From koeberle at mpiib-berlin.mpg.de Thu Mar 10 13:22:13 2005 From: koeberle at mpiib-berlin.mpg.de (=?ISO-8859-1?Q?Christian_K=F6berle?=) Date: Thu Mar 10 13:18:48 2005 Subject: [Biojava-l] SequencePanel Message-ID: <42309055.6050205@mpiib-berlin.mpg.de> Hi, I have a problem with SequencePanel. If I put this in a JScrollPane it is visible, but it shows additional to the rendered Area a empty Area. If I put the SequencePanel in a JPanel it shows no rendered Stuff. What dose it mean? Thanks Christian From christoph.gille at charite.de Thu Mar 10 13:36:14 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Thu Mar 10 13:58:07 2005 Subject: [Biojava-l] biojava and STRAP Message-ID: <38040.192.168.220.204.1110479774.squirrel@webmail.charite.de> Hi, I would like to ask whether my program STRAP could benefit from BioJava and vice versa. Is it worth to develop converters to exchange objects like protein objects between both? http://www.charite.de/bioinf/strap/ STRAP is a multi purpose multiple sequences alignment tool. It contains wrapper classes for the alignment procedures SequenceAligner, ClustalW,Mafft5, T_Coffee, Muscle, Dialign, DialignT, Probcons2, NeoBio, JAligner and for the 3D-superposition program CE/CL and for transmembrane helix and secondary structure and coiled coil prediction. Further it has a very fast PDB and DSSP parsers (30ms per PDB-file). There is a wrapper for Rasmol and Pymol and a specialized multi-model 3D-wire viewer. These classes could be made available in BioJava. I guess one has to create classes that implement certain interfaces of BioJava. BioJava looks very objectified. However, for performance reasons I had to use byte arrays for sequences in STRAP. Otherwise I tried to follow the basic rules of modern programming. As BioJava it defines many interfaces. E.g. all different alignment procedures are implementations of the interface SequenceAligner. I would like to know what additional functionality STRAP could gain by BioJava. I would highly appreciate your opinion of this matter. Many thanks Christoph From krebsj at cip.ifi.lmu.de Thu Mar 10 20:03:42 2005 From: krebsj at cip.ifi.lmu.de (Joerg Krebs) Date: Thu Mar 10 19:58:22 2005 Subject: [Biojava-l] SwissProt FeatureTable Message-ID: <1110503022.6472.2.camel@thesystem.lepido.homelinux.com> Hi, does anyone know how to parse the FeatureTable Entries of a SwissProt File via the biojava package. With getAnnotation I can only get the annotation entries without the FeatureTable-Entries :( In the Source-Code of biojava 1.4pre1 exists a SwissprotFeatureTableParser.java in src/org/biojava/bio/seq/io/ but it seems to be not yet ready to use. Maybe someone can help me with my Problem. Thanks Joerg -- Joerg Krebs From mark.schreiber at group.novartis.com Thu Mar 10 20:55:18 2005 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Thu Mar 10 20:50:02 2005 Subject: [Biojava-l] biojava and STRAP Message-ID: > >I would like to ask whether my program STRAP could benefit from >BioJava and vice versa. Is it worth to develop converters to exchange >objects like protein objects between both? > >http://www.charite.de/bioinf/strap/ > > >STRAP is a multi purpose multiple sequences alignment tool. It >contains wrapper classes for the alignment procedures >SequenceAligner, ClustalW,Mafft5, T_Coffee, Muscle, Dialign, DialignT, >Probcons2, NeoBio, JAligner and for the 3D-superposition program CE/CL >and for transmembrane helix and secondary structure and coiled coil >prediction. > I think many of these things would be new to biojava. We have a lot of parsers but one of the things we lack is wrappers to launch processes. There is a class called ProcessTools which can be used to make things like this but there are none that I know of in BioJava right now. Your GUI components for structure and alignment viewing look quite nice too! >Further it has a very fast PDB and DSSP parsers (30ms per PDB-file). Biojava has an experimental PDB parser and model in the development version but I don't think we have DSSP. Not sure of the speed. I think that your parsers could implement one of the interfaces >There is a wrapper for Rasmol and Pymol and a specialized multi-model >3D-wire viewer. These would also