Monate kostenlos testen. http://www.pc-sicherheit.web.de/startseite/?mc=022220 From markjschreiber at gmail.com Wed Aug 29 10:30:45 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Wed, 29 Aug 2007 22:30:45 +0800 Subject: [Biojava-l] problems with the profilehmm demo In-Reply-To: <1728297875@web.de> References: <1728297875@web.de> Message-ID: <93b45ca50708290730t75c8db2chd41ed2531d214307@mail.gmail.com> Hi Daniel - Your suggestion for the cause of the bug makes sense. I will take a look at this tomorrow when I have access to the CVS. A possible solution might be to make AlphabetIndexers listen to their underlying Alphabets for changes to the number of Symbols. Thanks for your help! If you think of a solution before I wake up tomorrow you can be biojava hero of the month : ) - Mark On 8/29/07, daniel.rohrbach at web.de wrote: > Hi all, hi Mark > > thanks for the fast Answer. > > I looked at the code and perhaps solved the problem. > > During initialisation of the ProfileHMM ( bevore method connectModel() is called ) the transWeights are set with SimpleDistributions sd. These sd again are initialized with an empty Alphabet (no symbol). (*) > > These Distributions keeps an indexer Object which is used during the training process where the exception occurs. > > because of (*) the number of indexed symbols is 0 (indexer.symbols.length == 0) and the (FiniteAlphabet)indexer.alphaRef.get() has length 0 too. > (Indexer is of type LinearAlphabetIndex) > > When connectModel() is called the Alphabets ( which are the same as indexer.alphaRef ) are filled with some symbols (EmissionState, DotState ...) (**) BUT the indexer.symbols.length will not be changed (***). > > This causes the following exception: > In SimpleDistribution.Trainer.trainImpl is a method called getWeights(). This will return a double list of length indexer.getAlphabet() which is the same of indexer.alphaRef. Because of (**) this will have a length n>0. So that the for loop in this piece of code runs from 0 to n. Here the exception occurs. indexer.symbolForIndex(i) (0<=i > I think it must be changed the symbols of the indexer Object in the connectModel() method too. But I'm not really sure because I didn't worked with biojava so long. > > I'm sorry for my bad English but I hope that I could help a little. > Many greetings > Daniel > > > -----Urspr?ngliche Nachricht----- > > Von: "Mark Schreiber" > > Gesendet: 28.08.07 16:28:23 > > An: "Daniel Rohrbach" > > CC: biojava-l at lists.open-bio.org > > Betreff: Re: [Biojava-l] problems with the profilehmm demo > > > > > > Hi - > > > > This is a bug that has been submitted to bugzilla. Strangely it was > > not an issue in the pre-releases of biojava. I was kind of hoping > > someone else would fix it but I guess I will have to find time to take > > a look. > > > > - Mark > > > > On 8/28/07, Daniel Rohrbach wrote: > > > Hi all, > > > > > > i'm trying to run the "How do I make a ProfileHMM" example but it doesn't want to work. I copied the code to my program and when I start it I get the following exceptions: > > > > > > Exception in thread "main" java.lang.IndexOutOfBoundsException: Can't find symbol for index 0 > > > at org.biojava.bio.symbol.LinearAlphabetIndex.symbolForIndex(LinearAlphabetIndex.java:106) > > > at org.biojava.bio.dist.SimpleDistribution$Trainer.trainImpl(SimpleDistribution.java:332) > > > at org.biojava.bio.dist.SimpleDistribution$Trainer.train(SimpleDistribution.java:306) > > > at org.biojava.bio.dist.SimpleDistributionTrainerContext.train(SimpleDistributionTrainerContext.java:126) > > > at biojavatests.HMMTest.main(HMMTest.java:71) > > > > > > The error occurs at mt.train(). It seems that there was no, wrong or empty alphabet set for the trainer that shall be used. > > > > > > here the link to the examplepage: http://biojava.org/wiki/BioJava:CookBook:DP:HMM > > > any help on this topic? > > > > > > Thanks in advance > > > __________________________________________________________________________ > > > Erweitern Sie FreeMail zu einem noch leistungsst?rkeren E-Mail-Postfach! > > > Mehr Infos unter http://produkte.web.de/club/?mc=021131 > > > > > > > > > _______________________________________________ > > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > > _______________________________________________________________________ > Jetzt neu! Sch?tzen Sie Ihren PC mit McAfee und WEB.DE. 3 Monate > kostenlos testen. http://www.pc-sicherheit.web.de/startseite/?mc=022220 > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From markjschreiber at gmail.com Wed Aug 29 10:36:21 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Wed, 29 Aug 2007 22:36:21 +0800 Subject: [Biojava-l] problems with the profilehmm demo In-Reply-To: <1728297875@web.de> References: <1728297875@web.de> Message-ID: <93b45ca50708290736h4c57e8c5m8acf1d9e0c27f1da@mail.gmail.com> Just looked at the CVS on line. You are very likely correct. There used to be a listener for changes in the Alphabet but this was mistakenly removed as it was thought to be redundant. A diff view is here (http://code.open-bio.org/cgi/viewcvs.cgi/biojava-live/src/org/biojava/bio/symbol/LinearAlphabetIndex.java.diff?r1=1.12&r2=1.13&cvsroot=biojava) I will check it back in tomorrow unless some one beats me to it. A JUnit test is also required to make sure this works. - Mark On 8/29/07, daniel.rohrbach at web.de wrote: > Hi all, hi Mark > > thanks for the fast Answer. > > I looked at the code and perhaps solved the problem. > > During initialisation of the ProfileHMM ( bevore method connectModel() is called ) the transWeights are set with SimpleDistributions sd. These sd again are initialized with an empty Alphabet (no symbol). (*) > > These Distributions keeps an indexer Object which is used during the training process where the exception occurs. > > because of (*) the number of indexed symbols is 0 (indexer.symbols.length == 0) and the (FiniteAlphabet)indexer.alphaRef.get() has length 0 too. > (Indexer is of type LinearAlphabetIndex) > > When connectModel() is called the Alphabets ( which are the same as indexer.alphaRef ) are filled with some symbols (EmissionState, DotState ...) (**) BUT the indexer.symbols.length will not be changed (***). > > This causes the following exception: > In SimpleDistribution.Trainer.trainImpl is a method called getWeights(). This will return a double list of length indexer.getAlphabet() which is the same of indexer.alphaRef. Because of (**) this will have a length n>0. So that the for loop in this piece of code runs from 0 to n. Here the exception occurs. indexer.symbolForIndex(i) (0<=i > I think it must be changed the symbols of the indexer Object in the connectModel() method too. But I'm not really sure because I didn't worked with biojava so long. > > I'm sorry for my bad English but I hope that I could help a little. > Many greetings > Daniel > > > -----Urspr?ngliche Nachricht----- > > Von: "Mark Schreiber" > > Gesendet: 28.08.07 16:28:23 > > An: "Daniel Rohrbach" > > CC: biojava-l at lists.open-bio.org > > Betreff: Re: [Biojava-l] problems with the profilehmm demo > > > > > > Hi - > > > > This is a bug that has been submitted to bugzilla. Strangely it was > > not an issue in the pre-releases of biojava. I was kind of hoping > > someone else would fix it but I guess I will have to find time to take > > a look. > > > > - Mark > > > > On 8/28/07, Daniel Rohrbach wrote: > > > Hi all, > > > > > > i'm trying to run the "How do I make a ProfileHMM" example but it doesn't want to work. I copied the code to my program and when I start it I get the following exceptions: > > > > > > Exception in thread "main" java.lang.IndexOutOfBoundsException: Can't find symbol for index 0 > > > at org.biojava.bio.symbol.LinearAlphabetIndex.symbolForIndex(LinearAlphabetIndex.java:106) > > > at org.biojava.bio.dist.SimpleDistribution$Trainer.trainImpl(SimpleDistribution.java:332) > > > at org.biojava.bio.dist.SimpleDistribution$Trainer.train(SimpleDistribution.java:306) > > > at org.biojava.bio.dist.SimpleDistributionTrainerContext.train(SimpleDistributionTrainerContext.java:126) > > > at biojavatests.HMMTest.main(HMMTest.java:71) > > > > > > The error occurs at mt.train(). It seems that there was no, wrong or empty alphabet set for the trainer that shall be used. > > > > > > here the link to the examplepage: http://biojava.org/wiki/BioJava:CookBook:DP:HMM > > > any help on this topic? > > > > > > Thanks in advance > > > __________________________________________________________________________ > > > Erweitern Sie FreeMail zu