From pwilkinson at videotron.ca Thu Sep 4 09:18:42 2003 From: pwilkinson at videotron.ca (Peter Wilkinson) Date: Thu Sep 4 09:18:03 2003 Subject: [Biojava-l] Test In-Reply-To: <20030829030745.54302.qmail@web60104.mail.yahoo.com> Message-ID: <5.2.0.9.0.20030904091812.00b21028@pop.videotron.ca> This is a test Administrator From Mason.Christopher at mayo.edu Sun Sep 7 17:15:20 2003 From: Mason.Christopher at mayo.edu (Christopher Mason) Date: Sun Sep 7 17:14:21 2003 Subject: [Biojava-l] Biosql performance numbers? Message-ID: <93113309.1062951320@[172.23.198.245]> Howdy, Has anyone tried recently importing all of Swiss Prot, NCBInr, etc. into a biosql database on any RDBMS (postgres, mysql, oracle, etc.)? If so, can you give me (even approximate) performance numbers (for loading, finding a specific sequence entry, iterating over all sequences, etc.) and ultimate database size on disk? I'm trying to determine if using biosql is a viable way of architecting my application (which needs to do things to all sequences and then things to a specific, user chosen sequence). I've tried loading all of sprot.dat to Postgres using bioperl, but this was a less than raging success (see my recent post to bioperl-l for details). I'll try again with UploadFlat (which I found after I started using bioperl). Thanks, -c -- [ Christopher Mason MPRC Bioinformatics cjm37@mayo.edu ] From Eric.Jain at isb-sib.ch Mon Sep 8 02:39:30 2003 From: Eric.Jain at isb-sib.ch (Eric Jain) Date: Mon Sep 8 02:38:01 2003 Subject: [Biojava-l] Re: Biosql performance numbers? References: <93113309.1062951320@[172.23.198.245]> Message-ID: <004501c375d3$f5791bd0$c300000a@caliente> > Has anyone tried recently importing all of Swiss Prot, NCBInr, etc. > into a biosql database on any RDBMS (postgres, mysql, oracle, etc.)? Can't give you any numbers, but if your database is only used for querying, you may be better off only storing data that is actually used in queries into the database, and keeping the actual entries in indexed text files. -- Eric Jain From jan.wuerthner at uni-duesseldorf.de Mon Sep 8 03:15:56 2003 From: jan.wuerthner at uni-duesseldorf.de (Jan =?iso-8859-15?q?W=FCrthner?=) Date: Mon Sep 8 03:14:00 2003 Subject: [Biojava-l] reading sequences from xml files... Message-ID: <200309080915.56828.jan.wuerthner@uni-duesseldorf.de> Hi, does anyone know, if there is a biojava way to construct a Sequence object by reading sequence data from an XML file? I store all the information in XML files (e.g. connecting via http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=Nucleotide&dopt=XML&uid=1234). I know that SeqIOTools offers methods for reading sequences from files (fileToBioJava()), but unfortunately XML is not among the supported formats. kind regards Jan W?rthner -- Jan W?rthner Institute for Medical Microbiology Building 22.21 Heinrich-Heine-University Universit?tsstra?e 1 40225 Duesseldorf Tel. +49 (0) 211 81 14545 URL: www.medmikro.uni-duesseldorf.de From matthew_pocock at yahoo.co.uk Mon Sep 8 05:40:16 2003 From: matthew_pocock at yahoo.co.uk (=?iso-8859-1?q?Matthew=20Pocock?=) Date: Mon Sep 8 05:38:51 2003 Subject: [Biojava-l] reading sequences from xml files... In-Reply-To: <200309080915.56828.jan.wuerthner@uni-duesseldorf.de> Message-ID: <20030908094016.48245.qmail@web14907.mail.yahoo.com> --- Jan W?rthner wrote: > > Hi, > > does anyone know, if there is a biojava way to > construct a Sequence object by > reading sequence data from an XML file? Hi Jan, Asking if we have parsers for XML is a bit like asking if we have parsers for ASCII - there are loads of ways to encode the same data with XML. We currently support (to a greater or lesser extent) game, agave, das-xml and XFF. > > I store all the information in XML files (e.g. > connecting via > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=Nucleotide&dopt=XML&uid=1234). OK - reading this now. It looks like a semi-sane XML version of genbank/embl. You should fairly easily be able to write a sax or stax handler for this that calls methods on a SeqIOListener. > I know that SeqIOTools offers methods for reading > sequences from files > (fileToBioJava()), but unfortunately XML is not > among the supported formats. What do you do at the moment? Do you have your own parsers, or do you use somebody elses? > > kind regards > Jan W?rthner Matthew ________________________________________________________________________ Want to chat instantly with your online friends? Get the FREE Yahoo! Messenger http://mail.messenger.yahoo.co.uk From jan.wuerthner at uni-duesseldorf.de Mon Sep 8 07:35:49 2003 From: jan.wuerthner at uni-duesseldorf.de (Jan =?iso-8859-1?q?W=FCrthner?=) Date: Mon Sep 8 07:33:53 2003 Subject: [Biojava-l] reading sequences from xml files... In-Reply-To: <20030908094016.48245.qmail@web14907.mail.yahoo.com> References: <20030908094016.48245.qmail@web14907.mail.yahoo.com> Message-ID: <200309081335.49373.jan.wuerthner@uni-duesseldorf.de> Am Monday 08 September 2003 11:40 schrieb Matthew Pocock: > >> [...] > > What do you do at the moment? Do you have your own > parsers, or do you use somebody elses? I have written an XML parser (Handler) for NCBI's blast output, constructing SeqSimilaritySearchResult instances by hand. I first tried to use the BlastXMLParser, but run into trouble dealing with the dtds. The documentation of the BlastXMLParser suggests to modify the ncbi xml documents, but I wanted to parse the inputstream. Is there a place where people can upload/download new parsers? Jan > > kind regards > > Jan W?rthner > > Matthew > > ________________________________________________________________________ > Want to chat instantly with your online friends? Get the FREE Yahoo! > Messenger http://mail.messenger.yahoo.co.uk -- Jan W?rthner Institute for Medical Microbiology Building 22.21 Heinrich-Heine-University Universit?tsstra?e 1 40225 Duesseldorf Tel. +49 (0) 211 81 14545 URL: www.medmikro.uni-duesseldorf.de From ihab at stanford.edu Mon Sep 8 18:53:18 2003 From: ihab at stanford.edu (Ihab A.B. Awad) Date: Mon Sep 8 18:52:18 2003 Subject: [Biojava-l] Best way to represent multiple annotation "tracks" Message-ID: Hi folks, I'm working on a gene expression data visualization program -- http://genetics.stanford.edu/~ihab/caryoscope/ I have not used BioJava yet for the data model, but I would like to migrate in that direction. It seems that my data model is very similar to BioJava's, except for one thing that puzzles me: How would you folks represent multiple "tracks" of annotation values? The way I have things modeled -- http://genetics.stanford.edu/~ihab/caryoscope/doc/api/edu/stanford/genomics/domain/Dataset.html a Dataset object maps a Feature to a data object (or null). I see you folks implement this a bit differently: a Feature implements interface Annotatable, whereby it becomes responsible for knowing about its own Annotations. Hence my question -- how would you represent a "track" of annotations as a single entity? Thanks a lot for any help you can provide in pointing me in the right direction. Peace, Ihab -- Ihab A.B. Awad Snr Scientific Programmer, Dept of Genetics From mark.schreiber at agresearch.co.nz Mon Sep 8 19:06:03 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Mon Sep 8 19:05:17 2003 Subject: [Biojava-l] Best way to represent multiple annotation "tracks" Message-ID: Hi - In biojava Annotations have no location. They are global to the Annotatable object. They can be localized to a region by being applied to a Feature. So to generate a track of "annotations" you would instead create a track of annotated Features. - Mark -----Original Message----- From: Ihab A.B. Awad [mailto:ihab@stanford.edu] Sent: Tue 9/09/2003 10:53 a.m. To: biojava-l@biojava.org Cc: Subject: [Biojava-l] Best way to represent multiple annotation "tracks" Hi folks, I'm working on a gene expression data visualization program -- http://genetics.stanford.edu/~ihab/caryoscope/ I have not used BioJava yet for the data model, but I would like to migrate in that direction. It seems that my data model is very similar to BioJava's, except for one thing that puzzles me: How would you folks represent multiple "tracks" of annotation values? The way I have things modeled -- http://genetics.stanford.edu/~ihab/caryoscope/doc/api/edu/stanford/genomics/domain/Dataset.html a Dataset object maps a Feature to a data object (or null). I see you folks implement this a bit differently: a Feature implements interface Annotatable, whereby it becomes responsible for knowing about its own Annotations. Hence my question -- how would you represent a "track" of annotations as a single entity? Thanks a lot for any help you can provide in pointing me in the right direction. Peace, Ihab -- Ihab A.B. Awad Snr Scientific Programmer, Dept of Genetics _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From ihab at stanford.edu Mon Sep 8 19:12:47 2003 From: ihab at stanford.edu (Ihab A.B. Awad) Date: Mon Sep 8 19:11:28 2003 Subject: [Biojava-l] Best way to represent multiple annotation "tracks" In-Reply-To: References: Message-ID: Hi Mark & all, Thank you for the tip.... >In biojava Annotations have no location. They are global to the >Annotatable object. They can be localized to a region by being >applied to a Feature. So to generate a track of "annotations" you >would instead create a track of annotated Features. > > I have not used BioJava yet for the data model, but I would like to > migrate in that direction. It seems that my data model is very > similar to BioJava's, except for one thing that puzzles me: How would > you folks represent multiple "tracks" of annotation values? So, let's say I have a bunch of ESTs, each of which has been mapped to a location on the genome. To each EST, my data maps a floating point number indicating the expression level. In this case, each Feature would represent one of the ESTs, right? So what would be the Feature(s) representing the annotation track? Would they be Features owned by the EST Feature (via the inheritance of FeatureHolder by interface Feature)? Or -- ?? Thanks again & peace, Ihab -- Ihab A.B. Awad Snr Scientific Programmer, Dept of Genetics From ihab at stanford.edu Mon Sep 8 19:53:09 2003 From: ihab at stanford.edu (Ihab A.B. Awad) Date: Mon Sep 8 19:51:55 2003 Subject: [Biojava-l] Best way to represent multiple annotation "tracks" In-Reply-To: References: Message-ID: Hi again, [ Pls excuse the poor netiquette for posting a followup to my own message.... ] >So, let's say I have a bunch of ESTs, each of which has been mapped >to a location on the genome. To each EST, my data maps a floating >point number indicating the expression level. > >In this case, each Feature would represent one of the ESTs, right? >So what would be the Feature(s) representing the annotation track? >Would they be Features owned by the EST Feature (via the inheritance >of FeatureHolder by interface Feature)? Or -- ?? Alternatively, would each EST be a SubSequence with Features attached to it, with each Feature representing one of the data "tracks"? If so, then how does one decide when something is a Feature or a SubSequence? I'm not a biologist, so I'm probably way confused here, but it seems to me there is a gray area (ORFs?). So I guess there are several competing implementations. 1. SEQUENCE BASED, FEATURES REPRESENT DATA TRACKS "Chromosome 1" : Sequence "AA504327" : SubSequence "RAT2N" : Feature : Annotation "Value" => 2.34312 "RAT2_MEAN": Feature : Annotation "Value" => 1.8342 "AA432030" : SubSequence ... 2. SEQUENCE BASED, ANNOTATIONS REPRESENT DATA TRACKS "Chromosome 1" : Sequence "AA504327" : SubSequence "Microarray Experiment B2341v" : Feature : Annotation "RAT2N" => 2.34312 "RAT2_MEAN" => 1.8342 "AA432030" : SubSequence ... 3. FEATURE BASED, SUB-FEATURES REPRESENT DATA TRACKS (Very similar to #1, except using Feature instead of SubSequence.) "Chromosome 1" : Sequence "AA504327" : Feature "RAT2N" : Feature : Annotation "Value" => 2.34312 "RAT2_MEAN": Feature : Annotation "Value" => 1.8342 "AA432030" : SubSequence ... 4. FEATURE BASED, ANNOTATIONS REPRESENT DATA TRACKS (Very similar to #2, except using Feature instead of SubSequence.) "Chromosome 1" : Sequence "AA504327" : Feature "Microarray Experiment B2341v" : Feature : Annotation "RAT2N" => 2.34312 "RAT2_MEAN" => 1.8342 "AA432030" : SubSequence ... Thanks a lot again & peace, Ihab -- Ihab A.B. Awad Snr Scientific Programmer, Dept of Genetics From gdelrio at buckinstitute.org Wed Sep 10 12:06:00 2003 From: gdelrio at buckinstitute.org (Gabriel del Rio Guerra) Date: Wed Sep 10 12:05:17 2003 Subject: [Biojava-l] Reformating multiple sequence alignments Message-ID: <4AA34A707932424EBE2D973764D226A91B98D7@inverness.buckcenter.org> Hi, I am interesting in using or developing a program to inter-convert different sequence alignments formats. In particular I want to translate HSSP alignments into MSF format. Does anyone knows if this is possible with Biojava at this point? Thanks, Gabriel -----Original Message----- From: Kenny Yu [mailto:kyu@biodiscovery.com] Sent: Wednesday, April 30, 2003 8:45 AM To: biojava-l@biojava.org Subject: [Biojava-l] unified consolidated annotation system Both biosql and biodas are concerned with retrieving annotation on the basis of known features. They are not optimized for large-scale cross-system queries and data mining on the basis of annotations. I am interested in consolidating annotations from various sources (such as genbank and unigene) into a unified form on which I can run queries like "find features that are linked to DNA repair function in human but not in mouse" and "find feature whose molecular functions overlap with those of Accession Number nnnn". Similar mechanisms may exist in LION's SRS (http://www.lionbioscience.com/solutions/products/srs/relational). What I am contemplating is essentially a data warehouse for annotations. I'll borrow data warehouse and OLAP techniques in the design. It's a hybrid of relational, nested-relational and multidimensional database. Feature entity, or gene, and annotation are the dimensions. It models textual values as well as binary objects such as pathway diagrams as annot! ation values. I intend to make my work open-source and would call it UCAsql. Currently the schema design, with some documentation and java API, is available to anyone upon request by email to myself at kyu@biodiscovery.com. _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From charles.girardot at libertysurf.fr Wed Sep 10 14:13:41 2003 From: charles.girardot at libertysurf.fr (=?iso-8859-1?Q?charles.girardot@libertysurf.fr?=) Date: Wed Sep 10 14:12:17 2003 Subject: [Biojava-l] Parsing location from gbk files Message-ID: Hi, I am using biojava to extract mRNA, CDS and gene boundaries from genbank annotation files (e.g., "hs_chr19.gbs" from ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_19/). I've just switched from the biojava 1.22 to latest 1.3 release (biojava-1.30-jdk14.jar and bytecode-0.92.jar) and I get lots of exception (see below, the peace of code generating this follows as well). Don't known if it's important but ".gbs" files do not hold the contig sequences but only annotations. Nota: I am using the jdk 1.4.1. Thanks for your help. Charles Girardot ======================================= java.lang.IllegalArgumentException: Location 59817 is outside 1..0 at org.biojava.bio.seq.impl.SimpleFeature.(SimpleFeature.java:306) at org.biojava.bio.seq.impl.SimpleStrandedFeature.(SimpleStrandedFeature.java:74) at sun.reflect.GeneratedConstructorAccessor1.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:274) at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:138) rethrown as org.biojava.bio.BioException: Couldn't realize feature at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:144) at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:94) at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:198) at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:204) at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:168) at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:87) at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:98) at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:101) at org.gc.test.GenbankParserTest.main(GenbankParserTest.java:34) ========================================== package org.gc.test; import java.io.BufferedReader; import java.io.File; import java.io.FileReader; import org.biojava.bio.seq.Sequence; import org.biojava.bio.seq.SequenceIterator; import org.biojava.bio.seq.io.SeqIOTools; /** * @author unknown * * To change the template for this generated type comment go to * Window>Preferences>Java>Code Generation>Code and Comments */ public class GenbankParserTest { public static void main(String[] args) { System.out.println("Main starts ..."); try { File f = new File("D:\\Travail\\data\\Hs_chr19.gbs"); BufferedReader bf = new BufferedReader(new FileReader(f)); SequenceIterator it = SeqIOTools.readGenbank(bf); while (it.hasNext()) { System.out.println("getting next seq..."); Sequence s = it.nextSequence(); } } catch (Exception e) { System.out.println(e.getStackTrace()); } System.out.println("End of main"); } } ********** L'ADSL A 20 EUR/MOIS********** Avec Tiscali, l'ADSL est ? 20 EUR/mois. Vous pourrez chercher longtemps avant de trouver moins cher ! Pour profiter de cette offre exceptionnelle, cliquez ici : http://register.tiscali.fr/adsl/ Offre soumise ? conditions. From mark.schreiber at agresearch.co.nz Wed Sep 10 17:40:34 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Wed Sep 10 17:39:15 2003 Subject: [Biojava-l] Reformating multiple sequence alignments Message-ID: Hi - I'm not too familiar with what you are trying to do but... A lot of the biojava Alignment API can be found in org.biojava.bio.alignment parsers for reading and writing different formats are in org.biojava.bio.seq.io.* SeqIOTools is especially useful. Hope this helps: - Mark -----Original Message----- From: Gabriel del Rio Guerra [mailto:gdelrio@buckinstitute.org] Sent: Thu 11/09/2003 4:06 a.m. To: biojava-l@biojava.org Cc: Subject: [Biojava-l] Reformating multiple sequence alignments Hi, I am interesting in using or developing a program to inter-convert different sequence alignments formats. In particular I want to translate HSSP alignments into MSF format. Does anyone knows if this is possible with Biojava at this point? Thanks, Gabriel -----Original Message----- From: Kenny Yu [mailto:kyu@biodiscovery.com] Sent: Wednesday, April 30, 2003 8:45 AM To: biojava-l@biojava.org Subject: [Biojava-l] unified consolidated annotation system Both biosql and biodas are concerned with retrieving annotation on the basis of known features. They are not optimized for large-scale cross-system queries and data mining on the basis of annotations. I am interested in consolidating annotations from various sources (such as genbank and unigene) into a unified form on which I can run queries like "find features that are linked to DNA repair function in human but not in mouse" and "find feature whose molecular functions overlap with those of Accession Number nnnn". Similar mechanisms may exist in LION's SRS (http://www.lionbioscience.com/solutions/products/srs/relational). What I am contemplating is essentially a data warehouse for annotations. I'll borrow data warehouse and OLAP techniques in the design. It's a hybrid of relational, nested-relational and multidimensional database. Feature entity, or gene, and annotation are the dimensions. It models textual values as well as binary objects such as pathway diagrams as annot! ation values. I intend to make my work open-source and would call it UCAsql. Currently the schema design, with some documentation and java API, is available to anyone upon request by email to myself at kyu@biodiscovery.com. _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From mark.schreiber at agresearch.co.nz Wed Sep 10 17:44:04 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Wed Sep 10 17:42:38 2003 Subject: [Biojava-l] Parsing location from gbk files Message-ID: Hi - This is a recurring problem as more files are being deposited that contain only references to other contigs but contain annotation and features. A model where a DummySequence of appropriate length is instantiated if the contig files are not available may be useful. Possibley a GBS parser would be useful? Has anyone hacked out something like this? - Mark -----Original Message----- From: charles.girardot@libertysurf.fr [mailto:charles.girardot@libertysurf.fr] Sent: Thu 11/09/2003 6:13 a.m. To: biojava-l Cc: Subject: [Biojava-l] Parsing location from gbk files Hi, I am using biojava to extract mRNA, CDS and gene boundaries from genbank annotation files (e.g., "hs_chr19.gbs" from ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_19/). I've just switched from the biojava 1.22 to latest 1.3 release (biojava-1.30-jdk14.jar and bytecode-0.92.jar) and I get lots of exception (see below, the peace of code generating this follows as well). Don't known if it's important but ".gbs" files do not hold the contig sequences but only annotations. Nota: I am using the jdk 1.4.1. Thanks for your help. Charles Girardot ======================================= java.lang.IllegalArgumentException: Location 59817 is outside 1..0 at org.biojava.bio.seq.impl.SimpleFeature.