From frederik at genohm.com Tue Aug 4 11:12:11 2009 From: frederik at genohm.com (Frederik Decouttere) Date: Tue, 04 Aug 2009 17:12:11 +0200 Subject: [Biojava-l] SimpleGappedSequence using RichSequence objects In-Reply-To: Message-ID: Hi While migrating to biojavax (and biojava 1.7 in general), I don?t see a replacement for SimpleGappedSequence that is using RichSequence objects instead of the ?old? Sequence objects. Am I missing something, or isn?t there a SimpleGappedSequence yet based on RichSequence ? kr Frederik Decouttere From holland at eaglegenomics.com Tue Aug 4 11:30:47 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Tue, 4 Aug 2009 16:30:47 +0100 Subject: [Biojava-l] SimpleGappedSequence using RichSequence objects In-Reply-To: References: Message-ID: <83834A0F-A971-4999-9A0E-F97BC18BA687@eaglegenomics.com> Nope, you're not missing anything - it hasn't been implemented. cheers, Richard On 4 Aug 2009, at 16:12, Frederik Decouttere wrote: > Hi > > While migrating to biojavax (and biojava 1.7 in general), I don?t > see a > replacement for SimpleGappedSequence that is using RichSequence > objects > instead of the ?old? Sequence objects. > Am I missing something, or isn?t there a SimpleGappedSequence yet > based on > RichSequence ? > > kr > Frederik Decouttere > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From andreas.draeger at uni-tuebingen.de Tue Aug 4 13:05:34 2009 From: andreas.draeger at uni-tuebingen.de (Andreas Draeger) Date: Tue, 04 Aug 2009 19:05:34 +0200 Subject: [Biojava-l] Sequence logo Message-ID: <4A786A5E.7040202@uni-tuebingen.de> Dear all, Just a question: I assume you all know this visualization of position frequency matrices, in which A, T, G, and C appear according to their frequency within the matrix with different sizes and all letters are colored differently (green, red, blue, yellow). Is there a class in BioJava that produces this kind of visualization? Cheers Andreas -- Dipl.-Bioinform. Andreas Dr?ger Eberhard Karls University T?bingen Center for Bioinformatics (ZBIT) Sand 1 72076 T?bingen Germany Phone: +49-7071-29-70436 Fax: +49-7071-29-5091 From mark.schreiber at novartis.com Wed Aug 5 01:35:23 2009 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Wed, 5 Aug 2009 13:35:23 +0800 Subject: [Biojava-l] Sequence logo In-Reply-To: <4A786A5E.7040202@uni-tuebingen.de> Message-ID: Hi - There is some code for a Swing component in one of the GUI packages. It is useful for making a single position but not an entire logo. In the past I have used the code that does the drawing and modified it to work on a Distribution[]. The code shouldn't really be in a Swing component it should be in a class that generates drawing instructions for a Graphics2D object. This is a lot more flexible because you can then draw into a Frame or Canvas if you want a GUI, or a BufferedImage if you want a graphics file, or a Batik Graphics2D object if you want to make an SVG file. Also the code in BioJava doesn't let you modify the g2 object at all so you can't turn on anti-aliasing (highly recommended). The idea of separating BioJava's graphics and GUI capabilities has been on the cards for a while. If you do this for the Sequence Logo it would be great to feed it back to the group as an example of how it should be done. - Mark biojava-l-bounces at lists.open-bio.org wrote on 08/05/2009 01:05:34 AM: > Dear all, > > Just a question: I assume you all know this visualization of position > frequency matrices, in which A, T, G, and C appear according to their > frequency within the matrix with different sizes and all letters are > colored differently (green, red, blue, yellow). > > Is there a class in BioJava that produces this kind of visualization? > > Cheers > Andreas > > -- > Dipl.-Bioinform. Andreas Dr?ger > Eberhard Karls University T?bingen > Center for Bioinformatics (ZBIT) > Sand 1 > 72076 T?bingen > Germany > > Phone: +49-7071-29-70436 > Fax: +49-7071-29-5091 > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l _________________________ CONFIDENTIALITY NOTICE The information contained in this e-mail message is intended only for the exclusive use of the individual or entity named above and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivery of the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately by e-mail and delete the material from any computer. Thank you. From nathan.genome at gmail.com Wed Aug 5 06:38:28 2009 From: nathan.genome at gmail.com (nathan genome) Date: Wed, 5 Aug 2009 12:38:28 +0200 Subject: [Biojava-l] (no subject) Message-ID: hi i am working on genomic variations. i am interested to initially visualize mappings from clone-ends to reference sequence. i have data in the following tab. format : CAX100A01FOR1 1 748 scaffold_116 507411 508161CAX100A01REV1 1 702 scaffold_116 512322 511611 1st & 7th cols. represent clone-ends, the numbers are positions, 4th col. indicates the reference. How do i visualize this pair alignment in a window with biojava. thanks Natthan From nathan.genome at gmail.com Wed Aug 5 06:45:31 2009 From: nathan.genome at gmail.com (nathan genome) Date: Wed, 5 Aug 2009 12:45:31 +0200 Subject: [Biojava-l] visualization Message-ID: i am interested to initially visualize mappings from clone-ends to reference sequence. i have data in the following tab. format : CAX100A01FOR1 1 748 scaffold_116 507411 508161 CAX100A01REV1 1 702 scaffold_116 512322 511611 1st & 7th cols. represent clone-ends, the numbers are positions, 4th col. indicates the reference. idea is to visualize as a browser which is similar to gbrowse thanks Natthan From andreas.draeger at uni-tuebingen.de Wed Aug 5 09:18:29 2009 From: andreas.draeger at uni-tuebingen.de (Andreas Draeger) Date: Wed, 05 Aug 2009 15:18:29 +0200 Subject: [Biojava-l] Upper case symbols Message-ID: <4A7986A5.7000608@uni-tuebingen.de> Dear all, Thank you for this very quick answer regarding Sequence logos! The code works fine. However, would it also be possible to tell the DNATools class that upper case letters should be used instead of lower case "a", "c", "g", and "t"? I think it is more common to apply upper case symbols in sequence logos. Cheers Andreas -- Dipl.-Bioinform. Andreas Dr?ger Eberhard Karls University T?bingen Center for Bioinformatics (ZBIT) Sand 1 72076 T?bingen Germany Phone: +49-7071-29-70436 Fax: +49-7071-29-5091 From thien.nguyen at berkeley.edu Wed Aug 5 15:40:50 2009 From: thien.nguyen at berkeley.edu (Thien Nguyen) Date: Wed, 5 Aug 2009 12:40:50 -0700 (PDT) Subject: [Biojava-l] chromatogram question: get confident value of the called base Message-ID: <56495.136.152.170.253.1249501250.squirrel@calmail.berkeley.edu> Hello all, I'm new to BioJava. I start using Chromatogram package to read a number of .ab1 files and save some statistics. Reading the API, I don't see how to get some sort of quality/confidence metric for each location, but only the called base and the raw offset numbers. Here is what I know: . ChromatogramFactory to create Chromatogram object from a file .ChromatogramTools.getDNASequence to get the called bases, or TraceOffsetArray to get the raw offset array. Is there an available method that get the confidence of each called bases? Thank you Thien Nguyen From d.johnson at reading.ac.uk Thu Aug 6 13:03:24 2009 From: d.johnson at reading.ac.uk (David Johnson) Date: Thu, 6 Aug 2009 18:03:24 +0100 Subject: [Biojava-l] ParseException when using interleaved Nexus file Message-ID: Hi everyone, A quick question about the BioJava Nexus parser. I've been trying to use the Nexus file parser, simply by doing something like: NexusFileBuilder builder = new NexusFileBuilder(); NexusFileFormat.parseFile(builder, f); However, when parsing Nexus files that are interleaved, I get a ParseException. Is there a way to setup the parser provided by BioJava to handle interleaved Nexus files? Thanks, -David -- David Johnson School of Biological Sciences University of Reading From andreas.draeger at uni-tuebingen.de Thu Aug 6 13:47:35 2009 From: andreas.draeger at uni-tuebingen.de (=?ISO-8859-1?Q?Andreas_Dr=E4ger?=) Date: Thu, 06 Aug 2009 19:47:35 +0200 Subject: [Biojava-l] Upper case symbols In-Reply-To: <4A79F96C.5050909@u.washington.edu> References: <4A7986A5.7000608@uni-tuebingen.de> <4A79F96C.5050909@u.washington.edu> Message-ID: <4A7B1737.6010200@uni-tuebingen.de> Thank you, Eric! This XML file works greatly! Cheers Andreas From andreas at sdsc.edu Thu Aug 6 16:36:02 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 6 Aug 2009 13:36:02 -0700 Subject: [Biojava-l] blast parsing question In-Reply-To: <3DD69071F4A8490D9D1D7EEB172FEFC0@zillumina> References: <3DD69071F4A8490D9D1D7EEB172FEFC0@zillumina> Message-ID: <59a41c430908061336n1f71c6d6ocf064db05fdfb236@mail.gmail.com> Hi Bernd, not sure if you got a reply to your mail off-list. Did you manage to solve your problem in the meanwhile? Andreas On Wed, Jul 29, 2009 at 6:16 AM, Bernd Jagla wrote: > Hi, > > > > I am new to BioJava. I want to test what is going on here in order to > potentially integrate it with KNIME. > > My first project is parsing BLAST output for large files. The example in > the > codebook is very good and I had no problems integrating everything in > Eclipse and geting it to work. > > > > Now here is my problem: > > I am interested in parsing the summary table in the beginning of the > blast-output, and I haven't found a way to get at this information. > > > > I am blasting short sequences (20nt - 300nt) against genomic databases > (mouse/human/refseq/miRBase). I want to know if a given sequence (out of a > set of sequences) aligns to a specific genome with high identity. I want to > then separate the input source fasta file into a set that aligns to the > genome and one that doesn't (potentially another list of dubious sequences > where there is no clear answer). For this I only need the length of the > query sequence and score and the first few characters of the header line. > > At least that's the way I am currently doing it. I have set the blast > parameters to only give me the first alignment, but the first 50 or so in > the summary. > > > > Any help, comments are appreciated. > > > > Thanks, > > > > Bernd > > > > > > > > > > > > Bernd Jagla > Bioinformatician > > Institut Pasteur > Plate-forme puces a ADN > Genopole / Institut Pasteur > 28 rue du Docteur Roux > 75724 Paris Cedex 15 > France > > > bernd.jagla at pasteur.fr > > > tel: > > > < > http://www.plaxo.com/click_to_call?lang=en&src=jj_signature&To=%2B33+%280%2 > 9+140+61+35+13&Email=berndjagla at yahoo.com> > +33 (0) 140 61 35 13 > > > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From holland at eaglegenomics.com Fri Aug 7 04:57:38 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Fri, 7 Aug 2009 09:57:38 +0100 Subject: [Biojava-l] ParseException when using interleaved Nexus file In-Reply-To: References: Message-ID: <30109C99-0ADF-461D-AB8A-B9800C4111D1@eaglegenomics.com> Could you point me to an example of an interleaved file? And also the full stack trace of the exception that gets thrown? cheers, Richard On 6 Aug 2009, at 18:03, David Johnson wrote: > Hi everyone, > > A quick question about the BioJava Nexus parser. I've been trying to > use the Nexus file parser, simply by doing something like: > > NexusFileBuilder builder = new NexusFileBuilder(); > NexusFileFormat.parseFile(builder, f); > > However, when parsing Nexus files that are interleaved, I get a > ParseException. > > Is there a way to setup the parser provided by BioJava to handle > interleaved Nexus files? > > Thanks, > -David > -- > David Johnson > School of Biological Sciences > University of Reading > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From holland at eaglegenomics.com Fri Aug 7 05:57:37 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Fri, 7 Aug 2009 10:57:37 +0100 Subject: [Biojava-l] ParseException when using interleaved Nexus file In-Reply-To: References: <30109C99-0ADF-461D-AB8A-B9800C4111D1@eaglegenomics.com> Message-ID: Thanks David. One more quick question - is this the exact file that is throwing the exception? I haven't tested it yet - but if I could test against the real file that is throwing the problem, that would help me find out exactly what's going wrong. For what it's worth, the exception is normally thrown when more than one interleave=yes/no token is found in the header of the Data or Characters block, or when the interleave token appears in a line other than the Format line of the header. cheers, Richard On 7 Aug 2009, at 10:28, David Johnson wrote: > Hi Richard, > > Thanks for your mail. An example of an interleaved file can be found > here: > > http://www.molecularevolution.org/si/resources/fileformats/files/dna.nex > > where the link pointing to the example file is from > http://www.molecularevolution.org/si/resources/fileformats/ and under > the NEXUS section. > > The specific error message is: "org.biojava.bio.seq.io.ParseException: > Found unexpected token interleave=yes in CHARACTERS block" > > So it looks like the error is thrown reading the "interleave" > parameter in the top of the data block, and before reaching the actual > interleaved matrix data. Full stacktrace in attached .txt. > > Cheers, > -David > > 2009/8/7 Richard Holland : >> Could you point me to an example of an interleaved file? >> >> And also the full stack trace of the exception that gets thrown? >> >> cheers, >> Richard >> >> On 6 Aug 2009, at 18:03, David Johnson wrote: >> >>> Hi everyone, >>> >>> A quick question about the BioJava Nexus parser. I've been trying to >>> use the Nexus file parser, simply by doing something like: >>> >>> NexusFileBuilder builder = new NexusFileBuilder(); >>> NexusFileFormat.parseFile(builder, f); >>> >>> However, when parsing Nexus files that are interleaved, I get a >>> ParseException. >>> >>> Is there a way to setup the parser provided by BioJava to handle >>> interleaved Nexus files? >>> >>> Thanks, >>> -David >>> -- >>> David Johnson >>> School of Biological Sciences >>> University of Reading >>> _______________________________________________ >>> Biojava-l mailing list - Biojava-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >> >> -- >> Richard Holland, BSc MBCS >> Operations and Delivery Director, Eagle Genomics Ltd >> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com >> http://www.eaglegenomics.com/ >> >> > > > > -- > David Johnson > Post-doc Research Assistant > School of Biological Sciences > 506, Philip Lyle Research Building > University of Reading > Whiteknights > Reading, RG6 6BX > UK > > Tel: +44 (0) 118 378 4415 > email: d.johnson at reading.ac.uk > web: http://www.rdg.ac.uk/~sis07dj > -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From d.johnson at reading.ac.uk Fri Aug 7 06:10:46 2009 From: d.johnson at reading.ac.uk (David Johnson) Date: Fri, 7 Aug 2009 11:10:46 +0100 Subject: [Biojava-l] ParseException when using interleaved Nexus file In-Reply-To: References: <30109C99-0ADF-461D-AB8A-B9800C4111D1@eaglegenomics.com> Message-ID: Hi Richard, Actually the original exception was thrown in a different file that my supervisor tried uploading to a Web app I'm developing that uses the BioJava Nexus parser, but can't get hold of that particular file today. So the one I provided the link for was just another example of an interleaved Nexus file I Googled for when I got your first email this morning, as I figured they'd probably be the same formatting. But I remember it's definitely the same exception in both cases. I had a quick look in the example I provided today, and the interleave=yes token is definitely in the header of the data block, and is also definitely in the Format line. Oh, just FYI, I'm using the BioJava 1.7 binary distribution (http://www.biojava.org/download/bj17/bin/biojava.jar). Cheers, -David 2009/8/7 Richard Holland : > Thanks David. One more quick question - is this the exact file that is > throwing the exception? I haven't tested it yet - but if I could test > against the real file that is throwing the problem, that would help me find > out exactly what's going wrong. > > For what it's worth, the exception is normally thrown when more than one > interleave=yes/no token is found in the header of the Data or Characters > block, or when the interleave token appears in a line other than the Format > line of the header. > > cheers, > Richard > > On 7 Aug 2009, at 10:28, David Johnson wrote: > >> Hi Richard, >> >> Thanks for your mail. An example of an interleaved file can be found here: >> >> http://www.molecularevolution.org/si/resources/fileformats/files/dna.nex >> >> where the link pointing to the example file is from >> http://www.molecularevolution.org/si/resources/fileformats/ and under >> the NEXUS section. >> >> The specific error message is: "org.biojava.bio.seq.io.ParseException: >> Found unexpected token interleave=yes in CHARACTERS block" >> >> So it looks like the error is thrown reading the "interleave" >> parameter in the top of the data block, and before reaching the actual >> interleaved matrix data. Full stacktrace in attached .txt. >> >> Cheers, >> -David >> >> 2009/8/7 Richard Holland : >>> >>> Could you point me to an example of an interleaved file? >>> >>> And also the full stack trace of the exception that gets thrown? >>> >>> cheers, >>> Richard >>> >>> On 6 Aug 2009, at 18:03, David Johnson wrote: >>> >>>> Hi everyone, >>>> >>>> A quick question about the BioJava Nexus parser. I've been trying to >>>> use the Nexus file parser, simply by doing something like: >>>> >>>> ? ? ?NexusFileBuilder builder = new NexusFileBuilder(); >>>> ? ? ?NexusFileFormat.parseFile(builder, f); >>>> >>>> However, when parsing Nexus files that are interleaved, I get a >>>> ParseException. >>>> >>>> Is there a way to setup the parser provided by BioJava to handle >>>> interleaved Nexus files? >>>> >>>> Thanks, >>>> -David >>>> -- >>>> From vincent.rouilly03 at imperial.ac.uk Sat Aug 8 13:33:02 2009 From: vincent.rouilly03 at imperial.ac.uk (Rouilly, Vincent) Date: Sat, 8 Aug 2009 18:33:02 +0100 Subject: [Biojava-l] BioJava, Dazzle and Google App Engine (Java version) Message-ID: Hi, first of all, congratulations and thanks to all BioJava contributors for providing such a great library. Over the last few days, I have been trying to use BioJava on the Google App Engine (with its latest Java support). http://code.google.com/appengine/docs/java/gettingstarted/ Has anyone got experience with that ? I am especially interested in setting up a Dazzle DAS server on the google app engine (basic configuration). It would be a great way for people to easily share their data through DAS. However, whatever DAS request, I always get the exceptions: DataSourceException("Basic installation only covers flat namespace of data-sources"); Any suggestions ? many thanks, Vincent. From holland at eaglegenomics.com Sat Aug 8 17:15:43 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Sat, 8 Aug 2009 22:15:43 +0100 Subject: [Biojava-l] BioJava, Dazzle and Google App Engine (Java version) In-Reply-To: References: Message-ID: <0F80A206-C826-492F-9BE9-2D0F2D7934C6@eaglegenomics.com> Hello. Dazzle/DAS is not BioJava, but I happen to know that Jon Warren at the Sanger Centre is an expert in all things DAS, so he might be able to help you. I've copied him on this. cheers, Richard On 8 Aug 2009, at 18:33, Rouilly, Vincent wrote: > Hi, > > first of all, congratulations and thanks to all BioJava contributors > for providing such a great library. > > Over the last few days, I have been trying to use BioJava on the > Google App Engine (with its latest Java support). > http://code.google.com/appengine/docs/java/gettingstarted/ > > Has anyone got experience with that ? > > I am especially interested in setting up a Dazzle DAS server on the > google app engine (basic configuration). > It would be a great way for people to easily share their data > through DAS. > > However, whatever DAS request, I always get the exceptions: > DataSourceException("Basic installation only covers flat namespace > of data-sources"); > > Any suggestions ? > > many thanks, > > Vincent. > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From andreas at sdsc.edu Sat Aug 8 17:59:14 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Sat, 8 Aug 2009 14:59:14 -0700 Subject: [Biojava-l] Fwd: BioJava, Dazzle and Google App Engine (Java version) In-Reply-To: <59a41c430908081350m1c55ce2ag1f7b51a6673756fe@mail.gmail.com> References: <59a41c430908081350m1c55ce2ag1f7b51a6673756fe@mail.gmail.com> Message-ID: <59a41c430908081459j10589fa6y2fd1f3249130bc99@mail.gmail.com> Hi Vincent, did you try following the instructions at http://biojava.org/wiki/Dazzle ? I have never tried to run it using the google app engine, but it works fine for me using Eclipse or standalone... Also have a look at http://biojava.org/wiki/Dazzle:deployment Hope that helps, Andreas On Sat, Aug 8, 2009 at 10:33 AM, Rouilly, Vincent < vincent.rouilly03 at imperial.ac.uk> wrote: > Hi, > > first of all, congratulations and thanks to all BioJava contributors for > providing such a great library. > > Over the last few days, I have been trying to use BioJava on the Google App > Engine (with its latest Java support). > http://code.google.com/appengine/docs/java/gettingstarted/ > > Has anyone got experience with that ? > > I am especially interested in setting up a Dazzle DAS server on the google > app engine (basic configuration). > It would be a great way for people to easily share their data through DAS. > > However, whatever DAS request, I always get the exceptions: > DataSourceException("Basic installation only covers flat namespace of > data-sources"); > > Any suggestions ? > > many thanks, > > Vincent. > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From rabee.a.aa at m.titech.ac.jp Sun Aug 9 00:43:05 2009 From: rabee.a.aa at m.titech.ac.jp (rabee.a.aa at m.titech.ac.jp) Date: Sun, 9 Aug 2009 13:43:05 +0900 Subject: [Biojava-l] BioJava, Bioperl and R Message-ID: <1249792985464413.9007@mail3.nap.gsic.titech.ac.jp> Dear All, I'm quite new to Bioinfromatics field, i want to ask which is best language to use in analysis of next generation sequencing data is it Biojava, Bioperl or R (Bioconductor) Best Regards, Rabe From vincent.rouilly03 at imperial.ac.uk Sun Aug 9 06:50:33 2009 From: vincent.rouilly03 at imperial.ac.uk (Rouilly, Vincent) Date: Sun, 9 Aug 2009 11:50:33 +0100 Subject: [Biojava-l] BioJava, Dazzle and Google App Engine (Java version) In-Reply-To: <59a41c430908081350m1c55ce2ag1f7b51a6673756fe@mail.gmail.com> References: , <59a41c430908081350m1c55ce2ag1f7b51a6673756fe@mail.gmail.com> Message-ID: Hi, thanks for your quick replies. Sorry, I forgot to mention that I am also using the stand-alone Google Engine for now, with the Eclipse plug-in. And, my development platform is a Mac OS 10.4.11, with JRE 1.6 from Soylatte, and Eclipse v3.4.2. I have read through the dazzle documentation, but I still can't get it to work within the Google App Engine / Eclipse environment. I am not very familiar with Eclipse, so it is very likely that I am not doing things right. Here is the process I have followed to give Dazzle a try to on the Google Engine. But remember, this process doesn't work for me. I hope it makes sense, and that someone can point me to the right direction. many thanks, Vincent. 