einem noch leistungsst?rkeren E-Mail-Postfach! > > > Mehr Infos unter http://produkte.web.de/club/?mc=021131 > > > > > > > > > _______________________________________________ > > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > > _______________________________________________________________________ > Jetzt neu! Sch?tzen Sie Ihren PC mit McAfee und WEB.DE. 3 Monate > kostenlos testen. http://www.pc-sicherheit.web.de/startseite/?mc=022220 > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From koen.bruynseels at cropdesign.com Wed Aug 29 12:13:32 2007 From: koen.bruynseels at cropdesign.com (koen.bruynseels at cropdesign.com) Date: Wed, 29 Aug 2007 18:13:32 +0200 Subject: [Biojava-l] Koen Bruynseels is out of the office. Message-ID: I will be out of the office starting 29/08/2007 and will not return until 06/09/2007. I will respond to your message when I return. From mcolosimo at mitre.org Wed Aug 29 12:53:19 2007 From: mcolosimo at mitre.org (Colosimo, Marc E.) Date: Wed, 29 Aug 2007 12:53:19 -0400 Subject: [Biojava-l] Maven Project Message-ID: I'm look for information about maven versions for biojava. I guess ant is the default method, since there is an ant build.xml file. I am asking because I found several maven repositories for biojava with various versions on the web (via google), but nothing here. I hope some of those people are on this list so that we might get their work put into the main version (pom.xml and metadata files). Also, it would be nice to have biojava host the biojava m2repo for biojava. Thanks Marc From holland at ebi.ac.uk Thu Aug 30 03:42:29 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Thu, 30 Aug 2007 08:42:29 +0100 Subject: [Biojava-l] Maven Project In-Reply-To: References: Message-ID: <46D674E5.9050701@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 There is no Maven repository for the official BioJava. Some years ago a BioJava2 project was branched which did use Maven. However, this branch of the project was never completed and is no longer maintained to the best of my knowledge. The main BioJava project uses Ant, although we are considering looking to move to Maven in future. cheers, Richard Colosimo, Marc E. wrote: > I'm look for information about maven > versions for biojava. I guess ant is the default method, since there is > an ant build.xml file. I am asking because I found several maven > repositories for biojava with various versions on the web (via google), > but nothing here. I hope some of those people are on this list so that > we might get their work put into the main version (pom.xml and metadata > files). Also, it would be nice to have biojava host the biojava m2repo > for biojava. > > Thanks > Marc > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFG1nTl4C5LeMEKA/QRAmXdAJ9LkI7OIaO7zh/phG8IOcOagLpbLQCfWY+Q 8MLStvIqnesvZX9AqI5EZzM= =ZYLp -----END PGP SIGNATURE----- From daniel.rohrbach at web.de Thu Aug 30 05:01:32 2007 From: daniel.rohrbach at web.de (daniel.rohrbach at web.de) Date: Thu, 30 Aug 2007 11:01:32 +0200 Subject: [Biojava-l] problems with the profilehmm demo Message-ID: <1729896514@web.de> thanks a lot for the support. I had changed the code, if I'd have got access to the CVS. When you changed the code, I will be very grateful if you can inform me . I need it for a work on a project for the university. Daniel > -----Urspr?ngliche Nachricht----- > Von: "Mark Schreiber" > Gesendet: 29.08.07 16:36:38 > An: "daniel.rohrbach at web.de" > CC: biojava-l at lists.open-bio.org > Betreff: Re: [Biojava-l] problems with the profilehmm demo > > Just looked at the CVS on line. You are very likely correct. > > There used to be a listener for changes in the Alphabet but this was > mistakenly removed as it was thought to be redundant. A diff view is > here (http://code.open-bio.org/cgi/viewcvs.cgi/biojava-live/src/org/biojava/bio/symbol/LinearAlphabetIndex.java.diff?r1=1.12&r2=1.13&cvsroot=biojava) > > I will check it back in tomorrow unless some one beats me to it. A > JUnit test is also required to make sure this works. > > - Mark > > On 8/29/07, daniel.rohrbach at web.de wrote: > > Hi all, hi Mark > > > > thanks for the fast Answer. > > > > I looked at the code and perhaps solved the problem. > > > > During initialisation of the ProfileHMM ( bevore method connectModel() is called ) the transWeights are set with SimpleDistributions sd. These sd again are initialized with an empty Alphabet (no symbol). (*) > > > > These Distributions keeps an indexer Object which is used during the training process where the exception occurs. > > > > because of (*) the number of indexed symbols is 0 (indexer.symbols.length == 0) and the (FiniteAlphabet)indexer.alphaRef.get() has length 0 too. > > (Indexer is of type LinearAlphabetIndex) > > > > When connectModel() is called the Alphabets ( which are the same as indexer.alphaRef ) are filled with some symbols (EmissionState, DotState ...) (**) BUT the indexer.symbols.length will not be changed (***). > > > > This causes the following exception: > > In SimpleDistribution.Trainer.trainImpl is a method called getWeights(). This will return a double list of length indexer.getAlphabet() which is the same of indexer.alphaRef. Because of (**) this will have a length n>0. So that the for loop in this piece of code runs from 0 to n. Here the exception occurs. indexer.symbolForIndex(i) (0<=i > > > I think it must be changed the symbols of the indexer Object in the connectModel() method too. But I'm not really sure because I didn't worked with biojava so long. > > > > I'm sorry for my bad English but I hope that I could help a little. > > Many greetings > > Daniel > > > > > -----Urspr?ngliche Nachricht----- > > > Von: "Mark Schreiber" > > > Gesendet: 28.08.07 16:28:23 > > > An: "Daniel Rohrbach" > > > CC: biojava-l at lists.open-bio.org > > > Betreff: Re: [Biojava-l] problems with the profilehmm demo > > > > > > > > > > Hi - > > > > > > This is a bug that has been submitted to bugzilla. Strangely it was > > > not an issue in the pre-releases of biojava. I was kind of hoping > > > someone else would fix it but I guess I will have to find time to take > > > a look. > > > > > > - Mark > > > > > > On 8/28/07, Daniel Rohrbach wrote: > > > > Hi all, > > > > > > > > i'm trying to run the "How do I make a ProfileHMM" example but it doesn't want to work. I copied the code to my program and when I start it I get the following exceptions: > > > > > > > > Exception in thread "main" java.lang.IndexOutOfBoundsException: Can't find symbol for index 0 > > > > at org.biojava.bio.symbol.LinearAlphabetIndex.symbolForIndex(LinearAlphabetIndex.java:106) > > > > at org.biojava.bio.dist.SimpleDistribution$Trainer.trainImpl(SimpleDistribution.java:332) > > > > at org.biojava.bio.dist.SimpleDistribution$Trainer.train(SimpleDistribution.java:306) > > > > at org.biojava.bio.dist.SimpleDistributionTrainerContext.train(SimpleDistributionTrainerContext.java:126) > > > > at biojavatests.HMMTest.main(HMMTest.java:71) > > > > > > > > The error occurs at mt.train(). It seems that there was no, wrong or empty alphabet set for the trainer that shall be used. > > > > > > > > here the link to the examplepage: http://biojava.org/wiki/BioJava:CookBook:DP:HMM > > > > any help on this topic? > > > > > > > > Thanks in advance > > > > __________________________________________________________________________ > > > > Erweitern Sie FreeMail zu einem noch leistungsst?rkeren E-Mail-Postfach! > > > > Mehr Infos unter http://produkte.web.de/club/?mc=021131 > > > > > > > > > > > > _______________________________________________ > > > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > > > > > > > _______________________________________________________________________ > > Jetzt neu! Sch?tzen Sie Ihren PC mit McAfee und WEB.DE. 3 Monate > > kostenlos testen. http://www.pc-sicherheit.web.de/startseite/?mc=022220 > > > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > _____________________________________________________________________ Der WEB.DE SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! http://smartsurfer.web.de/?mc=100071&distributionid=000000000066 From markjschreiber at gmail.com Thu Aug 30 05:58:56 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Thu, 30 Aug 2007 17:58:56 +0800 Subject: [Biojava-l] problems with the profilehmm demo In-Reply-To: <1729896514@web.de> References: <1729896514@web.de> Message-ID: <93b45ca50708300258we282b2cqb025cac4bcea1b37@mail.gmail.com> Hi - I have put the ChangeListeners back in and commited to CVS. Some