(SimpleFeature.java:306) at org.biojava.bio.seq.impl.SimpleStrandedFeature.(SimpleStrandedFeature.java:74) at sun.reflect.GeneratedConstructorAccessor1.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:274) at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:138) rethrown as org.biojava.bio.BioException: Couldn't realize feature at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:144) at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:94) at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:198) at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:204) at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:168) at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:87) at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:98) at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:101) at org.gc.test.GenbankParserTest.main(GenbankParserTest.java:34) ========================================== package org.gc.test; import java.io.BufferedReader; import java.io.File; import java.io.FileReader; import org.biojava.bio.seq.Sequence; import org.biojava.bio.seq.SequenceIterator; import org.biojava.bio.seq.io.SeqIOTools; /** * @author unknown * * To change the template for this generated type comment go to * Window>Preferences>Java>Code Generation>Code and Comments */ public class GenbankParserTest { public static void main(String[] args) { System.out.println("Main starts ..."); try { File f = new File("D:\\Travail\\data\\Hs_chr19.gbs"); BufferedReader bf = new BufferedReader(new FileReader(f)); SequenceIterator it = SeqIOTools.readGenbank(bf); while (it.hasNext()) { System.out.println("getting next seq..."); Sequence s = it.nextSequence(); } } catch (Exception e) { System.out.println(e.getStackTrace()); } System.out.println("End of main"); } } ********** L'ADSL A 20 EUR/MOIS********** Avec Tiscali, l'ADSL est ? 20 EUR/mois. Vous pourrez chercher longtemps avant de trouver moins cher ! Pour profiter de cette offre exceptionnelle, cliquez ici : http://register.tiscali.fr/adsl/ Offre soumise ? conditions. _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From matthew_pocock at yahoo.co.uk Thu Sep 11 05:58:16 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Thu Sep 11 05:58:52 2003 Subject: [Biojava-l] Parsing location from gbk files In-Reply-To: References: Message-ID: <3F604738.6080504@yahoo.co.uk> Schreiber, Mark wrote: >Hi - > >This is a recurring problem as more files are being deposited that contain only references to other contigs but contain annotation and features. > >A model where a DummySequence of appropriate length is instantiated if the contig files are not available may be useful. Possibley a GBS parser would be useful? Has anyone hacked out something like this? > >- Mark > > It should be possible to create a dummy sequence of the right length and then populate the feature table with component features for the assembly info. Perhaps if we wrote a ComponentFeature that held an LSID - then tries to resolve itself on demand via the LSID framework? I don't have the time right now, but somebody should get keen. Matthew > -----Original Message----- > From: charles.girardot@libertysurf.fr [mailto:charles.girardot@libertysurf.fr] > Sent: Thu 11/09/2003 6:13 a.m. > To: biojava-l > Cc: > Subject: [Biojava-l] Parsing location from gbk files > > > > Hi, > > I am using biojava to extract mRNA, CDS and gene boundaries from genbank annotation files (e.g., "hs_chr19.gbs" from ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_19/). > I've just switched from the biojava 1.22 to latest 1.3 release (biojava-1.30-jdk14.jar and bytecode-0.92.jar) > and I get lots of exception (see below, the peace of code generating this follows as well). Don't known if it's important but ".gbs" files do not hold the contig sequences but only annotations. > > Nota: I am using the jdk 1.4.1. > > Thanks for your help. > > Charles Girardot > > > ======================================= > java.lang.IllegalArgumentException: Location 59817 is outside 1..0 > at org.biojava.bio.seq.impl.SimpleFeature.(SimpleFeature.java:306) > at org.biojava.bio.seq.impl.SimpleStrandedFeature.(SimpleStrandedFeature.java:74) > at sun.reflect.GeneratedConstructorAccessor1.newInstance(Unknown Source) > at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) > at java.lang.reflect.Constructor.newInstance(Constructor.java:274) > at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:138) > rethrown as org.biojava.bio.BioException: Couldn't realize feature > at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:144) > at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:94) > at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:198) > at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:204) > at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:168) > at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:87) > at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:98) > at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:101) > at org.gc.test.GenbankParserTest.main(GenbankParserTest.java:34) > > > > ========================================== > > package org.gc.test; > > import java.io.BufferedReader; > import java.io.File; > import java.io.FileReader; > > import org.biojava.bio.seq.Sequence; > import org.biojava.bio.seq.SequenceIterator; > import org.biojava.bio.seq.io.SeqIOTools; > > /** > * @author unknown > * > * To change the template for this generated type comment go to > * Window>Preferences>Java>Code Generation>Code and Comments > */ > public class GenbankParserTest { > > public static void main(String[] args) { > System.out.println("Main starts ..."); > try { > > File f = new File("D:\\Travail\\data\\Hs_chr19.gbs"); > BufferedReader bf = new BufferedReader(new FileReader(f)); > SequenceIterator it = SeqIOTools.readGenbank(bf); > while (it.hasNext()) { > System.out.println("getting next seq..."); > Sequence s = it.nextSequence(); > } > } catch (Exception e) { > System.out.println(e.getStackTrace()); > } > System.out.println("End of main"); > } > } > > > ********** L'ADSL A 20 EUR/MOIS********** > Avec Tiscali, l'ADSL est ? 20 EUR/mois. Vous pourrez chercher longtemps avant de trouver moins cher ! > Pour profiter de cette offre exceptionnelle, cliquez ici : http://register.tiscali.fr/adsl/ > Offre soumise ? conditions. > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > > > >======================================================================= >Attention: The information contained in this message and/or attachments >from AgResearch Limited is intended only for the persons or entities >to which it is addressed and may contain confidential and/or privileged >material. Any review, retransmission, dissemination or other use of, or >taking of any action in reliance upon, this information by persons or >entities other than the intended recipients is prohibited by AgResearch >Limited. If you have received this message in error, please notify the >sender immediately. >======================================================================= > >_______________________________________________ >Biojava-l mailing list - Biojava-l@biojava.org >http://biojava.org/mailman/listinfo/biojava-l > > > From r.stones at csl.gov.uk Thu Sep 11 06:24:00 2003 From: r.stones at csl.gov.uk (Robert Stones) Date: Thu Sep 11 06:22:43 2003 Subject: [Biojava-l] Protein digest References: <200309111000.h8BA0GMj021409@portal.open-bio.org> Message-ID: <3F604D40.70D66C20@csl.gov.uk> Hi Does anyone have any example code to digest proteins and work out the mass of the peptides generated? biojava-l-request@portal.open-bio.org wrote: > > Send Biojava-l mailing list submissions to > biojava-l@biojava.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://biojava.org/mailman/listinfo/biojava-l > or, via email, send a message with subject or body 'help' to > biojava-l-request@biojava.org > > You can reach the person managing the list at > biojava-l-owner@biojava.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Biojava-l digest..." > > Today's Topics: > > 1. RE: Best way to represent multiple annotation "tracks" > (Ihab A.B. Awad) > 2. Reformating multiple sequence alignments (Gabriel del Rio Guerra) > 3. Parsing location from gbk files > ( charles.girardot@libertysurf.fr ) > 4. RE: Reformating multiple sequence alignments (Schreiber, Mark) > 5. RE: Parsing location from gbk files (Schreiber, Mark) > 6. Re: Parsing location from gbk files (Matthew Pocock) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 8 Sep 2003 16:53:09 -0700 > From: "Ihab A.B. Awad" > Subject: RE: [Biojava-l] Best way to represent multiple annotation > "tracks" > To: "Schreiber, Mark" , > > Message-ID: > Content-Type: text/plain; charset="us-ascii" ; format="flowed" > > Hi again, > > [ Pls excuse the poor netiquette for posting a followup to my own message.... ] > > >So, let's say I have a bunch of ESTs, each of which has been mapped > >to a location on the genome. To each EST, my data maps a floating > >point number indicating the expression level. > > > >In this case, each Feature would represent one of the ESTs, right? > >So what would be the Feature(s) representing the annotation track? > >Would they be Features owned by the EST Feature (via the inheritance > >of FeatureHolder by interface Feature)? Or -- ?? > > Alternatively, would each EST be a SubSequence with Features attached > to it, with each Feature representing one of the data "tracks"? If > so, then how does one decide when something is a Feature or a > SubSequence? I'm not a biologist, so I'm probably way confused here, > but it seems to me there is a gray area (ORFs?). > > So I guess there are several competing implementations. > > 1. SEQUENCE BASED, FEATURES REPRESENT DATA TRACKS > > "Chromosome 1" : Sequence > "AA504327" : SubSequence > "RAT2N" : Feature > : Annotation > "Value" => 2.34312 > "RAT2_MEAN": Feature > : Annotation > "Value" => 1.8342 > "AA432030" : SubSequence > ... > > 2. SEQUENCE BASED, ANNOTATIONS REPRESENT DATA TRACKS > > "Chromosome 1" : Sequence > "AA504327" : SubSequence > "Microarray Experiment B2341v" : Feature > : Annotation > "RAT2N" => 2.34312 > "RAT2_MEAN" => 1.8342 > "AA432030" : SubSequence > ... > > 3. FEATURE BASED, SUB-FEATURES REPRESENT DATA TRACKS > > (Very similar to #1, except using Feature instead of SubSequence.) > > "Chromosome 1" : Sequence > "AA504327" : Feature > "RAT2N" : Feature > : Annotation > "Value" => 2.34312 > "RAT2_MEAN": Feature > : Annotation > "Value" => 1.8342 > "AA432030" : SubSequence > ... > > 4. FEATURE BASED, ANNOTATIONS REPRESENT DATA TRACKS > > (Very similar to #2, except using Feature instead of SubSequence.) > > "Chromosome 1" : Sequence > "AA504327" : Feature > "Microarray Experiment B2341v" : Feature > : Annotation > "RAT2N" => 2.34312 > "RAT2_MEAN" => 1.8342 > "AA432030" : SubSequence > ... > > Thanks a lot again & peace, > > Ihab > > -- > Ihab A.B. Awad > Snr Scientific Programmer, Dept of Genetics > > ------------------------------ > > Message: 2 > Date: Wed, 10 Sep 2003 09:06:00 -0700 > From: "Gabriel del Rio Guerra" > Subject: [Biojava-l] Reformating multiple sequence alignments > To: > Message-ID: > <4AA34A707932424EBE2D973764D226A91B98D7@inverness.buckcenter.org> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I am interesting in using or developing a program to inter-convert > different sequence alignments formats. In particular I want to translate > HSSP alignments into MSF format. Does anyone knows if this is possible > with Biojava at this point? > > Thanks, > > Gabriel > > -----Original Message----- > From: Kenny Yu [mailto:kyu@biodiscovery.com] > Sent: Wednesday, April 30, 2003 8:45 AM > To: biojava-l@biojava.org > Subject: [Biojava-l] unified consolidated annotation system > > Both biosql and biodas are concerned with retrieving annotation on the > basis of known features. They are not optimized for large-scale > cross-system queries and data mining on the basis of annotations. I am > interested in consolidating annotations from various sources (such as > genbank and unigene) into a unified form on which I can run queries like > "find features that are linked to DNA repair function in human but not > in mouse" and "find feature whose molecular functions overlap with > those of Accession Number nnnn". Similar mechanisms may exist in LION's > SRS (http://www.lionbioscience.com/solutions/products/srs/relational). > What I am contemplating is essentially a data warehouse for annotations. > I'll borrow data warehouse and OLAP techniques in the design. It's a > hybrid of relational, nested-relational and multidimensional database. > Feature entity, or gene, and annotation are the dimensions. It models > textual values as well as binary objects such as pathway diagrams as > annot! > ation values. I intend to make my work open-source and would call it > UCAsql. Currently the schema design, with some documentation and java > API, is available to anyone upon request by email to myself at > kyu@biodiscovery.com. > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > > ------------------------------ > > Message: 3 > Date: Wed, 10 Sep 2003 20:13:41 +0200 > From: " charles.girardot@libertysurf.fr " > > Subject: [Biojava-l] Parsing location from gbk files > To: " biojava-l " > Message-ID: > Content-Type: text/plain; charset=iso-8859-1 > > Hi, > > I am using biojava to extract mRNA, CDS and gene boundaries from genbank annotation files (e.g., "hs_chr19.gbs" from ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_19/). > I've just switched from the biojava 1.22 to latest 1.3 release (biojava-1.30-jdk14.jar and bytecode-0.92.jar) > and I get lots of exception (see below, the peace of code generating this follows as well). Don't known if it's important but ".gbs" files do not hold the contig sequences but only annotations. > > Nota: I am using the jdk 1.4.1. > > Thanks for your help. > > Charles Girardot > > ======================================= > java.lang.IllegalArgumentException: Location 59817 is outside 1..0 > at org.biojava.bio.seq.impl.SimpleFeature.(SimpleFeature.java:306) > at org.biojava.bio.seq.impl.SimpleStrandedFeature.(SimpleStrandedFeature.java:74) > at sun.reflect.GeneratedConstructorAccessor1.newInstance(Unknown Source) > at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) > at java.lang.reflect.Constructor.newInstance(Constructor.java:274) > at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:138) > rethrown as org.biojava.bio.BioException: Couldn't realize feature > at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:144) > at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:94) > at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:198) > at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:204) > at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:168) > at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:87) > at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:98) > at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:101) > at org.gc.test.GenbankParserTest.main(GenbankParserTest.java:34) > > > ========================================== > > package org.gc.test; > > import java.io.BufferedReader; > import java.io.File; > import java.io.FileReader; > > import org.biojava.bio.seq.Sequence; > import org.biojava.bio.seq.SequenceIterator; > import org.biojava.bio.seq.io.SeqIOTools; > > /** > * @author unknown > * > * To change the template for this generated type comment go to > * Window>Preferences>Java>Code Generation>Code and Comments > */ > public class GenbankParserTest { > > public static void main(String[] args) { > System.out.println("Main starts ..."); > try { > > File f = new File("D:\\Travail\\data\\Hs_chr19.gbs"); > BufferedReader bf = new BufferedReader(new FileReader(f)); > SequenceIterator it = SeqIOTools.readGenbank(bf); > while (it.hasNext()) { > System.out.println("getting next seq..."); > Sequence s = it.nextSequence(); > } > } catch (Exception e) { > System.out.println(e.getStackTrace()); > } > System.out.println("End of main"); > } > } > > ********** L'ADSL A 20 EUR/MOIS********** > Avec Tiscali, l'ADSL est ? 20 EUR/mois. Vous pourrez chercher longtemps avant de trouver moins cher ! > Pour profiter de cette offre exceptionnelle, cliquez ici : http://register.tiscali.fr/adsl/ > Offre soumise ? conditions. > > ------------------------------ > > Message: 4 > Date: Thu, 11 Sep 2003 09:40:34 +1200 > From: "Schreiber, Mark" > Subject: RE: [Biojava-l] Reformating multiple sequence alignments > To: "Gabriel del Rio Guerra" , > > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Hi - > > I'm not too familiar with what you are trying to do but... > > A lot of the biojava Alignment API can be found in org.biojava.bio.alignment parsers for reading and writing different formats are in org.biojava.bio.seq.io.* SeqIOTools is especially useful. > > Hope this helps: > > - Mark > > > -----Original Message----- > From: Gabriel del Rio Guerra [mailto:gdelrio@buckinstitute.org] > Sent: Thu 11/09/2003 4:06 a.m. > To: biojava-l@biojava.org > Cc: > Subject: [Biojava-l] Reformating multiple sequence alignments > > > > Hi, > > I am interesting in using or developing a program to inter-convert > different sequence alignments formats. In particular I want to translate > HSSP alignments into MSF format. Does anyone knows if this is possible > with Biojava at this point? > > Thanks, > > Gabriel > > -----Original Message----- > From: Kenny Yu [mailto:kyu@biodiscovery.com] > Sent: Wednesday, April 30, 2003 8:45 AM > To: biojava-l@biojava.org > Subject: [Biojava-l] unified consolidated annotation system > > Both biosql and biodas are concerned with retrieving annotation on the > basis of known features. They are not optimized for large-scale > cross-system queries and data mining on the basis of annotations. I am > interested in consolidating annotations from various sources (such as > genbank and unigene) into a unified form on which I can run queries like > "find features that are linked to DNA repair function in human but not > in mouse" and "find feature whose molecular functions overlap with > those of Accession Number nnnn". Similar mechanisms may exist in LION's > SRS (http://www.lionbioscience.com/solutions/products/srs/relational). > What I am contemplating is essentially a data warehouse for annotations. > I'll borrow data warehouse and OLAP techniques in the design. It's a > hybrid of relational, nested-relational and multidimensional database. > Feature entity, or gene, and annotation are the dimensions. It models > textual values as well as binary objects such as pathway diagrams as > annot! > ation values. I intend to make my work open-source and would call it > UCAsql. Currently the schema design, with some documentation and java > API, is available to anyone upon request by email to myself at > kyu@biodiscovery.com. > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > > > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > > ------------------------------ > > Message: 5 > Date: Thu, 11 Sep 2003 09:44:04 +1200 > From: "Schreiber, Mark" > Subject: RE: [Biojava-l] Parsing location from gbk files > To: , "biojava-l" > > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Hi - > > This is a recurring problem as more files are being deposited that contain only references to other contigs but contain annotation and features. > > A model where a DummySequence of appropriate length is instantiated if the contig files are not available may be useful. Possibley a GBS parser would be useful? Has anyone hacked out something like this? > > - Mark > > -----Original Message----- > From: charles.girardot@libertysurf.fr [mailto:charles.girardot@libertysurf.fr] > Sent: Thu 11/09/2003 6:13 a.m. > To: biojava-l > Cc: > Subject: [Biojava-l] Parsing location from gbk files > > > > Hi, > > I am using biojava to extract mRNA, CDS and gene boundaries from genbank annotation files (e.g., "hs_chr19.gbs" from ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_19/). > I've just switched from the biojava 1.22 to latest 1.3 release (biojava-1.30-jdk14.jar and bytecode-0.92.jar) > and I get lots of exception (see below, the peace of code generating this follows as well). Don't known if it's important but ".gbs" files do not hold the contig sequences but only annotations. > > Nota: I am using the jdk 1.4.1. > > Thanks for your help. > > Charles Girardot > > > ======================================= > java.lang.IllegalArgumentException: Location 59817 is outside 1..0 > at org.biojava.bio.seq.impl.SimpleFeature.