1- Download 'dazzle' in /tmp/ using subversion (http://biojava.org/wiki/Dazzle): svn checkout http://www.derkholm.net/svn/repos/dazzle/trunk /tmp/dazzle 2- Create new Google App Engine project from Eclipse (after Google Engine plugin installation): Project name: dazzle Package: org.biojava.servlets.dazzle Uncheck 'Use Google Web Toolkit' Finish 3- Import 'dazzle' Jar files into 'dazzle google engine' project import from /tmp/dazzle/jars: bioJava.jar, bytecode.jar, dasmi-model.jar, servlet-api-2.3.jar In Eclipse, 'dazzle' project Properties -> Java Build Path -> Add External Jars 4- Import 'dazzle' src files into 'dazzle google engine' project drag-and-drop /tmp/dazzle/src/org folder into 'Eclipse:/ dazzle/src' folder 5- Import 'dazzle' ressources folder into 'dazzle google engine' project drag-and-drop /tmp/dazzle/resources folder into 'Eclipse:/dazzle' folder 5- Import WEB-INF files into 'dazzle google engine' project drag-and-drop files from /tmp/dazzle/dazzle-webapp into Eclipse:/dazzle/war/. 6- Update web.xml file in Eclipse:/dazzle/war/WEB-INF/ DazzleServerMain org.biojava.servlets.dazzle.DazzleServlet DazzleServerMain /* welcome-file-list: dazzle-welcome.html 6- Run application as web Application in Eclipse check with web browser: http://localhost:8080/das/dsn ________________________________________ From: andreas.prlic at gmail.com [andreas.prlic at gmail.com] On Behalf Of Andreas Prlic [andreas at sdsc.edu] Sent: Saturday, August 08, 2009 9:50 PM To: Rouilly, Vincent Subject: Re: [Biojava-l] BioJava, Dazzle and Google App Engine (Java version) Hi Vincent, did you try following the instructions at http://biojava.org/wiki/Dazzle ? I have never tried to run it using the google app engine, but it works fine for me using Eclipse or standalone... Also have a look at http://biojava.org/wiki/Dazzle:deployment Hope that helps, Andreas On Sat, Aug 8, 2009 at 10:33 AM, Rouilly, Vincent > wrote: Hi, first of all, congratulations and thanks to all BioJava contributors for providing such a great library. Over the last few days, I have been trying to use BioJava on the Google App Engine (with its latest Java support). http://code.google.com/appengine/docs/java/gettingstarted/ Has anyone got experience with that ? I am especially interested in setting up a Dazzle DAS server on the google app engine (basic configuration). It would be a great way for people to easily share their data through DAS. However, whatever DAS request, I always get the exceptions: DataSourceException("Basic installation only covers flat namespace of data-sources"); Any suggestions ? many thanks, Vincent. _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From vincent.rouilly03 at imperial.ac.uk Tue Aug 11 05:16:41 2009 From: vincent.rouilly03 at imperial.ac.uk (Rouilly, Vincent) Date: Tue, 11 Aug 2009 10:16:41 +0100 Subject: [Biojava-l] BioJava, Dazzle and Google App Engine (Java version) In-Reply-To: References: , <59a41c430908081350m1c55ce2ag1f7b51a6673756fe@mail.gmail.com> , Message-ID: Hi, thanks a lot for those who provided me advices. I finally got 'dazzle' to work on the Google App Engine. In short, it means that you can get a free/scalable DAS server on the Google Cloud. check: http://dazzle-das.appspot.com/das/dsn http://dazzle-das.appspot.com/das/test/entry_points If you are interested, you can find below the process I followed. My next target is to get 'dazzle' to fetch annotation directly from the Google Data Store provided in the Google App Engine (as opposed to from a flat file). best, Vincent. ---------------------- Prerequisites: - Java 1.5 - Eclipse 3.4.1 + Google App Engine plug-in from http://code.google.com/appengine/docs/java/tools/eclipse.html - Dazzle code into /tmp/dazzle from: svn checkout http://www.derkholm.net/svn/repos/dazzle/trunk /tmp/dazzle 1- Create new Google App Engine project from Eclipse (after Google Engine plug-in installation): Project name: dazzle Package: org.biojava.servlets.dazzle Uncheck 'Use Google Web Toolkit' Finish 2- Import 'dazzle' Jar files into 'dazzle google engine' project In Eclipse, 'dazzle' project Properties -> Java Build Path -> Add External Jars Import from /tmp/dazzle/jars: bioJava.jar, bytecode.jar, dasmi-model.jar, servlet-api-2.3.jar 3- Import 'dazzle' ressources folder into 'dazzle google engine' project drag-and-drop /tmp/dazzle/resources folder into 'Eclipse:/dazzle' folder 4- Import 'dazzle' src files into 'dazzle google engine' project drag-and-drop /tmp/dazzle/src/org folder into 'Eclipse:/ dazzle/src' folder Comment: you should have 3 errors due to the use of Context in 'MysqlFeatureCache'. For now, I just commented the 2 lines involved. 5- Import /tmp/dazzle/dazzle-webapp files into 'dazzle google engine' project drag-and-drop files from /tmp/dazzle/dazzle-webapp into Eclipse:/dazzle/war/. (do not select WEB-INF folder) 6- Import Jars to WEB-INF/lib drag and drop jar files from /tmp/dazzle/jars into 'dazzle google engine' Eclipse:/dazzle/war/WEB-INF/lib biojava.jar, bytecode.jar, dasmi-model.jar, servelt-api-2.3.jar, dazzle.jar 6- Update web.xml file in Eclipse:/dazzle/war/WEB-INF/ [....] Dazzle org.biojava.servlets.dazzle.DazzleServlet Dazzle /das/* das_welcome.html [...] 6- Run application in Eclipse as web Application (standalone test) check with your web browser: http://localhost:8080/das/dsn 7- If it works, you can create a Google App Engine Application ID and deploy your dazzle server on the cloud. http://code.google.com/appengine/docs/java/tools/uploadinganapp.html ________________________________________ From: Jonathan Warren [jw12 at sanger.ac.uk] Sent: Monday, August 10, 2009 5:28 PM To: Rouilly, Vincent Cc: Andreas Prlic; Richard Holland Subject: Re: [Biojava-l] BioJava, Dazzle and Google App Engine (Java version) I had a look at this and it seems the container works differently from tomcat and resin. I think you may have to change the way dazzle gets it's datasource information? The problem is that the google servlet adds dazzle to this nameComponents list whereas tomcat and resin don't when reading the xml config: public Set getDataSourceIDs(List nameComponents, HttpServletRequest req) throws DataSourceException { System.err.println("Address: " + req.getRemoteAddr()); System.err.println("Host: " + req.getRemoteHost()); if (nameComponents.size() != 0) { System.out.println(nameComponents.toString()); throw new DataSourceException("Basic installation only covers flat namespace of data-sources"); } I got some requests to work by adding /dazzle/* in the web.xml like this: DazzleServerMain /dazzle/* however some requests then work and others don't. Maybe the other guys have some ideas, but I couldn't see a particular reason or quick hack to overcome the difference. On 9 Aug 2009, at 11:50, Rouilly, Vincent wrote: Hi, thanks for your quick replies. Sorry, I forgot to mention that I am also using the stand-alone Google Engine for now, with the Eclipse plug-in. And, my development platform is a Mac OS 10.4.11, with JRE 1.6 from Soylatte, and Eclipse v3.4.2. I have read through the dazzle documentation, but I still can't get it to work within the Google App Engine / Eclipse environment. I am not very familiar with Eclipse, so it is very likely that I am not doing things right. Here is the process I have followed to give Dazzle a try to on the Google Engine. But remember, this process doesn't work for me. I hope it makes sense, and that someone can point me to the right direction. many thanks, Vincent. 1- Download 'dazzle' in /tmp/ using subversion (http://biojava.org/wiki/Dazzle): svn checkout http://www.derkholm.net/svn/repos/dazzle/trunk /tmp/dazzle 2- Create new Google App Engine project from Eclipse (after Google Engine plugin installation): Project name: dazzle Package: org.biojava.servlets.dazzle Uncheck 'Use Google Web Toolkit' Finish 3- Import 'dazzle' Jar files into 'dazzle google engine' project import from /tmp/dazzle/jars: bioJava.jar, bytecode.jar, dasmi-model.jar, servlet-api-2.3.jar In Eclipse, 'dazzle' project Properties -> Java Build Path -> Add External Jars 4- Import 'dazzle' src files into 'dazzle google engine' project drag-and-drop /tmp/dazzle/src/org folder into 'Eclipse:/ dazzle/src' folder 5- Import 'dazzle' ressources folder into 'dazzle google engine' project drag-and-drop /tmp/dazzle/resources folder into 'Eclipse:/dazzle' folder 5- Import WEB-INF files into 'dazzle google engine' project drag-and-drop files from /tmp/dazzle/dazzle-webapp into Eclipse:/dazzle/war/. 6- Update web.xml file in Eclipse:/dazzle/war/WEB-INF/ DazzleServerMain org.biojava.servlets.dazzle.DazzleServlet DazzleServerMain /* welcome-file-list: dazzle-welcome.html 6- Run application as web Application in Eclipse check with web browser: http://localhost:8080/das/dsn ________________________________________ From: andreas.prlic at gmail.com [andreas.prlic at gmail.com] On Behalf Of Andreas Prlic [andreas at sdsc.edu] Sent: Saturday, August 08, 2009 9:50 PM To: Rouilly, Vincent Subject: Re: [Biojava-l] BioJava, Dazzle and Google App Engine (Java version) Hi Vincent, did you try following the instructions at http://biojava.org/wiki/Dazzle ? I have never tried to run it using the google app engine, but it works fine for me using Eclipse or standalone... Also have a look at http://biojava.org/wiki/Dazzle:deployment Hope that helps, Andreas On Sat, Aug 8, 2009 at 10:33 AM, Rouilly, Vincent > wrote: Hi, first of all, congratulations and thanks to all BioJava contributors for providing such a great library. Over the last few days, I have been trying to use BioJava on the Google App Engine (with its latest Java support). http://code.google.com/appengine/docs/java/gettingstarted/ Has anyone got experience with that ? I am especially interested in setting up a Dazzle DAS server on the google app engine (basic configuration). It would be a great way for people to easily share their data through DAS. However, whatever DAS request, I always get the exceptions: DataSourceException("Basic installation only covers flat namespace of data-sources"); Any suggestions ? many thanks, Vincent. _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l Jonathan Warren Senior Developer and DAS coordinator jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE. From holland at eaglegenomics.com Tue Aug 11 05:17:03 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Tue, 11 Aug 2009 10:17:03 +0100 Subject: [Biojava-l] ParseException when using interleaved Nexus file In-Reply-To: References: <30109C99-0ADF-461D-AB8A-B9800C4111D1@eaglegenomics.com> Message-ID: <32FD8C34-2F30-4159-A9FB-D809784B7ED0@eaglegenomics.com> I've found the problem - "interleave=yes" is not valid according to the official NEXUS format spec which the parser was written against. (Maddison et al., 1997) Interleaved file are supposed to only include the word "interleave" - it takes no parameters. Non-interleaved files shouldn't mention it at all. I've modified the parser to tolerate this but I'd be interested to know where the invalid token came from - was it added manually, or by an existing piece of publically available software? The modification has been made in the trunk of the biojava-live subversion repository. cheers, Richard On 7 Aug 2009, at 11:10, David Johnson wrote: > Hi Richard, > > Actually the original exception was thrown in a different file that my > supervisor tried uploading to a Web app I'm developing that uses the > BioJava Nexus parser, but can't get hold of that particular file > today. So the one I provided the link for was just another example of > an interleaved Nexus file I Googled for when I got your first email > this morning, as I figured they'd probably be the same formatting. But > I remember it's definitely the same exception in both cases. > > I had a quick look in the example I provided today, and the > interleave=yes token is definitely in the header of the data block, > and is also definitely in the Format line. > > Oh, just FYI, I'm using the BioJava 1.7 binary distribution > (http://www.biojava.org/download/bj17/bin/biojava.jar). > > Cheers, > -David > > 2009/8/7 Richard Holland : >> Thanks David. One more quick question - is this the exact file that >> is >> throwing the exception? I haven't tested it yet - but if I could test >> against the real file that is throwing the problem, that would help >> me find >> out exactly what's going wrong. >> >> For what it's worth, the exception is normally thrown when more >> than one >> interleave=yes/no token is found in the header of the Data or >> Characters >> block, or when the interleave token appears in a line other than >> the Format >> line of the header. >> >> cheers, >> Richard >> >> On 7 Aug 2009, at 10:28, David Johnson wrote: >> >>> Hi Richard, >>> >>> Thanks for your mail. An example of an interleaved file can be >>> found here: >>> >>> http://www.molecularevolution.org/si/resources/fileformats/files/dna.nex >>> >>> where the link pointing to the example file is from >>> http://www.molecularevolution.org/si/resources/fileformats/ and >>> under >>> the NEXUS section. >>> >>> The specific error message is: >>> "org.biojava.bio.seq.io.ParseException: >>> Found unexpected token interleave=yes in CHARACTERS block" >>> >>> So it looks like the error is thrown reading the "interleave" >>> parameter in the top of the data block, and before reaching the >>> actual >>> interleaved matrix data. Full stacktrace in attached .txt. >>> >>> Cheers, >>> -David >>> >>> 2009/8/7 Richard Holland : >>>> >>>> Could you point me to an example of an interleaved file? >>>> >>>> And also the full stack trace of the exception that gets thrown? >>>> >>>> cheers, >>>> Richard >>>> >>>> On 6 Aug 2009, at 18:03, David Johnson wrote: >>>> >>>>> Hi everyone, >>>>> >>>>> A quick question about the BioJava Nexus parser. I've been >>>>> trying to >>>>> use the Nexus file parser, simply by doing something like: >>>>> >>>>> NexusFileBuilder builder = new NexusFileBuilder(); >>>>> NexusFileFormat.parseFile(builder, f); >>>>> >>>>> However, when parsing Nexus files that are interleaved, I get a >>>>> ParseException. >>>>> >>>>> Is there a way to setup the parser provided by BioJava to handle >>>>> interleaved Nexus files? >>>>> >>>>> Thanks, >>>>> -David >>>>> -- >>>>> -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From d.johnson at reading.ac.uk Tue Aug 11 06:12:18 2009 From: d.johnson at reading.ac.uk (David Johnson) Date: Tue, 11 Aug 2009 11:12:18 +0100 Subject: [Biojava-l] ParseException when using interleaved Nexus file In-Reply-To: <32FD8C34-2F30-4159-A9FB-D809784B7ED0@eaglegenomics.com> References: <30109C99-0ADF-461D-AB8A-B9800C4111D1@eaglegenomics.com> <32FD8C34-2F30-4159-A9FB-D809784B7ED0@eaglegenomics.com> Message-ID: Hi Richard, OK that's good to know... I suppose that's the problem with specifications - people don't always follow them! But I get the impression either some people think that using interleave=yes/no is standard practice, or it could be being generated by some other phylo software (e.g. maybe PAUP or some other tools). I had a talk with my supervisor and he actually can't find the specific programs that have been putting that in, but looking at a range of his Nexus files, there's quite a few that seem to use put in the yes/no bits, some files he received from other researchers. Are the modifications available in the latest automated build (on CruiseControl)? Cheers, -David 2009/8/11 Richard Holland > I've found the problem - "interleave=yes" is not valid according to the > official NEXUS format spec which the parser was written against. (Maddison > et al., 1997) > > Interleaved file are supposed to only include the word "interleave" - it > takes no parameters. Non-interleaved files shouldn't mention it at all. > > I've modified the parser to tolerate this but I'd be interested to know > where the invalid token came from - was it added manually, or by an existing > piece of publically available software? > > The modification has been made in the trunk of the biojava-live subversion > repository. > > cheers, > Richard > > > From holland at eaglegenomics.com Tue Aug 11 06:50:50 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Tue, 11 Aug 2009 11:50:50 +0100 Subject: [Biojava-l] ParseException when using interleaved Nexus file In-Reply-To: References: <30109C99-0ADF-461D-AB8A-B9800C4111D1@eaglegenomics.com> <32FD8C34-2F30-4159-A9FB-D809784B7ED0@eaglegenomics.com> Message-ID: It should already be on CruiseControl. Standards in bioinformatics are a pain - people write them to describe the format of files their software outputs, then the very same people then produce files that break those standards without any additional documentation or explanation. (Genbank are one of the biggest offenders!) It makes it very hard to write parsers, because if you stick to the official spec there will always be files that don't work yet people insist are still valid, yet without prior documented evidence of invalid files that are considered to be valid, it is impossible to write a parser to cater for them. :) cheers, Richard On 11 Aug 2009, at 11:12, David Johnson wrote: > Hi Richard, > > OK that's good to know... I suppose that's the problem with > specifications - people don't always follow them! > > But I get the impression either some people think