quick tests show everything seems to work (even Serialization!!). I will commit some formal unit tests shortly. I will leave the bugzilla bug open until I have some unit tests in place to make sure it doesn't happen again. Thanks for your work in solving this bug. Best regards, - Mark On 8/30/07, daniel.rohrbach at web.de wrote: > > > thanks a lot for the support. I had changed the code, if I'd have got > access to the CVS. When you changed the code, I will be very grateful if > you can inform me . I need it for a work on a project for the university. > > Daniel > > > -----Urspr?ngliche Nachricht----- > > Von: "Mark Schreiber" > > Gesendet: 29.08.07 16:36:38 > > An: "daniel.rohrbach at web.de" > > CC: biojava-l at lists.open-bio.org > > Betreff: Re: [Biojava-l] problems with the profilehmm demo > > > > > > Just looked at the CVS on line. You are very likely correct. > > > > There used to be a listener for changes in the Alphabet but this was > > mistakenly removed as it was thought to be redundant. A diff view is > > here ( > http://code.open-bio.org/cgi/viewcvs.cgi/biojava-live/src/org/biojava/bio/symbol/LinearAlphabetIndex.java.diff?r1=1.12&r2=1.13&cvsroot=biojava > ) > > > > I will check it back in tomorrow unless some one beats me to it. A > > JUnit test is also required to make sure this works. > > > > - Mark > > > > On 8/29/07, daniel.rohrbach at web.de wrote: > > > Hi all, hi Mark > > > > > > thanks for the fast Answer. > > > > > > I looked at the code and perhaps solved the problem. > > > > > > During initialisation of the ProfileHMM ( bevore method connectModel() > is called ) the transWeights are set with SimpleDistributions sd. These sd > again are initialized with an empty Alphabet (no symbol). (*) > > > > > > These Distributions keeps an indexer Object which is used during the > training process where the exception occurs. > > > > > > because of (*) the number of indexed symbols is 0 ( > indexer.symbols.length == 0) and the > (FiniteAlphabet)indexer.alphaRef.get() has length 0 too. > > > (Indexer is of type LinearAlphabetIndex) > > > > > > When connectModel() is called the Alphabets ( which are the same as > indexer.alphaRef ) are filled with some symbols (EmissionState, DotState > ...) (**) BUT the indexer.symbols.length will not be changed (***). > > > > > > This causes the following exception: > > > In SimpleDistribution.Trainer.trainImpl is a method called > getWeights(). This will return a double list of length indexer.getAlphabet() > which is the same of indexer.alphaRef. Because of (**) this will have a > length n>0. So that the for loop in this piece of code runs from 0 to n. > Here the exception occurs. indexer.symbolForIndex(i) (0<=i error because of (***) indexer.symbols are empty. > > > > > > I think it must be changed the symbols of the indexer Object in the > connectModel() method too. But I'm not really sure because I didn't worked > with biojava so long. > > > > > > I'm sorry for my bad English but I hope that I could help a little. > > > Many greetings > > > Daniel > > > > > > > -----Urspr?ngliche Nachricht----- > > > > Von: "Mark Schreiber" > > > > Gesendet: 28.08.07 16:28:23 > > > > An: "Daniel Rohrbach" > > > > CC: biojava-l at lists.open-bio.org > > > > Betreff: Re: [Biojava-l] problems with the profilehmm demo > > > > > > > > > > > > > > Hi - > > > > > > > > This is a bug that has been submitted to bugzilla. Strangely it was > > > > not an issue in the pre-releases of biojava. I was kind of hoping > > > > someone else would fix it but I guess I will have to find time to > take > > > > a look. > > > > > > > > - Mark > > > > > > > > On 8/28/07, Daniel Rohrbach wrote: > > > > > Hi all, > > > > > > > > > > i'm trying to run the "How do I make a ProfileHMM" example but it > doesn't want to work. I copied the code to my program and when I start it I > get the following exceptions: > > > > > > > > > > Exception in thread "main" java.lang.IndexOutOfBoundsException: > Can't find symbol for index 0 > > > > > at > org.biojava.bio.symbol.LinearAlphabetIndex.symbolForIndex( > LinearAlphabetIndex.java:106) > > > > > at > org.biojava.bio.dist.SimpleDistribution$Trainer.trainImpl( > SimpleDistribution.java:332) > > > > > at org.biojava.bio.dist.SimpleDistribution$Trainer.train( > SimpleDistribution.java:306) > > > > > at > org.biojava.bio.dist.SimpleDistributionTrainerContext.train( > SimpleDistributionTrainerContext.java:126) > > > > > at biojavatests.HMMTest.main(HMMTest.java:71) > > > > > > > > > > The error occurs at mt.train(). It seems that there was no, wrong > or empty alphabet set for the trainer that shall be used. > > > > > > > > > > here the link to the examplepage: > http://biojava.org/wiki/BioJava:CookBook:DP:HMM > > > > > any help on this topic? > > > > > > > > > > Thanks in advance > > > > > > __________________________________________________________________________ > > > > > Erweitern Sie FreeMail zu einem noch leistungsst?rkeren > E-Mail-Postfach! > > > > > Mehr Infos unter http://produkte.web.de/club/?mc=021131 > > > > > > > > > > > > > > > _______________________________________________ > > > > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > > > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > > > > > > > > > > > > > _______________________________________________________________________ > > > Jetzt neu! Sch?tzen Sie Ihren PC mit McAfee und WEB.DE. 3 Monate > > > kostenlos testen. > http://www.pc-sicherheit.web.de/startseite/?mc=022220 > > > > > > > > > _______________________________________________ > > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > > _____________________________________________________________________ > Der WEB.DE SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! > http://smartsurfer.web.de/?mc=100071&distributionid=000000000066 > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From raphael.bauer at charite.de Thu Aug 30 15:58:52 2007 From: raphael.bauer at charite.de (Raphael A. Bauer) Date: Thu, 30 Aug 2007 15:58:52 -0400 Subject: [Biojava-l] Maven Project In-Reply-To: <46D674E5.9050701@ebi.ac.uk> References: <46D674E5.9050701@ebi.ac.uk> Message-ID: <46D7217C.2040005@charite.de> Richard Holland wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > There is no Maven repository for the official BioJava. Some years ago a > BioJava2 project was branched which did use Maven. However, this branch ... I am currently using biojava.jar manually imported into my m2 repository. And then I am using this as dependency in my pom.xml. Works pretty nice for all functions I am using - if you are using external biojava functions you have to have them included as well I guess. Raphael From holland at ebi.ac.uk Fri Aug 31 05:42:23 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Fri, 31 Aug 2007 10:42:23 +0100 Subject: [Biojava-l] UK industry users of BioJava Message-ID: <46D7E27F.9080700@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello all. We would like to find out who is using BioJava in industry in the UK, for purposes of a funding proposal we are writing. The proposal requires us to include at least one industry developer as a collaborator. The definition of industry excludes universities and government-owned research establishments. Please could you let me know ASAP if you are such a person and would be willing to collaborate on major future BioJava development work. The best way to respond is simply to reply directly to this email. cheers, Richard -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFG1+J/4C5LeMEKA/QRAuesAJwMCXT98c4EjSgWrFsj32tNR9by2ACfTL5P hsx3ZZtqKi0CCZs3Oj1RtGo= =XtQv -----END PGP SIGNATURE----- From andrew.craig at cambridgebluegnome.com Fri Aug 31 12:18:51 2007 From: andrew.craig at cambridgebluegnome.com (Andrew Craig) Date: Fri, 31 Aug 2007 17:18:51 +0100 Subject: [Biojava-l] BioJava 1.5 in Matlab and DNATools Class Message-ID: <002501c7ebea$9eec9d50$1001a8c0@FRANKLIN> Dear List, I am trying to use BioJava-1.5 from Matlab (7.2), in order to retrieve the raw chromatogram data from some .AB1 files. I have added biojava-1.5.jar to the Matlab java class path. I then import the following classes. import java.io.*; import java.util.*; import org.biojava.bio.*; import org.biojava.bio.chromatogram.*; import org.biojava.bio.program.abi.*; import org.biojava.bio.seq.*; import org.biojava.bio.seq.impl.*; import org.biojava.bio.seq.io.*; import org.biojava.bio.symbol.