(SimpleFeature.java:306) > at org.biojava.bio.seq.impl.SimpleStrandedFeature.(SimpleStrandedFeature.java:74) > at sun.reflect.GeneratedConstructorAccessor1.newInstance(Unknown Source) > at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) > at java.lang.reflect.Constructor.newInstance(Constructor.java:274) > at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:138) > rethrown as org.biojava.bio.BioException: Couldn't realize feature > at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:144) > at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:94) > at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:198) > at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:204) > at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:168) > at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:87) > at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:98) > at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:101) > at org.gc.test.GenbankParserTest.main(GenbankParserTest.java:34) > > > > ========================================== > > package org.gc.test; > > import java.io.BufferedReader; > import java.io.File; > import java.io.FileReader; > > import org.biojava.bio.seq.Sequence; > import org.biojava.bio.seq.SequenceIterator; > import org.biojava.bio.seq.io.SeqIOTools; > > /** > * @author unknown > * > * To change the template for this generated type comment go to > * Window>Preferences>Java>Code Generation>Code and Comments > */ > public class GenbankParserTest { > > public static void main(String[] args) { > System.out.println("Main starts ..."); > try { > > File f = new File("D:\\Travail\\data\\Hs_chr19.gbs"); > BufferedReader bf = new BufferedReader(new FileReader(f)); > SequenceIterator it = SeqIOTools.readGenbank(bf); > while (it.hasNext()) { > System.out.println("getting next seq..."); > Sequence s = it.nextSequence(); > } > } catch (Exception e) { > System.out.println(e.getStackTrace()); > } > System.out.println("End of main"); > } > } > > > ********** L'ADSL A 20 EUR/MOIS********** > Avec Tiscali, l'ADSL est ? 20 EUR/mois. Vous pourrez chercher longtemps avant de trouver moins cher ! > Pour profiter de cette offre exceptionnelle, cliquez ici : http://register.tiscali.fr/adsl/ > Offre soumise ? conditions. > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > > > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > > ------------------------------ > > Message: 6 > Date: Thu, 11 Sep 2003 10:58:16 +0100 > From: Matthew Pocock > Subject: Re: [Biojava-l] Parsing location from gbk files > To: "Schreiber, Mark" > Cc: biojava-l > Message-ID: <3F604738.6080504@yahoo.co.uk> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Schreiber, Mark wrote: > > >Hi - > > > >This is a recurring problem as more files are being deposited that contain only references to other contigs but contain annotation and features. > > > >A model where a DummySequence of appropriate length is instantiated if the contig files are not available may be useful. Possibley a GBS parser would be useful? Has anyone hacked out something like this? > > > >- Mark > > > > > It should be possible to create a dummy sequence of the right length and > then populate the feature table with component features for the assembly > info. Perhaps if we wrote a ComponentFeature that held an LSID - then > tries to resolve itself on demand via the LSID framework? > > I don't have the time right now, but somebody should get keen. > > Matthew > > > -----Original Message----- > > From: charles.girardot@libertysurf.fr [mailto:charles.girardot@libertysurf.fr] > > Sent: Thu 11/09/2003 6:13 a.m. > > To: biojava-l > > Cc: > > Subject: [Biojava-l] Parsing location from gbk files > > > > > > > > Hi, > > > > I am using biojava to extract mRNA, CDS and gene boundaries from genbank annotation files (e.g., "hs_chr19.gbs" from ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_19/). > > I've just switched from the biojava 1.22 to latest 1.3 release (biojava-1.30-jdk14.jar and bytecode-0.92.jar) > > and I get lots of exception (see below, the peace of code generating this follows as well). Don't known if it's important but ".gbs" files do not hold the contig sequences but only annotations. > > > > Nota: I am using the jdk 1.4.1. > > > > Thanks for your help. > > > > Charles Girardot > > > > > > ======================================= > > java.lang.IllegalArgumentException: Location 59817 is outside 1..0 > > at org.biojava.bio.seq.impl.SimpleFeature.(SimpleFeature.java:306) > > at org.biojava.bio.seq.impl.SimpleStrandedFeature.(SimpleStrandedFeature.java:74) > > at sun.reflect.GeneratedConstructorAccessor1.newInstance(Unknown Source) > > at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) > > at java.lang.reflect.Constructor.newInstance(Constructor.java:274) > > at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:138) > > rethrown as org.biojava.bio.BioException: Couldn't realize feature > > at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:144) > > at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:94) > > at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:198) > > at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:204) > > at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:168) > > at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:87) > > at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:98) > > at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:101) > > at org.gc.test.GenbankParserTest.main(GenbankParserTest.java:34) > > > > > > > > ========================================== > > > > package org.gc.test; > > > > import java.io.BufferedReader; > > import java.io.File; > > import java.io.FileReader; > > > > import org.biojava.bio.seq.Sequence; > > import org.biojava.bio.seq.SequenceIterator; > > import org.biojava.bio.seq.io.SeqIOTools; > > > > /** > > * @author unknown > > * > > * To change the template for this generated type comment go to > > * Window>Preferences>Java>Code Generation>Code and Comments > > */ > > public class GenbankParserTest { > > > > public static void main(String[] args) { > > System.out.println("Main starts ..."); > > try { > > > > File f = new File("D:\\Travail\\data\\Hs_chr19.gbs"); > > BufferedReader bf = new BufferedReader(new FileReader(f)); > > SequenceIterator it = SeqIOTools.readGenbank(bf); > > while (it.hasNext()) { > > System.out.println("getting next seq..."); > > Sequence s = it.nextSequence(); > > } > > } catch (Exception e) { > > System.out.println(e.getStackTrace()); > > } > > System.out.println("End of main"); > > } > > } > > > > > > ********** L'ADSL A 20 EUR/MOIS********** > > Avec Tiscali, l'ADSL est ? 20 EUR/mois. Vous pourrez chercher longtemps avant de trouver moins cher ! > > Pour profiter de cette offre exceptionnelle, cliquez ici : http://register.tiscali.fr/adsl/ > > Offre soumise ? conditions. > > > > > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l@biojava.org > > http://biojava.org/mailman/listinfo/biojava-l > > > > > > > >======================================================================= > >Attention: The information contained in this message and/or attachments > >from AgResearch Limited is intended only for the persons or entities > >to which it is addressed and may contain confidential and/or privileged > >material. Any review, retransmission, dissemination or other use of, or > >taking of any action in reliance upon, this information by persons or > >entities other than the intended recipients is prohibited by AgResearch > >Limited. If you have received this message in error, please notify the > >sender immediately. > >======================================================================= > > > >_______________________________________________ > >Biojava-l mailing list - Biojava-l@biojava.org > >http://biojava.org/mailman/listinfo/biojava-l > > > > > > > > ------------------------------ > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > > End of Biojava-l Digest, Vol 9, Issue 2 > *************************************** ________________________________________________________________________ This e-mail has been scanned for all viruses by Star Internet. The service is powered by MessageLabs. For more information on a proactive anti-virus service working around the clock, around the globe, visit: http://www.star.net.uk ________________________________________________________________________ From fred.criscuolo at pfizer.com Thu Sep 11 12:26:52 2003 From: fred.criscuolo at pfizer.com (Criscuolo, Fred) Date: Thu Sep 11 12:25:38 2003 Subject: [Biojava-l] Parse error with negative strand CDS Message-ID: <6300328FB7CFD511AACF0002A589357D08F78D6B@lajgrdexm04.agouron.com> Hi, I am using BioJava 1.3.0 to process a GenBank file that has a CDS on the negative strand. I am using the SeqIOTools.readGenbank(BufferedReader) method to parse the file. I get the following error for any CDS on the negative strand: This line could not be parsed: CDS complement(518..1597) The GenBank files I'm working with are produced by the VectorNTI application. I'm using Java 1.4.2. I've searched the biojava mailing list but have not seen a reference to this particular problem. Any idea what's wrong? Thanks. Fred Fred Criscuolo Research Informatics - Pfizer, Inc. 858.622.7307 LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately. From mark.schreiber at agresearch.co.nz Thu Sep 11 18:04:46 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Thu Sep 11 18:03:17 2003 Subject: [Biojava-l] Parse error with negative strand CDS Message-ID: Hi - This looks odd. It may be that the Genbank produced by VectorNTI is not quite right. Can you post the file, or at least the few lines surrounding the CDS feature? - Mark -----Original Message----- From: Criscuolo, Fred [mailto:fred.criscuolo@pfizer.com] Sent: Friday, 12 September 2003 4:27 a.m. To: 'biojava-l@biojava.org' Subject: [Biojava-l] Parse error with negative strand CDS Hi, I am using BioJava 1.3.0 to process a GenBank file that has a CDS on the negative strand. I am using the SeqIOTools.readGenbank(BufferedReader) method to parse the file. I get the following error for any CDS on the negative strand: This line could not be parsed: CDS complement(518..1597) The GenBank files I'm working with are produced by the VectorNTI application. I'm using Java 1.4.2. I've searched the biojava mailing list but have not seen a reference to this particular problem. Any idea what's wrong? Thanks. Fred Fred Criscuolo Research Informatics - Pfizer, Inc. 858.622.7307 LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately. _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From y_liu88 at yahoo.com Fri Sep 12 00:13:20 2003 From: y_liu88 at yahoo.com (Yong Liu) Date: Fri Sep 12 00:11:47 2003 Subject: [Biojava-l] HELP: Relative URI "NCBI_BlastOutput.dtd"; can not be resolved without a base URI. Message-ID: <20030912041320.22806.qmail@web20609.mail.yahoo.com> Hi, I am new to Biojava. I just checked out biojava-live from the cvs.biojava, and compiled the whole packages and demos successfully. I want to run the BlastParser, but I got the following errors. Can anybody tell me how I run this program? Thanks very much! -Yong %java -classpath .:../biojava.jar blastxml.BlastParser ./blastxml/input.xml org.xml.sax.SAXParseException: Relative URI "NCBI_BlastOutput.dtd"; can not be resolved without a base URI. at org.apache.crimson.parser.Parser2.fatal(Parser2.java:3339) at org.apache.crimson.parser.Parser2.fatal(Parser2.java:3333) at org.apache.crimson.parser.Parser2.resolveURI(Parser2.java:2915) at org.apache.crimson.parser.Parser2.maybeExternalID(Parser2.java:2887) at org.apache.crimson.parser.Parser2.maybeDoctypeDecl(Parser2.java:1276) at org.apache.crimson.parser.Parser2.parseInternal(Parser2.java:623) at org.apache.crimson.parser.Parser2.parse(Parser2.java:333) at org.apache.crimson.parser.XMLReaderImpl.parse(XMLReaderImpl.java:448) at org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade.parse(BlastXMLParserFacade.java:167) at blastxml.BlastParser.main(BlastParser.java:47) __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software http://sitebuilder.yahoo.com From pwilkinson at videotron.ca Fri Sep 12 09:38:54 2003 From: pwilkinson at videotron.ca (Peter Wilkinson) Date: Fri Sep 12 09:37:28 2003 Subject: [Biojava-l] Parse error with negative strand CDS In-Reply-To: Message-ID: <5.2.0.9.0.20030912093129.00b5c570@pop.videotron.ca> Well ... Fred. Having worked for the company that makes VectorNTI (Informax), I can tell you that there are some modifications to the format that should be benign ... but that is not always true. The output of GenBank files from VectorNTI are slightly different, but Iwould not have expected them to break the parser. the annotations within VectorNTI are added into the comments fields, which should not be a problem. One thing to check is whether biojava parser is updated to the current genbank format, and whether the output from vectorNTI produces the same 'version' of the genbank file. If they don't then the biojava parser may not handle the vectorNTI output. if you could send the file I can see what the problem is, the line on its own does not seem like a problem. It might be some spacing issues (version of the formatting) in the file generated on the previous line somewhere. Peter At 10:04 AM 12/09/2003 +1200, Schreiber, Mark wrote: >Hi - > >This looks odd. It may be that the Genbank produced by VectorNTI is not >quite right. Can you post the file, or at least the few lines surrounding >the CDS feature? > >- Mark > > >-----Original Message----- >From: Criscuolo, Fred [mailto:fred.criscuolo@pfizer.com] >Sent: Friday, 12 September 2003 4:27 a.m. >To: 'biojava-l@biojava.org' >Subject: [Biojava-l] Parse error with negative strand CDS > > >Hi, >I am using BioJava 1.3.0 to process a GenBank file that has a CDS on the >negative strand. I am using the SeqIOTools.readGenbank(BufferedReader) >method to parse the file. I get the following error for any CDS on the >negative strand: > > This line could not be parsed: CDS complement(518..1597) > >The GenBank files I'm working with are produced by the VectorNTI >application. I'm using Java 1.4.2. I've searched the biojava mailing list >but have not seen a reference to this particular problem. Any idea what's >wrong? Thanks. Fred > >Fred Criscuolo >Research Informatics - Pfizer, Inc. >858.622.7307 > > > >LEGAL NOTICE >Unless expressly stated otherwise, this message is confidential and may be >privileged. It is intended for the addressee(s) only. Access to this >E-mail by anyone else is unauthorized. If you are not an addressee, any >disclosure or copying of the contents of this E-mail or any action taken >(or not taken) in reliance on it is unauthorized and may be unlawful. If >you are not an addressee, please inform the sender immediately. >_______________________________________________ >Biojava-l mailing list - Biojava-l@biojava.org >http://biojava.org/mailman/listinfo/biojava-l >======================================================================= >Attention: The information contained in this message and/or attachments >from AgResearch Limited is intended only for the persons or entities >to which it is addressed and may contain confidential and/or privileged >material. Any review, retransmission, dissemination or other use of, or >taking of any action in reliance upon, this information by persons or >entities other than the intended recipients is prohibited by AgResearch >Limited. If you have received this message in error, please notify the >sender immediately. >======================================================================= > >_______________________________________________ >Biojava-l mailing list - Biojava-l@biojava.org >http://biojava.org/mailman/listinfo/biojava-l ------------------------------------- Peter Wilkinson Bioinformatics Consultant ------------------------------------- From facemann at yahoo.com Fri Sep 12 20:05:10 2003 From: facemann at yahoo.com (Andy Hammer) Date: Fri Sep 12 20:03:36 2003 Subject: [Biojava-l] Performance of SymbolList.subStr() function Message-ID: <20030913000510.87331.qmail@web13406.mail.yahoo.com> This blows my mind! In both blocks of code: seq = si.nextSequence(); //just a protein sequence In this block of code, my system would take hours and often crash with an out of memory error. for(int i = 1; i <= seqLength; i++){ String seqString = seq.subStr(i,i); char protein = seqString.charAt(0); newSeq = newSeq.append(newCodon(protein));//add a 3 char string to the newSeq StringBuffer } I altered the above block to: String seqString = seq.seqString(); for(int i = 0; i < seqLength; i++){ char protein = seqString.charAt(i); newSeq = newSeq.append(newCodon(protein)); } This program used to take 4 hours to complete. With this simple change it is now done in 30 minutes! Obviously, the SymbolList.subStr() function was severly hampering my efficiency. I guess it was poor use of the SymbolList.subStr() function. My rational was that I didn't want to create an unneeded String simply to represent my already existing SymbolList. I am just trying to learn from this to become a better programmer and would appreciate any comments on this. Thanks! __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software http://sitebuilder.yahoo.com From facemann at yahoo.com Fri Sep 12 21:31:29 2003 From: facemann at yahoo.com (Andy Hammer) Date: Fri Sep 12 21:29:55 2003 Subject: [Biojava-l] Build errors Message-ID: <20030913013129.30335.qmail@web13407.mail.yahoo.com> I am getting some build errors. I even deleted /biojava-live and started over. Lastly from ./biojava-live/ ant clean = build successful cvs update -d = appeared successful ant = [ahammer@westwater biojava-live]$ ant Buildfile: build.xml init: [echo] JUnit present: ${junit.present} [echo] JUnit supported by Ant: true prepare: [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build prepare-core: [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/src/main [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/classes/main [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/src/tests [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/classes/tests [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/src/demos [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/classes/demos [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/src/apps [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/classes/apps [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/src/docs [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/docs [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/docs/api [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/lib [copy] Copying 1191 files to /home/ahammer/downloads/biojava-live/ant-build/src/main [copy] Copied 23 empty directories to /home/ahammer/downloads/biojava-live/ant-build/src/main [copy] Copying 147 files to /home/ahammer/downloads/biojava-live/ant-build/src/tests [copy] Copied 1 empty directory to /home/ahammer/downloads/biojava-live/ant-build/src/tests [copy] Copying 180 files to /home/ahammer/downloads/biojava-live/ant-build/src/demos [copy] Copied 5 empty directories to /home/ahammer/downloads/biojava-live/ant-build/src/demos [copy] Copying 2 files to /home/ahammer/downloads/biojava-live/ant-build/src/apps [copy] Copying 15 files to /home/ahammer/downloads/biojava-live/ant-build/src/docs [copy] Copying 1 file to /home/ahammer/downloads/biojava-live/ant-build/src/main [copy] Copying 1 file to /home/ahammer/downloads/biojava-live/ant-build/src/demos [copy] Copying 1 file to /home/ahammer/downloads/biojava-live/ant-build/src/apps [copy] Copying 17 files to /home/ahammer/downloads/biojava-live/ant-build/classes/main [copy] Copied 1 empty directory to /home/ahammer/downloads/biojava-live/ant-build/classes/main [copy] Copying 3 files to /home/ahammer/downloads/biojava-live/ant-build prepare-src: compile: [javac] Compiling 1091 source files to /home/ahammer/downloads/biojava-live/ant-build/classes/main [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/impl/RevCompSequence.java:47: reference to ProjectedFeatureHolder is ambiguous, both class org.biojava.bio.seq.projection.ProjectedFeatureHolder in org.biojava.bio.seq.projection and class org.biojava.bio.seq.ProjectedFeatureHolder in org.biojava.bio.seq match [javac] private ProjectedFeatureHolder pfh; [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/impl/RevCompSequence.java:65: reference to ProjectedFeatureHolder is ambiguous, both class org.biojava.bio.seq.projection.ProjectedFeatureHolder in org.biojava.bio.seq.projection and class org.biojava.bio.seq.ProjectedFeatureHolder in org.biojava.bio.seq match [javac] pfh = new ProjectedFeatureHolder(new TranslateFlipContext(this,seq,seq.length()+1,true)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:301: cannot resolve symbol [javac] symbol : method make_checkcast (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] proxyIV.add(ByteCode.make_checkcast(ourContextC)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:366: cannot resolve symbol [javac] symbol : method make_checkcast (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] proxyIV.add(ByteCode.make_checkcast(ourContextC) ); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:436: cannot resolve symbol [javac] symbol : variable TYPE_OBJECT [javac] location: class org.biojava.utils.bytecode.CodeUtils [javac] CodeClass c_baseClass = CodeUtils.TYPE_OBJECT; [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:447: cannot resolve symbol [javac] symbol : variable TYPE_OBJECT [javac] location: class org.biojava.utils.bytecode.CodeUtils [javac] = CodeUtils.TYPE_OBJECT.getConstructor(CodeUtils.EMPTY_LIST); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:482: cannot resolve symbol [javac] symbol : method make_checkcast (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] revTIV.add(ByteCode.make_checkcast(c_FeatureTemplate)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:492: cannot resolve symbol [javac] symbol : method getFields () [javac] location: interface org.biojava.utils.bytecode.CodeClass [javac] for(Iterator fi = c_ourTemplate.getFields().iterator(); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:522: cannot resolve symbol [javac] symbol : method make_checkcast (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] revIV.add(ByteCode.make_checkcast(c_ourTemplate)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:524: cannot resolve symbol [javac] symbol : method make_checkcast (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] revIV.add(ByteCode.make_checkcast(c_ourContext)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:526: cannot resolve symbol [javac] symbol : method make_checkcast (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] revIV.add(ByteCode.make_checkcast(c_ourTemplate)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:198: cannot resolve symbol [javac] symbol : method make_checkcast (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] walkIV.add(ByteCode.make_checkcast(c_ourVisitor)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:227: cannot resolve symbol [javac] symbol : method forMethod (java.lang.reflect.Method) [javac] location: class org.biojava.utils.bytecode.IntrospectedCodeClass [javac] CodeMethod m_getFilter = IntrospectedCodeClass.forMethod(m); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:245: cannot resolve symbol [javac] symbol : method make_checkcast (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] wfiv.add(ByteCode.make_checkcast(c_ourFilter)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:260: cannot resolve symbol [javac] symbol : method make_instanceof (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] wrapperIV.add(ByteCode.make_instanceof(c_ourFilter)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:291: cannot resolve symbol [javac] symbol : method forMethod (java.lang.reflect.Method) [javac] location: class org.biojava.utils.bytecode.IntrospectedCodeClass [javac] CodeMethod ourMeth = IntrospectedCodeClass.forMethod(meth); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:297: cannot resolve symbol [javac] symbol : method make_checkcast (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] bodyIV.add(ByteCode.make_checkcast(c_thisFiltType)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:306: cannot resolve symbol [javac] symbol : method make_instanceof (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] walkIV.add(ByteCode.make_instanceof(c_thisFiltType)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:328: cannot resolve symbol [javac] symbol : variable TYPE_OBJECT [javac] location: class org.biojava.utils.bytecode.CodeUtils [javac] CodeUtils.TYPE_OBJECT, [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:358: cannot resolve symbol [javac] symbol : variable TYPE_OBJECT [javac] location: class org.biojava.utils.bytecode.CodeUtils [javac] CodeUtils.TYPE_OBJECT, [javac] ^ [javac] 20 errors BUILD FAILED file:/home/ahammer/downloads/biojava-live/build.xml:278: Compile failed; see the compiler error output for details. I think last time I bothered to build was around 1.3. It has always worked in the past. . . Any ideas would be appreciated. facemann __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software http://sitebuilder.yahoo.com From mark.schreiber at agresearch.co.nz Fri Sep 12 21:31:44 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Fri Sep 12 21:30:34 2003 Subject: [Biojava-l] Parse error with negative strand CDS Message-ID: The problem appears to be in the way that VNTI represents the coordinates of locations that cross the origin of a circular molecule. It is not done in the "NCBI way" so the parser gets a little confused. I think we can make the parser more tolerant but we need to sort out a few issues in the deep dark bowels of biojava seqio first. - Mark -----Original Message----- From: Peter Wilkinson [mailto:pwilkinson@videotron.ca] Sent: Sat 13/09/2003 1:38 a.m. To: Schreiber, Mark; Criscuolo, Fred; biojava-l@biojava.org Cc: Subject: RE: [Biojava-l] Parse error with negative strand CDS Well ... Fred. Having worked for the company that makes VectorNTI (Informax), I can tell you that there are some modifications to the format that should be benign ... but that is not always true. The output of GenBank files from VectorNTI are slightly different, but Iwould not have expected them to break the parser. the annotations within VectorNTI are added into the comments fields, which should not be a problem. One thing to check is whether biojava parser is updated to the current genbank format, and whether the output from vectorNTI produces the same 'version' of the genbank file. If they don't then the biojava parser may not handle the vectorNTI output. if you could send the file I can see what the problem is, the line on its own does not seem like a problem. It might be some spacing issues (version of the formatting) in the file generated on the previous line somewhere. Peter At 10:04 AM 12/09/2003 +1200, Schreiber, Mark wrote: >Hi - > >This looks odd. It may be that the Genbank produced by VectorNTI is not >quite right. Can you post the file, or at least the few lines surrounding >the CDS feature? > >- Mark > > >-----Original Message----- >From: Criscuolo, Fred [mailto:fred.criscuolo@pfizer.com] >Sent: Friday, 12 September 2003 4:27 a.m. >To: 'biojava-l@biojava.org' >Subject: [Biojava-l] Parse error with negative strand CDS > > >Hi, >I am using BioJava 1.3.0 to process a GenBank file that has a CDS on the >negative strand. I am using the SeqIOTools.readGenbank(BufferedReader) >method to parse the file. I get the following error for any CDS on the >negative strand: > > This line could not be parsed: CDS complement(518..1597) > >The GenBank files I'm working with are produced by the VectorNTI >application. I'm using Java 1.4.2. I've searched the biojava mailing list >but have not seen a reference to this particular problem. Any idea what's >wrong? Thanks. Fred > >Fred Criscuolo >Research Informatics - Pfizer, Inc. >858.622.7307 > > > >LEGAL NOTICE >Unless expressly stated otherwise, this message is confidential and may be >privileged. It is intended for the addressee(s) only. Access to this >E-mail by anyone else is unauthorized. If you are not an addressee, any >disclosure or copying of the contents of this E-mail or any action taken >(or not taken) in reliance on it is unauthorized and may be unlawful. If >you are not an addressee, please inform the sender immediately. >_______________________________________________ >Biojava-l mailing list - Biojava-l@biojava.org >http://biojava.org/mailman/listinfo/biojava-l >======================================================================= >Attention: The information contained in this message and/or attachments >from AgResearch Limited is intended only for the persons or entities >to which it is addressed and may contain confidential and/or privileged >material. Any review, retransmission, dissemination or other use of, or >taking of any action in reliance upon, this information by persons or >entities other than the intended recipients is prohibited by AgResearch >Limited. If you have received this message in error, please notify the >sender immediately. >======================================================================= > >_______________________________________________ >Biojava-l mailing list - Biojava-l@biojava.org >http://biojava.org/mailman/listinfo/biojava-l ------------------------------------- Peter Wilkinson Bioinformatics Consultant ------------------------------------- ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From mark.schreiber at agresearch.co.nz Fri Sep 12 21:38:51 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Fri Sep 12 21:37:24 2003 Subject: [Biojava-l] Performance of SymbolList.subStr() function Message-ID: Andy - String manipulation is nortoriously slow in Java (due to the Security model which needs Strings to be immutable) so every manipulation reqiures a new String. If you are dealing with a small alphabet and are going to be treating each Symbol as a String then it may pay to create one of each String "a", "c" etc and intern them using the String.intern() method. I'm not sure if it will imporve performance but you might be able to avoid using Strings and chars at all by using Edits and cross product alphabets. see the alphabets and symbols section of http://www.biojava.org/docs/bj_in_anger/ and also http://www.biojava.org/docs/bj_in_anger/edit.htm Hope this helps, Mark -----Original Message----- From: Andy Hammer [mailto:facemann@yahoo.com] Sent: Sat 13/09/2003 12:05 p.m. To: bio java Cc: Subject: [Biojava-l] Performance of SymbolList.subStr() function This blows my mind! In both blocks of code: seq = si.nextSequence(); //just a protein sequence In this block of code, my system would take hours and often crash with an out of memory error. for(int i = 1; i <= seqLength; i++){ String seqString = seq.subStr(i,i); char protein = seqString.charAt(0); newSeq = newSeq.append(newCodon(protein));//add a 3 char string to the newSeq StringBuffer } I altered the above block to: String seqString = seq.seqString(); for(int i = 0; i < seqLength; i++){ char protein = seqString.charAt(i); newSeq = newSeq.append(newCodon(protein)); } This program used to take 4 hours to complete. With this simple change it is now done in 30 minutes! Obviously, the SymbolList.subStr() function was severly hampering my efficiency. I guess it was poor use of the SymbolList.subStr() function. My rational was that I didn't want to create an unneeded String simply to represent my already existing SymbolList. I am just trying to learn from this to become a better programmer and would appreciate any comments on this. Thanks! __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software http://sitebuilder.yahoo.com _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From pwilkinson at videotron.ca Fri Sep 12 23:09:38 2003 From: pwilkinson at videotron.ca (Peter Wilkinson) Date: Fri Sep 12 23:08:20 2003 Subject: [Biojava-l] Parse error with negative strand CDS Message-ID: <5.2.0.9.0.20030912230738.023ac7e0@pop.videotron.ca> So .... Well ... the rep_origin is supposed to be a single digit, where replication starts. 5191..31 is not expected. for example: source 1..2245 /organism="Escherichia coli" /plasmid="Plasmid Z" /strain="K12" rep_origin 6 /direction=LEFT /note="ori" CDS join(complement(567..795)complement(21..349)) /gene="trbC" /product="transfer protein C" CDS 803..1344 AND NOT as you have it. Try to change the annotation within vectorNTI to show the exact origin. otherwise it must be in the following format to represent a 'fuzzy' annotation: (5191.31) #### see below, this seems like a circular reference, I think only something like (5191.5231 will work). The problem is I am not sure how well vectorNTI supports the 'fuzzy' annotations. I remember that genomax did not. And I dont think Vector Does unless you imported a file with the annotation first. you will have to try it. Here is a list of formats for location descriptors: Location Description 467 Points to a single base in the presented sequence 340..565 Points to a continuous range of bases bounded by and including the starting and ending bases <345..500 Indicates that the exact lower boundary point of a feature is unknown. The location begins at some base previous to the first base specified (which need not be contained in the presented sequence) and con- tinues to and includes the ending base <1..888 The feature starts before the first sequenced base and continues to and includes base 888 (102.110) Indicates that the exact location is unknown but that it is one of the bases between bases 102 and 110, in- clusive (23.45)..600 Specifies that the starting point is one of the bases be- tween bases 23 and 45, inclusive, and the end point is base 600 (122.133)..(204.221) The feature starts at a base between 122 and 133, in- clusive, and ends at a base between 204 and 221, in- clusive 123^124 Points to a site between bases 123 and 124 145^177 Points to a site between two adjacent bases anywhere between bases 145 and 177 join(12..78,134..202) Regions 12 to 78 and 134 to 202 should be joined to form one contiguous sequence complement(join(2691..4571,4918..5163)) Joins regions 2691 to 4571 and 4918 to 5163, then complements the joined segments (the feature is on the strand complementary to the presented strand) join(complement(4918..5163),complement(2691..4571)) Complements regions 4918 to 5163 and 2691 to 4571, then joins the complemented segments (the feature is on the strand complementary to the presented strand) complement(34..(122.126)) Start at one of the bases complementary to those between 122 and 126 on the presented strand and finish at the base complementary to base 34 (the feature is on the strand complementary to the presented strand) J00194:100..202 Points to bases 100 to 202, inclusive, in the entry (in this database) with primary accession number 'J00194' rep_origin 5191..31 /vntifkey="33" /label=SV40_ORI /note=" SV40 replication origin core region; 0.67 " misc_signal complement(21..27) /locus_tag="SV40gp1" /note="early mRNA promoter element; 0.66 [66],[78],[79]" misc_feature complement(21..27) /vntifkey="21" /label=E_P /note=" SV40 early mRNA promoter element; 0.66 " rep_origin 32..83 /vntifkey="33" /label=AUX_ORI /note=" SV40 replication origin auxiliary region; 0.67 " repeat_region complement(40..60) At 10:39 AM 12/09/2003 -0400, you wrote: >Hi Peter, >Thanks for your assistance. I've attached a gb formatted file produced by >VectorNTI, whose features generate parsing exceptions in BioJava. I believe >I have isolated at least one problem associated with a feature whose start >location is greater than its end location as in an origin of replication. >The gb file produced by VectorNTI has a different format than one downloaded >from NCBI. > >VectorNTI: rep_origin 5191..31 >NCBI: rep_origin join(5191..5243,1..31) > >If I edit the VectorNTI output to the NCBI format, I do not get any parsing >errors. I will contact the scientist who supplied my test files to see what >version of VectorNTI generated them and if there have been any subsequent >updates. >Thanks again >Fred > > > >-----Original Message----- >From: Peter Wilkinson [mailto:pwilkinson@videotron.ca] >Sent: Friday, September 12, 2003 6:39 AM >To: Schreiber, Mark; Criscuolo, Fred; biojava-l@biojava.org >Subject: RE: [Biojava-l] Parse error with negative strand CDS > > >Well ... Fred. > >Having worked for the company that makes VectorNTI (Informax), I can tell >you that there are some modifications to the format that should be benign >... but that is not always true. The output of GenBank files from VectorNTI >are slightly different, but Iwould not have expected them to break the >parser. > >the annotations within VectorNTI are added into the comments fields, which >should not be a problem. > >One thing to check is whether biojava parser is updated to the current >genbank format, and whether the output from vectorNTI produces the same >'version' of the genbank file. If they don't then the biojava parser may >not handle the vectorNTI output. > >if you could send the file I can see what the problem is, the line on its >own does not seem like a problem. It might be some spacing issues (version >of the formatting) in the file generated on the previous line somewhere. > >Peter > >At 10:04 AM 12/09/2003 +1200, Schreiber, Mark wrote: > >Hi - > > > >This looks odd. It may be that the Genbank produced by VectorNTI is not > >quite right. Can you post the file, or at least the few lines surrounding > >the CDS feature? > > > >- Mark > > > > > >-----Original Message----- > >From: Criscuolo, Fred [mailto:fred.criscuolo@pfizer.com] > >Sent: Friday, 12 September 2003 4:27 a.m. > >To: 'biojava-l@biojava.org' > >Subject: [Biojava-l] Parse error with negative strand CDS > > > > > >Hi, > >I am using BioJava 1.3.0 to process a GenBank file that has a CDS on the > >negative strand. I am using the SeqIOTools.readGenbank(BufferedReader) > >method to parse the file. I get the following error for any CDS on the > >negative strand: > > > > This line could not be parsed: CDS complement(518..1597) > > > >The GenBank files I'm working with are produced by the VectorNTI > >application. I'm using Java 1.4.2. I've searched the biojava mailing list > >but have not seen a reference to this particular problem. Any idea what's > >wrong? Thanks. Fred > > > >Fred Criscuolo > >Research Informatics - Pfizer, Inc. > >858.622.7307 > > > > > > > >LEGAL NOTICE > >Unless expressly stated otherwise, this message is confidential and may be > >privileged. It is intended for the addressee(s) only. Access to this > >E-mail by anyone else is unauthorized. If you are not an addressee, any > >disclosure or copying of the contents