that using > interleave=yes/no is standard practice, or it could be being > generated by some other phylo software (e.g. maybe PAUP or some > other tools). > > I had a talk with my supervisor and he actually can't find the > specific programs that have been putting that in, but looking at a > range of his Nexus files, there's quite a few that seem to use put > in the yes/no bits, some files he received from other researchers. > > Are the modifications available in the latest automated build (on > CruiseControl)? > > Cheers, > -David > > 2009/8/11 Richard Holland > I've found the problem - "interleave=yes" is not valid according to > the official NEXUS format spec which the parser was written against. > (Maddison et al., 1997) > > Interleaved file are supposed to only include the word "interleave" > - it takes no parameters. Non-interleaved files shouldn't mention it > at all. > > I've modified the parser to tolerate this but I'd be interested to > know where the invalid token came from - was it added manually, or > by an existing piece of publically available software? > > The modification has been made in the trunk of the biojava-live > subversion repository. > > cheers, > Richard > > -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From andreas at sdsc.edu Tue Aug 11 17:04:11 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 11 Aug 2009 14:04:11 -0700 Subject: [Biojava-l] BioJava, Dazzle and Google App Engine (Java version) In-Reply-To: References: <59a41c430908081350m1c55ce2ag1f7b51a6673756fe@mail.gmail.com> Message-ID: <59a41c430908111404o4bbabe9cw3a263fad6a9ee58a@mail.gmail.com> Hi Vincent, interesting approach... Want to add your notes to the wiki pages as well? Thanks, Andreas On Tue, Aug 11, 2009 at 2:16 AM, Rouilly, Vincent < vincent.rouilly03 at imperial.ac.uk> wrote: > Hi, > > thanks a lot for those who provided me advices. > I finally got 'dazzle' to work on the Google App Engine. > > In short, it means that you can get a free/scalable DAS server on the > Google Cloud. > > check: > http://dazzle-das.appspot.com/das/dsn > http://dazzle-das.appspot.com/das/test/entry_points > > If you are interested, you can find below the process I followed. > My next target is to get 'dazzle' to fetch annotation directly from the > Google Data Store provided in the Google App Engine (as opposed to from a > flat file). > > best, > > Vincent. > ---------------------- > > Prerequisites: > - Java 1.5 > - Eclipse 3.4.1 + Google App Engine plug-in from > http://code.google.com/appengine/docs/java/tools/eclipse.html > - Dazzle code into /tmp/dazzle from: svn checkout > http://www.derkholm.net/svn/repos/dazzle/trunk /tmp/dazzle > > > 1- Create new Google App Engine project from Eclipse (after Google Engine > plug-in installation): > Project name: dazzle > Package: org.biojava.servlets.dazzle > Uncheck 'Use Google Web Toolkit' > Finish > > 2- Import 'dazzle' Jar files into 'dazzle google engine' project > In Eclipse, 'dazzle' project Properties -> Java Build Path -> Add > External Jars > Import from /tmp/dazzle/jars: bioJava.jar, bytecode.jar, > dasmi-model.jar, servlet-api-2.3.jar > > 3- Import 'dazzle' ressources folder into 'dazzle google engine' project > drag-and-drop /tmp/dazzle/resources folder into 'Eclipse:/dazzle' > folder > > 4- Import 'dazzle' src files into 'dazzle google engine' project > drag-and-drop /tmp/dazzle/src/org folder into 'Eclipse:/ dazzle/src' > folder > Comment: you should have 3 errors due to the use of Context in > 'MysqlFeatureCache'. For now, I just commented the 2 lines involved. > > 5- Import /tmp/dazzle/dazzle-webapp files into 'dazzle google engine' > project > drag-and-drop files from /tmp/dazzle/dazzle-webapp into > Eclipse:/dazzle/war/. (do not select WEB-INF folder) > > 6- Import Jars to WEB-INF/lib > drag and drop jar files from /tmp/dazzle/jars into 'dazzle google > engine' Eclipse:/dazzle/war/WEB-INF/lib > biojava.jar, bytecode.jar, dasmi-model.jar, servelt-api-2.3.jar, > dazzle.jar > > 6- Update web.xml file in Eclipse:/dazzle/war/WEB-INF/ > > [....] > > Dazzle > > org.biojava.servlets.dazzle.DazzleServlet > > > > Dazzle > /das/* > > > > das_welcome.html > > [...] > > 6- Run application in Eclipse as web Application (standalone test) > check with your web browser: http://localhost:8080/das/dsn > > 7- If it works, you can create a Google App Engine Application ID and > deploy your dazzle server on the cloud. > http://code.google.com/appengine/docs/java/tools/uploadinganapp.html > > ________________________________________ > From: Jonathan Warren [jw12 at sanger.ac.uk] > Sent: Monday, August 10, 2009 5:28 PM > To: Rouilly, Vincent > Cc: Andreas Prlic; Richard Holland > Subject: Re: [Biojava-l] BioJava, Dazzle and Google App Engine (Java > version) > > I had a look at this and it seems the container works differently from > tomcat and resin. I think you may have to change the way dazzle gets it's > datasource information? > The problem is that the google servlet adds dazzle to this nameComponents > list whereas tomcat and resin don't when reading the xml config: > > public Set getDataSourceIDs(List nameComponents, HttpServletRequest req) > throws DataSourceException > { > System.err.println("Address: " + req.getRemoteAddr()); > System.err.println("Host: " + req.getRemoteHost()); > > > if (nameComponents.size() != 0) { > System.out.println(nameComponents.toString()); > throw new DataSourceException("Basic installation only covers flat > namespace of data-sources"); > } > > > > I got some requests to work by adding > /dazzle/* in the web.xml like this: > > DazzleServerMain > /dazzle/* > > > however some requests then work and others don't. > > Maybe the other guys have some ideas, but I couldn't see a particular > reason or quick hack to overcome the difference. > > On 9 Aug 2009, at 11:50, Rouilly, Vincent wrote: > > > Hi, > > thanks for your quick replies. > > Sorry, I forgot to mention that I am also using the stand-alone Google > Engine for now, with the Eclipse plug-in. > And, my development platform is a Mac OS 10.4.11, with JRE 1.6 from > Soylatte, and Eclipse v3.4.2. > > I have read through the dazzle documentation, but I still can't get it to > work within the Google App Engine / Eclipse environment. > I am not very familiar with Eclipse, so it is very likely that I am not > doing things right. > > Here is the process I have followed to give Dazzle a try to on the Google > Engine. But remember, this process doesn't work for me. > I hope it makes sense, and that someone can point me to the right > direction. > > many thanks, > Vincent. > > 1- Download 'dazzle' in /tmp/ using subversion ( > http://biojava.org/wiki/Dazzle): > svn checkout http://www.derkholm.net/svn/repos/dazzle/trunk /tmp/dazzle > > 2- Create new Google App Engine project from Eclipse (after Google Engine > plugin installation): > Project name: dazzle > Package: org.biojava.servlets.dazzle > Uncheck 'Use Google Web Toolkit' > Finish > > 3- Import 'dazzle' Jar files into 'dazzle google engine' project > import from /tmp/dazzle/jars: bioJava.jar, bytecode.jar, dasmi-model.jar, > servlet-api-2.3.jar > In Eclipse, 'dazzle' project Properties -> Java Build Path -> Add External > Jars > > 4- Import 'dazzle' src files into 'dazzle google engine' project > drag-and-drop /tmp/dazzle/src/org folder into 'Eclipse:/ dazzle/src' folder > > 5- Import 'dazzle' ressources folder into 'dazzle google engine' project > drag-and-drop /tmp/dazzle/resources folder into 'Eclipse:/dazzle' folder > > 5- Import WEB-INF files into 'dazzle google engine' project > drag-and-drop files from /tmp/dazzle/dazzle-webapp into > Eclipse:/dazzle/war/. > > 6- Update web.xml file in Eclipse:/dazzle/war/WEB-INF/ > > DazzleServerMain > > org.biojava.servlets.dazzle.DazzleServlet > > > > DazzleServerMain > /* > > > welcome-file-list: dazzle-welcome.html > > 6- Run application as web Application in Eclipse > check with web browser: http://localhost:8080/das/dsn > > > > ________________________________________ > From: andreas.prlic at gmail.com [ > andreas.prlic at gmail.com] On Behalf Of > Andreas Prlic [andreas at sdsc.edu] > Sent: Saturday, August 08, 2009 9:50 PM > To: Rouilly, Vincent > Subject: Re: [Biojava-l] BioJava, Dazzle and Google App Engine (Java > version) > > Hi Vincent, > > did you try following the instructions at > http://biojava.org/wiki/Dazzle ? > > I have never tried to run it using the google app engine, but it works fine > for me using Eclipse or standalone... Also have a look at > http://biojava.org/wiki/Dazzle:deployment > > Hope that helps, > Andreas > > > > On Sat, Aug 8, 2009 at 10:33 AM, Rouilly, Vincent < > vincent.rouilly03 at imperial.ac.uk> > wrote: > Hi, > > first of all, congratulations and thanks to all BioJava contributors for > providing such a great library. > > Over the last few days, I have been trying to use BioJava on the Google App > Engine (with its latest Java support). > http://code.google.com/appengine/docs/java/gettingstarted/ > > Has anyone got experience with that ? > > I am especially interested in setting up a Dazzle DAS server on the google > app engine (basic configuration). > It would be a great way for people to easily share their data through DAS. > > However, whatever DAS request, I always get the exceptions: > DataSourceException("Basic installation only covers flat namespace of > data-sources"); > > Any suggestions ? > > many thanks, > > Vincent. > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org Biojava-l at lists.open-bio.org> > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > Jonathan Warren > Senior Developer and DAS coordinator > jw12 at sanger.ac.uk > Ext: 2314 > Telephone: 01223 492314 > > > > > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a compa ny > registered in England with number 2742969, whose registered office is 2 15 > Euston Road, London, NW1 2BE. > From gwaldon at geneinfinity.org Sun Aug 16 12:27:07 2009 From: gwaldon at geneinfinity.org (George Waldon) Date: Sun, 16 Aug 2009 12:27:07 -0400 Subject: [Biojava-l] Where notes are coming from? Message-ID: <20090816162707.90836.qmail@mxw1102.verio-web.com> Hi, Simple question, I am using a ChangeForwarder.Retyper to forward note changes. When I receive a ChangeEvent with the ChangeType Note.VALUE, how do I find out the RichFeature the change is coming from? What is the intended design? Thanks, George From holland at eaglegenomics.com Sun Aug 16 12:51:50 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Sun, 16 Aug 2009 17:51:50 +0100 Subject: [Biojava-l] Where notes are coming from? In-Reply-To: <20090816162707.90836.qmail@mxw1102.verio-web.com> References: <20090816162707.90836.qmail@mxw1102.verio-web.com> Message-ID: Good question - I don't think you can, as the relationship is unidirectional (it wasn't intended for notes to be passed around independent of their features). In the case of ChangeForwarders listening only for notes, this causes a bit of a problem - but I think you will also get a Change event against the Feature itself to say a note has been added, in which case you might be able to write logic to associate the two Change events to work out what's going on. On 16 Aug 2009, at 17:27, George Waldon wrote: > Hi, > > Simple question, I am using a ChangeForwarder.Retyper to forward > note changes. When I receive a ChangeEvent with the ChangeType > Note.VALUE, how do I find out the RichFeature the change is coming > from? What is the intended design? > > Thanks, > George > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From andreas at sdsc.edu Sun Aug 16 17:41:03 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Sun, 16 Aug 2009 14:41:03 -0700 Subject: [Biojava-l] plans for next months Message-ID: <59a41c430908161441l3ae3ebao524237a1b7b868fe@mail.gmail.com> Hi, Here a quick summary of what I propose to be our action plan for the next months for BioJava: * I would like to call for a code-freeze in 2 weeks (or so) in order to finalize the new modularized and mavenized version of biojava for the developers. The current developmental trunk will remain permanently frozen and all future work should continue at a new location in SVN. As such it will be important that all developers commit any changes they are working on before that. * We will update the documentation for how to obtain a new mavenized checkout on the wiki. * After the change the new modules need to be tested and if no major problems are found, the ok will be given to continue working on the new modules (at the new location) * All developers should obtain a new checkout. * We need to identify sub-module leaders who will take over leadership of the sub-modules. In order to come up with a new release of biojava we should continue development on the new modules for a few months. Talking off list with Richard Holland it looks like we will have a hackaton in January in Cambridge, U.K. (details to be finalized and announced). I suggest that we use that opportunity to focus on further developing the modules and make a new public BioJava release shortly after that. At the present I see the following topics that would be great to work on until and during the hackaton in order to prepare a shiny new version of BioJava for public release: + Work on standardizing the organization of the modules (tests, examples, source, docu etc.) + Add new modules + Improve existing modules + Anything the module leaders deem necessary for their modules. + Use OSGI for visualisation related modules I can post a more detailed and specific list of things to work on if people are interested. Andreas From andreas at sdsc.edu Wed Aug 19 17:30:17 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Wed, 19 Aug 2009 14:30:17 -0700 Subject: [Biojava-l] BioJava PDB question In-Reply-To: References: <59a41c430908051056o7a0aa0a0x6ea3aece8a2714c@mail.gmail.com> Message-ID: <59a41c430908191430q573f8567qce49fff240829717@mail.gmail.com> Hi Scooter, A while ago you asked me about H-Bond calculations for biojava. I committed some code for this yesterday. Check out org.biojava.bio.structure.secstruc.SecStruc It is still a bit unrefined, but once complete this code should be able to calculate a secondary structure assignment. So far it creates virtual H-atoms and uses them to calculate H-Bond energies and tracks H-bond patterns ... Cheers, Andreas From christoph.gille at charite.de Sun Aug 23 17:06:44 2009 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Sun, 23 Aug 2009 23:06:44 +0200 Subject: [Biojava-l] How STRAP can contribute to BJ3 Message-ID: <6dc74c5b9b77a93f3c508d3246b10978.squirrel@webmail.charite.de> Hi, As the developer of STRAP http://3d-alignment.eu I am following with interest the discussion on the new Biojava (BJ3) design. STRAP is a free workbench for proteins similar to Jalview or Cinema. Here I would like to open a discussion on "How STRAP could contribute to the Biojava BJ3" and vice versa "How Biojava can be used to extend the functionality of STRAP". While STRAP is heavily used as a stand alone application and is a protein/alignment viewer in currently 7 Web-services such as PDBSum and Prodom, it has been used as an API/toolbox only by a few people. In most of these cases Biojava and STRAP had been used simultaneously because the functionalities of both toolkits are complementary. I start the discussion by explaining the plugin interface of STRAP. For this purpose I created the Web page http://3d-alignment.eu/biojava/PluginsForStrap.html The page explains how plugins with Biojava are written and deployed on Web-pages. It contains two examples which are ready to be clicked on a computer with Java-Web-Start. The basic idea is that by clicking a Web link a communication between the Browser and STRAP is started which results in loading a remote Jar file together with the most recent Biojava.jar through a customized ClassLoader. The plugin can then act in response to other mouse clicks in the Web page. STRAP contains different graphical dialogs for different types of plugins. E.g. plugins that implement the interface Superimpose3D are opened in the superimposition-dialog. Conversely, plugins that implement SecondaryStructure_Predictor are opened in the dialog for predicting 3D-structure from sequence. The advantage is that the developer of a plugin does not need to provide a GUI and can concentrate on the logic of the algorithm. Here is the Web-form of one of the examples in the above Web-page.
The important Web-variable is "script". It contains the script command script name-of-plugin-class , Jar-files for the plugin. To use Biojava, the jar-file biojava.jar is contained in the list of jar-files. Cheers Christoph From andreas at sdsc.edu Mon Aug 24 00:18:14 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Sun, 23 Aug 2009 21:18:14 -0700 Subject: [Biojava-l] BioJava code freeze, modularization and action items for sub modules Message-ID: <59a41c430908232118k2fff9564of1a45fba447eb922@mail.gmail.com> Hi, In order to push the modularization and migration to Maven, I would like to declare a code freeze on the current developmental trunk. Please commit all new changes by Thursday 27th of August 23:00 GMT. In the week after I would like to refactor the code base and commit the initial set of modules to a new developmental trunk. All future development will happen on that new trunk. You will be able to follow the ongoing status of this at http://biojava.org/wiki/BioJava:MavenMigration Once the modules are in place it is a good moment to hand over the leadership of the sub-modules to the new module-project leaders. It will be up to the module-lead to take the modules into the direction that he/she feels important. I would like to take this opportunity to suggest a couple of people as module-leaders and propose some action items for the modules. Feel free to comment or make additional suggestions... Here a list of modules / action items and the people that I would propose to become module leaders: Module: biojava-core Lead: Andreas Prlic - break the new modules out of core - bring up to modern Java standards, use Generics - declare old/unused code obsolete - don;t break backwards compatibility Module: biojava-sequence Lead: Richard Holland - Bring in Richard's new code that he started to develop on the biojava-3 branch. - provide a more scaleable and efficient basis for dealing with large sequence files Module: biojava-alignment Lead: Andreas Draeger - allow better access to underlying dynamic programming data structures - allow more customizable display of pairwise alignments (HTML/plain text, etc) Module : biojava-blast Lead: still looking for a leader - provide access to all details of the blast output - add support for RPS blast Module: biojava-phylo Lead: Scooter Willis - provide improved NJtree /Jalview Module: biojava-biosql Lead: Richard Holland - merge the new biojava-sequence module with the current biojava-biosql code Module: biojava-structure Lead: Andreas Prlic - add support for SCOP file parsing - add support for easy access of domains (in terms of coordinates) - add secondary structure assignment - improve structure alignments - better integration with 3D viewers (Jmol, RCSB viewers) Module: biojava-web services: The details seem still to be under discussion and perhaps we need multiple modules here? also what about REST vs. SOAP? To be discussed. People who expressed interest are: Niall Haslam,Scooter Willis, Sylvain Foisy Module?: biojava-ws-blast Module?: biojava-ws-biolit Module: biojava-sequencing Lead: ??? - support FastQ files - support parsing of output for various new sequencing machines This is only an initial set of modules and I think it is safe to say that more modules will be added after more discussions (and people volunteering to contribute). Andreas From andreas at sdsc.edu Mon Aug 24 01:36:36 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Sun, 23 Aug 2009 22:36:36 -0700 Subject: [Biojava-l] How STRAP can contribute to BJ3 In-Reply-To: <6dc74c5b9b77a93f3c508d3246b10978.squirrel@webmail.charite.de> References: <6dc74c5b9b77a93f3c508d3246b10978.squirrel@webmail.charite.de> Message-ID: <59a41c430908232236y191778a5g3fa9bd981246ebe7@mail.gmail.com> Hi Christoph, In principle there are the following ways to support BioJava: * You can help and answer support emails on the mailing lists. * You can provide and/or maintain documentation in the biojava wiki. * You can submit bug fixes by email or to the mailing lists * You can contribute to the source code. Regarding your question how BioJava can help Strap, I am not sure how much biojava code is already used by the software and there seems to be some overlap in functionality. I tried to have a look at the Strap code, but I could find a link to the source. The project page says the license is GPL, so just a thought: if you are interested in making your project more transparent, you might consider hosting it at sourceforge or google code ... In case you are interested to learn more about BioJava, the Cookbook provides an overview of some frequently used features: http://biojava.org/wiki/BioJava:CookBook Hope that helps, Andreas On Sun, Aug 23, 2009 at 2:06 PM, Dr. Christoph Gille wrote: > > Hi, > > As the developer of STRAP http://3d-alignment.eu I am following with > interest the discussion on the new Biojava (BJ3) design. > > STRAP is a free workbench for proteins similar to Jalview or Cinema. > > Here I would like to open a discussion on > > "How STRAP could contribute to the Biojava BJ3" > > and vice versa > > "How Biojava can be used to extend the functionality of STRAP". > > While STRAP is heavily used as a stand alone application and is a > protein/alignment viewer in currently 7 Web-services such as PDBSum > and Prodom, it has been used as an API/toolbox only by a few people. > In most of these cases Biojava and STRAP had been used simultaneously > because the functionalities of both toolkits are complementary. > > I start the discussion by explaining the plugin interface of STRAP. > > For this purpose I created the Web page > http://3d-alignment.eu/biojava/PluginsForStrap.html > > The page explains how plugins with Biojava are written and deployed on > Web-pages. It contains two examples which are ready to be clicked on a > computer with Java-Web-Start. > > The basic idea is that by clicking a Web link a communication between > the Browser and STRAP is started which results in loading a remote Jar > file together with the most recent Biojava.jar through a customized > ClassLoader. The plugin can then act in response to other mouse clicks in the Web page. > > STRAP contains different graphical dialogs for different types of > plugins. ?E.g. plugins that implement the interface Superimpose3D are > opened in the superimposition-dialog. ?Conversely, plugins that > implement SecondaryStructure_Predictor are opened in the dialog for > predicting 3D-structure from sequence. The advantage is that the > developer of a plugin does not need to provide a GUI and can > concentrate on the logic of the algorithm. > > Here is the Web-form of one of the examples in the above Web-page. > >