be useful. >These classes could be made available in BioJava. I guess one has to >create classes that implement certain interfaces of BioJava. That would be the best way to go. One of the nice things about biojava is that almost everything happens behind an interface. This means that as long as you provide the methods required by the interfaces you use your implementation can be anything. You could probably even leave most of your code as is and just write wrappers for your sequence objects etc to make them look like biojava sequence objects. >BioJava looks very objectified. However, for performance reasons I had >to use byte arrays for sequences in STRAP. Otherwise I tried >to follow the basic rules of modern programming. As BioJava it >defines many interfaces. E.g. all different alignment procedures are >implementations of the interface SequenceAligner. If you want to keep your byte array implementations then you simply need to wrap them as a BioJava SymbolList or Sequence object. They remain essentially the same but look like BioJava sequence objects. Behind the scenes (Interfaces) biojava can do some bit packing of large sequences. I'm not sure of the performance of these versus yours. Probably easier to stick with what you have and provide wrappers. >I would like to know what additional functionality STRAP could gain by >BioJava. Hope this helps. As always contributions are greatly appreciated. - Mark From mark.schreiber at group.novartis.com Thu Mar 10 21:02:49 2005 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Thu Mar 10 20:57:24 2005 Subject: [Biojava-l] SwissProt FeatureTable Message-ID: Hello Joerg, Biojava usually places feature information in the FeatureHolder of the Sequence that is generated when parsing the file. As you state the annotation entries end up in the Annotation object. You can get an Iterator over the FeatureHolder using sequence.features(). Each feature will contain some basic information such as the type and location plus it will also contain an Annotation bundle itself with any annotations specific to that feature. To view where everything will end up after parsing take a look at: http://www.biojava.org/docs/bj_in_anger/filter.htm - Mark Joerg Krebs Sent by: biojava-l-bounces@portal.open-bio.org 03/11/2005 09:03 AM To: biojava-l@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] SwissProt FeatureTable Hi, does anyone know how to parse the FeatureTable Entries of a SwissProt File via the biojava package. With getAnnotation I can only get the annotation entries without the FeatureTable-Entries :( In the Source-Code of biojava 1.4pre1 exists a SwissprotFeatureTableParser.java in src/org/biojava/bio/seq/io/ but it seems to be not yet ready to use. Maybe someone can help me with my Problem. Thanks Joerg -- Joerg Krebs _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From ap3 at sanger.ac.uk Fri Mar 11 04:52:58 2005 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Fri Mar 11 04:46:36 2005 Subject: [Biojava-l] biojava and STRAP In-Reply-To: <38040.192.168.220.204.1110479774.squirrel@webmail.charite.de> References: <38040.192.168.220.204.1110479774.squirrel@webmail.charite.de> Message-ID: Hi Christoph! > Further it has a very fast PDB and DSSP parsers (30ms per PDB-file). I contributed a PDB parser and data model to biojava - CVS a while ago. The parser mainly parses the coordinate section of the PDB files, so it would be nice to get the header section parsed as well. - though I think that parsing of either header or atoms should be optional. Is your parser event-based? That would be an improvement to the current one and it would allow fine tuned (and therefore fast) parsing of PDB files according to people/algorithm needs. E.g. It would be interesting to have event listeners that only parse Ca atoms - or only the mainchain atoms, etc. depending on the application. The current implementation will create an all atom representation of the PDB file. The PDB data model is designed so it can deal with various exceptions that occur within protein structures and the idea was that it should be possible to develop algorithms on top of it. regarding DSSP: yes would be nice to have a parser for it. :-) > There