of this E-mail or any action taken > >(or not taken) in reliance on it is unauthorized and may be unlawful. If > >you are not an addressee, please inform the sender immediately. > >_______________________________________________ > >Biojava-l mailing list - Biojava-l@biojava.org > >http://biojava.org/mailman/listinfo/biojava-l > >======================================================================= > >Attention: The information contained in this message and/or attachments > >from AgResearch Limited is intended only for the persons or entities > >to which it is addressed and may contain confidential and/or privileged > >material. Any review, retransmission, dissemination or other use of, or > >taking of any action in reliance upon, this information by persons or > >entities other than the intended recipients is prohibited by AgResearch > >Limited. If you have received this message in error, please notify the > >sender immediately. > >======================================================================= > > > >_______________________________________________ > >Biojava-l mailing list - Biojava-l@biojava.org > >http://biojava.org/mailman/listinfo/biojava-l > > >------------------------------------- >Peter Wilkinson >Bioinformatics Consultant > >------------------------------------- > > > > >LEGAL NOTICE >Unless expressly stated otherwise, this message is confidential and may be >privileged. It is intended for the addressee(s) only. Access to this >E-mail by anyone else is unauthorized. If you are not an addressee, any >disclosure or copying of the contents of this E-mail or any action taken >(or not taken) in reliance on it is unauthorized and may be unlawful. If >you are not an addressee, please inform the sender immediately. ------------------------------------- Peter Wilkinson Bioinformatics Consultant ------------------------------------- From mark.schreiber at agresearch.co.nz Sat Sep 13 00:38:28 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Sat Sep 13 00:37:10 2003 Subject: [Biojava-l] Build errors Message-ID: Looks like you might not have the bytecode.jar file which is odd. Do you see it in your biojava-live directory? - Mark -----Original Message----- From: Andy Hammer [mailto:facemann@yahoo.com] Sent: Sat 13/09/2003 1:31 p.m. To: bio java Cc: Subject: [Biojava-l] Build errors I am getting some build errors. I even deleted /biojava-live and started over. Lastly from ./biojava-live/ ant clean = build successful cvs update -d = appeared successful ant = [ahammer@westwater biojava-live]$ ant Buildfile: build.xml init: [echo] JUnit present: ${junit.present} [echo] JUnit supported by Ant: true prepare: [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build prepare-core: [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/src/main [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/classes/main [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/src/tests [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/classes/tests [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/src/demos [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/classes/demos [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/src/apps [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/classes/apps [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/src/docs [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/docs [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/docs/api [mkdir] Created dir: /home/ahammer/downloads/biojava-live/ant-build/lib [copy] Copying 1191 files to /home/ahammer/downloads/biojava-live/ant-build/src/main [copy] Copied 23 empty directories to /home/ahammer/downloads/biojava-live/ant-build/src/main [copy] Copying 147 files to /home/ahammer/downloads/biojava-live/ant-build/src/tests [copy] Copied 1 empty directory to /home/ahammer/downloads/biojava-live/ant-build/src/tests [copy] Copying 180 files to /home/ahammer/downloads/biojava-live/ant-build/src/demos [copy] Copied 5 empty directories to /home/ahammer/downloads/biojava-live/ant-build/src/demos [copy] Copying 2 files to /home/ahammer/downloads/biojava-live/ant-build/src/apps [copy] Copying 15 files to /home/ahammer/downloads/biojava-live/ant-build/src/docs [copy] Copying 1 file to /home/ahammer/downloads/biojava-live/ant-build/src/main [copy] Copying 1 file to /home/ahammer/downloads/biojava-live/ant-build/src/demos [copy] Copying 1 file to /home/ahammer/downloads/biojava-live/ant-build/src/apps [copy] Copying 17 files to /home/ahammer/downloads/biojava-live/ant-build/classes/main [copy] Copied 1 empty directory to /home/ahammer/downloads/biojava-live/ant-build/classes/main [copy] Copying 3 files to /home/ahammer/downloads/biojava-live/ant-build prepare-src: compile: [javac] Compiling 1091 source files to /home/ahammer/downloads/biojava-live/ant-build/classes/main [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/impl/RevCompSequence.java:47: reference to ProjectedFeatureHolder is ambiguous, both class org.biojava.bio.seq.projection.ProjectedFeatureHolder in org.biojava.bio.seq.projection and class org.biojava.bio.seq.ProjectedFeatureHolder in org.biojava.bio.seq match [javac] private ProjectedFeatureHolder pfh; [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/impl/RevCompSequence.java:65: reference to ProjectedFeatureHolder is ambiguous, both class org.biojava.bio.seq.projection.ProjectedFeatureHolder in org.biojava.bio.seq.projection and class org.biojava.bio.seq.ProjectedFeatureHolder in org.biojava.bio.seq match [javac] pfh = new ProjectedFeatureHolder(new TranslateFlipContext(this,seq,seq.length()+1,true)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:301: cannot resolve symbol [javac] symbol : method make_checkcast (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] proxyIV.add(ByteCode.make_checkcast(ourContextC)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:366: cannot resolve symbol [javac] symbol : method make_checkcast (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] proxyIV.add(ByteCode.make_checkcast(ourContextC) ); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:436: cannot resolve symbol [javac] symbol : variable TYPE_OBJECT [javac] location: class org.biojava.utils.bytecode.CodeUtils [javac] CodeClass c_baseClass = CodeUtils.TYPE_OBJECT; [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:447: cannot resolve symbol [javac] symbol : variable TYPE_OBJECT [javac] location: class org.biojava.utils.bytecode.CodeUtils [javac] = CodeUtils.TYPE_OBJECT.getConstructor(CodeUtils.EMPTY_LIST); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:482: cannot resolve symbol [javac] symbol : method make_checkcast (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] revTIV.add(ByteCode.make_checkcast(c_FeatureTemplate)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:492: cannot resolve symbol [javac] symbol : method getFields () [javac] location: interface org.biojava.utils.bytecode.CodeClass [javac] for(Iterator fi = c_ourTemplate.getFields().iterator(); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:522: cannot resolve symbol [javac] symbol : method make_checkcast (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] revIV.add(ByteCode.make_checkcast(c_ourTemplate)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:524: cannot resolve symbol [javac] symbol : method make_checkcast (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] revIV.add(ByteCode.make_checkcast(c_ourContext)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:526: cannot resolve symbol [javac] symbol : method make_checkcast (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] revIV.add(ByteCode.make_checkcast(c_ourTemplate)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:198: cannot resolve symbol [javac] symbol : method make_checkcast (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] walkIV.add(ByteCode.make_checkcast(c_ourVisitor)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:227: cannot resolve symbol [javac] symbol : method forMethod (java.lang.reflect.Method) [javac] location: class org.biojava.utils.bytecode.IntrospectedCodeClass [javac] CodeMethod m_getFilter = IntrospectedCodeClass.forMethod(m); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:245: cannot resolve symbol [javac] symbol : method make_checkcast (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] wfiv.add(ByteCode.make_checkcast(c_ourFilter)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:260: cannot resolve symbol [javac] symbol : method make_instanceof (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] wrapperIV.add(ByteCode.make_instanceof(c_ourFilter)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:291: cannot resolve symbol [javac] symbol : method forMethod (java.lang.reflect.Method) [javac] location: class org.biojava.utils.bytecode.IntrospectedCodeClass [javac] CodeMethod ourMeth = IntrospectedCodeClass.forMethod(meth); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:297: cannot resolve symbol [javac] symbol : method make_checkcast (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] bodyIV.add(ByteCode.make_checkcast(c_thisFiltType)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:306: cannot resolve symbol [javac] symbol : method make_instanceof (org.biojava.utils.bytecode.CodeClass) [javac] location: class org.biojava.utils.bytecode.ByteCode [javac] walkIV.add(ByteCode.make_instanceof(c_thisFiltType)); [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:328: cannot resolve symbol [javac] symbol : variable TYPE_OBJECT [javac] location: class org.biojava.utils.bytecode.CodeUtils [javac] CodeUtils.TYPE_OBJECT, [javac] ^ [javac] /home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:358: cannot resolve symbol [javac] symbol : variable TYPE_OBJECT [javac] location: class org.biojava.utils.bytecode.CodeUtils [javac] CodeUtils.TYPE_OBJECT, [javac] ^ [javac] 20 errors BUILD FAILED file:/home/ahammer/downloads/biojava-live/build.xml:278: Compile failed; see the compiler error output for details. I think last time I bothered to build was around 1.3. It has always worked in the past. . . Any ideas would be appreciated. facemann __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software http://sitebuilder.yahoo.com _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From Robin.Emig at maxygen.com Sun Sep 14 23:04:30 2003 From: Robin.Emig at maxygen.com (Emig, Robin) Date: Sun Sep 14 23:02:52 2003 Subject: [Biojava-l] Simple alignment Message-ID: Is there any objection to making SimpleAlignment take a TreeMap instead of a simple Map? The reason is that order of the sequences in the alignment is often of importance. I suppose the alternative is to create a new alignment called OrderedAlignment. -Robin From mark.schreiber at agresearch.co.nz Mon Sep 15 04:28:53 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Mon Sep 15 04:27:19 2003 Subject: [Biojava-l] Simple alignment Message-ID: Robin - How about overloading the constructor? That way if you provide a TreeMap the result is ordered. If not you get what you get. Many classes are dependent on SimpleAlignment so it may not pay to change it too much. - Mark -----Original Message----- From: Emig, Robin [mailto:Robin.Emig@maxygen.com] Sent: Mon 15/09/2003 3:04 p.m. To: bio java Cc: Subject: [Biojava-l] Simple alignment Is there any objection to making SimpleAlignment take a TreeMap instead of a simple Map? The reason is that order of the sequences in the alignment is often of importance. I suppose the alternative is to create a new alignment called OrderedAlignment. -Robin _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From matthew_pocock at yahoo.co.uk Mon Sep 15 05:12:31 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Mon Sep 15 05:14:02 2003 Subject: [Biojava-l] Simple alignment In-Reply-To: References: Message-ID: <3F65827F.10400@yahoo.co.uk> Doesn't TreeMap extend/implement Map? Is there a reason you can't just pass a TreeMap into the constructor? Matthew Schreiber, Mark wrote: >Robin - > >How about overloading the constructor? That way if you provide a TreeMap the result is ordered. If not you get what you get. Many classes are dependent on SimpleAlignment so it may not pay to change it too much. > >- Mark > > > >-----Original Message----- >From: Emig, Robin [mailto:Robin.Emig@maxygen.com] >Sent: Mon 15/09/2003 3:04 p.m. >To: bio java >Cc: >Subject: [Biojava-l] Simple alignment > > > > Is there any objection to making SimpleAlignment take a TreeMap instead of a simple Map? The reason is that order of the sequences in the alignment is often of importance. I suppose the alternative is to create a new alignment called OrderedAlignment. > -Robin > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > > > >======================================================================= >Attention: The information contained in this message and/or attachments >from AgResearch Limited is intended only for the persons or entities >to which it is addressed and may contain confidential and/or privileged >material. Any review, retransmission, dissemination or other use of, or >taking of any action in reliance upon, this information by persons or >entities other than the intended recipients is prohibited by AgResearch >Limited. If you have received this message in error, please notify the >sender immediately. >======================================================================= > >_______________________________________________ >Biojava-l mailing list - Biojava-l@biojava.org >http://biojava.org/mailman/listinfo/biojava-l > > > From Robin.Emig at maxygen.com Mon Sep 15 11:18:34 2003 From: Robin.Emig at maxygen.com (Emig, Robin) Date: Mon Sep 15 11:16:55 2003 Subject: [Biojava-l] Simple alignment Message-ID: Well, The problem is that the code in biojava is "safe", so it copies the Map first thing, but it copies it into a HashMap. So, since what I really need is the have the same order from an iterator that the file was read, all that needs to be done is to have all instances of HashMap in MSFAlignmentFormat, FastaAlignmentFormat and SimpleAlignment to be changed to LinkedHashMap. Then there should be no changes needed to any "interfaces". I think we should also have a unit test built to verify this as well. -Robin -----Original Message----- From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] Sent: Monday, September 15, 2003 2:13 AM To: Schreiber, Mark Cc: Emig, Robin; bio java Subject: Re: [Biojava-l] Simple alignment Doesn't TreeMap extend/implement Map? Is there a reason you can't just pass a TreeMap into the constructor? Matthew Schreiber, Mark wrote: >Robin - > >How about overloading the constructor? That way if you provide a TreeMap the result is ordered. If not you get what you get. Many classes are dependent on SimpleAlignment so it may not pay to change it too much. > >- Mark > > > >-----Original Message----- >From: Emig, Robin [mailto:Robin.Emig@maxygen.com] >Sent: Mon 15/09/2003 3:04 p.m. >To: bio java >Cc: >Subject: [Biojava-l] Simple alignment > > > > Is there any objection to making SimpleAlignment take a TreeMap instead of a simple Map? The reason is that order of the sequences in the alignment is often of importance. I suppose the alternative is to create a new alignment called OrderedAlignment. > -Robin > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > > > >======================================================================= >Attention: The information contained in this message and/or attachments >from AgResearch Limited is intended only for the persons or entities >to which it is addressed and may contain confidential and/or privileged >material. Any review, retransmission, dissemination or other use of, or >taking of any action in reliance upon, this information by persons or >entities other than the intended recipients is prohibited by AgResearch >Limited. If you have received this message in error, please notify the >sender immediately. >======================================================================= > >_______________________________________________ >Biojava-l mailing list - Biojava-l@biojava.org >http://biojava.org/mailman/listinfo/biojava-l > > > From matthew_pocock at yahoo.co.uk Mon Sep 15 11:33:11 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Mon Sep 15 11:34:40 2003 Subject: [Biojava-l] Simple alignment In-Reply-To: References: Message-ID: <3F65DBB7.8070809@yahoo.co.uk> Emig, Robin wrote: > Well, The problem is that the code in biojava is "safe", so it copies the Map first thing, but it copies it into a HashMap. So, since what I really need is the have the same order from an iterator that the file was read, all that needs to be done is to have all instances of HashMap in MSFAlignmentFormat, FastaAlignmentFormat and SimpleAlignment to be changed to LinkedHashMap. Then there should be no changes needed to any "interfaces". I think we should also have a unit test built to verify this as well. >-Robin > > I'm fairly sure that Map.clone() will do the sane thing. Cloning is generally evil, but for collections they got so may bug reports that it does work (or so they tell me). Any way, go ahead and diddle the constructor guts so that it works for you. If you add the order-preserving behavior to a unit test, update the javadocs on the class to document the behavior as well. Matthew From heuermh at acm.org Mon Sep 15 11:36:44 2003 From: heuermh at acm.org (Michael Heuer) Date: Mon Sep 15 12:10:25 2003 Subject: [Biojava-l] Simple alignment In-Reply-To: Message-ID: I think it might make more sense to create an interface OrderedAlignment as you suggest than to change an implementation detail in the existing code. michael On Mon, 15 Sep 2003, Emig, Robin wrote: > Well, The problem is that the code in biojava is "safe", so it copies the Map first thing, but it copies it into a HashMap. So, since what I really need is the have the same order from an iterator that the file was read, all that needs to be done is to have all instances of HashMap in MSFAlignmentFormat, FastaAlignmentFormat and SimpleAlignment to be changed to LinkedHashMap. Then there should be no changes needed to any "interfaces". I think we should also have a unit test built to verify this as well. > -Robin > > -----Original Message----- > From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] > Sent: Monday, September 15, 2003 2:13 AM > To: Schreiber, Mark > Cc: Emig, Robin; bio java > Subject: Re: [Biojava-l] Simple alignment > > > Doesn't TreeMap extend/implement Map? Is there a reason you can't just > pass a TreeMap into the constructor? > > Matthew > > Schreiber, Mark wrote: > > >Robin - > > > >How about overloading the constructor? That way if you provide a TreeMap the result is ordered. If not you get what you get. Many classes are dependent on SimpleAlignment so it may not pay to change it too much. > > > >- Mark > > > > > > > >-----Original Message----- > >From: Emig, Robin [mailto:Robin.Emig@maxygen.com] > >Sent: Mon 15/09/2003 3:04 p.m. > >To: bio java > >Cc: > >Subject: [Biojava-l] Simple alignment > > > > > > > > Is there any objection to making SimpleAlignment take a TreeMap instead of a simple Map? The reason is that order of the sequences in the alignment is often of importance. I suppose the alternative is to create a new alignment called OrderedAlignment. > > -Robin > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l@biojava.org > > http://biojava.org/mailman/listinfo/biojava-l > > > > > > > >======================================================================= > >Attention: The information contained in this message and/or attachments > >from AgResearch Limited is intended only for the persons or entities > >to which it is addressed and may contain confidential and/or privileged > >material. Any review, retransmission, dissemination or other use of, or > >taking of any action in reliance upon, this information by persons or > >entities other than the intended recipients is prohibited by AgResearch > >Limited. If you have received this message in error, please notify the > >sender immediately. > >======================================================================= > > > >_______________________________________________ > >Biojava-l mailing list - Biojava-l@biojava.org > >http://biojava.org/mailman/listinfo/biojava-l > > > > > > > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > From matthew_pocock at yahoo.co.uk Mon Sep 15 12:42:21 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Mon Sep 15 12:43:59 2003 Subject: [Biojava-l] Simple alignment In-Reply-To: References: Message-ID: <3F65EBED.60400@yahoo.co.uk> Michael Heuer wrote: >I think it might make more sense to create an interface OrderedAlignment >as you suggest than to change an implementation detail in the existing >code. > > michael > > But adding ordering doesn't break any old code that wasn't relying on ordering. It's not like removing ordering from a previously ordered implementation. Existing code will run without noticing any difference. Anyway, this should probably be continued on the -dev list. Matthew From ambesi at tigem.it Mon Sep 15 16:37:18 2003 From: ambesi at tigem.it (Alberto Ambesi) Date: Mon Sep 15 16:35:39 2003 Subject: [Biojava-l] how do you run a similarity search through biojava classes? Message-ID: <666BCABA-E7BC-11D7-B40E-003065C1C706@tigem.it> I need to find the best similarity match of a query sequence against bigger sequence (say, a chromosome region of 100 kb). what I need as output is the identity % of the match and the position (start/end). please any suggestions or sample code are apreciated. Thank you, Alberto Ambesi From lach at cantv.net Mon Sep 15 17:43:07 2003 From: lach at cantv.net (lach@cantv.net) Date: Mon Sep 15 17:41:27 2003 Subject: [Biojava-l] BioJava GUI and applets question Message-ID: <149350-22003911521437541@cantv.net> Hi! I programmed an applet (Swing) and I used several classes from GUI Packages (FeatureTree, MultiLineRenderer, SequencePanel, etc.). All Applet's components works properly with AppletViewer but not in any Browser. The most calls to BioJava methods apparently are ignored when applet is loaded from IE6 or Nestcape 7, the other applet's components run properly. Not any error or exception is generated. I don't really know what is happening. Somebody can help me? Simply I don't understand it =s Thanks Luis Ch. lach@cantv.net From mark.schreiber at agresearch.co.nz Tue Sep 16 00:52:51 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Tue Sep 16 00:52:12 2003 Subject: [Biojava-l] how do you run a similarity search through biojavaclasses? Message-ID: Hi - The weight matrices and DP examples from http://www.biojava.org/docs/bj_in_anger/index.htm might be useful. - Mark -----Original Message----- From: Alberto Ambesi [mailto:ambesi@tigem.it] Sent: Tue 16/09/2003 8:37 a.m. To: biojava-l@biojava.org Cc: Subject: [Biojava-l] how do you run a similarity search through biojavaclasses? I need to find the best similarity match of a query sequence against bigger sequence (say, a chromosome region of 100 kb). what I need as output is the identity % of the match and the position (start/end). please any suggestions or sample code are apreciated. Thank you, Alberto Ambesi _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From matthew_pocock at yahoo.co.uk Tue Sep 16 05:18:32 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Tue Sep 16 05:20:17 2003 Subject: [Biojava-l] BioJava GUI and applets question In-Reply-To: <149350-22003911521437541@cantv.net> References: <149350-22003911521437541@cantv.net> Message-ID: <3F66D568.8000700@yahoo.co.uk> Hi, Are you using the Java Plugin from Sun for the browsers? The default VM may well be very out of date (the ie one doesn't even support java 1.2). Matthew lach@cantv.net wrote: >Hi! > >I programmed an applet (Swing) and I used several classes from GUI Packages >(FeatureTree, MultiLineRenderer, SequencePanel, etc.). All Applet's >components works properly with AppletViewer but not in any Browser. The >most calls to BioJava methods apparently are ignored when applet is loaded >from IE6 or Nestcape 7, the other applet's components run properly. Not any >error or exception is generated. I don't really know what is happening. > >Somebody can help me? > > >Simply I don't understand it >=s > >Thanks >Luis Ch. >lach@cantv.net > >_______________________________________________ >Biojava-l mailing list - Biojava-l@biojava.org >http://biojava.org/mailman/listinfo/biojava-l > > > From wux at mail.cbi.pku.edu.cn Wed Sep 17 04:26:29 2003 From: wux at mail.cbi.pku.edu.cn (wux@mail.cbi.pku.edu.cn) Date: Wed Sep 17 04:28:55 2003 Subject: [Biojava-l] proxy problem Message-ID: <200309170830.h8H8UH9g009996@mail.cbi.pku.edu.cn> Dear all: I think there is a proxy problem in org.biojava.directory package. When a guy uses a computer which needs a proxy to link abroad, it will fail to use biofetch(as far as I know, this situation is often in many labs to save money).So I suggest when biojava uses a netIO,it should be able to use a proxy.Any ideas? ¡¡¡¡ ¡¡¡¡¡¡¡¡¡¡¡¡ Yours faithfully, ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ wux ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ wux@mail.cbi.pku.edu.cn ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ 2003-09-17 ***************************************************** WuXin Ph.D student of CBI (Center of Bioinformatics) Peking University 100871 P.R.China Email: wux@mail.cbi.pku.edu.cn Tel: 010-62762409 (dorm) 010-62755206 (office) Address: Building 47#2026 Peking University ***************************************************** From bioinformatics4suman at yahoo.com Wed Sep 17 17:19:36 2003 From: bioinformatics4suman at yahoo.com (Suman Kanuganti) Date: Wed Sep 17 17:17:52 2003 Subject: [Biojava-l] Detect seq? Message-ID: <20030917211936.43589.qmail@web60103.mail.yahoo.com> Ok; is there any best method to tell what is the seq type is in biojava? I mean is that a dna sequence or protein sequence etc. I have seen SeqAlignReadWrite.guessFileType but this is no approriate and does work, Thanks, Suman K ===== Suman K BioInformatics Associate, Genomics Research, University of Missouri - Columbia. __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software http://sitebuilder.yahoo.com From mark.schreiber at agresearch.co.nz Wed Sep 17 18:03:01 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Wed Sep 17 18:01:24 2003 Subject: [Biojava-l] Detect seq? Message-ID: Hi Suman, If you are trying to determine the Alphabet of a BJ Sequence or SymbolList you would say something like seq.getAlphabet().getName() which will return "DNA" or RNA etc. Unfortunately there is not a good (fool proof) way to guess the sequence type from a "flat file" unless that file specifically says the type. Often you can infer it (ie GenBank is DNA, SwissProt is protein) but for Fasta you often cannot unless it contains a symbol not found in the DNA alphabet (including ambiguities). - Mark -----Original Message----- From: Suman Kanuganti [mailto:bioinformatics4suman@yahoo.com] Sent: Thursday, 18 September 2003 9:20 a.m. To: biojava-l@biojava.org Subject: [Biojava-l] Detect seq? Ok; is there any best method to tell what is the seq type is in biojava? I mean is that a dna sequence or protein sequence etc. I have seen SeqAlignReadWrite.guessFileType but this is no approriate and does work, Thanks, Suman K ===== Suman K BioInformatics Associate, Genomics Research, University of Missouri - Columbia. __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software http://sitebuilder.yahoo.com _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From cox at mshri.on.ca Thu Sep 11 19:06:35 2003 From: cox at mshri.on.ca (Brian Cox) Date: Wed Sep 17 19:29:06 2003 Subject: [Biojava-l] position weight matrix Message-ID: <008201c378b9$5bb6b7d0$eafac5c0@rossdell> I wrote a program to find TF binding sites using a WeightMatrixAnnotator, but when I try to annotate a sequence if the sequences has any N or X then everything matches. How do I get the WeightMatrixAnnotator to ignore the Ns or Xs? thanks, Brian Cox Samuel Lunenfeld Research Institute Mount Sinai Hospital, Rm 884 Toronto, Ontario Canada 416-586-8266 From phirnee123 at yahoo.com Wed Sep 17 09:40:34 2003 From: phirnee123 at yahoo.com (bharani kumar) Date: Wed Sep 17 19:29:58 2003 Subject: [Biojava-l] sequence allignment Message-ID: <20030917134034.65912.qmail@web13407.mail.yahoo.com> hi, this program i found in the src of biojava and is already a precompiled one but when i compile this it is gemnerating the following errors. import java.io.*; import org.biojava.bio.symbol.*; import org.biojava.bio.seq.*; import org.biojava.bio.seq.io.*; public class Align { private static FastaSequence seq1 = new FastaSequence(); private static FastaSequence seq2 = new FastaSequence(); private static String filename = new String("pam250"); private static String scorematrix = new String("pam250"); private static int openGapPenalty = -12; private static int extensionGapPenalty = -3; private static Alignment alignment; public static void main(String[] argv) { int a = argv.length; try { // read some command-line arguments if (a>4 || a==0) Usage(); if (a==4) extensionGapPenalty = Integer.parseInt(argv[3]); if (a>=3) openGapPenalty = Integer.parseInt(argv[2]); if (a>=2) scorematrix = argv[1]; if (a>=1) filename = argv[0]; // read the first two sequences of the specified fasta-file seq1.readFasta(filename,1); seq2.readFasta(filename,2); // create the Alignment-object alignment alignment = new Alignment(seq1, seq2, scorematrix); // call method fillEditMatrix() of object alignment // alignment.fillEditMatrix(); /* for a global alignment with i) linear, ii) linear affine gap costs, call */ alignment.fillEditMatrix(openGapPenalty); alignment.backTracking(openGapPenalty); // print alignment alignment.print(); } catch (NumberFormatException e) {System.out.println(e.getMessage() + " is not an integer.\n");Usage();} catch (ErrorInSequenceException e) {System.out.println(e.getMessage());} catch (ErrorInScoreMatrixException e) {System.out.println(e.getMessage());} catch (FileNotFoundException e) {System.out.println("File not found: " + e.getMessage());} catch (IOException e){System.out.println("IOException: " + e.getMessage());} catch (ArrayIndexOutOfBoundsException e){System.out.println("ArrayIndexOutOfBoundsException: " + e.getMessage());} } public static void Usage() { System.out.println("usage: java Align "); System.out.println("\t\t[scoring matrix (default = pam250)]"); System.out.println("\t\t[opening gap penalty (default = 12)]"); System.out.println("\t\t[extending gap penalty (default = 3)]"); System.exit(1); } } COMPILATION ERRORS: Align.java [8:1] cannot resolve symbol symbol : class FastaSequence location: class Align private static FastaSequence seq1 = new FastaSequence(); ^ Align.java [9:1] cannot resolve symbol symbol : class FastaSequence location: class Align private static FastaSequence seq2 = new FastaSequence(); ^ Align.java [8:1] cannot resolve symbol symbol : class FastaSequence location: class Align private static FastaSequence seq1 = new FastaSequence(); ^ Align.java [9:1] cannot resolve symbol symbol : class FastaSequence location: class Align private static FastaSequence seq2 = new FastaSequence(); ^ Align.java [38:1] org.biojava.bio.symbol.Alignment is abstract; cannot be instantiated alignment = new Alignment(seq1, seq2, scorematrix); ^ Align.java [47:1] cannot resolve symbol symbol : method fillEditMatrix (int) location: interface org.biojava.bio.symbol.Alignment alignment.fillEditMatrix(openGapPenalty); ^ Align.java [50:1] cannot resolve symbol symbol : method backTracking (int) location: interface org.biojava.bio.symbol.Alignment alignment.backTracking(openGapPenalty); ^ Align.java [54:1] cannot resolve symbol symbol : method print () location: interface org.biojava.bio.symbol.Alignment alignment.print(); ^ Align.java [60:1] cannot resolve symbol symbol : class ErrorInSequenceException location: class Align catch (ErrorInSequenceException e) {System.out.println(e.getMessage());} ^ Align.java [61:1] cannot resolve symbol symbol : class ErrorInScoreMatrixException location: class Align catch (ErrorInScoreMatrixException e) {System.out.println(e.getMessage());} ^ 10 errors Errors compiling Align. *********************************************************************************** "The secret of success is to know something nobody else knows." BHARANI KUMAR.P.S CUBIC, UNIVERSITÄT ZU KÖLN, Zülpicher Str. 47 50674 Köln Germany Fon +49 221 7212018, +49 176 21000597 phirnee123@yahoo.com ************************************************************ --------------------------------- Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software From mark.schreiber at agresearch.co.nz Wed Sep 17 19:45:09 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Wed Sep 17 19:43:31 2003 Subject: [Biojava-l] position weight matrix Message-ID: Hi Brian, Technically this is correct as N or X do actually match everything. Are wanting to rule out any motif with an N or are you wanting to penalize a motif with an N (or other ambiguity)? If you are working with DNA you could use org.biojava.bio.seq.NucleotideTools, this class can be used to access the nucleotide alphabet that treats all symbols as Atomic, even if they are normally IUPAC ambiguity symbols. If you did this and set the weight of N in the marix to 0.0 it would exclude those motifs. - Mark -----Original Message----- From: Brian Cox [mailto:cox@mshri.on.ca] Sent: Friday, 12 September 2003 11:07 a.m. To: biojava-l@biojava.org Subject: [Biojava-l] position weight matrix I wrote a program to find TF binding sites using a WeightMatrixAnnotator, but when I try to annotate a sequence if the sequences has any N or X then everything matches. How do I get the WeightMatrixAnnotator to ignore the Ns or Xs? thanks, Brian Cox Samuel Lunenfeld Research Institute Mount Sinai Hospital, Rm 884 Toronto, Ontario Canada 416-586-8266 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From mark.schreiber at agresearch.co.nz Wed Sep 17 23:30:25 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Wed Sep 17 23:28:53 2003 Subject: [Biojava-l] position weight matrix Message-ID: Brian, I think we should change WeightMatrix so that N only scores a quater match of A where as R would score a half match. Do others feel this is sensible? - Mark -----Original Message----- From: Brian Cox [mailto:cox@mshri.on.ca] Sent: Thu 18/09/2003 2:35 p.m. To: Schreiber, Mark Cc: Subject: RE: [Biojava-l] position weight matrix Thanks, That sounds like what I was looking for, I wanted to penalize the use of an N in the sequence. Not sure yet how to implement this but I'll give it a shot. thanks for the reply, BRian -----Original Message----- From: Schreiber, Mark To: Brian Cox; biojava-l@biojava.org Sent: 9/17/03 7:45 PM Subject: RE: [Biojava-l] position weight matrix Hi Brian, Technically this is correct as N or X do actually match everything. Are wanting to rule out any motif with an N or are you wanting to penalize a motif with an N (or other ambiguity)? If you are working with DNA you could use org.biojava.bio.seq.NucleotideTools, this class can be used to access the nucleotide alphabet that treats all symbols as Atomic, even if they are normally IUPAC ambiguity symbols. If you did this and set the weight of N in the marix to 0.0 it would exclude those motifs. - Mark -----Original Message----- From: Brian Cox [mailto:cox@mshri.on.ca] Sent: Friday, 12 September 2003 11:07 a.m. To: biojava-l@biojava.org Subject: [Biojava-l] position weight matrix I wrote a program to find TF binding sites using a WeightMatrixAnnotator, but when I try to annotate a sequence if the sequences has any N or X then everything matches. How do I get the WeightMatrixAnnotator to ignore the Ns or Xs? thanks, Brian Cox Samuel Lunenfeld Research Institute Mount Sinai Hospital, Rm 884 Toronto, Ontario Canada 416-586-8266 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From wux at mail.cbi.pku.edu.cn Thu Sep 18 04:45:06 2003 From: wux at mail.cbi.pku.edu.cn (wux@mail.cbi.pku.edu.cn) Date: Thu Sep 18 04:47:31 2003 Subject: [Biojava-l] http proxy Message-ID: <200309180849.h8I8mw9g020812@mail.cbi.pku.edu.cn> Dear all: There is a problem in biojava when using biofetch behind a firewall. There is no way to get the httpURLconnection object and set the http proxy. I think there are two solutions: 1. Modify biofetch of the OBDA proctocol, add proxyHost, proxyPort, Login, password to the tag-value pairs. 2. Hard code to the BioFetchSequenceDBProvider and BioFetchSequenceDB with http proxy and let user set it. Is there another way to handle it? What's your opinion? Any suggestions? Thanks. ¡¡¡¡ ¡¡¡¡¡¡¡¡¡¡¡¡ Yours faithfully, ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ wux ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ wux@mail.cbi.pku.edu.cn ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ 2003-09-18 ***************************************************** WuXin Ph.D student of CBI (Center of Bioinformatics) Peking University 100871 P.R.China Email: wux@mail.cbi.pku.edu.cn Tel: 010-62762409 (dorm) 010-62755206 (office) Address: Building 47#2026 Peking University ***************************************************** From td2 at sanger.ac.uk Thu Sep 18 05:04:17 2003 From: td2 at sanger.ac.uk (Thomas Down) Date: Thu Sep 18 05:02:34 2003 Subject: [Biojava-l] http proxy In-Reply-To: <200309180849.h8I8mw9g020812@mail.cbi.pku.edu.cn> References: <200309180849.h8I8mw9g020812@mail.cbi.pku.edu.cn> Message-ID: <20030918090417.GA328858@jabba.sanger.ac.uk> On Thu, Sep 18, 2003 at 04:45:06PM +0800, wux@mail.cbi.pku.edu.cn wrote: > Dear all: > > There is a problem in biojava when using biofetch behind a firewall. There is no way > to get the httpURLconnection object and set the http proxy. I think there are two solutions: > 1. Modify biofetch of the OBDA proctocol, add proxyHost, proxyPort, Login, password > to the tag-value pairs. > 2. Hard code to the BioFetchSequenceDBProvider and BioFetchSequenceDB with http proxy > and let user set it. One other option: in Java, it's possible to set up proxies on a per-application basis by setting some system properties, e.g.: java -Dhttp.proxyHost=gate.derkholm.net -Dhttp.proxyPort=8088 MyApp Or put these in a system properties file. Other than that... yes, adding explicit proxy support to OBDA sounds like it might be a good idea. But if so, I think it should be done as part of the OBDA spec (option 1) rather than a unilateral BioJava feature. Thomas. From matthew_pocock at yahoo.co.uk Thu Sep 18 05:14:36 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Thu Sep 18 05:13:24 2003 Subject: [Biojava-l] position weight matrix In-Reply-To: References: Message-ID: <3F69777C.20001@yahoo.co.uk> Schreiber, Mark wrote: >Brian, > >I think we should change WeightMatrix so that N only scores a quater match of A where as R would score a half match. > >Do others feel this is sensible? > >- Mark > > We should be taking the odds score between the weight matrix matching at that pos and the null model - that way, ambiguity symbols devide out. I'm tied up today (writing lectures - damn those students), but it should be easy to modify WeightMatrixAnnotator to accept a ScoreType instance. For reasons that we can argue about on -dev or off-line, you can't in the general case just divide scores for columns containing an N by 4, or portion them out relative to the null model. That's why the ScoreType objects were added to the DP package. Matthew > -----Original Message----- > From: Brian Cox [mailto:cox@mshri.on.ca] > Sent: Thu 18/09/2003 2:35 p.m. > To: Schreiber, Mark > Cc: > Subject: RE: [Biojava-l] position weight matrix > > > > Thanks, > That sounds like what I was looking for, I wanted to penalize the use of an > N in the sequence. Not sure yet how to implement this but I'll give it a > shot. > thanks for the reply, > BRian > > -----Original Message----- > From: Schreiber, Mark > To: Brian Cox; biojava-l@biojava.org > Sent: 9/17/03 7:45 PM > Subject: RE: [Biojava-l] position weight matrix > > Hi Brian, > > Technically this is correct as N or X do actually match everything. Are > wanting to rule out any motif with an N or are you wanting to penalize a > motif with an N (or other ambiguity)? > > If you are working with DNA you could use > org.biojava.bio.seq.NucleotideTools, this class can be