> ? > ? > ? >
> > The important Web-variable is "script". It contains the script command > > ?script ? name-of-plugin-class , ?Jar-files for the plugin. > > To use Biojava, the jar-file biojava.jar is contained in the list of jar-files. > > > Cheers > > Christoph > > > > _______________________________________________ > 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 Mon Aug 24 12:14:50 2009 From: koen.bruynseels at cropdesign.com (koen.bruynseels at cropdesign.com) Date: Mon, 24 Aug 2009 18:14:50 +0200 Subject: [Biojava-l] Koen Bruynseels is out of the office. Message-ID: I will be out of the office starting 08/21/2009 and will not return until 08/27/2009. I will respond to your message when I return. From holland at eaglegenomics.com Mon Aug 24 13:30:31 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Mon, 24 Aug 2009 18:30:31 +0100 Subject: [Biojava-l] [Biojava-dev] Adding profile-profile alignment algorithms to Biojava In-Reply-To: <9551386.424471251132481047.JavaMail.coremail@app180.163.com> References: <9551386.424471251132481047.JavaMail.coremail@app180.163.com> Message-ID: Contributions of code would be welcome! Are you volunteering? :) cheers, Richard On 24 Aug 2009, at 17:48, simpleyrx wrote: > > Experts, > > Profile-profile alignment or HMM-HMM alignments have > become more important in protein bioinformation field than ever > before. So I think, if we can implement Profile-profile alignment > and HMM-HMM alignments algorithms in Biojava package, it will be > more useful to the researchers who interested in protein > bioinformatics. > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From heuermh at acm.org Thu Aug 27 13:01:31 2009 From: heuermh at acm.org (Michael Heuer) Date: Thu, 27 Aug 2009 13:01:31 -0400 (EDT) Subject: [Biojava-l] [Biojava-dev] BioJava code freeze, modularization and action items for sub modules In-Reply-To: <59a41c430908232118k2fff9564of1a45fba447eb922@mail.gmail.com> Message-ID: Andreas Prlic wrote: > Here a list of modules / action items and the people that I would propose to > become module leaders: > ... > > Module: biojava-sequencing Lead: Michael Heuer > - support FastQ files > - support parsing of output for various new sequencing machines I have volunteered on the open-bio mailing list to implement FASTQ support. A nice collection of test data is being created in collaboration with the other open-bio projects. If anyone has interest in a particular data set, please let me know, as I will also need data for performance tuning. michael From andreas at sdsc.edu Thu Aug 27 13:30:08 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 27 Aug 2009 10:30:08 -0700 Subject: [Biojava-l] [Biojava-dev] BioJava code freeze, modularization and action items for sub modules In-Reply-To: References: <59a41c430908232118k2fff9564of1a45fba447eb922@mail.gmail.com> Message-ID: <59a41c430908271030p7318c468u8d145f5750369cb3@mail.gmail.com> Great, thanks for "volunteering", Michael. To add another Module: biojava-das : Lead: Jonathan Warren probably deprecate the old DAS code in BJ and replace it with the up to date Dasobert library Thanks to Jonathan for volunteering as well. Andreas On Thu, Aug 27, 2009 at 10:01 AM, Michael Heuer wrote: > Andreas Prlic wrote: > >> Here a list of modules / action items and the people that I would propose to >> become module leaders: >> ... >> >> Module: biojava-sequencing Lead: ?Michael Heuer >> ? - support FastQ files >> ? - support parsing of output for various new sequencing machines > > I have volunteered on the open-bio mailing list to implement FASTQ > support. ?A nice collection of test data is being created in collaboration > with the other open-bio projects. ?If anyone has interest in a particular > data set, please let me know, as I will also need data for performance > tuning. > > ? michael > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From markjschreiber at gmail.com Fri Aug 28 01:37:59 2009 From: markjschreiber at gmail.com (Mark Schreiber) Date: Fri, 28 Aug 2009 13:37:59 +0800 Subject: [Biojava-l] [Biojava-dev] BioJava code freeze, modularization and action items for sub modules In-Reply-To: <59a41c430908271030p7318c468u8d145f5750369cb3@mail.gmail.com> References: <59a41c430908232118k2fff9564of1a45fba447eb922@mail.gmail.com> <59a41c430908271030p7318c468u8d145f5750369cb3@mail.gmail.com> Message-ID: <93b45ca50908272237k2485a1d8le343a8b1dc10ae12@mail.gmail.com> I'm happy to volunteer code for: 1. BLASTXML parser as long as I can change the ssbind APIs (other parsers could go into a legacy module??). Actually I would prefer to completely decouple from the sequence/ feature module as many people would like a blast parser without the rest of biojava thrown in. 2. BioSQL/ JPA bindings. I have already generated JPA compliant entity beans for mapping to BioSQL as well as JPA handler code that makes sure modifications presist properly. Currently the object model very closely follows the BioSQL table structure. Also the current beans are what people call Anaemic beans in that they hold data and provide getters and setters but no biological behaivour. I can easily provide bio-smarts to the beans but it might be better to hold off until there is a module that contains sequence/feature interfaces which the beans could implement. 3. Happy to provide code for an enterprise module if there is sufficient interest. This would probably take the form of SessionBeans and WebServices that can be deployed to Glassfish/ JBoss etc to provide biological services for people who want to make client server or SOA apps. - Mark On Fri, Aug 28, 2009 at 1:30 AM, Andreas Prlic wrote: > Great, thanks for "volunteering", Michael. > > To add another Module: > > biojava-das : Lead: Jonathan Warren > probably deprecate the old DAS code in BJ and replace it with > the up to date Dasobert library > > Thanks to Jonathan for volunteering as well. > > Andreas > > > > > On Thu, Aug 27, 2009 at 10:01 AM, Michael Heuer wrote: > > Andreas Prlic wrote: > > > >> Here a list of modules / action items and the people that I would > propose to > >> become module leaders: > >> ... > >> > >> Module: biojava-sequencing Lead: Michael Heuer > >> - support FastQ files > >> - support parsing of output for various new sequencing machines > > > > I have volunteered on the open-bio mailing list to implement FASTQ > > support. A nice collection of test data is being created in > collaboration > > with the other open-bio projects. If anyone has interest in a particular > > data set, please let me know, as I will also need data for performance > > tuning. > > > > michael > > > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From andreas at sdsc.edu Fri Aug 28 11:10:03 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Fri, 28 Aug 2009 08:10:03 -0700 Subject: [Biojava-l] [Biojava-dev] BioJava code freeze, modularization and action items for sub modules In-Reply-To: <93b45ca50908272237k2485a1d8le343a8b1dc10ae12@mail.gmail.com> References: <59a41c430908232118k2fff9564of1a45fba447eb922@mail.gmail.com> <59a41c430908271030p7318c468u8d145f5750369cb3@mail.gmail.com> <93b45ca50908272237k2485a1d8le343a8b1dc10ae12@mail.gmail.com> Message-ID: <59a41c430908280810s1720cfckbc36168f2fbc73a8@mail.gmail.com> Thanks, Mark. Guess we should start collecting all this info on a wiki page. I started to edit http://biojava.org/wiki/BioJava:Modules module leaders: feel free to edit the plans for your module... Andreas On Thu, Aug 27, 2009 at 10:37 PM, Mark Schreiber wrote: - Show quoted text - On Thu, Aug 27, 2009 at 10:37 PM, Mark Schreiber wrote: > I'm happy to volunteer code for: > > BLASTXML parser as long as I can change the ssbind APIs (other parsers could > go into a legacy module??). Actually I would prefer to completely decouple > from the sequence/ feature module as many people would like a blast parser > without the rest of biojava thrown in. > BioSQL/ JPA bindings. I have already generated JPA compliant entity beans > for mapping to BioSQL as well as JPA handler code that makes sure > modifications presist properly. Currently the object model very closely > follows the BioSQL table structure.? Also the current beans are what people > call Anaemic beans in that they hold data and provide getters and setters > but no biological behaivour. I can easily provide bio-smarts to the beans > but it might be better to hold off until there is a module that contains > sequence/feature interfaces which the beans could implement. > Happy to provide code for an enterprise module if there is sufficient > interest. This would probably take the form of SessionBeans and WebServices > that can be deployed to Glassfish/ JBoss etc to provide biological services > for people who want to make client server or SOA apps. > > - Mark > > > On Fri, Aug 28, 2009 at 1:30 AM, Andreas Prlic wrote: >> >> Great, thanks for "volunteering", Michael. >> >> To add another Module: >> >> biojava-das : Lead: Jonathan Warren >> probably deprecate the old DAS code in BJ and replace it with >> the up to date Dasobert library >> >> Thanks to Jonathan for volunteering as well. >> >> Andreas >> >> >> >> >> On Thu, Aug 27, 2009 at 10:01 AM, Michael Heuer wrote: >> > Andreas Prlic wrote: >> > >> >> Here a list of modules / action items and the people that I would >> >> propose to >> >> become module leaders: >> >> ... >> >> >> >> Module: biojava-sequencing Lead: ?Michael Heuer >> >> ? - support FastQ files >> >> ? - support parsing of output for various new sequencing machines >> > >> > I have volunteered on the open-bio mailing list to implement FASTQ >> > support. ?A nice collection of test data is being created in >> > collaboration >> > with the other open-bio projects. ?If anyone has interest in a >> > particular >> > data set, please let me know, as I will also need data for performance >> > tuning. >> > >> > ? michael >> > >> > _______________________________________________ >> > biojava-dev mailing list >> > biojava-dev at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > >> >> _______________________________________________ >> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l > > From ehaugen at u.washington.edu Wed Aug 5 17:59:02 2009 From: ehaugen at u.washington.edu (Eric Haugen) Date: Wed, 05 Aug 2009 21:59:02 -0000 Subject: [Biojava-l] Upper case symbols In-Reply-To: <4A7986A5.7000608@uni-tuebingen.de> References: <4A7986A5.7000608@uni-tuebingen.de> Message-ID: <4A79F96C.5050909@u.washington.edu> Andreas Draeger wrote: > Dear all, > > Thank you for this very quick answer regarding Sequence logos! The code > works fine. However, would it also be possible to tell the DNATools > class that upper case letters should be used instead of lower case "a", > "c", "g", and "t"? I think it is more common to apply upper case symbols > in sequence logos. > > Cheers > Andreas > Hi Andreas, The way I did it was to uppercase the letters in the AlphabetManager.xml file, replacing the AlphabetManager.xml inside my biojava.jar. See the attached version. Maybe there's an easier way I don't know about... Best regards, Eric -- Eric Haugen Software Engineer Stam lab, UW Genome Sciences University of Washington 2211 Elliott Avenue, 6th Floor Seattle, WA 98121 -------------- next part -------------- A non-text attachment was scrubbed... Name: AlphabetManager.xml Type: text/xml Size: 28062 bytes Desc: not available URL: From d.johnson at reading.ac.uk Fri Aug 7 05:28:39 2009 From: d.johnson at reading.ac.uk (David Johnson) Date: Fri, 07 Aug 2009 09:28:39 -0000 Subject: [Biojava-l] ParseException when using interleaved Nexus file In-Reply-To: <30109C99-0ADF-461D-AB8A-B9800C4111D1@eaglegenomics.com> References: <30109C99-0ADF-461D-AB8A-B9800C4111D1@eaglegenomics.com> Message-ID: Hi Richard, Thanks for your mail. An example of an interleaved file can be found here: http://www.molecularevolution.org/si/resources/fileformats/files/dna.nex where the link pointing to the example file is from http://www.molecularevolution.org/si/resources/fileformats/ and under the NEXUS section. The specific error message is: "org.biojava.bio.seq.io.ParseException: Found unexpected token interleave=yes in CHARACTERS block" So it looks like the error is thrown reading the "interleave" parameter in the top of the data block, and before reaching the actual interleaved matrix data. Full stacktrace in attached .txt. Cheers, -David 2009/8/7 Richard Holland : > Could you point me to an example of an interleaved file? > > And also the full stack trace of the exception that gets thrown? > > cheers, > Richard > > On 6 Aug 2009, at 18:03, David Johnson wrote: > >> Hi everyone, >> >> A quick question about the BioJava Nexus parser. I've been trying to >> use the Nexus file parser, simply by doing something like: >> >> ? ? ? NexusFileBuilder builder = new NexusFileBuilder(); >> ? ? ? NexusFileFormat.parseFile(builder, f); >> >> However, when parsing Nexus files that are interleaved, I get a >> ParseException. >> >> Is there a way to setup the parser provided by BioJava to handle >> interleaved Nexus files? >> >> Thanks, >> -David >> -- >> David Johnson >> School of Biological Sciences >> University of Reading >> _______________________________________________ >> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > > -- David Johnson Post-doc Research Assistant School of Biological Sciences 506, Philip Lyle Research Building University of Reading Whiteknights Reading, RG6 6BX UK Tel: +44 (0) 118 378 4415 email: d.johnson at reading.ac.uk web: http://www.rdg.ac.uk/~sis07dj -------------- next part -------------- Message ID org.biojava.bio.seq.io.ParseException Complete Message Found unexpected token interleave=yes in CHARACTERS block at org.biojavax.bio.phylo.io.nexus.CharactersBlockParser.parseToken(CharactersBlockParser.java:1177) at org.biojavax.bio.phylo.io.nexus.NexusFileListener$Abstract.parseToken(NexusFileListener.java:256) at org.biojavax.bio.phylo.io.nexus.NexusFileFormat$TokenParser.parseToken(NexusFileFormat.java:345) at org.biojavax.bio.phylo.io.nexus.NexusFileFormat$TokenParser.access$100(NexusFileFormat.java:296) at org.biojavax.bio.phylo.io.nexus.NexusFileFormat.parse(NexusFileFormat.java:266) at org.biojavax.bio.phylo.io.nexus.NexusFileFormat.parseReader(NexusFileFormat.java:117) at org.biojavax.bio.phylo.io.nexus.NexusFileFormat.parseFile(NexusFileFormat.java:79) at uk.ac.rdg.evo.portal.NexusUtil.parseFile(NexusUtil.java:24) at uk.ac.rdg.evo.portal.panels.BayesPhyloJobStep1Panel$UploadNexusForm.onSubmit(BayesPhyloJobStep1Panel.java:65) at org.apache.wicket.markup.html.form.Form.delegateSubmit(Form.java:1518) at org.apache.wicket.markup.html.form.Form.process(Form.java:914) at org.apache.wicket.markup.html.form.Form.onFormSubmitted(Form.java:876) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.apache.wicket.RequestListenerInterface.invoke(RequestListenerInterface.java:182) at org.apache.wicket.request.target.component.listener.ListenerInterfaceRequestTarget.processEvents(ListenerInterfaceRequestTarget.java:73) at org.apache.wicket.request.AbstractRequestCycleProcessor.processEvents(AbstractRequestCycleProcessor.java:92) at org.apache.wicket.RequestCycle.processEventsAndRespond(RequestCycle.java:1241) at org.apache.wicket.RequestCycle.step(RequestCycle.java:1320) at org.apache.wicket.RequestCycle.steps(RequestCycle.java:1419) at org.apache.wicket.RequestCycle.request(RequestCycle.java:545) at org.apache.wicket.protocol.http.WicketFilter.doGet(WicketFilter.java:456) at org.apache.wicket.protocol.http.WicketFilter.doFilter(WicketFilter.java:289) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:230) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:198) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:288) at org.apache.catalina.core.StandardContextValve.invokeInternal(StandardContextValve.java:271) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:202) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:632) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:577) at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:94) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:206) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:632) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:577) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:571) at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:1080) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:150) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:632) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:577) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:571) at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:1080) at org.apache.coyote.tomcat5.CoyoteAdapter.service(CoyoteAdapter.java:272) at com.sun.enterprise.web.connector.grizzly.DefaultProcessorTask.invokeAdapter(DefaultProcessorTask.java:637) at com.sun.enterprise.web.connector.grizzly.DefaultProcessorTask.doProcess(DefaultProcessorTask.java:568) at com.sun.enterprise.web.connector.grizzly.DefaultProcessorTask.process(DefaultProcessorTask.java:813) at com.sun.enterprise.web.connector.grizzly.DefaultReadTask.executeProcessorTask(DefaultReadTask.java:341) at com.sun.enterprise.web.connector.grizzly.DefaultReadTask.doTask(DefaultReadTask.java:263) at com.sun.enterprise.web.connector.grizzly.DefaultReadTask.doTask(DefaultReadTask.java:214) at com.sun.enterprise.web.connector.grizzly.TaskBase.run(TaskBase.java:265) at com.sun.enterprise.web.connector.grizzly.ssl.SSLWorkerThread.run(SSLWorkerThread.java:106) From frederik at genohm.com Tue Aug 4 15:12:11 2009 From: frederik at genohm.com (Frederik Decouttere) Date: Tue, 04 Aug 2009 17:12:11 +0200 Subject: [Biojava-l] SimpleGappedSequence using RichSequence objects In-Reply-To: Message-ID: Hi While migrating to biojavax (and biojava 1.7 in general), I don?t see a replacement for SimpleGappedSequence that is using RichSequence objects instead of the ?old? Sequence objects. Am I missing something, or isn?t there a SimpleGappedSequence yet based on RichSequence ? kr Frederik Decouttere From holland at eaglegenomics.com Tue Aug 4 15:30:47 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Tue, 4 Aug 2009 16:30:47 +0100 Subject: [Biojava-l] SimpleGappedSequence using RichSequence objects In-Reply-To: References: Message-ID: <83834A0F-A971-4999-9A0E-F97BC18BA687@eaglegenomics.com> Nope, you're not missing anything - it hasn't been implemented. cheers, Richard On 4 Aug 2009, at 16:12, Frederik Decouttere wrote: > Hi > > While migrating to biojavax (and biojava 1.7 in general), I don?t > see a > replacement for SimpleGappedSequence that is using RichSequence > objects > instead of the ?old? Sequence objects. > Am I missing something, or isn?t there a SimpleGappedSequence yet > based on > RichSequence ? > > kr > Frederik Decouttere > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From andreas.draeger at uni-tuebingen.de Tue Aug 4 17:05:34 2009 From: andreas.draeger at uni-tuebingen.de (Andreas Draeger) Date: Tue, 04 Aug 2009 19:05:34 +0200 Subject: [Biojava-l] Sequence logo Message-ID: <4A786A5E.7040202@uni-tuebingen.de> Dear all, Just a question: I assume you all know this visualization of position frequency matrices, in which A, T, G, and C appear according to their frequency within the matrix with different sizes and all letters are colored differently (green, red, blue, yellow). Is there a class in BioJava that produces this kind of visualization? Cheers Andreas -- Dipl.