is a wrapper for Rasmol and Pymol and a specialized multi-model > 3D-wire viewer. wrapper to rasmol ? Does this mean you pipe rasmol script commands to it? Personally, I usually recommend the Jmol viewer - also "speaks" rasmol :-) Gruesze, Andreas ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK From kavkrao at yahoo.co.in Thu Mar 17 00:58:40 2005 From: kavkrao at yahoo.co.in (kollipara koteswararao) Date: Thu Mar 17 00:53:05 2005 Subject: [Biojava-l] Message-ID: <20050317055840.59077.qmail@web8404.mail.in.yahoo.com> if anybody uses in their projects/programs the gui packages org.biojava.bio.gui org.biojava.bio.gui.sequence plese help me how to use the functions and classes so that if i have given the input a sequence(aligned sequences) file, the output should be coloured/gui sequence file. if anybody have worked in this packages, please send the source files. I am confusing in using the biojava-api for the above said purpose. Regards, K.A.V.Koteswararao,M.Tech Pondicherry University. --------------------------------- Do you Yahoo!? Yahoo! Small Business - Try our new resources site! From joel.bjorkman at gmail.com Fri Mar 18 04:20:34 2005 From: joel.bjorkman at gmail.com (=?ISO-8859-1?Q?Joel_Bj=F6rkman?=) Date: Fri Mar 18 04:16:41 2005 Subject: [Biojava-l] BioJava and DAS Message-ID: Hello! I'm new to org.biojava.bio.program.das and I have a couple of questions regarding fetching features and sequences from dazzle servers... At the moment I'm only interested in getting the sequence and annotations from ensembl's database, which should make the problem easier. It's quite obvious when you're browsing http://servlet.sanger.ac.uk:8080/das/ that ensemble got a lot of data. What I'm concerned about is when I look at the different segment sizes Some of them are really big. Taking a peek at the demo that follows with biojava-live shows that you are supposed to download the entire sequence and then make operations on it (eg substring). DASSequenceDB dasDB = new DASSequenceDB(dbURL); DASSequence dasSeq = (DASSequence) dasDB.getSequence(seqName); System.out.println("1st 10 bases: " + dasSeq.subStr(1, 10)); Isn't there any way that's more efficient and nicer to the server? Is there any way to throw requests like this: http://servlet.sanger.ac.uk:8080/das/ensembl_Homo_sapiens_core_28_35a/dna?segment=21:1,10 regards Joel From td2 at sanger.ac.uk Fri Mar 18 05:57:32 2005 From: td2 at sanger.ac.uk (Thomas Down) Date: Fri Mar 18 05:51:54 2005 Subject: [Biojava-l] BioJava and DAS In-Reply-To: References: Message-ID: On 18 Mar 2005, at 09:20, Joel Bj?rkman wrote: > Hello! > > I'm new to org.biojava.bio.program.das and I have a couple of > questions regarding fetching features and sequences from dazzle > servers... > > At the moment I'm only interested in getting the sequence and > annotations from ensembl's database, which should make the problem > easier. > > It's quite obvious when you're browsing > http://servlet.sanger.ac.uk:8080/das/ that ensemble got a lot of data. > > What I'm concerned about is when I look at the different segment sizes > > Some of them are really big. > > Taking a peek at the demo that follows with biojava-live shows that > you are supposed to download the entire sequence and then make > operations on it (eg substring). > > DASSequenceDB dasDB = new DASSequenceDB(dbURL); > DASSequence dasSeq = (DASSequence) dasDB.getSequence(seqName); > System.out.println("1st 10 bases: " + dasSeq.subStr(1, 10)); > > Isn't there any way that's more efficient and nicer to the server? Is > there any way to throw requests like this: > http://servlet.sanger.ac.uk:8080/das/ensembl_Homo_sapiens_core_28_35a/ > dna?segment=21:1,10 Hi, The "getSequence" call in that program doesn't actually retrieve all the sequence data from the DAS server, it just creates an object which can make calls to the DAS server as necessary. Currently, the actual DAS client code which is hidden behind the Sequence object you get back fetches the sequence data in chunks from the DAS server (50kb chunks, if I remember correctly) -- you certainly won't end up pulling down the full sequence of chr21 just to look at a few bases. Another issue with DAS is that although the XML