*; Next I read the raw chromatogram file with myTrace = ChromatogramFactory.create(myFile); Then I try to retrieve the raw data for the a base using raw_a = myTrace.getTrace(DNATools.a()); This works fine for a, t and g bases. My problem is when I call DNATools.c() it returns the following error ??? No method 'c' with matching signature found for class 'org.biojava.bio.seq.DNATools' Can anyone diagnose what is wrong and why only the .c method is giving an error? I can get around this by using DNATools.complement(G) but I would prefer to understand what is going on and get things working properly. Best regards, Andrew Craig ____________________________________________________________________ This email is confidential and privileged.If you are not the intended recipient pleaseaccept our apologies; please do not disclose, copy, or distribute information in this email nor take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Please inform us that this message has gone astray before deleting it. Thank you for your co-operation. Andrew Craig andrew.craig at cambridgebluegnome.com BlueGnome Limited http://www.cambridgebluegnome.com Breaks House Mill Court Great Shelford Cambridge CB2 5LD Tel: 01223 844441 Fax: 01223 844445 US: 1 800 418 9656 ____________________________________________________________________ From Joseph.Bedell at sial.com Fri Aug 31 17:01:08 2007 From: Joseph.Bedell at sial.com (Joseph Bedell) Date: Fri, 31 Aug 2007 16:01:08 -0500 Subject: [Biojava-l] Joseph Bedell is out of the office. Message-ID: I will be out of the office starting 08/30/2007 and will not return until 09/05/2007. I have all day meetings on 8/30, 8/31, and 9/4. I will be checking email intermittently. From markjschreiber at gmail.com Fri Aug 31 21:46:41 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Sat, 1 Sep 2007 09:46:41 +0800 Subject: [Biojava-l] BioJava 1.5 in Matlab and DNATools Class In-Reply-To: <002501c7ebea$9eec9d50$1001a8c0@FRANKLIN> References: <002501c7ebea$9eec9d50$1001a8c0@FRANKLIN> Message-ID: <93b45ca50708311846g2257389fqefdd0198481b88b6@mail.gmail.com> Hi - I know that some parts of matlab use biojava. Probably version 1.4 or 1.3. It may be that it is using this jar file instead of the one you want it not. I'm not a matlab expert so I don't know how you can resolve this. - Mark On 9/1/07, Andrew Craig wrote: > Dear List, > > I am trying to use BioJava-1.5 from Matlab (7.2), in order to retrieve the > raw chromatogram data from some .AB1 files. > > I have added biojava-1.5.jar to the Matlab java class path. I then import > the following classes. > import java.io.*; > import java.util.*; > import org.biojava.bio.*; > import org.biojava.bio.chromatogram.*; > import org.biojava.bio.program.abi.*; > import org.biojava.bio.seq.*; > import org.biojava.bio.seq.impl.*; > import org.biojava.bio.seq.io.*; > import org.biojava.bio.symbol.*; > > Next I read the raw chromatogram file with > > myTrace = ChromatogramFactory.create(myFile); > > Then I try to retrieve the raw data for the a base using > > raw_a = myTrace.getTrace(DNATools.a()); > > This works fine for a, t and g bases. My problem is when I call DNATools.c() > it returns the following error > > ??? No method 'c' with matching signature found for class > 'org.biojava.bio.seq.DNATools' > > Can anyone diagnose what is wrong and why only the .c method is giving an > error? I can get around this by using DNATools.complement(G) but I would > prefer to understand what is going on and get things working properly. > > Best regards, > > Andrew Craig > > ____________________________________________________________________ > > This email is confidential and privileged.If you are not the > intended recipient pleaseaccept our apologies; please do not > disclose, copy, or distribute information in this email nor take any > action in reliance on its contents: to do so is strictly prohibited > and may be unlawful. > > Please inform us that this message has gone astray before deleting > it. > > Thank you for your co-operation. > > Andrew Craig andrew.craig at cambridgebluegnome.com > BlueGnome Limited http://www.cambridgebluegnome.com > > Breaks House > Mill Court > Great Shelford > Cambridge > CB2 5LD > > Tel: 01223 844441 Fax: 01223 844445 > US: 1 800 418 9656 > ____________________________________________________________________ > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l >