-Bioinform. Andreas Dr?ger Eberhard Karls University T?bingen Center for Bioinformatics (ZBIT) Sand 1 72076 T?bingen Germany Phone: +49-7071-29-70436 Fax: +49-7071-29-5091 From mark.schreiber at novartis.com Wed Aug 5 05:35:23 2009 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Wed, 5 Aug 2009 13:35:23 +0800 Subject: [Biojava-l] Sequence logo In-Reply-To: <4A786A5E.7040202@uni-tuebingen.de> Message-ID: Hi - There is some code for a Swing component in one of the GUI packages. It is useful for making a single position but not an entire logo. In the past I have used the code that does the drawing and modified it to work on a Distribution[]. The code shouldn't really be in a Swing component it should be in a class that generates drawing instructions for a Graphics2D object. This is a lot more flexible because you can then draw into a Frame or Canvas if you want a GUI, or a BufferedImage if you want a graphics file, or a Batik Graphics2D object if you want to make an SVG file. Also the code in BioJava doesn't let you modify the g2 object at all so you can't turn on anti-aliasing (highly recommended). The idea of separating BioJava's graphics and GUI capabilities has been on the cards for a while. If you do this for the Sequence Logo it would be great to feed it back to the group as an example of how it should be done. - Mark biojava-l-bounces at lists.open-bio.org wrote on 08/05/2009 01:05:34 AM: > Dear all, > > Just a question: I assume you all know this visualization of position > frequency matrices, in which A, T, G, and C appear according to their > frequency within the matrix with different sizes and all letters are > colored differently (green, red, blue, yellow). > > Is there a class in BioJava that produces this kind of visualization? > > Cheers > Andreas > > -- > Dipl.-Bioinform. Andreas Dr?ger > Eberhard Karls University T?bingen > Center for Bioinformatics (ZBIT) > Sand 1 > 72076 T?bingen > Germany > > Phone: +49-7071-29-70436 > Fax: +49-7071-29-5091 > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l _________________________ CONFIDENTIALITY NOTICE The information contained in this e-mail message is intended only for the exclusive use of the individual or entity named above and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivery of the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately by e-mail and delete the material from any computer. Thank you. From nathan.genome at gmail.com Wed Aug 5 10:38:28 2009 From: nathan.genome at gmail.com (nathan genome) Date: Wed, 5 Aug 2009 12:38:28 +0200 Subject: [Biojava-l] (no subject) Message-ID: hi i am working on genomic variations. i am interested to initially visualize mappings from clone-ends to reference sequence. i have data in the following tab. format : CAX100A01FOR1 1 748 scaffold_116 507411 508161CAX100A01REV1 1 702 scaffold_116 512322 511611 1st & 7th cols. represent clone-ends, the numbers are positions, 4th col. indicates the reference. How do i visualize this pair alignment in a window with biojava. thanks Natthan From nathan.genome at gmail.com Wed Aug 5 10:45:31 2009 From: nathan.genome at gmail.com (nathan genome) Date: Wed, 5 Aug 2009 12:45:31 +0200 Subject: [Biojava-l] visualization Message-ID: i am interested to initially visualize mappings from clone-ends to reference sequence. i have data in the following tab. format : CAX100A01FOR1 1 748 scaffold_116 507411 508161 CAX100A01REV1 1 702 scaffold_116 512322 511611 1st & 7th cols. represent clone-ends, the numbers are positions, 4th col. indicates the reference. idea is to visualize as a browser which is similar to gbrowse thanks Natthan From andreas.draeger at uni-tuebingen.de Wed Aug 5 13:18:29 2009 From: andreas.draeger at uni-tuebingen.de (Andreas Draeger) Date: Wed, 05 Aug 2009 15:18:29 +0200 Subject: [Biojava-l] Upper case symbols Message-ID: <4A7986A5.7000608@uni-tuebingen.de> Dear all, Thank you for this very quick answer regarding Sequence logos! The code works fine. However, would it also be possible to tell the DNATools class that upper case letters should be used instead of lower case "a", "c", "g", and "t"? I think it is more common to apply upper case symbols in sequence logos. Cheers Andreas -- Dipl.-Bioinform. Andreas Dr?ger Eberhard Karls University T?bingen Center for Bioinformatics (ZBIT) Sand 1 72076 T?bingen Germany Phone: +49-7071-29-70436 Fax: +49-7071-29-5091 From thien.nguyen at berkeley.edu Wed Aug 5 19:40:50 2009 From: thien.nguyen at berkeley.edu (Thien Nguyen) Date: Wed, 5 Aug 2009 12:40:50 -0700 (PDT) Subject: [Biojava-l] chromatogram question: get confident value of the called base Message-ID: <56495.136.152.170.253.1249501250.squirrel@calmail.berkeley.edu> Hello all, I'm new to BioJava. I start using Chromatogram package to read a number of .ab1 files and save some statistics. Reading the API, I don't see how to get some sort of quality/confidence metric for each location, but only the called base and the raw offset numbers. Here is what I know: . ChromatogramFactory to create Chromatogram object from a file .ChromatogramTools.getDNASequence to get the called bases, or TraceOffsetArray to get the raw offset array. Is there an available method that get the confidence of each called bases? Thank you Thien Nguyen From d.johnson at reading.ac.uk Thu Aug 6 17:03:24 2009 From: d.johnson at reading.ac.uk (David Johnson) Date: Thu, 6 Aug 2009 18:03:24 +0100 Subject: [Biojava-l] ParseException when using interleaved Nexus file Message-ID: Hi everyone, A quick question about the BioJava Nexus parser. I've been trying to use the Nexus file parser, simply by doing something like: NexusFileBuilder builder = new NexusFileBuilder(); NexusFileFormat.parseFile(builder, f); However, when parsing Nexus files that are interleaved, I get a ParseException. Is there a way to setup the parser provided by BioJava to handle interleaved Nexus files? Thanks, -David -- David Johnson School of Biological Sciences University of Reading From andreas.draeger at uni-tuebingen.de Thu Aug 6 17:47:35 2009 From: andreas.draeger at uni-tuebingen.de (=?ISO-8859-1?Q?Andreas_Dr=E4ger?=) Date: Thu, 06 Aug 2009 19:47:35 +0200 Subject: [Biojava-l] Upper case symbols In-Reply-To: <4A79F96C.5050909@u.washington.edu> References: <4A7986A5.7000608@uni-tuebingen.de> <4A79F96C.5050909@u.washington.edu> Message-ID: <4A7B1737.6010200@uni-tuebingen.de> Thank you, Eric! This XML file works greatly! Cheers Andreas From andreas at sdsc.edu Thu Aug 6 20:36:02 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 6 Aug 2009 13:36:02 -0700 Subject: [Biojava-l] blast parsing question In-Reply-To: <3DD69071F4A8490D9D1D7EEB172FEFC0@zillumina> References: <3DD69071F4A8490D9D1D7EEB172FEFC0@zillumina> Message-ID: <59a41c430908061336n1f71c6d6ocf064db05fdfb236@mail.gmail.com> Hi Bernd, not sure if you got a reply to your mail off-list. Did you manage to solve your problem in the meanwhile? Andreas On Wed, Jul 29, 2009 at 6:16 AM, Bernd Jagla wrote: > Hi, > > > > I am new to BioJava. I want to test what is going on here in order to > potentially integrate it with KNIME. > > My first project is parsing BLAST output for large files. The example in > the > codebook is very good and I had no problems integrating everything in > Eclipse and geting it to work. > > > > Now here is my problem: > > I am interested in parsing the summary table in the beginning of the > blast-output, and I haven't found a way to get at this information. > > > > I am blasting short sequences (20nt - 300nt) against genomic databases > (mouse/human/refseq/miRBase). I want to know if a given sequence (out of a > set of sequences) aligns to a specific genome with high identity. I want to > then separate the input source fasta file into a set that aligns to the > genome and one that doesn't (potentially another list of dubious sequences > where there is no clear answer). For this I only need the length of the > query sequence and score and the first few characters of the header line. > > At least that's the way I am currently doing it. I have set the blast > parameters to only give me the first alignment, but the first 50 or so in > the summary. > > > > Any help, comments are appreciated. > > > > Thanks, > > > > Bernd > > > > > > > > > > > > Bernd Jagla > Bioinformatician > > Institut Pasteur > Plate-forme puces a ADN > Genopole / Institut Pasteur > 28 rue du Docteur Roux > 75724 Paris Cedex 15 > France > > > bernd.jagla at pasteur.fr > > > tel: > > > < > http://www.plaxo.com/click_to_call?lang=en&src=jj_signature&To=%2B33+%280%2 > 9+140+61+35+13&Email=berndjagla at yahoo.com> > +33 (0) 140 61 35 13 > > > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From holland at eaglegenomics.com Fri Aug 7 08:57:38 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Fri, 7 Aug 2009 09:57:38 +0100 Subject: [Biojava-l] ParseException when using interleaved Nexus file In-Reply-To: References: Message-ID: <30109C99-0ADF-461D-AB8A-B9800C4111D1@eaglegenomics.com> Could you point me to an example of an interleaved file? And also the full stack trace of the exception that gets thrown? cheers, Richard On 6 Aug 2009, at 18:03, David Johnson wrote: > Hi everyone, > > A quick question about the BioJava Nexus parser. I've been trying to > use the Nexus file parser, simply by doing something like: > > NexusFileBuilder builder = new NexusFileBuilder(); > NexusFileFormat.parseFile(builder, f); > > However, when parsing Nexus files that are interleaved, I get a > ParseException. > > Is there a way to setup the parser provided by BioJava to handle > interleaved Nexus files? > > Thanks, > -David > -- > David Johnson > School of Biological Sciences > University of Reading > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From holland at eaglegenomics.com Fri Aug 7 09:57:37 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Fri, 7 Aug 2009 10:57:37 +0100 Subject: [Biojava-l] ParseException when using interleaved Nexus file In-Reply-To: References: <30109C99-0ADF-461D-AB8A-B9800C4111D1@eaglegenomics.com> Message-ID: Thanks David. One more quick question - is this the exact file that is throwing the exception? I haven't tested it yet - but if I could test against the real file that is throwing the problem, that would help me find out exactly what's going wrong. For what it's worth, the exception is normally thrown when more than one interleave=yes/no token is found in the header of the Data or Characters block, or when the interleave token appears in a line other than the Format line of the header. cheers, Richard On 7 Aug 2009, at 10:28, David Johnson wrote: > Hi Richard, > > Thanks for your mail. An example of an interleaved file can be found > here: > > http://www.molecularevolution.org/si/resources/fileformats/files/dna.nex > > where the link pointing to the example file is from > http://www.molecularevolution.org/si/resources/fileformats/ and under > the NEXUS section. > > The specific error message is: "org.biojava.bio.seq.io.ParseException: > Found unexpected token interleave=yes in CHARACTERS block" > > So it looks like the error is thrown reading the "interleave" > parameter in the top of the data block, and before reaching the actual > interleaved matrix data. Full stacktrace in attached .txt. > > Cheers, > -David > > 2009/8/7 Richard Holland : >> Could you point me to an example of an interleaved file? >> >> And also the full stack trace of the exception that gets thrown? >> >> cheers, >> Richard >> >> On 6 Aug 2009, at 18:03, David Johnson wrote: >> >>> Hi everyone, >>> >>> A quick question about the BioJava Nexus parser. I've been trying to >>> use the Nexus file parser, simply by doing something like: >>> >>> NexusFileBuilder builder = new NexusFileBuilder(); >>> NexusFileFormat.parseFile(builder, f); >>> >>> However, when parsing Nexus files that are interleaved, I get a >>> ParseException. >>> >>> Is there a way to setup the parser provided by BioJava to handle >>> interleaved Nexus files? >>> >>> Thanks, >>> -David >>> -- >>> David Johnson >>> School of Biological Sciences >>> University of Reading >>> _______________________________________________ >>> Biojava-l mailing list - Biojava-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >> >> -- >> Richard Holland, BSc MBCS >> Operations and Delivery Director, Eagle Genomics Ltd >> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com >> http://www.eaglegenomics.com/ >> >> > > > > -- > David Johnson > Post-doc Research Assistant > School of Biological Sciences > 506, Philip Lyle Research Building > University of Reading > Whiteknights > Reading, RG6 6BX > UK > > Tel: +44 (0) 118 378 4415 > email: d.johnson at reading.ac.uk > web: http://www.rdg.ac.uk/~sis07dj > -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From d.johnson at reading.ac.uk Fri Aug 7 10:10:46 2009 From: d.johnson at reading.ac.uk (David Johnson) Date: Fri, 7 Aug 2009 11:10:46 +0100 Subject: [Biojava-l] ParseException when using interleaved Nexus file In-Reply-To: References: <30109C99-0ADF-461D-AB8A-B9800C4111D1@eaglegenomics.com> Message-ID: Hi Richard, Actually the original exception was thrown in a different file that my supervisor tried uploading to a Web app I'm developing that uses the BioJava Nexus parser, but can't get hold of that particular file today. So the one I provided the link for was just another example of an interleaved Nexus file I Googled for when I got your first email this morning, as I figured they'd probably be the same formatting. But I remember it's definitely the same exception in both cases. I had a quick look in the example I provided today, and the interleave=yes token is definitely in the header of the data block, and is also definitely in the Format line. Oh, just FYI, I'm using the BioJava 1.7 binary distribution (http://www.biojava.org/download/bj17/bin/biojava.jar). Cheers, -David 2009/8/7 Richard Holland : > Thanks David. One more quick question - is this the exact file that is > throwing the exception? I haven't tested it yet - but if I could test > against the real file that is throwing the problem, that would help me find > out exactly what's going wrong. > > For what it's worth, the exception is normally thrown when more than one > interleave=yes/no token is found in the header of the Data or Characters > block, or when the interleave token appears in a line other than the Format > line of the header. > > cheers, > Richard > > On 7 Aug 2009, at 10:28, David Johnson wrote: > >> Hi Richard, >> >> Thanks for your mail. An example of an interleaved file can be found here: >> >> http://www.molecularevolution.org/si/resources/fileformats/files/dna.nex >> >> where the link pointing to the example file is from >> http://www.molecularevolution.org/si/resources/fileformats/ and under >> the NEXUS section. >> >> The specific error message is: "org.biojava.bio.seq.io.ParseException: >> Found unexpected token interleave=yes in CHARACTERS block" >> >> So it looks like the error is thrown reading the "interleave" >> parameter in the top of the data block, and before reaching the actual >> interleaved matrix data. Full stacktrace in attached .txt. >> >> Cheers, >> -David >> >> 2009/8/7 Richard Holland : >>> >>> Could you point me to an example of an interleaved file? >>> >>> And also the full stack trace of the exception that gets thrown? >>> >>> cheers, >>> Richard >>> >>> On 6 Aug 2009, at 18:03, David Johnson wrote: >>> >>>> Hi everyone, >>>> >>>> A quick question about the BioJava Nexus parser. I've been trying to >>>> use the Nexus file parser, simply by doing something like: >>>> >>>> ? ? ?NexusFileBuilder builder = new NexusFileBuilder(); >>>> ? ? ?NexusFileFormat.parseFile(builder, f); >>>> >>>> However, when parsing Nexus files that are interleaved, I get a >>>> ParseException. >>>> >>>> Is there a way to setup the parser provided by BioJava to handle >>>> interleaved Nexus files? >>>> >>>> Thanks, >>>> -David >>>> -- >>>> From vincent.rouilly03 at imperial.ac.uk Sat Aug 8 17:33:02 2009 From: vincent.rouilly03 at imperial.ac.uk (Rouilly, Vincent) Date: Sat, 8 Aug 2009 18:33:02 +0100 Subject: [Biojava-l] BioJava, Dazzle and Google App Engine (Java version) Message-ID: Hi, first of all, congratulations and thanks to all BioJava contributors for providing such a great library. Over the last few days, I have been trying to use BioJava on the Google App Engine (with its latest Java support). http://code.google.com/appengine/docs/java/gettingstarted/ Has anyone got experience with that ? I am especially interested in setting up a Dazzle DAS server on the google app engine (basic configuration). It would be a great way for people to easily share their data through DAS. However, whatever DAS request, I always get the exceptions: DataSourceException("Basic installation only covers flat namespace of data-sources"); Any suggestions ? many thanks, Vincent. From holland at eaglegenomics.com Sat Aug 8 21:15:43 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Sat, 8 Aug 2009 22:15:43 +0100 Subject: [Biojava-l] BioJava, Dazzle and Google App Engine (Java version) In-Reply-To: References: Message-ID: <0F80A206-C826-492F-9BE9-2D0F2D7934C6@eaglegenomics.com> Hello. Dazzle/DAS is not BioJava, but I happen to know that Jon Warren at the Sanger Centre is an expert in all things DAS, so he might be able to help you. I've copied him on this. cheers, Richard On 8 Aug 2009, at 18:33, Rouilly, Vincent wrote: > Hi, > > first of all, congratulations and thanks to all BioJava contributors > for providing such a great library. > > Over the last few days, I have been trying to use BioJava on the > Google App Engine (with its latest Java support). > http://code.google.com/appengine/docs/java/gettingstarted/ > > Has anyone got experience with that ? > > I am especially interested in setting up a Dazzle DAS server on the > google app engine (basic configuration). > It would be a great way for people to easily share their data > through DAS. > > However, whatever DAS request, I always get the exceptions: > DataSourceException("Basic installation only covers flat namespace > of data-sources"); > > Any suggestions ? > > many thanks, > > Vincent. > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From andreas at sdsc.edu Sat Aug 8 21:59:14 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Sat, 8 Aug 2009 14:59:14 -0700 Subject: [Biojava-l] Fwd: BioJava, Dazzle and Google App Engine (Java version) In-Reply-To: <59a41c430908081350m1c55ce2ag1f7b51a6673756fe@mail.gmail.com> References: <59a41c430908081350m1c55ce2ag1f7b51a6673756fe@mail.gmail.com> Message-ID: <59a41c430908081459j10589fa6y2fd1f3249130bc99@mail.gmail.com> Hi Vincent, did you try following the instructions at http://biojava.org/wiki/Dazzle ? I have never tried to run it using the google app engine, but it works fine for me using Eclipse or standalone... Also have a look at http://biojava.org/wiki/Dazzle:deployment Hope that helps, Andreas On Sat, Aug 8, 2009 at 10:33 AM, Rouilly, Vincent < vincent.rouilly03 at imperial.ac.uk> wrote: > Hi, > > first of all, congratulations and thanks to all BioJava contributors for > providing such a great library. > > Over the last few days, I have been trying to use BioJava on the Google App > Engine (with its latest Java support). > http://code.google.com/appengine/docs/java/gettingstarted/ > > Has anyone got experience with that ? > > I am especially interested in setting up a Dazzle DAS server on the google > app engine (basic configuration). > It would be a great way for people to easily share their data through DAS. > > However, whatever DAS request, I always get the exceptions: > DataSourceException("Basic installation only covers flat namespace of > data-sources"); > > Any suggestions ? > > many thanks, > > Vincent. > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From rabee.a.aa at m.titech.ac.jp Sun Aug 9 04:43:05 2009 From: rabee.a.aa at m.titech.ac.jp (rabee.a.aa at m.titech.ac.jp) Date: Sun, 9 Aug 2009 13:43:05 +0900 Subject: [Biojava-l] BioJava, Bioperl and R Message-ID: <1249792985464413.9007@mail3.nap.gsic.titech.ac.jp> Dear All, I'm quite new to Bioinfromatics field, i want to ask which is best language to use in analysis of next generation sequencing data is it Biojava, Bioperl or R (Bioconductor) Best Regards, Rabe From vincent.rouilly03 at imperial.ac.uk Sun Aug 9 10:50:33 2009 From: vincent.rouilly03 at imperial.ac.uk (Rouilly, Vincent) Date: Sun, 9 Aug 2009 11:50:33 +0100 Subject: [Biojava-l] BioJava, Dazzle and Google App Engine (Java version) In-Reply-To: <59a41c430908081350m1c55ce2ag1f7b51a6673756fe@mail.gmail.com> References: , <59a41c430908081350m1c55ce2ag1f7b51a6673756fe@mail.gmail.com> Message-ID: Hi, thanks for your quick replies. Sorry, I forgot to mention that I am also using the stand-alone Google Engine for now, with the Eclipse plug-in. And, my development platform is a Mac OS 10.4.11, with JRE 1.6 from Soylatte, and Eclipse v3.4.2. I have read through the dazzle documentation, but I still can't get it to work within the Google App Engine / Eclipse environment. I am not very familiar with Eclipse, so it is very likely that I am not doing things right. Here is the process I have followed to give Dazzle a try to on the Google Engine. But remember, this process doesn't work for me. I hope it makes sense, and that someone can point me to the right direction. many thanks, Vincent. 