used to access > the nucleotide alphabet that treats all symbols as Atomic, even if they > are normally IUPAC ambiguity symbols. If you did this and set the weight > of N in the marix to 0.0 it would exclude those motifs. > > - Mark > > > > -----Original Message----- > From: Brian Cox [mailto:cox@mshri.on.ca] > Sent: Friday, 12 September 2003 11:07 a.m. > To: biojava-l@biojava.org > Subject: [Biojava-l] position weight matrix > > > I wrote a program to find TF binding sites using a > WeightMatrixAnnotator, but when I try to annotate a sequence if the > sequences has any N or X then everything matches. How do I get the > WeightMatrixAnnotator to ignore the Ns or Xs? > thanks, > Brian Cox > Samuel Lunenfeld Research Institute > Mount Sinai Hospital, Rm 884 > Toronto, Ontario > Canada > > 416-586-8266 > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > > > >======================================================================= >Attention: The information contained in this message and/or attachments >from AgResearch Limited is intended only for the persons or entities >to which it is addressed and may contain confidential and/or privileged >material. Any review, retransmission, dissemination or other use of, or >taking of any action in reliance upon, this information by persons or >entities other than the intended recipients is prohibited by AgResearch >Limited. If you have received this message in error, please notify the >sender immediately. >======================================================================= > >_______________________________________________ >Biojava-l mailing list - Biojava-l@biojava.org >http://biojava.org/mailman/listinfo/biojava-l > > > From lach at cantv.net Thu Sep 18 09:28:38 2003 From: lach at cantv.net (lach@cantv.net) Date: Thu Sep 18 09:26:53 2003 Subject: [Biojava-l] Biojava GUI and Applets Message-ID: <35401-220039418132838162@cantv.net> Hi, I updated Java Plugin, it didn't work. I could notice the following exceptions through Java Console: org.biojava.bio.BioError: Couldn't locate AlphabetManager.xml. This probably means that your biojava.jar file is corrupt or incorrectly built rethrown as org.biojava.bio.BioError: Unable to initialize DNATools ... AND java.lang.NoClassDefFoundError at org.biojava.bio.seq.io.SeqIOTools.getDNAParser(SeqIOTools.java:907) ... at org.biojava.bio.seq.io.SeqIOTools.fileToBiojava(SeqIOTools.java:787) ... I replaced biojava.jar, exceptions remain Where should I put .jar files to run my applet properly? One more time, Thanks Luis Ch. lach@cantv.net From matthew_pocock at yahoo.co.uk Thu Sep 18 09:59:57 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Thu Sep 18 09:58:42 2003 Subject: [Biojava-l] Biojava GUI and Applets In-Reply-To: <35401-220039418132838162@cantv.net> References: <35401-220039418132838162@cantv.net> Message-ID: <3F69BA5D.7010804@yahoo.co.uk> Hi, If you remove biojava.jar either from the web server or from the applet tags, do you get exactly the same error? If so, then it looks like the applet's path is not being searched. What is the tag you are using to load the applet? Matthew lach@cantv.net wrote: >Hi, > >I updated Java Plugin, it didn't work. > >I could notice the following exceptions through Java Console: > >org.biojava.bio.BioError: Couldn't locate AlphabetManager.xml. This >probably means that your biojava.jar file is corrupt or incorrectly built >rethrown as org.biojava.bio.BioError: Unable to initialize DNATools >... > >AND > >java.lang.NoClassDefFoundError >at org.biojava.bio.seq.io.SeqIOTools.getDNAParser(SeqIOTools.java:907) >... >at org.biojava.bio.seq.io.SeqIOTools.fileToBiojava(SeqIOTools.java:787) >... > >I replaced biojava.jar, exceptions remain > >Where should I put .jar files to run my applet properly? > > >One more time, Thanks > > >Luis Ch. >lach@cantv.net > >_______________________________________________ >Biojava-l mailing list - Biojava-l@biojava.org >http://biojava.org/mailman/listinfo/biojava-l > > > From mark.schreiber at agresearch.co.nz Thu Sep 18 13:08:29 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Thu Sep 18 13:07:29 2003 Subject: [Biojava-l] http proxy Message-ID: Hi - Unfortunately setting those parameters doesn't work for authenticating firewalls that require usernames and passwords. There needs to be a way to provide a Proxy to biofetch (or at least an input stream). - Mark -----Original Message----- From: Thomas Down [mailto:td2@sanger.ac.uk] Sent: Thu 18/09/2003 9:04 p.m. To: wux@mail.cbi.pku.edu.cn Cc: biojava-l@biojava.org Subject: Re: [Biojava-l] http proxy On Thu, Sep 18, 2003 at 04:45:06PM +0800, wux@mail.cbi.pku.edu.cn wrote: > Dear all: > > There is a problem in biojava when using biofetch behind a firewall. There is no way > to get the httpURLconnection object and set the http proxy. I think there are two solutions: > 1. Modify biofetch of the OBDA proctocol, add proxyHost, proxyPort, Login, password > to the tag-value pairs. > 2. Hard code to the BioFetchSequenceDBProvider and BioFetchSequenceDB with http proxy > and let user set it. One other option: in Java, it's possible to set up proxies on a per-application basis by setting some system properties, e.g.: java -Dhttp.proxyHost=gate.derkholm.net -Dhttp.proxyPort=8088 MyApp Or put these in a system properties file. Other than that... yes, adding explicit proxy support to OBDA sounds like it might be a good idea. But if so, I think it should be done as part of the OBDA spec (option 1) rather than a unilateral BioJava feature. Thomas. _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From mark.schreiber at agresearch.co.nz Thu Sep 18 13:12:16 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Thu Sep 18 13:11:01 2003 Subject: [Biojava-l] Biojava GUI and Applets Message-ID: Hi - It may also be that you compiled biojava without using Ant. If this is the case you need to place the files in biojava-live/resources into your classpath. - Mark -----Original Message----- From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] Sent: Fri 19/09/2003 1:59 a.m. To: lach@cantv.net Cc: biojava-l Subject: Re: [Biojava-l] Biojava GUI and Applets Hi, If you remove biojava.jar either from the web server or from the applet tags, do you get exactly the same error? If so, then it looks like the applet's path is not being searched. What is the tag you are using to load the applet? Matthew lach@cantv.net wrote: >Hi, > >I updated Java Plugin, it didn't work. > >I could notice the following exceptions through Java Console: > >org.biojava.bio.BioError: Couldn't locate AlphabetManager.xml. This >probably means that your biojava.jar file is corrupt or incorrectly built >rethrown as org.biojava.bio.BioError: Unable to initialize DNATools >... > >AND > >java.lang.NoClassDefFoundError >at org.biojava.bio.seq.io.SeqIOTools.getDNAParser(SeqIOTools.java:907) >... >at org.biojava.bio.seq.io.SeqIOTools.fileToBiojava(SeqIOTools.java:787) >... > >I replaced biojava.jar, exceptions remain > >Where should I put .jar files to run my applet properly? > > >One more time, Thanks > > >Luis Ch. >lach@cantv.net > >_______________________________________________ >Biojava-l mailing list - Biojava-l@biojava.org >http://biojava.org/mailman/listinfo/biojava-l > > > _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From lach at cantv.net Thu Sep 18 13:24:47 2003 From: lach at cantv.net (lach@cantv.net) Date: Thu Sep 18 13:23:01 2003 Subject: [Biojava-l] Biojava GUI and Applets Message-ID: <157240-220039418172447363@cantv.net> Hi, Yes, if I remove biojava.jar I get the same error I tried with and Errors remain CLASSPATH is set to C:\biojava.jar;C:\xerces.jar;C:\bytecode.jar;. Also there is a copy of .jar files in C:\Archivos de programa\Java\j2re1.4.1_04\lib\applet, without this copy Applet doesn't load. so, What am I doing bad? Thanks ----------- Mensaje Original -------------- Hi, If you remove biojava.jar either from the web server or from the applet tags, do you get exactly the same error? If so, then it looks like the applet's path is not being searched. What is the tag you are using to load the applet? Matthew Luis Ch. lach@cantv.net From matthew_pocock at yahoo.co.uk Fri Sep 19 05:32:57 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Fri Sep 19 05:32:07 2003 Subject: [Biojava-l] Biojava GUI and Applets In-Reply-To: <157240-220039418172447363@cantv.net> References: <157240-220039418172447363@cantv.net> Message-ID: <3F6ACD49.8080201@yahoo.co.uk> Ah - I think I see potential problems. Firstly, you should have just one archive attribute with a list of archives seperated by spaces and optional white-space. Secondly, you are using file locations for the jars - they need to be URLs that are relative to your html page that contains the applet. So - try something more like this: and put the three jar files in the same directory as your applet and the html page. Matthew lach@cantv.net wrote: >Hi, > >Yes, if I remove biojava.jar I get the same error > >I tried with > > > >and > archive= "C:\biojava.jar" > archive= "C:\xerces.jar" > archive= "C:\bytecode.jar" width=600 height=400> > > >Errors remain > >CLASSPATH is set to C:\biojava.jar;C:\xerces.jar;C:\bytecode.jar;. >Also there is a copy of .jar files in C:\Archivos de >programa\Java\j2re1.4.1_04\lib\applet, without this copy Applet doesn't >load. > >so, What am I doing bad? > >Thanks > >----------- Mensaje Original -------------- >Hi, > >If you remove biojava.jar either from the web server or from the applet >tags, do you get exactly the same error? If so, then it looks like the >applet's path is not being searched. What is the tag you are using to >load the applet? > >Matthew > > >Luis Ch. >lach@cantv.net > >_______________________________________________ >Biojava-l mailing list - Biojava-l@biojava.org >http://biojava.org/mailman/listinfo/biojava-l > > > From matthew_pocock at yahoo.co.uk Fri Sep 19 07:28:34 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Fri Sep 19 07:27:41 2003 Subject: [Biojava-l] position weight matrix In-Reply-To: <3F69777C.20001@yahoo.co.uk> References: <3F69777C.20001@yahoo.co.uk> Message-ID: <3F6AE862.4090602@yahoo.co.uk> Hi Brian, If you get an up-to-date copy of biojava from cvs (now) or the nightly builds (tomorrow) then you will find that WeightMatrixAnnotator now allows you to specify a ScoreType. The one you want is ScoreType.ODDS. You will need a different threshold than you are used to - effectively it's the log odds at which you accept a weight matrix match. Let's get bayes: s is your sequence, m is your weight matrix p(m|s)p(s) = p(s|m)p(m) becomes... p(m|s) = p(s|m) p(m) / p(s) e.g. the probability of your weight matrix binding to a particular position is the score of the weight matrix at that position multiplied by the ratio of how much you belive the weight matrix and the sequence. Of course, in this context, that ratio is fairy meaningless - just what is p(m) anyway? We could re-write p(s) in terms of it being produced by your weight matrix or the null model, at which this nuisance term becomes the threshold at which you should accept a match. So, if you think there should only be one site every 1000 nt, then p(m) / p(s) can be set to 1/1000, take the log of this, and that's your threshold. That's a noddy explanation, but it's sort of how bioinformatics does these things, so hey ho. Matthew From lach at cantv.net Fri Sep 19 10:40:51 2003 From: lach at cantv.net (lach@cantv.net) Date: Fri Sep 19 10:39:03 2003 Subject: [Biojava-l] Biojava GUI and applets Message-ID: <210770-220039519144051980@cantv.net> Hi, Thanks Mathew! I followed your instructions I tried And I put .jar files into the same directory as the applet and html page But now, errors have changed: java.security.AccessControlException: access denied (java.util.ProperyPermission entityExpansionLimit read) ... rethrown as org.biojava.bio.BioError. Unable to initialize AlphabetManager at org.biojava.bio.symbol.AlphabetManager.(AlphabetManager.java:896) at.org.biojava.bio.seq.DNATools.(DNATools.java:54) rethrown as org.biojava.bio.BioError: Unable to initialize DNATools at.org.biojava.bio.seq.DNATools.(DNATools.java:85) at.org.biojava.bio.seq.io.SeqIOTools.getDNAParser(SeqIOTools.java:181) ... Thanks ----------- Mensaje Original -------------- De: Matthew Pocock [matthew_pocock@yahoo.co.uk] Para: lach@cantv.net [lach@cantv.net] Cc: biojava-l@biojava.org [biojava-l@biojava.org] Asunto: Re: [Biojava-l] Biojava GUI and Applets Fecha: 19/09/2003 06:15:52 Mensaje: Ah - I think I see potential problems. Firstly, you should have just one archive attribute with a list of archives seperated by spaces and optional white-space. Secondly, you are using file locations for the jars - they need to be URLs that are relative to your html page that contains the applet. So - try something more like this: and put the three jar files in the same directory as your applet and the html page. Matthew Luis Ch. lach@cantv.net From mark.schreiber at agresearch.co.nz Sun Sep 21 16:03:47 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Sun Sep 21 16:02:03 2003 Subject: [Biojava-l] Biojava GUI and applets Message-ID: Hi - This is cause the applet is trying to read AlphabetManager.xml which applets are not generally allowed to do (read files) due to the sand box. I beleive you will need to change your security policy. Not sure on the details but the Sun java site has some documentation. - Mark -----Original Message----- From: lach@cantv.net [mailto:lach@cantv.net] Sent: Sat 20/09/2003 2:40 a.m. To: biojava-l@biojava.org Cc: Subject: [Biojava-l] Biojava GUI and applets Hi, Thanks Mathew! I followed your instructions I tried And I put .jar files into the same directory as the applet and html page But now, errors have changed: java.security.AccessControlException: access denied (java.util.ProperyPermission entityExpansionLimit read) ... rethrown as org.biojava.bio.BioError. Unable to initialize AlphabetManager at org.biojava.bio.symbol.AlphabetManager.(AlphabetManager.java:896) at.org.biojava.bio.seq.DNATools.(DNATools.java:54) rethrown as org.biojava.bio.BioError: Unable to initialize DNATools at.org.biojava.bio.seq.DNATools.(DNATools.java:85) at.org.biojava.bio.seq.io.SeqIOTools.getDNAParser(SeqIOTools.java:181) ... Thanks ----------- Mensaje Original -------------- De: Matthew Pocock [matthew_pocock@yahoo.co.uk] Para: lach@cantv.net [lach@cantv.net] Cc: biojava-l@biojava.org [biojava-l@biojava.org] Asunto: Re: [Biojava-l] Biojava GUI and Applets Fecha: 19/09/2003 06:15:52 Mensaje: Ah - I think I see potential problems. Firstly, you should have just one archive attribute with a list of archives seperated by spaces and optional white-space. Secondly, you are using file locations for the jars - they need to be URLs that are relative to your html page that contains the applet. So - try something more like this: and put the three jar files in the same directory as your applet and the html page. Matthew Luis Ch. lach@cantv.net _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From hz5 at njit.edu Tue Sep 23 08:49:49 2003 From: hz5 at njit.edu (hz5@njit.edu) Date: Tue Sep 23 08:57:50 2003 Subject: [Biojava-l] Biojava GUI and applets Message-ID: <1064321389.3f70416d816d8@webmail.njit.edu> I think it might because you have other files that are needed for the applet, put them all in one others.jar file, and put the others.jar file in the archive param. Should work, I did that, it worked. ========================================================= Haibo Zhang, PhD student Computational Biology, NJIT & Rutgers University Center for Applied Genomics, PHRI http://afs13.njit.edu/~hz5 From hywang at scbit.org Tue Sep 23 22:55:18 2003 From: hywang at scbit.org (hywang@scbit.org) Date: Tue Sep 23 22:49:43 2003 Subject: [Biojava-l] About the six frame renderer again. Message-ID: <20030924025518.4728.qmail@scbit.org> Hi, I have wrote a renderer for six frame view based on your SixFrameRenderer, it can render a frame with the input parameter: moduloFrame which could only be 0,1,2 for the different start base of translation. strand which stands for the positive or negtive strand. I can get the expected effect of six lines of Amino arrays in zoom in mode, and different sticks drawed for stop codon in zoom out mode. But if a sequence is very long, for example about 100k, the scroll action in zoom in mode will be a bit slow. I think that is probably because of the wholy repainting all the amino strings, so I have tried getclip() function in the paint() method ,but the improvement seemed to be not a satisfaction. Any help would be greatly appreciated and would stop me pulling anymore hair out! Thanks. Best Wishes ! Hywang import org.biojava.utils.AbstractChangeable; import org.biojava.bio.gui.sequence.SequenceRenderer; import org.biojava.bio.gui.sequence.SequenceRenderContext; import org.biojava.bio.gui.sequence.SequenceViewerEvent; import org.biojava.bio.seq.StrandedFeature; import org.biojava.bio.seq.DNATools; import org.biojava.bio.seq.RNATools; import org.biojava.bio.seq.ProteinTools; import org.biojava.bio.seq.io.SymbolTokenization; import org.biojava.bio.symbol.*; import org.biojava.bio.BioRuntimeException; import java.awt.*; import java.awt.event.MouseEvent; import java.awt.geom.AffineTransform; import java.awt.geom.Rectangle2D; import java.util.List; /** * Created by IntelliJ IDEA. * User: administrator * Date: 2003-9-5 * Time: 10:03:58 * To change this template use Options | File Templates. */ public class OneFrameRenderer extends AbstractChangeable implements SequenceRenderer { private double depth = 14.0; private double blockWidth = 12.0; private Paint fontcolor = Color.black; private Paint linecolor = Color.black; private int moduloFrame; private StrandedFeature.Strand strand; public OneFrameRenderer(int moduloFrame, StrandedFeature.Strand strand) { this.moduloFrame = moduloFrame; this.strand = strand; } public double getDepth(SequenceRenderContext context) { return depth + 1.0; } public double getMinimumLeader(SequenceRenderContext context) { return 0.0; } public double getMinimumTrailer(SequenceRenderContext context) { return 0.0; } public void paint(Graphics2D g2, SequenceRenderContext context) { //Rectangle2D prevClip = g2.getClipBounds(); //seems no use AffineTransform prevTransform = g2.getTransform(); g2.setPaint(fontcolor); Font font = context.getFont(); Rectangle2D maxCharBounds = font.getMaxCharBounds(g2.getFontRenderContext()); double scale = context.getScale(); if (scale >= (maxCharBounds.getWidth() * 0.2) && scale >= (maxCharBounds.getHeight() * 0.2)) { double xFontOffset = 0.0; double yFontOffset = 0.0; // These offsets are not set quite correctly yet. The // Rectangle2D from getMaxCharBounds() seems slightly // off. The "correct" application of translations based on // the Rectangle2D seem to give the wrong results. The // values below are mostly fudges. if (context.getDirection() == SequenceRenderContext.HORIZONTAL) { xFontOffset = maxCharBounds.getCenterX() * 0.25; yFontOffset = -maxCharBounds.getCenterY() + (depth * 0.5); } else { xFontOffset = -maxCharBounds.getCenterX() + (depth * 0.5); yFontOffset = -maxCharBounds.getCenterY() * 3.0; } SymbolList seq1 = context.getSymbols(); if (strand == StrandedFeature.NEGATIVE) { try { seq1 = DNATools.reverseComplement(seq1); } catch (Exception ex) { throw new BioRuntimeException(ex); } } SymbolList seq = seq1.subList(1 + moduloFrame, seq1.length() - (seq1.length() - moduloFrame) % 3); //int min = context.getRange().getMin(); int min = 1; //int max = context.getRange().getMax(); int max = seq.length(); //transcribe to RNA SymbolTokenization toke = null; TranslationTable eup = RNATools.getGeneticCode(TranslationTable.UNIVERSAL); Alphabet protein_al = ProteinTools.getAlphabet(); SymbolList protein = null; try { toke = protein_al.getTokenization("token"); seq = RNATools.transcribe(seq); //veiw the RNA sequence as codons, this is done internally by RNATool.translate() seq = SymbolListViews.windowedSymbolList(seq, 3); //translate protein = SymbolListViews.translate(seq, eup); } catch (Exception ex) { throw new BioRuntimeException(ex); } //System.out.println(protein.seqString()); //g2.drawString(protein.seqString(),(float)context.sequenceToGraphics(1),(fl