documents -- especially the feature tables -- can be pretty huge, they compress down well. Given a suitable server implementation (Dazzle can certainly do this, not sure how many others can), the BioJava DAS client can use the HTTP "Accept-Encoding" mechanism to negotiate GZIP compression of all the DAS XML. Saves a lot of bandwidth. Thomas. From jolyon.holdstock at ogt.co.uk Tue Mar 22 13:34:48 2005 From: jolyon.holdstock at ogt.co.uk (Jolyon Holdstock) Date: Tue Mar 22 13:28:24 2005 Subject: [Biojava-l] Obtaining sequence range Message-ID: <588D0DD225D05746B5D8CAE1BE971F3F48CB52@EUCLID.internal.ogtip.com> Hi, I am constructing a GUI comprising 2 TranslatedSequencePanels. The lower panel has the detail provided by various renderers. The upper panel is meant to show the whole sequence with a section highlighted to reflect the part currently displayed in the lower window. I am having real trouble getting to the data describing the coordinates of the sequence shown in the lower panel. I have tried using the getRange() method from the lower panel but that always returns a min of 0 and a max of 1. I have also tried getRange() from the RulerRenderer that is in the lower panel. This too, has not been successful. I can pass the RangeLocation returned by the method but I get a NullPointerException when I use it to call getMin() and getMax(). Is there a way to do this more easily? Many thanks, Jolyon Holdstock From fab.schreiber at gmx.de Thu Mar 24 10:27:07 2005 From: fab.schreiber at gmx.de (Fabian Schreiber) Date: Fri Mar 25 04:54:57 2005 Subject: [Biojava-l] Why does Baum-welch does not work? Message-ID: Hello! I've a question. I want to use the Baum-Welch-algorithm to train my Markov-Modell. First i set all the transition- and emission-probabilities, so that i have a kind of basis modell. Now i want to train my modell with lots of sequences. After the training had finished, i looked up the probabilities of the markov modell to find changes. But all the probabilities has changed to "NaN", which is no good. Can someone tell me, where the mistake is? Here is my code: //Create Markov Modell - The method createCasino generates an Alphabet and sets //the probabilities for the transitions and emissions MarkovModel casino = createCasino(); DP dp=DPFactory.DEFAULT.createDP(casino); BaumWelchTrainer bwtrainer = new BaumWelchTrainer(dp); SequenceDB seqDB = new HashSequenceDB("hashdb"); // here the DB is filled with the sequences --> this works //Set the stopper StoppingCriteria stopper= new StoppingCriteria() {public boolean isTrainingComplete(TrainingAlgorithm ta) {return (ta.getCycle() > 10);}}; //Train the modell bwtrainer.train(seqDB, 1.0, stopper); Thats it. Can somebody help me, why all probabilitites changed from 0.xx to NaN? Thanks for your support. Fabian From fab.schreiber at gmx.de Fri Mar 25 05:08:40 2005 From: fab.schreiber at gmx.de (fabian schreiber) Date: Fri Mar 25 05:03:11 2005 Subject: [Biojava-l] Why does Baum-welch not work? Message-ID: Hello! I've a question. I want to use the Baum-Welch-algorithm to train my Markov-Modell. First i set all the transition- and emission-probabilities, so that i have a kind of basis modell. Now i want to train my modell with lots of sequences. After the training had finished, i looked up the probabilities of the markov modell to find changes. But all the probabilities has changed to "NaN", which is no good. Can someone tell me, where the mistake is? Here is my code: //Create Markov Modell - The method createCasino generates an Alphabet and sets //the probabilities for the transitions and emissions MarkovModel casino = createCasino(); DP dp=DPFactory.DEFAULT.createDP(casino); BaumWelchTrainer bwtrainer = new BaumWelchTrainer(dp); SequenceDB seqDB = new HashSequenceDB("hashdb"); // here the DB is filled with the sequences --> this works //Set the stopper StoppingCriteria stopper= new StoppingCriteria() {public boolean isTrainingComplete(TrainingAlgorithm ta) {return (ta.getCycle() > 10);}}; //Train the modell bwtrainer.train(seqDB, 1.0, stopper); Thats it. Can somebody help me, why all probabilitites changed from 0.xx to NaN? Thanks for your support. Fabian _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l