1- Download 'dazzle' in /tmp/ using subversion (http://biojava.org/wiki/Dazzle): svn checkout http://www.derkholm.net/svn/repos/dazzle/trunk /tmp/dazzle 2- Create new Google App Engine project from Eclipse (after Google Engine plugin installation): Project name: dazzle Package: org.biojava.servlets.dazzle Uncheck 'Use Google Web Toolkit' Finish 3- Import 'dazzle' Jar files into 'dazzle google engine' project import from /tmp/dazzle/jars: bioJava.jar, bytecode.jar, dasmi-model.jar, servlet-api-2.3.jar In Eclipse, 'dazzle' project Properties -> Java Build Path -> Add External Jars 4- Import 'dazzle' src files into 'dazzle google engine' project drag-and-drop /tmp/dazzle/src/org folder into 'Eclipse:/ dazzle/src' folder 5- Import 'dazzle' ressources folder into 'dazzle google engine' project drag-and-drop /tmp/dazzle/resources folder into 'Eclipse:/dazzle' folder 5- Import WEB-INF files into 'dazzle google engine' project drag-and-drop files from /tmp/dazzle/dazzle-webapp into Eclipse:/dazzle/war/. 6- Update web.xml file in Eclipse:/dazzle/war/WEB-INF/ DazzleServerMain org.biojava.servlets.dazzle.DazzleServlet DazzleServerMain /* welcome-file-list: dazzle-welcome.html 6- Run application as web Application in Eclipse check with web browser: http://localhost:8080/das/dsn ________________________________________ From: andreas.prlic at gmail.com [andreas.prlic at gmail.com] On Behalf Of Andreas Prlic [andreas at sdsc.edu] Sent: Saturday, August 08, 2009 9:50 PM To: Rouilly, Vincent Subject: Re: [Biojava-l] BioJava, Dazzle and Google App Engine (Java version) Hi Vincent, did you try following the instructions at http://biojava.org/wiki/Dazzle ? I have never tried to run it using the google app engine, but it works fine for me using Eclipse or standalone... Also have a look at http://biojava.org/wiki/Dazzle:deployment Hope that helps, Andreas On Sat, Aug 8, 2009 at 10:33 AM, Rouilly, Vincent > wrote: Hi, first of all, congratulations and thanks to all BioJava contributors for providing such a great library. Over the last few days, I have been trying to use BioJava on the Google App Engine (with its latest Java support). http://code.google.com/appengine/docs/java/gettingstarted/ Has anyone got experience with that ? I am especially interested in setting up a Dazzle DAS server on the google app engine (basic configuration). It would be a great way for people to easily share their data through DAS. However, whatever DAS request, I always get the exceptions: DataSourceException("Basic installation only covers flat namespace of data-sources"); Any suggestions ? many thanks, Vincent. _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From vincent.rouilly03 at imperial.ac.uk Tue Aug 11 09:16:41 2009 From: vincent.rouilly03 at imperial.ac.uk (Rouilly, Vincent) Date: Tue, 11 Aug 2009 10:16:41 +0100 Subject: [Biojava-l] BioJava, Dazzle and Google App Engine (Java version) In-Reply-To: References: , <59a41c430908081350m1c55ce2ag1f7b51a6673756fe@mail.gmail.com> , Message-ID: Hi, thanks a lot for those who provided me advices. I finally got 'dazzle' to work on the Google App Engine. In short, it means that you can get a free/scalable DAS server on the Google Cloud. check: http://dazzle-das.appspot.com/das/dsn http://dazzle-das.appspot.com/das/test/entry_points If you are interested, you can find below the process I followed. My next target is to get 'dazzle' to fetch annotation directly from the Google Data Store provided in the Google App Engine (as opposed to from a flat file). best, Vincent. ---------------------- Prerequisites: - Java 1.5 - Eclipse 3.4.1 + Google App Engine plug-in from http://code.google.com/appengine/docs/java/tools/eclipse.html - Dazzle code into /tmp/dazzle from: svn checkout http://www.derkholm.net/svn/repos/dazzle/trunk /tmp/dazzle 1- Create new Google App Engine project from Eclipse (after Google Engine plug-in installation): Project name: dazzle Package: org.biojava.servlets.dazzle Uncheck 'Use Google Web Toolkit' Finish 2- Import 'dazzle' Jar files into 'dazzle google engine' project In Eclipse, 'dazzle' project Properties -> Java Build Path -> Add External Jars Import from /tmp/dazzle/jars: bioJava.jar, bytecode.jar, dasmi-model.jar, servlet-api-2.3.jar 3- Import 'dazzle' ressources folder into 'dazzle google engine' project drag-and-drop /tmp/dazzle/resources folder into 'Eclipse:/dazzle' folder 4- Import 'dazzle' src files into 'dazzle google engine' project drag-and-drop /tmp/dazzle/src/org folder into 'Eclipse:/ dazzle/src' folder Comment: you should have 3 errors due to the use of Context in 'MysqlFeatureCache'. For now, I just commented the 2 lines involved. 5- Import /tmp/dazzle/dazzle-webapp files into 'dazzle google engine' project drag-and-drop files from /tmp/dazzle/dazzle-webapp into Eclipse:/dazzle/war/. (do not select WEB-INF folder) 6- Import Jars to WEB-INF/lib drag and drop jar files from /tmp/dazzle/jars into 'dazzle google engine' Eclipse:/dazzle/war/WEB-INF/lib biojava.jar, bytecode.jar, dasmi-model.jar, servelt-api-2.3.jar, dazzle.jar 6- Update web.xml file in Eclipse:/dazzle/war/WEB-INF/ [....] Dazzle org.biojava.servlets.dazzle.DazzleServlet Dazzle /das/* das_welcome.html [...] 6- Run application in Eclipse as web Application (standalone test) check with your web browser: http://localhost:8080/das/dsn 7- If it works, you can create a Google App Engine Application ID and deploy your dazzle server on the cloud. http://code.google.com/appengine/docs/java/tools/uploadinganapp.html ________________________________________ From: Jonathan Warren [jw12 at sanger.ac.uk] Sent: Monday, August 10, 2009 5:28 PM To: Rouilly, Vincent Cc: Andreas Prlic; Richard Holland Subject: Re: [Biojava-l] BioJava, Dazzle and Google App Engine (Java version) I had a look at this and it seems the container works differently from tomcat and resin. I think you may have to change the way dazzle gets it's datasource information? The problem is that the google servlet adds dazzle to this nameComponents list whereas tomcat and resin don't when reading the xml config: public Set getDataSourceIDs(List nameComponents, HttpServletRequest req) throws DataSourceException { System.err.println("Address: " + req.getRemoteAddr()); System.err.println("Host: " + req.getRemoteHost()); if (nameComponents.size() != 0) { System.out.println(nameComponents.toString()); throw new DataSourceException("Basic installation only covers flat namespace of data-sources"); } I got some requests to work by adding /dazzle/* in the web.xml like this: DazzleServerMain /dazzle/* however some requests then work and others don't. Maybe the other guys have some ideas, but I couldn't see a particular reason or quick hack to overcome the difference. On 9 Aug 2009, at 11:50, Rouilly, Vincent wrote: Hi, thanks for your quick replies. Sorry, I forgot to mention that I am also using the stand-alone Google Engine for now, with the Eclipse plug-in. And, my development platform is a Mac OS 10.4.11, with JRE 1.6 from Soylatte, and Eclipse v3.4.2. I have read through the dazzle documentation, but I still can't get it to work within the Google App Engine / Eclipse environment. I am not very familiar with Eclipse, so it is very likely that I am not doing things right. Here is the process I have followed to give Dazzle a try to on the Google Engine. But remember, this process doesn't work for me. I hope it makes sense, and that someone can point me to the right direction. many thanks, Vincent. 1- Download 'dazzle' in /tmp/ using subversion (http://biojava.org/wiki/Dazzle): svn checkout http://www.derkholm.net/svn/repos/dazzle/trunk /tmp/dazzle 2- Create new Google App Engine project from Eclipse (after Google Engine plugin installation): Project name: dazzle Package: org.biojava.servlets.dazzle Uncheck 'Use Google Web Toolkit' Finish 3- Import 'dazzle' Jar files into 'dazzle google engine' project import from /tmp/dazzle/jars: bioJava.jar, bytecode.jar, dasmi-model.jar, servlet-api-2.3.jar In Eclipse, 'dazzle' project Properties -> Java Build Path -> Add External Jars 4- Import 'dazzle' src files into 'dazzle google engine' project drag-and-drop /tmp/dazzle/src/org folder into 'Eclipse:/ dazzle/src' folder 5- Import 'dazzle' ressources folder into 'dazzle google engine' project drag-and-drop /tmp/dazzle/resources folder into 'Eclipse:/dazzle' folder 5- Import WEB-INF files into 'dazzle google engine' project drag-and-drop files from /tmp/dazzle/dazzle-webapp into Eclipse:/dazzle/war/. 6- Update web.xml file in Eclipse:/dazzle/war/WEB-INF/ DazzleServerMain org.biojava.servlets.dazzle.DazzleServlet DazzleServerMain /* welcome-file-list: dazzle-welcome.html 6- Run application as web Application in Eclipse check with web browser: http://localhost:8080/das/dsn ________________________________________ From: andreas.prlic at gmail.com [andreas.prlic at gmail.com] On Behalf Of Andreas Prlic [andreas at sdsc.edu] Sent: Saturday, August 08, 2009 9:50 PM To: Rouilly, Vincent Subject: Re: [Biojava-l] BioJava, Dazzle and Google App Engine (Java version) Hi Vincent, did you try following the instructions at http://biojava.org/wiki/Dazzle ? I have never tried to run it using the google app engine, but it works fine for me using Eclipse or standalone... Also have a look at http://biojava.org/wiki/Dazzle:deployment Hope that helps, Andreas On Sat, Aug 8, 2009 at 10:33 AM, Rouilly, Vincent > wrote: Hi, first of all, congratulations and thanks to all BioJava contributors for providing such a great library. Over the last few days, I have been trying to use BioJava on the Google App Engine (with its latest Java support). http://code.google.com/appengine/docs/java/gettingstarted/ Has anyone got experience with that ? I am especially interested in setting up a Dazzle DAS server on the google app engine (basic configuration). It would be a great way for people to easily share their data through DAS. However, whatever DAS request, I always get the exceptions: DataSourceException("Basic installation only covers flat namespace of data-sources"); Any suggestions ? many thanks, Vincent. _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l Jonathan Warren Senior Developer and DAS coordinator jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE. From holland at eaglegenomics.com Tue Aug 11 09:17:03 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Tue, 11 Aug 2009 10:17:03 +0100 Subject: [Biojava-l] ParseException when using interleaved Nexus file In-Reply-To: References: <30109C99-0ADF-461D-AB8A-B9800C4111D1@eaglegenomics.com> Message-ID: <32FD8C34-2F30-4159-A9FB-D809784B7ED0@eaglegenomics.com> I've found the problem - "interleave=yes" is not valid according to the official NEXUS format spec which the parser was written against. (Maddison et al., 1997) Interleaved file are supposed to only include the word "interleave" - it takes no parameters. Non-interleaved files shouldn't mention it at all. I've modified the parser to tolerate this but I'd be interested to know where the invalid token came from - was it added manually, or by an existing piece of publically available software? The modification has been made in the trunk of the biojava-live subversion repository. cheers, Richard On 7 Aug 2009, at 11:10, David Johnson wrote: > Hi Richard, > > Actually the original exception was thrown in a different file that my > supervisor tried uploading to a Web app I'm developing that uses the > BioJava Nexus parser, but can't get hold of that particular file > today. So the one I provided the link for was just another example of > an interleaved Nexus file I Googled for when I got your first email > this morning, as I figured they'd probably be the same formatting. But > I remember it's definitely the same exception in both cases. > > I had a quick look in the example I provided today, and the > interleave=yes token is definitely in the header of the data block, > and is also definitely in the Format line. > > Oh, just FYI, I'm using the BioJava 1.7 binary distribution > (http://www.biojava.org/download/bj17/bin/biojava.jar). > > Cheers, > -David > > 2009/8/7 Richard Holland : >> Thanks David. One more quick question - is this the exact file that >> is >> throwing the exception? I haven't tested it yet - but if I could test >> against the real file that is throwing the problem, that would help >> me find >> out exactly what's going wrong. >> >> For what it's worth, the exception is normally thrown when more >> than one >> interleave=yes/no token is found in the header of the Data or >> Characters >> block, or when the interleave token appears in a line other than >> the Format >> line of the header. >> >> cheers, >> Richard >> >> On 7 Aug 2009, at 10:28, David Johnson wrote: >> >>> Hi Richard, >>> >>> Thanks for your mail. An example of an interleaved file can be >>> found here: >>> >>> http://www.molecularevolution.org/si/resources/fileformats/files/dna.nex >>> >>> where the link pointing to the example file is from >>> http://www.molecularevolution.org/si/resources/fileformats/ and >>> under >>> the NEXUS section. >>> >>> The specific error message is: >>> "org.biojava.bio.seq.io.ParseException: >>> Found unexpected token interleave=yes in CHARACTERS block" >>> >>> So it looks like the error is thrown reading the "interleave" >>> parameter in the top of the data block, and before reaching the >>> actual >>> interleaved matrix data. Full stacktrace in attached .txt. >>> >>> Cheers, >>> -David >>> >>> 2009/8/7 Richard Holland : >>>> >>>> Could you point me to an example of an interleaved file? >>>> >>>> And also the full stack trace of the exception that gets thrown? >>>> >>>> cheers, >>>> Richard >>>> >>>> On 6 Aug 2009, at 18:03, David Johnson wrote: >>>> >>>>> Hi everyone, >>>>> >>>>> A quick question about the BioJava Nexus parser. I've been >>>>> trying to >>>>> use the Nexus file parser, simply by doing something like: >>>>> >>>>> NexusFileBuilder builder = new NexusFileBuilder(); >>>>> NexusFileFormat.parseFile(builder, f); >>>>> >>>>> However, when parsing Nexus files that are interleaved, I get a >>>>> ParseException. >>>>> >>>>> Is there a way to setup the parser provided by BioJava to handle >>>>> interleaved Nexus files? >>>>> >>>>> Thanks, >>>>> -David >>>>> -- >>>>> -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From d.johnson at reading.ac.uk Tue Aug 11 10:12:18 2009 From: d.johnson at reading.ac.uk (David Johnson) Date: Tue, 11 Aug 2009 11:12:18 +0100 Subject: [Biojava-l] ParseException when using interleaved Nexus file In-Reply-To: <32FD8C34-2F30-4159-A9FB-D809784B7ED0@eaglegenomics.com> References: <30109C99-0ADF-461D-AB8A-B9800C4111D1@eaglegenomics.com> <32FD8C34-2F30-4159-A9FB-D809784B7ED0@eaglegenomics.com> Message-ID: Hi Richard, OK that's good to know... I suppose that's the problem with specifications - people don't always follow them! But I get the impression either some people think that using interleave=yes/no is standard practice, or it could be being generated by some other phylo software (e.g. maybe PAUP or some other tools). I had a talk with my supervisor and he actually can't find the specific programs that have been putting that in, but looking at a range of his Nexus files, there's quite a few that seem to use put in the yes/no bits, some files he received from other researchers. Are the modifications available in the latest automated build (on CruiseControl)? Cheers, -David 2009/8/11 Richard Holland > I've found the problem - "interleave=yes" is not valid according to the > official NEXUS format spec which the parser was written against. (Maddison > et al., 1997) > > Interleaved file are supposed to only include the word "interleave" - it > takes no parameters. Non-interleaved files shouldn't mention it at all. > > I've modified the parser to tolerate this but I'd be interested to know > where the invalid token came from - was it added manually, or by an existing > piece of publically available software? > > The modification has been made in the trunk of the biojava-live subversion > repository. > > cheers, > Richard > > > From holland at eaglegenomics.com Tue Aug 11 10:50:50 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Tue, 11 Aug 2009 11:50:50 +0100 Subject: [Biojava-l] ParseException when using interleaved Nexus file In-Reply-To: References: <30109C99-0ADF-461D-AB8A-B9800C4111D1@eaglegenomics.com> <32FD8C34-2F30-4159-A9FB-D809784B7ED0@eaglegenomics.com> Message-ID: It should already be on CruiseControl. Standards in bioinformatics are a pain - people write them to describe the format of files their software outputs, then the very same people then produce files that break those standards without any additional documentation or explanation. (Genbank are one of the biggest offenders!) It makes it very hard to write parsers, because if you stick to the official spec there will always be files that don't work yet people insist are still valid, yet without prior documented evidence of invalid files that are considered to be valid, it is impossible to write a parser to cater for them. :) cheers, Richard On 11 Aug 2009, at 11:12, David Johnson wrote: > Hi Richard, > > OK that's good to know... I suppose that's the problem with > specifications - people don't always follow them! > > But I get the impression either some people think that using > interleave=yes/no is standard practice, or it could be being > generated by some other phylo software (e.g. maybe PAUP or some > other tools). > > I had a talk with my supervisor and he actually can't find the > specific programs that have been putting that in, but looking at a > range of his Nexus files, there's quite a few that seem to use put > in the yes/no bits, some files he received from other researchers. > > Are the modifications available in the latest automated build (on > CruiseControl)? > > Cheers, > -David > > 2009/8/11 Richard Holland > I've found the problem - "interleave=yes" is not valid according to > the official NEXUS format spec which the parser was written against. > (Maddison et al., 1997) > > Interleaved file are supposed to only include the word "interleave" > - it takes no parameters. Non-interleaved files shouldn't mention it > at all. > > I've modified the parser to tolerate this but I'd be interested to > know where the invalid token came from - was it added manually, or > by an existing piece of publically available software? > > The modification has been made in the trunk of the biojava-live > subversion repository. > > cheers, > Richard > > -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From andreas at sdsc.edu Tue Aug 11 21:04:11 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 11 Aug 2009 14:04:11 -0700 Subject: [Biojava-l] BioJava, Dazzle and Google App Engine (Java version) In-Reply-To: References: <59a41c430908081350m1c55ce2ag1f7b51a6673756fe@mail.gmail.com> Message-ID: <59a41c430908111404o4bbabe9cw3a263fad6a9ee58a@mail.gmail.com> Hi Vincent, interesting approach... Want to add your notes to the wiki pages as well? Thanks, Andreas On Tue, Aug 11, 2009 at 2:16 AM, Rouilly, Vincent < vincent.rouilly03 at imperial.ac.uk> wrote: > Hi, > > thanks a lot for those who provided me advices. > I finally got 'dazzle' to work on the Google App Engine. > > In short, it means that you can get a free/scalable DAS server on the > Google Cloud. > > check: > http://dazzle-das.appspot.com/das/dsn > http://dazzle-das.appspot.com/das/test/entry_points > > If you are interested, you can find below the process I followed. > My next target is to get 'dazzle' to fetch annotation directly from the > Google Data Store provided in the Google App Engine (as opposed to from a > flat file). > > best, > > Vincent. > ---------------------- > > Prerequisites: > - Java 1.5 > - Eclipse 3.4.1 + Google App Engine plug-in from > http://code.google.com/appengine/docs/java/tools/eclipse.html > - Dazzle code into /tmp/dazzle from: svn checkout > http://www.derkholm.net/svn/repos/dazzle/trunk /tmp/dazzle > > > 1- Create new Google App Engine project from Eclipse (after Google Engine > plug-in installation): > Project name: dazzle > Package: org.biojava.servlets.dazzle > Uncheck 'Use Google Web Toolkit' > Finish > > 2- Import 'dazzle' Jar files into 'dazzle google engine' project > In Eclipse, 'dazzle' project Properties -> Java Build Path -> Add > External Jars > Import from /tmp/dazzle/jars: bioJava.jar, bytecode.jar, > dasmi-model.jar, servlet-api-2.3.jar > > 3- Import 'dazzle' ressources folder into 'dazzle google engine' project > drag-and-drop /tmp/dazzle/resources folder into 'Eclipse:/dazzle' > folder > > 4- Import 'dazzle' src files into 'dazzle google engine' project > drag-and-drop /tmp/dazzle/src/org folder into 'Eclipse:/ dazzle/src' > folder > Comment: you should have 3 errors due to the use of Context in > 'MysqlFeatureCache'. For now, I just commented the 2 lines involved. > > 5- Import /tmp/dazzle/dazzle-webapp files into 'dazzle google engine' > project > drag-and-drop files from /tmp/dazzle/dazzle-webapp into > Eclipse:/dazzle/war/. (do not select WEB-INF folder) > > 6- Import Jars to WEB-INF/lib > drag and drop jar files from /tmp/dazzle/jars into 'dazzle google > engine' Eclipse:/dazzle/war/WEB-INF/lib > biojava.jar, bytecode.jar, dasmi-model.jar, servelt-api-2.3.jar, > dazzle.jar > > 6- Update web.xml file in Eclipse:/dazzle/war/WEB-INF/ > > [....] > > Dazzle > > org.biojava.servlets.dazzle.DazzleServlet > > > > Dazzle > /das/* > > > > das_welcome.html > > [...] > > 6- Run application in Eclipse as web Application (standalone test) > check with your web browser: http://localhost:8080/das/dsn > > 7- If it works, you can create a Google App Engine Application ID and > deploy your dazzle server on the cloud. > http://code.google.com/appengine/docs/java/tools/uploadinganapp.html > > ________________________________________ > From: Jonathan Warren [jw12 at sanger.ac.uk] > Sent: Monday, August 10, 2009 5:28 PM > To: Rouilly, Vincent > Cc: Andreas Prlic; Richard Holland > Subject: Re: [Biojava-l] BioJava, Dazzle and Google App Engine (Java > version) > > I had a look at this and it seems the container works differently from > tomcat and resin. I think you may have to change the way dazzle gets it's > datasource information? > The problem is that the google servlet adds dazzle to this nameComponents > list whereas tomcat and resin don't when reading the xml config: > > public Set getDataSourceIDs(List nameComponents, HttpServletRequest req) > throws DataSourceException > { > System.err.println("Address: " + req.getRemoteAddr()); > System.err.println("Host: " + req.getRemoteHost()); > > > if (nameComponents.size() != 0) { > System.out.println(nameComponents.toString()); > throw new DataSourceException("Basic installation only covers flat > namespace of data-sources"); > } > > > > I got some requests to work by adding > /dazzle/* in the web.xml like this: > > DazzleServerMain > /dazzle/* > > > however some requests then work and others don't. > > Maybe the other guys have some ideas, but I couldn't see a particular > reason or quick hack to overcome the difference. > > On 9 Aug 2009, at 11:50, Rouilly, Vincent wrote: > > > Hi, > > thanks for your quick replies. > > Sorry, I forgot to mention that I am also using the stand-alone Google > Engine for now, with the Eclipse plug-in. > And, my development platform is a Mac OS 10.4.11, with JRE 1.6 from > Soylatte, and Eclipse v3.4.2. > > I have read through the dazzle documentation, but I still can't get it to > work within the Google App Engine / Eclipse environment. > I am not very familiar with Eclipse, so it is very likely that I am not > doing things right. > > Here is the process I have followed to give Dazzle a try to on the Google > Engine. But remember, this process doesn't work for me. > I hope it makes sense, and that someone can point me to the right > direction. > > many thanks, > Vincent. > > 1- Download 'dazzle' in /tmp/ using subversion ( > http://biojava.org/wiki/Dazzle): > svn checkout http://www.derkholm.net/svn/repos/dazzle/trunk /tmp/dazzle > > 2- Create new Google App Engine project from Eclipse (after Google Engine > plugin installation): > Project name: dazzle > Package: org.biojava.servlets.dazzle > Uncheck 'Use Google Web Toolkit' > Finish > > 3- Import 'dazzle' Jar files into 'dazzle google engine' project > import from /tmp/dazzle/jars: bioJava.jar, bytecode.jar, dasmi-model.jar, > servlet-api-2.3.jar > In Eclipse, 'dazzle' project Properties -> Java Build Path -> Add External > Jars > > 4- Import 'dazzle' src files into 'dazzle google engine' project > drag-and-drop /tmp/dazzle/src/org folder into 'Eclipse:/ dazzle/src' folder > > 5- Import 'dazzle' ressources folder into 'dazzle google engine' project > drag-and-drop /tmp/dazzle/resources folder into 'Eclipse:/dazzle' folder > > 5- Import WEB-INF files into 'dazzle google engine' project > drag-and-drop files from /tmp/dazzle/dazzle-webapp into > Eclipse:/dazzle/war/. > > 6- Update web.xml file in Eclipse:/dazzle/war/WEB-INF/ > > DazzleServerMain > > org.biojava.servlets.dazzle.DazzleServlet > > > > DazzleServerMain > /* > > > welcome-file-list: dazzle-welcome.html > > 6- Run application as web Application in Eclipse > check with web browser: http://localhost:8080/das/dsn > > > > ________________________________________ > From: andreas.prlic at gmail.com [ > andreas.prlic at gmail.com] On Behalf Of > Andreas Prlic [andreas at sdsc.edu] > Sent: Saturday, August 08, 2009 9:50 PM > To: Rouilly, Vincent > Subject: Re: [Biojava-l] BioJava, Dazzle and Google App Engine (Java > version) > > Hi Vincent, > > did you try following the instructions at > http://biojava.org/wiki/Dazzle ? > > I have never tried to run it using the google app engine, but it works fine > for me using Eclipse or standalone... Also have a look at > http://biojava.org/wiki/Dazzle:deployment > > Hope that helps, > Andreas > > > > On Sat, Aug 8, 2009 at 10:33 AM, Rouilly, Vincent < > vincent.rouilly03 at imperial.ac.uk> > wrote: > Hi, > > first of all, congratulations and thanks to all BioJava contributors for > providing such a great library. > > Over the last few days, I have been trying to use BioJava on the Google App > Engine (with its latest Java support). > http://code.google.com/appengine/docs/java/gettingstarted/ > > Has anyone got experience with that ? > > I am especially interested in setting up a Dazzle DAS server on the google > app engine (basic configuration). > It would be a great way for people to easily share their data through DAS. > > However, whatever DAS request, I always get the exceptions: > DataSourceException("Basic installation only covers flat namespace of > data-sources"); > > Any suggestions ? > > many thanks, > > Vincent. > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org Biojava-l at lists.open-bio.org> > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > Jonathan Warren > Senior Developer and DAS coordinator > jw12 at sanger.ac.uk > Ext: 2314 > Telephone: 01223 492314 > > > > > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a compa ny > registered in England with number 2742969, whose registered office is 2 15 > Euston Road, London, NW1 2BE. > From gwaldon at geneinfinity.org Sun Aug 16 16:27:07 2009 From: gwaldon at geneinfinity.org (George Waldon) Date: Sun, 16 Aug 2009 12:27:07 -0400 Subject: [Biojava-l] Where notes are coming from? Message-ID: <20090816162707.90836.qmail@mxw1102.verio-web.com> Hi, Simple question, I am using a ChangeForwarder.Retyper to forward note changes. When I receive a ChangeEvent with the ChangeType Note.VALUE, how do I find out the RichFeature the change is coming from? What is the intended design? Thanks, George From holland at eaglegenomics.com Sun Aug 16 16:51:50 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Sun, 16 Aug 2009 17:51:50 +0100 Subject: [Biojava-l] Where notes are coming from? In-Reply-To: <20090816162707.90836.qmail@mxw1102.verio-web.com> References: <20090816162707.90836.qmail@mxw1102.verio-web.com> Message-ID: Good question - I don't think you can, as the relationship is unidirectional (it wasn't intended for notes to be passed around independent of their features). In the case of ChangeForwarders listening only for notes, this causes a bit of a problem - but I think you will also get a Change event against the Feature itself to say a note has been added, in which case you might be able to write logic to associate the two Change events to work out what's going on. On 16 Aug 2009, at 17:27, George Waldon wrote: > Hi, > > Simple question, I am using a ChangeForwarder.Retyper to forward > note changes. When I receive a ChangeEvent with the ChangeType > Note.VALUE, how do I find out the RichFeature the change is coming > from? What is the intended design? > > Thanks, > George > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From andreas at sdsc.edu Sun Aug 16 21:41:03 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Sun, 16 Aug 2009 14:41:03 -0700 Subject: [Biojava-l] plans for next months Message-ID: <59a41c430908161441l3ae3ebao524237a1b7b868fe@mail.gmail.com> Hi, Here a quick summary of what I propose to be our action plan for the next months for BioJava: * I would like to call for a code-freeze in 2 weeks (or so) in order to finalize the new modularized and mavenized version of biojava for the developers. The current developmental trunk will remain permanently frozen and all future work should continue at a new location in SVN. As such it will be important that all developers commit any changes they are working on before that. * We will update the documentation for how to obtain a new mavenized checkout on the wiki. * After the change the new modules need to be tested and if no major problems are found, the ok will be given to continue working on the new modules (at the new location) * All developers should obtain a new checkout. * We need to identify sub-module leaders who will take over leadership of the sub-modules. In order to come up with a new release of biojava we should continue development on the new modules for a few months. Talking off list with Richard Holland it looks like we will have a hackaton in January in Cambridge, U.K. (details to be finalized and announced). I suggest that we use that opportunity to focus on further developing the modules and make a new public BioJava release shortly after that. At the present I see the following topics that would be great to work on until and during the hackaton in order to prepare a shiny new version of BioJava for public release: + Work on standardizing the organization of the modules (tests, examples, source, docu etc.) + Add new modules + Improve existing modules + Anything the module leaders deem necessary for their modules. + Use OSGI for visualisation related modules I can post a more detailed and specific list of things to work on if people are interested. Andreas From andreas at sdsc.edu Wed Aug 19 21:30:17 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Wed, 19 Aug 2009 14:30:17 -0700 Subject: [Biojava-l] BioJava PDB question In-Reply-To: References: <59a41c430908051056o7a0aa0a0x6ea3aece8a2714c@mail.gmail.com> Message-ID: <59a41c430908191430q573f8567qce49fff240829717@mail.gmail.com> Hi Scooter, A while ago you asked me about H-Bond calculations for biojava. I committed some code for this yesterday. Check out org.biojava.bio.structure.secstruc.SecStruc It is still a bit unrefined, but once complete this code should be able to calculate a secondary structure assignment. So far it creates virtual H-atoms and uses them to calculate H-Bond energies and tracks H-bond patterns ... Cheers, Andreas From christoph.gille at charite.de Sun Aug 23 21:06:44 2009 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Sun, 23 Aug 2009 23:06:44 +0200 Subject: [Biojava-l] How STRAP can contribute to BJ3 Message-ID: <6dc74c5b9b77a93f3c508d3246b10978.squirrel@webmail.charite.de> Hi, As the developer of STRAP http://3d-alignment.eu I am following with interest the discussion on the new Biojava (BJ3) design. STRAP is a free workbench for proteins similar to Jalview or Cinema. Here I would like to open a discussion on "How STRAP could contribute to the Biojava BJ3" and vice versa "How Biojava can be used to extend the functionality of STRAP". While STRAP is heavily used as a stand alone application and is a protein/alignment viewer in currently 7 Web-services such as PDBSum and Prodom, it has been used as an API/toolbox only by a few people. In most of these cases Biojava and STRAP had been used simultaneously because the functionalities of both toolkits are complementary. I start the discussion by explaining the plugin interface of STRAP. For this purpose I created the Web page http://3d-alignment.eu/biojava/PluginsForStrap.html The page explains how plugins with Biojava are written and deployed on Web-pages. It contains two examples which are ready to be clicked on a computer with Java-Web-Start. The basic idea is that by clicking a Web link a communication between the Browser and STRAP is started which results in loading a remote Jar file together with the most recent Biojava.jar through a customized ClassLoader. The plugin can then act in response to other mouse clicks in the Web page. STRAP contains different graphical dialogs for different types of plugins. E.g. plugins that implement the interface Superimpose3D are opened in the superimposition-dialog. Conversely, plugins that implement SecondaryStructure_Predictor are opened in the dialog for predicting 3D-structure from sequence. The advantage is that the developer of a plugin does not need to provide a GUI and can concentrate on the logic of the algorithm. Here is the Web-form of one of the examples in the above Web-page.
The important Web-variable is "script". It contains the script command script name-of-plugin-class , Jar-files for the plugin. To use Biojava, the jar-file biojava.jar is contained in the list of jar-files. Cheers Christoph From andreas at sdsc.edu Mon Aug 24 04:18:14 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Sun, 23 Aug 2009 21:18:14 -0700 Subject: [Biojava-l] BioJava code freeze, modularization and action items for sub modules Message-ID: <59a41c430908232118k2fff9564of1a45fba447eb922@mail.gmail.com> Hi, In order to push the modularization and migration to Maven, I would like to declare a code freeze on the current developmental trunk. Please commit all new changes by Thursday 27th of August 23:00 GMT. In the week after I would like to refactor the code base and commit the initial set of modules to a new developmental trunk. All future development will happen on that new trunk. You will be able to follow the ongoing status of this at http://biojava.org/wiki/BioJava:MavenMigration Once the modules are in place it is a good moment to hand over the leadership of the sub-modules to the new module-project leaders. It will be up to the module-lead to take the modules into the direction that he/she feels important. I would like to take this opportunity to suggest a couple of people as module-leaders and propose some action items for the modules. Feel free to comment or make additional suggestions... Here a list of modules / action items and the people that I would propose to become module leaders: Module: biojava-core Lead: Andreas Prlic - break the new modules out of core - bring up to modern Java standards, use Generics - declare old/unused code obsolete - don;t break backwards compatibility Module: biojava-sequence Lead: Richard Holland - Bring in Richard's new code that he started to develop on the biojava-3 branch. - provide a more scaleable and efficient basis for dealing with large sequence files Module: biojava-alignment Lead: Andreas Draeger - allow better access to underlying dynamic programming data structures - allow more customizable display of pairwise alignments (HTML/plain text, etc) Module : biojava-blast Lead: still looking for a leader - provide access to all details of the blast output - add support for RPS blast Module: biojava-phylo Lead: Scooter Willis - provide improved NJtree /Jalview Module: biojava-biosql Lead: Richard Holland - merge the new biojava-sequence module with the current biojava-biosql code Module: biojava-structure Lead: Andreas Prlic - add support for SCOP file parsing - add support for easy access of domains (in terms of coordinates) - add secondary structure assignment - improve structure alignments - better integration with 3D viewers (Jmol, RCSB viewers) Module: biojava-web services: The details seem still to be under discussion and perhaps we need multiple modules here? also what about REST vs. SOAP? To be discussed. People who expressed interest are: Niall Haslam,Scooter Willis, Sylvain Foisy Module?: biojava-ws-blast Module?: biojava-ws-biolit Module: biojava-sequencing Lead: ??? - support FastQ files - support parsing of output for various new sequencing machines This is only an initial set of modules and I think it is safe to say that more modules will be added after more discussions (and people volunteering to contribute). Andreas From andreas at sdsc.edu Mon Aug 24 05:36:36 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Sun, 23 Aug 2009 22:36:36 -0700 Subject: [Biojava-l] How STRAP can contribute to BJ3 In-Reply-To: <6dc74c5b9b77a93f3c508d3246b10978.squirrel@webmail.charite.de> References: <6dc74c5b9b77a93f3c508d3246b10978.squirrel@webmail.charite.de> Message-ID: <59a41c430908232236y191778a5g3fa9bd981246ebe7@mail.gmail.com> Hi Christoph, In principle there are the following ways to support BioJava: * You can help and answer support emails on the mailing lists. * You can provide and/or maintain documentation in the biojava wiki. * You can submit bug fixes by email or to the mailing lists * You can contribute to the source code. Regarding your question how BioJava can help Strap, I am not sure how much biojava code is already used by the software and there seems to be some overlap in functionality. I tried to have a look at the Strap code, but I could find a link to the source. The project page says the license is GPL, so just a thought: if you are interested in making your project more transparent, you might consider hosting it at sourceforge or google code ... In case you are interested to learn more about BioJava, the Cookbook provides an overview of some frequently used features: http://biojava.org/wiki/BioJava:CookBook Hope that helps, Andreas On Sun, Aug 23, 2009 at 2:06 PM, Dr. Christoph Gille wrote: > > Hi, > > As the developer of STRAP http://3d-alignment.eu I am following with > interest the discussion on the new Biojava (BJ3) design. > > STRAP is a free workbench for proteins similar to Jalview or Cinema. > > Here I would like to open a discussion on > > "How STRAP could contribute to the Biojava BJ3" > > and vice versa > > "How Biojava can be used to extend the functionality of STRAP". > > While STRAP is heavily used as a stand alone application and is a > protein/alignment viewer in currently 7 Web-services such as PDBSum > and Prodom, it has been used as an API/toolbox only by a few people. > In most of these cases Biojava and STRAP had been used simultaneously > because the functionalities of both toolkits are complementary. > > I start the discussion by explaining the plugin interface of STRAP. > > For this purpose I created the Web page > http://3d-alignment.eu/biojava/PluginsForStrap.html > > The page explains how plugins with Biojava are written and deployed on > Web-pages. It contains two examples which are ready to be clicked on a > computer with Java-Web-Start. > > The basic idea is that by clicking a Web link a communication between > the Browser and STRAP is started which results in loading a remote Jar > file together with the most recent Biojava.jar through a customized > ClassLoader. The plugin can then act in response to other mouse clicks in the Web page. > > STRAP contains different graphical dialogs for different types of > plugins. ?E.g. plugins that implement the interface Superimpose3D are > opened in the superimposition-dialog. ?Conversely, plugins that > implement SecondaryStructure_Predictor are opened in the dialog for > predicting 3D-structure from sequence. The advantage is that the > developer of a plugin does not need to provide a GUI and can > concentrate on the logic of the algorithm. > > Here is the Web-form of one of the examples in the above Web-page. > >
> ? > ? > ? >
> > The important Web-variable is "script". It contains the script command > > ?script ? name-of-plugin-class , ?Jar-files for the plugin. > > To use Biojava, the jar-file biojava.jar is contained in the list of jar-files. > > > Cheers > > Christoph > > > > _______________________________________________ > 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 Mon Aug 24 16:14:50 2009 From: koen.bruynseels at cropdesign.com (koen.bruynseels at cropdesign.com) Date: Mon, 24 Aug 2009 18:14:50 +0200 Subject: [Biojava-l] Koen Bruynseels is out of the office. Message-ID: I will be out of the office starting 08/21/2009 and will not return until 08/27/2009. I will respond to your message when I return. From holland at eaglegenomics.com Mon Aug 24 17:30:31 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Mon, 24 Aug 2009 18:30:31 +0100 Subject: [Biojava-l] [Biojava-dev] Adding profile-profile alignment algorithms to Biojava In-Reply-To: <9551386.424471251132481047.JavaMail.coremail@app180.163.com> References: <9551386.424471251132481047.JavaMail.coremail@app180.163.com> Message-ID: Contributions of code would be welcome! Are you volunteering? :) cheers, Richard On 24 Aug 2009, at 17:48, simpleyrx wrote: > > Experts, > > Profile-profile alignment or HMM-HMM alignments have > become more important in protein bioinformation field than ever > before. So I think, if we can implement Profile-profile alignment > and HMM-HMM alignments algorithms in Biojava package, it will be > more useful to the researchers who interested in protein > bioinformatics. > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From heuermh at acm.org Thu Aug 27 17:01:31 2009 From: heuermh at acm.org (Michael Heuer) Date: Thu, 27 Aug 2009 13:01:31 -0400 (EDT) Subject: [Biojava-l] [Biojava-dev] BioJava code freeze, modularization and action items for sub modules In-Reply-To: <59a41c430908232118k2fff9564of1a45fba447eb922@mail.gmail.com> Message-ID: Andreas Prlic wrote: > Here a list of modules / action items and the people that I would propose to > become module leaders: > ... > > Module: biojava-sequencing Lead: Michael Heuer > - support FastQ files > - support parsing of output for various new sequencing machines I have volunteered on the open-bio mailing list to implement FASTQ support. A nice collection of test data is being created in collaboration with the other open-bio projects. If anyone has interest in a particular data set, please let me know, as I will also need data for performance tuning. michael From andreas at sdsc.edu Thu Aug 27 17:30:08 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 27 Aug 2009 10:30:08 -0700 Subject: [Biojava-l] [Biojava-dev] BioJava code freeze, modularization and action items for sub modules In-Reply-To: References: <59a41c430908232118k2fff9564of1a45fba447eb922@mail.gmail.com> Message-ID: <59a41c430908271030p7318c468u8d145f5750369cb3@mail.gmail.com> Great, thanks for "volunteering", Michael. To add another Module: biojava-das : Lead: Jonathan Warren probably deprecate the old DAS code in BJ and replace it with the up to date Dasobert library Thanks to Jonathan for volunteering as well. Andreas On Thu, Aug 27, 2009 at 10:01 AM, Michael Heuer wrote: > Andreas Prlic wrote: > >> Here a list of modules / action items and the people that I would propose to >> become module leaders: >> ... >> >> Module: biojava-sequencing Lead: ?Michael Heuer >> ? - support FastQ files >> ? - support parsing of output for various new sequencing machines > > I have volunteered on the open-bio mailing list to implement FASTQ > support. ?A nice collection of test data is being created in collaboration > with the other open-bio projects. ?If anyone has interest in a particular > data set, please let me know, as I will also need data for performance > tuning. > > ? michael > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From markjschreiber at gmail.com Fri Aug 28 05:37:59 2009 From: markjschreiber at gmail.com (Mark Schreiber) Date: Fri, 28 Aug 2009 13:37:59 +0800 Subject: [Biojava-l] [Biojava-dev] BioJava code freeze, modularization and action items for sub modules In-Reply-To: <59a41c430908271030p7318c468u8d145f5750369cb3@mail.gmail.com> References: <59a41c430908232118k2fff9564of1a45fba447eb922@mail.gmail.com> <59a41c430908271030p7318c468u8d145f5750369cb3@mail.gmail.com> Message-ID: <93b45ca50908272237k2485a1d8le343a8b1dc10ae12@mail.gmail.com> I'm happy to volunteer code for: 1. BLASTXML parser as long as I can change the ssbind APIs (other parsers could go into a legacy module??). Actually I would prefer to completely decouple from the sequence/ feature module as many people would like a blast parser without the rest of biojava thrown in. 2. BioSQL/ JPA bindings. I have already generated JPA compliant entity beans for mapping to BioSQL as well as JPA handler code that makes sure modifications presist properly. Currently the object model very closely follows the BioSQL table structure. Also the current beans are what people call Anaemic beans in that they hold data and provide getters and setters but no biological behaivour. I can easily provide bio-smarts to the beans but it might be better to hold off until there is a module that contains sequence/feature interfaces which the beans could implement. 3. Happy to provide code for an enterprise module if there is sufficient interest. This would probably take the form of SessionBeans and WebServices that can be deployed to Glassfish/ JBoss etc to provide biological services for people who want to make client server or SOA apps. - Mark On Fri, Aug 28, 2009 at 1:30 AM, Andreas Prlic wrote: > Great, thanks for "volunteering", Michael. > > To add another Module: > > biojava-das : Lead: Jonathan Warren > probably deprecate the old DAS code in BJ and replace it with > the up to date Dasobert library > > Thanks to Jonathan for volunteering as well. > > Andreas > > > > > On Thu, Aug 27, 2009 at 10:01 AM, Michael Heuer wrote: > > Andreas Prlic wrote: > > > >> Here a list of modules / action items and the people that I would > propose to > >> become module leaders: > >> ... > >> > >> Module: biojava-sequencing Lead: Michael Heuer > >> - support FastQ files > >> - support parsing of output for various new sequencing machines > > > > I have volunteered on the open-bio mailing list to implement FASTQ > > support. A nice collection of test data is being created in > collaboration > > with the other open-bio projects. If anyone has interest in a particular > > data set, please let me know, as I will also need data for performance > > tuning. > > > > michael > > > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From andreas at sdsc.edu Fri Aug 28 15:10:03 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Fri, 28 Aug 2009 08:10:03 -0700 Subject: [Biojava-l] [Biojava-dev] BioJava code freeze, modularization and action items for sub modules In-Reply-To: <93b45ca50908272237k2485a1d8le343a8b1dc10ae12@mail.gmail.com> References: <59a41c430908232118k2fff9564of1a45fba447eb922@mail.gmail.com> <59a41c430908271030p7318c468u8d145f5750369cb3@mail.gmail.com> <93b45ca50908272237k2485a1d8le343a8b1dc10ae12@mail.gmail.com> Message-ID: <59a41c430908280810s1720cfckbc36168f2fbc73a8@mail.gmail.com> Thanks, Mark. Guess we should start collecting all this info on a wiki page. I started to edit http://biojava.org/wiki/BioJava:Modules module leaders: feel free to edit the plans for your module... Andreas On Thu, Aug 27, 2009 at 10:37 PM, Mark Schreiber wrote: - Show quoted text - On Thu, Aug 27, 2009 at 10:37 PM, Mark Schreiber wrote: > I'm happy to volunteer code for: > > BLASTXML parser as long as I can change the ssbind APIs (other parsers could > go into a legacy module??). Actually I would prefer to completely decouple > from the sequence/ feature module as many people would like a blast parser > without the rest of biojava thrown in. > BioSQL/ JPA bindings. I have already generated JPA compliant entity beans > for mapping to BioSQL as well as JPA handler code that makes sure > modifications presist properly. Currently the object model very closely > follows the BioSQL table structure.? Also the current beans are what people > call Anaemic beans in that they hold data and provide getters and setters > but no biological behaivour. I can easily provide bio-smarts to the beans > but it might be better to hold off until there is a module that contains > sequence/feature interfaces which the beans could implement. > Happy to provide code for an enterprise module if there is sufficient > interest. This would probably take the form of SessionBeans and WebServices > that can be deployed to Glassfish/ JBoss etc to provide biological services > for people who want to make client server or SOA apps. > > - Mark > > > On Fri, Aug 28, 2009 at 1:30 AM, Andreas Prlic wrote: >> >> Great, thanks for "volunteering", Michael. >> >> To add another Module: >> >> biojava-das : Lead: Jonathan Warren >> probably deprecate the old DAS code in BJ and replace it with >> the up to date Dasobert library >> >> Thanks to Jonathan for volunteering as well. >> >> Andreas >> >> >> >> >> On Thu, Aug 27, 2009 at 10:01 AM, Michael Heuer wrote: >> > Andreas Prlic wrote: >> > >> >> Here a list of modules / action items and the people that I would >> >> propose to >> >> become module leaders: >> >> ... >> >> >> >> Module: biojava-sequencing Lead: ?Michael Heuer >> >> ? - support FastQ files >> >> ? - support parsing of output for various new sequencing machines >> > >> > I have volunteered on the open-bio mailing list to implement FASTQ >> > support. ?A nice collection of test data is being created in >> > collaboration >> > with the other open-bio projects. ?If anyone has interest in a >> > particular >> > data set, please let me know, as I will also need data for performance >> > tuning. >> > >> > ? michael >> > >> > _______________________________________________ >> > biojava-dev mailing list >> > biojava-dev at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > >> >> _______________________________________________ >> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l > > From ehaugen at u.washington.edu Wed Aug 5 21:59:02 2009 From: ehaugen at u.washington.edu (Eric Haugen) Date: Wed, 05 Aug 2009 21:59:02 -0000 Subject: [Biojava-l] Upper case symbols In-Reply-To: <4A7986A5.7000608@uni-tuebingen.de> References: <4A7986A5.7000608@uni-tuebingen.de> Message-ID: <4A79F96C.5050909@u.washington.edu> Andreas Draeger wrote: > Dear all, > > Thank you for this very quick answer regarding Sequence logos! The code > works fine. However, would it also be possible to tell the DNATools > class that upper case letters should be used instead of lower case "a", > "c", "g", and "t"? I think it is more common to apply upper case symbols > in sequence logos. > > Cheers > Andreas > Hi Andreas, The way I did it was to uppercase the letters in the AlphabetManager.xml file, replacing the AlphabetManager.xml inside my biojava.jar. See the attached version. Maybe there's an easier way I don't know about... Best regards, Eric -- Eric Haugen Software Engineer Stam lab, UW Genome Sciences University of Washington 2211 Elliott Avenue, 6th Floor Seattle, WA 98121 -------------- next part -------------- A non-text attachment was scrubbed... Name: AlphabetManager.xml Type: text/xml Size: 28062 bytes Desc: not available URL: From d.johnson at reading.ac.uk Fri Aug 7 09:28:39 2009 From: d.johnson at reading.ac.uk (David Johnson) Date: Fri, 07 Aug 2009 09:28:39 -0000 Subject: [Biojava-l] ParseException when using interleaved Nexus file In-Reply-To: <30109C99-0ADF-461D-AB8A-B9800C4111D1@eaglegenomics.com> References: <30109C99-0ADF-461D-AB8A-B9800C4111D1@eaglegenomics.com> Message-ID: Hi Richard, Thanks for your mail. An example of an interleaved file can be found here: http://www.molecularevolution.org/si/resources/fileformats/files/dna.nex where the link pointing to the example file is from http://www.molecularevolution.org/si/resources/fileformats/ and under the NEXUS section. The specific error message is: "org.biojava.bio.seq.io.ParseException: Found unexpected token interleave=yes in CHARACTERS block" So it looks like the error is thrown reading the "interleave" parameter in the top of the data block, and before reaching the actual interleaved matrix data. Full stacktrace in attached .txt. Cheers, -David 2009/8/7 Richard Holland : > Could you point me to an example of an interleaved file? > > And also the full stack trace of the exception that gets thrown? > > cheers, > Richard > > On 6 Aug 2009, at 18:03, David Johnson wrote: > >> Hi everyone, >> >> A quick question about the BioJava Nexus parser. I've been trying to >> use the Nexus file parser, simply by doing something like: >> >> ? ? ? NexusFileBuilder builder = new NexusFileBuilder(); >> ? ? ? NexusFileFormat.parseFile(builder, f); >> >> However, when parsing Nexus files that are interleaved, I get a >> ParseException. >> >> Is there a way to setup the parser provided by BioJava to handle >> interleaved Nexus files? >> >> Thanks, >> -David >> -- >> David Johnson >> School of Biological Sciences >> University of Reading >> _______________________________________________ >> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > > -- David Johnson Post-doc Research Assistant School of Biological Sciences 506, Philip Lyle Research Building University of Reading Whiteknights Reading, RG6 6BX UK Tel: +44 (0) 118 378 4415 email: d.johnson at reading.ac.uk web: http://www.rdg.ac.uk/~sis07dj -------------- next part -------------- Message ID org.biojava.bio.seq.io.ParseException Complete Message Found unexpected token interleave=yes in CHARACTERS block at org.biojavax.bio.phylo.io.nexus.CharactersBlockParser.parseToken(CharactersBlockParser.java:1177) at org.biojavax.bio.phylo.io.nexus.NexusFileListener$Abstract.parseToken(NexusFileListener.java:256) at org.biojavax.bio.phylo.io.nexus.NexusFileFormat$TokenParser.parseToken(NexusFileFormat.java:345) at org.biojavax.bio.phylo.io.nexus.NexusFileFormat$TokenParser.access$100(NexusFileFormat.java:296) at org.biojavax.bio.phylo.io.nexus.NexusFileFormat.parse(NexusFileFormat.java:266) at org.biojavax.bio.phylo.io.nexus.NexusFileFormat.parseReader(NexusFileFormat.java:117) at org.biojavax.bio.phylo.io.nexus.NexusFileFormat.parseFile(NexusFileFormat.java:79) at uk.ac.rdg.evo.portal.NexusUtil.parseFile(NexusUtil.java:24) at uk.ac.rdg.evo.portal.panels.BayesPhyloJobStep1Panel$UploadNexusForm.onSubmit(BayesPhyloJobStep1Panel.java:65) at org.apache.wicket.markup.html.form.Form.delegateSubmit(Form.java:1518) at org.apache.wicket.markup.html.form.Form.process(Form.java:914) at org.apache.wicket.markup.html.form.Form.onFormSubmitted(Form.java:876) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.apache.wicket.RequestListenerInterface.invoke(RequestListenerInterface.java:182) at org.apache.wicket.request.target.component.listener.ListenerInterfaceRequestTarget.processEvents(ListenerInterfaceRequestTarget.java:73) at org.apache.wicket.request.AbstractRequestCycleProcessor.processEvents(AbstractRequestCycleProcessor.java:92) at org.apache.wicket.RequestCycle.processEventsAndRespond(RequestCycle.java:1241) at org.apache.wicket.RequestCycle.step(RequestCycle.java:1320) at org.apache.wicket.RequestCycle.steps(RequestCycle.java:1419) at org.apache.wicket.RequestCycle.request(RequestCycle.java:545) at org.apache.wicket.protocol.http.WicketFilter.doGet(WicketFilter.java:456) at org.apache.wicket.protocol.http.WicketFilter.doFilter(WicketFilter.java:289) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:230) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:198) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:288) at org.apache.catalina.core.StandardContextValve.invokeInternal(StandardContextValve.java:271) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:202) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:632) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:577) at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:94) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:206) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:632) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:577) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:571) at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:1080) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:150) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:632) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:577) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:571) at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:1080) at org.apache.coyote.tomcat5.CoyoteAdapter.service(CoyoteAdapter.java:272) at com.sun.enterprise.web.connector.grizzly.DefaultProcessorTask.invokeAdapter(DefaultProcessorTask.java:637) at com.sun.enterprise.web.connector.grizzly.DefaultProcessorTask.doProcess(DefaultProcessorTask.java:568) at com.sun.enterprise.web.connector.grizzly.DefaultProcessorTask.process(DefaultProcessorTask.java:813) at com.sun.enterprise.web.connector.grizzly.DefaultReadTask.executeProcessorTask(DefaultReadTask.java:341) at com.sun.enterprise.web.connector.grizzly.DefaultReadTask.doTask(DefaultReadTask.java:263) at com.sun.enterprise.web.connector.grizzly.DefaultReadTask.doTask(DefaultReadTask.java:214) at com.sun.enterprise.web.connector.grizzly.TaskBase.run(TaskBase.java:265) at com.sun.enterprise.web.connector.grizzly.ssl.SSLWorkerThread.run(SSLWorkerThread.java:106)