oat)yFontOffset); //---the same slow for (int sPos = min; sPos <= max; sPos++) { if (context.getDirection() == SequenceRenderContext.HORIZONTAL && sPos % 3 == 0) { double gPos = context.sequenceToGraphics(sPos - 1 + moduloFrame); String s = "*"; try { s = toke.tokenizeSymbol(protein.symbolAt(sPos / 3)); //s = protein.symbolAt(sPos).toString(); } catch (Exception ex) { // We'll ignore the case of not being able to tokenize it } g2.drawString(s,(float)(gPos+ xFontOffset),(float)yFontOffset); /* char [] tmpc = s.toCharArray(); g2.drawChars(tmpc,0,1, (int) (gPos),// + xFontOffset), (int) yFontOffset);*/ } } } else { renderOneFrame(g2, context, context.getRange(), false); } //g2.setClip(prevClip);// ---seems no use g2.setTransform(prevTransform); } public SequenceViewerEvent processMouseEvent(SequenceRenderContext context, MouseEvent me, List path) { path.add(this); int sPos = context.graphicsToSequence(me.getPoint()); return new SequenceViewerEvent(this, null, sPos, me, path); } private boolean isStop(SymbolList seq, int base, StrandedFeature.Strand strand) { // tests whether there is a stop at given location. // the triplet is either base, +1, +2 or -1, -2 // depending on the strand searched if (strand == StrandedFeature.POSITIVE) { // check that search does not exceed bounds if (base + 2 > seq.length()) return false; // search top strand // first base must be t if (seq.symbolAt(base) != DNATools.t()) return false; // second base cannot be c or t if (seq.symbolAt(base + 1) == DNATools.c()) return false; if (seq.symbolAt(base + 1) == DNATools.t()) return false; // if second base is g, the third must be a if (seq.symbolAt(base + 1) == DNATools.g()) { if (seq.symbolAt(base + 2) != DNATools.a()) return false; } else { // second base is a: third must be a or g. if (seq.symbolAt(base + 2) == DNATools.c()) return false; if (seq.symbolAt(base + 2) == DNATools.t()) return false; } // oh well, must be a stop, innit? return true; } else { // check bounds if (base - 2 < 1) return false; // search bottom strand // first base must be t if (seq.symbolAt(base) != DNATools.a()) return false; // second base cannot be c or t on reverse strand if (seq.symbolAt(base - 1) == DNATools.a()) return false; if (seq.symbolAt(base - 1) == DNATools.g()) return false; // if second base is g, the third must be a if (seq.symbolAt(base - 1) == DNATools.c()) { if (seq.symbolAt(base - 2) != DNATools.t()) return false; } else { // second base is a: third must be a or g. if (seq.symbolAt(base - 2) == DNATools.a()) return false; if (seq.symbolAt(base - 2) == DNATools.g()) return false; } // ach! a stop! return true; } } private void renderOneFrame( Graphics2D g, SequenceRenderContext src, RangeLocation range, boolean onceOnly) { // method to draw by checking succeeding triplets for // stop codons. // write it for horizontal rendering first. SymbolList seq = src.getSymbols(); // get extent of sequence to render // hope it agrees with clip region! int minS = range.getMin(); int maxS = range.getMax(); // we start at the first triplet whose first base is within // the range. /* if (minS % 3 > moduloFrame) { // first triplet of my frame is in next mod-zero triplet minS = (minS / 3 + 1) * 3 + moduloFrame; } else if (minS % 3 != moduloFrame) { // first triplet is in current mod-zero triplet minS = (minS / 3) * 3 + moduloFrame; }*/ // now we search every triplet from minS upward seeking stops. for (int base = minS+moduloFrame; base <= maxS; base += 3) { // check for stop if (!isStop(seq, base, strand)) continue; // we have a stop, render a line drawLine(g, src, base, strand); // do I call it quits now? if (onceOnly) return; } } public void drawLine( Graphics2D g, SequenceRenderContext src, int base, StrandedFeature.Strand strand) { Paint prevPaint = g.getPaint(); g.setPaint(linecolor); // compute the frame to use. //int moduloFrame = base%3; // System.out.println("drawLine: base,strand,modulo" + base + " " + strand + " " + moduloFrame); // get required offset for frame double offset = 0;//modi by hywang // compute position of line to be drawn int lineP = (int) src.sequenceToGraphics(base); // draw the line if (src.getDirection() == src.HORIZONTAL) { g.drawLine(lineP, (int) offset, lineP, (int) (offset + blockWidth)); } else { g.drawLine((int) offset, lineP, (int) (offset + blockWidth), lineP); } g.setPaint(prevPaint); } } From matthew_pocock at yahoo.co.uk Wed Sep 24 06:03:23 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Wed Sep 24 06:03:30 2003 Subject: [Biojava-l] Re: [Biojava-dev] About the six frame renderer again. In-Reply-To: <20030924025518.4728.qmail@scbit.org> References: <20030924025518.4728.qmail@scbit.org> Message-ID: <3F716BEB.6010107@yahoo.co.uk> Hi, I recently added code for optimizing rendering to the current clip. If you get a recent biojava (preferably source-code - try cvs or the nightly builds), then you will see some new-in-1.4 code in the .gui.sequence package. Take a look at SymbolSequenceREnderer, arround line #117 for how to get the minimally visible range. Matthew hywang@scbit.org wrote: > Hi, > I have wrote a renderer for six frame view based on your > SixFrameRenderer, it can render a frame with the input > parameter: > moduloFrame > which could only be 0,1,2 for the different start base of translation. > strand > which stands for the positive or negtive strand. > I can get the expected effect of six lines of Amino arrays in zoom in > mode, > and different sticks drawed for stop codon in zoom out mode. > But if a sequence is very long, for example about 100k, > the scroll action in zoom in mode will be a bit slow. > I think that is probably because of the wholy repainting all the amino > strings, so I have tried getclip() function in the paint() method > ,but the improvement seemed to be not a satisfaction. > Any help would be greatly appreciated and would stop me pulling > anymore hair out! > Thanks. > Best Wishes ! > Hywang From andrew at anatomy.otago.ac.nz Fri Sep 26 00:52:29 2003 From: andrew at anatomy.otago.ac.nz (Andrew Macgregor) Date: Fri Sep 26 00:50:33 2003 Subject: [Biojava-l] Unigene and Biosql Message-ID: <3BA76034-EFDD-11D7-9CD9-00039399CEDC@anatomy.otago.ac.nz> Hi, Has anyone got something using biojava that is equivalent to the load_seqdatabase.pl script that comes with bioperl-db? That is something that will allow me to load a unigene file into a biosql db using biojava? Cheers, Andrew. From andrew at anatomy.otago.ac.nz Fri Sep 26 17:42:00 2003 From: andrew at anatomy.otago.ac.nz (andrew@anatomy.otago.ac.nz) Date: Fri Sep 26 17:31:48 2003 Subject: [Biojava-l] Unigene and Biosql In-Reply-To: References: <3BA76034-EFDD-11D7-9CD9-00039399CEDC@anatomy.otago.ac.nz> Message-ID: <59356.203.109.254.50.1064612520.squirrel@anatomy2.otago.ac.nz> Hi Michael, Thanks Michael. Yes I'm aware that you can input with Perl and extract with Java. I'm just interested in whether the input can also be done with Java so I could, for example, do it from within an application. -- Andrew. > Hello Andrew, > > The biosql database is meant to be language neutral, so if you import a > sequence into biosql db with the perl script, biojava should pull it out > just fine. > > michael > > On Fri, 26 Sep 2003, Andrew Macgregor wrote: > >> Hi, >> >> Has anyone got something using biojava that is equivalent to the >> load_seqdatabase.pl script that comes with bioperl-db? That is >> something that will allow me to load a unigene file into a biosql db >> using biojava? >> >> Cheers, Andrew. >> >> _______________________________________________ >> Biojava-l mailing list - Biojava-l@biojava.org >> http://biojava.org/mailman/listinfo/biojava-l From msouthern at exsar.com Mon Sep 29 14:00:47 2003 From: msouthern at exsar.com (Mark Southern) Date: Mon Sep 29 13:58:51 2003 Subject: [Biojava-l] Sequence serialization exception In-Reply-To: <2C879FB52902524C85E8B616CF276F1A0CA6B3@cartasrv.carta.local> Message-ID: <2C879FB52902524C85E8B616CF276F1A0CA6B4@cartasrv.carta.local> I am getting the following exception when trying to serialize a protein sequence. I am using biojava 1.3. Can anyone please explain to me why? Many thanks, Mark. java.io.InvalidObjectException: Couldn't resolve symbol:SER at org.biojava.bio.symbol.AlphabetManager$WellKnownAtomicSymbol$OPH.readResolve (AlphabetManager.java:1441) 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:324) at java.io.ObjectStreamClass.invokeReadResolve(ObjectStreamClass.java:911) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1655) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.readArray(ObjectInputStream.java:1603) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1271) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.defaultReadObject(ObjectInputStream.java:452) at org.biojava.bio.seq.impl.SimpleSequence.readObject(SimpleSequence.java:119) 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:324) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.defaultReadObject(ObjectInputStream.java:452) at org.biojava.bio.seq.ViewSequence.readObject(ViewSequence.java:93) 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:324) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:324) at java.util.HashMap.readObject(HashMap.java:985) at sun.reflect.GeneratedMethodAccessor6.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl .java:25) at java.lang.reflect.Method.invoke(Method.java:324) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:324) at java.util.HashMap.readObject(HashMap.java:986) at sun.reflect.GeneratedMethodAccessor6.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl .java:25) at java.lang.reflect.Method.invoke(Method.java:324) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:324) at com.exsar.hdex.model.calc.Test.main(Test.java:104) From msouthern at exsar.com Mon Sep 29 18:45:07 2003 From: msouthern at exsar.com (Mark Southern) Date: Mon Sep 29 18:43:12 2003 Subject: [Biojava-l] RE: Sequence serialization exception - AlphabetManager problem? In-Reply-To: <2C879FB52902524C85E8B616CF276F1A0CA6B4@cartasrv.carta.local> Message-ID: <2C879FB52902524C85E8B616CF276F1A1CC459@cartasrv.carta.local> Appologies for following up on my own post. What follows is a simpler test than the serialization I attempted before. Consider the bit of code below and corresponding error message; For some reason, the protein sequence is being treated as a dna sequence. Is there something I am missing with respect to how AlphabetManager treats dna and protein alphabets? Any explainations would be most welcome. Thanks again, Mark. //------------------------------------------------------------------------ public static void main(String[] args) throws Exception{ String seqFile = "c:\\temp\\KAP0_BOVIN.swiss"; SequenceIterator iter = (SequenceIterator) SeqIOTools.fileToBiojava(SeqIOConstants.SWISSPROT ,new BufferedReader( new FileReader( seqFile ) ) ); Sequence seq = iter.nextSequence(); SeqIOTools.biojavaToFile( SeqIOConstants.SWISSPROT, System.out, seq ); } org.biojava.bio.symbol.IllegalSymbolException: Symbol ALA not found in alphabet DNA at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:278) at org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper.val idate(AlphabetManager.java:1423) at org.biojava.bio.seq.io.CharacterTokenization._tokenizeSymbol(CharacterTokeni zation.java:178) at org.biojava.bio.seq.io.CharacterTokenization.tokenizeSymbol(CharacterTokeniz ation.java:191) at org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper.tokenize Symbol(AlphabetManager.java:1276) at org.biojava.bio.seq.io.AbstractGenEmblFileFormer.formatTokenBlock(AbstractGe nEmblFileFormer.java:337) at org.biojava.bio.seq.io.EmblFileFormer.addSymbols(EmblFileFormer.java:211) rethrown as org.biojava.bio.symbol.IllegalAlphabetException: DNA not tokenizing at org.biojava.bio.seq.io.EmblFileFormer.addSymbols(EmblFileFormer.java:224) at org.biojava.bio.seq.io.SeqIOEventEmitter.getSeqIOEvents(SeqIOEventEmitter.ja va:125) rethrown as org.biojava.bio.BioError: An internal error occurred processing symbols at org.biojava.bio.seq.io.SeqIOEventEmitter.getSeqIOEvents(SeqIOEventEmitter.ja va:137) at org.biojava.bio.seq.io.EmblLikeFormat.writeSequence(EmblLikeFormat.java:289) at org.biojava.bio.seq.io.EmblLikeFormat.writeSequence(EmblLikeFormat.java:253) at org.biojava.bio.seq.io.SeqIOTools.writeSwissprot(SeqIOTools.java:316) at org.biojava.bio.seq.io.SeqIOTools.seqToFile(SeqIOTools.java:1078) at org.biojava.bio.seq.io.SeqIOTools.biojavaToFile(SeqIOTools.java:870) at com.exsar.test.SerializeTest.main(SerializeTest.java:24) -----Original Message----- From: Mark Southern [mailto:msouthern@exsar.com] Sent: Monday, September 29, 2003 2:01 PM Cc: 'biojava-l@biojava.org' Subject: Sequence serialization exception I am getting the following exception when trying to serialize a protein sequence. I am using biojava 1.3. Can anyone please explain to me why? Many thanks, Mark. java.io.InvalidObjectException: Couldn't resolve symbol:SER at org.biojava.bio.symbol.AlphabetManager$WellKnownAtomicSymbol$OPH.readResolve (AlphabetManager.java:1441) 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:324) at java.io.ObjectStreamClass.invokeReadResolve(ObjectStreamClass.java:911) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1655) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.readArray(ObjectInputStream.java:1603) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1271) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.defaultReadObject(ObjectInputStream.java:452) at org.biojava.bio.seq.impl.SimpleSequence.readObject(SimpleSequence.java:119) 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:324) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.defaultReadObject(ObjectInputStream.java:452) at org.biojava.bio.seq.ViewSequence.readObject(ViewSequence.java:93) 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:324) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:324) at java.util.HashMap.readObject(HashMap.java:985) at sun.reflect.GeneratedMethodAccessor6.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl .java:25) at java.lang.reflect.Method.invoke(Method.java:324) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:324) at java.util.HashMap.readObject(HashMap.java:986) at sun.reflect.GeneratedMethodAccessor6.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl .java:25) at java.lang.reflect.Method.invoke(Method.java:324) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:324) at com.exsar.hdex.model.calc.Test.main(Test.java:104) From facemann at yahoo.com Mon Sep 29 21:15:57 2003 From: facemann at yahoo.com (Andy Hammer) Date: Mon Sep 29 21:13:49 2003 Subject: [Biojava-l] Build errors Message-ID: <20030930011557.9748.qmail@web13401.mail.yahoo.com> Yes, the bytecode.jar file is present and is 91K in size. Andy =-=-=-=-=-= Looks like you might not have the bytecode.jar file which is odd. Do you see it in your biojava-live directory? - Mark __________________________________ Do you Yahoo!? The New Yahoo! Shopping - with improved product search http://shopping.yahoo.com From matthew_pocock at yahoo.co.uk Tue Sep 30 05:12:48 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Tue Sep 30 05:14:36 2003 Subject: [Biojava-l] Build errors In-Reply-To: <20030913013129.30335.qmail@web13407.mail.yahoo.com> References: <20030913013129.30335.qmail@web13407.mail.yahoo.com> Message-ID: <3F794910.6000807@yahoo.co.uk> This usually happens because you are trying to build biojava from source while you have an old biojava.jar in your classpath. Matthew Andy Hammer wrote: >I am getting some build errors. >I even deleted /biojava-live and started over. >Lastly from ./biojava-live/ >ant clean = build successful >cvs update -d = appeared successful >ant = >[ahammer@westwater biojava-live]$ ant >Buildfile: build.xml > >init: > [echo] JUnit present: >${junit.present} > [echo] JUnit supported by Ant: true > >prepare: > [mkdir] Created dir: >/home/ahammer/downloads/biojava-live/ant-build > >prepare-core: > [mkdir] Created dir: >/home/ahammer/downloads/biojava-live/ant-build/src/main > [mkdir] Created dir: >/home/ahammer/downloads/biojava-live/ant-build/classes/main > [mkdir] Created dir: >/home/ahammer/downloads/biojava-live/ant-build/src/tests > [mkdir] Created dir: >/home/ahammer/downloads/biojava-live/ant-build/classes/tests > [mkdir] Created dir: >/home/ahammer/downloads/biojava-live/ant-build/src/demos > [mkdir] Created dir: >/home/ahammer/downloads/biojava-live/ant-build/classes/demos > [mkdir] Created dir: >/home/ahammer/downloads/biojava-live/ant-build/src/apps > [mkdir] Created dir: >/home/ahammer/downloads/biojava-live/ant-build/classes/apps > [mkdir] Created dir: >/home/ahammer/downloads/biojava-live/ant-build/src/docs > [mkdir] Created dir: >/home/ahammer/downloads/biojava-live/ant-build/docs > [mkdir] Created dir: >/home/ahammer/downloads/biojava-live/ant-build/docs/api > [mkdir] Created dir: >/home/ahammer/downloads/biojava-live/ant-build/lib > [copy] Copying 1191 files to >/home/ahammer/downloads/biojava-live/ant-build/src/main > [copy] Copied 23 empty directories to >/home/ahammer/downloads/biojava-live/ant-build/src/main > [copy] Copying 147 files to >/home/ahammer/downloads/biojava-live/ant-build/src/tests > [copy] Copied 1 empty directory to >/home/ahammer/downloads/biojava-live/ant-build/src/tests > [copy] Copying 180 files to >/home/ahammer/downloads/biojava-live/ant-build/src/demos > [copy] Copied 5 empty directories to >/home/ahammer/downloads/biojava-live/ant-build/src/demos > [copy] Copying 2 files to >/home/ahammer/downloads/biojava-live/ant-build/src/apps > [copy] Copying 15 files to >/home/ahammer/downloads/biojava-live/ant-build/src/docs > [copy] Copying 1 file to >/home/ahammer/downloads/biojava-live/ant-build/src/main > [copy] Copying 1 file to >/home/ahammer/downloads/biojava-live/ant-build/src/demos > [copy] Copying 1 file to >/home/ahammer/downloads/biojava-live/ant-build/src/apps > [copy] Copying 17 files to >/home/ahammer/downloads/biojava-live/ant-build/classes/main > [copy] Copied 1 empty directory to >/home/ahammer/downloads/biojava-live/ant-build/classes/main > [copy] Copying 3 files to >/home/ahammer/downloads/biojava-live/ant-build > >prepare-src: > >compile: > [javac] Compiling 1091 source files to >/home/ahammer/downloads/biojava-live/ant-build/classes/main > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/impl/RevCompSequence.java:47: >reference to ProjectedFeatureHolder is ambiguous, both >class >org.biojava.bio.seq.projection.ProjectedFeatureHolder >in org.biojava.bio.seq.projection and class >org.biojava.bio.seq.ProjectedFeatureHolder in >org.biojava.bio.seq match > [javac] private ProjectedFeatureHolder pfh; > [javac] ^ > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/impl/RevCompSequence.java:65: >reference to ProjectedFeatureHolder is ambiguous, both >class >org.biojava.bio.seq.projection.ProjectedFeatureHolder >in org.biojava.bio.seq.projection and class >org.biojava.bio.seq.ProjectedFeatureHolder in >org.biojava.bio.seq match > [javac] pfh = new >ProjectedFeatureHolder(new >TranslateFlipContext(this,seq,seq.length()+1,true)); > [javac] ^ > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:301: >cannot resolve symbol > [javac] symbol : method make_checkcast >(org.biojava.utils.bytecode.CodeClass) > [javac] location: class >org.biojava.utils.bytecode.ByteCode > [javac] >proxyIV.add(ByteCode.make_checkcast(ourContextC)); > [javac] ^ > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:366: >cannot resolve symbol > [javac] symbol : method make_checkcast >(org.biojava.utils.bytecode.CodeClass) > [javac] location: class >org.biojava.utils.bytecode.ByteCode > [javac] >proxyIV.add(ByteCode.make_checkcast(ourContextC) ); > [javac] ^ > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:436: >cannot resolve symbol > [javac] symbol : variable TYPE_OBJECT > [javac] location: class >org.biojava.utils.bytecode.CodeUtils > [javac] CodeClass c_baseClass = >CodeUtils.TYPE_OBJECT; > [javac] ^ > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:447: >cannot resolve symbol > [javac] symbol : variable TYPE_OBJECT > [javac] location: class >org.biojava.utils.bytecode.CodeUtils > [javac] = >CodeUtils.TYPE_OBJECT.getConstructor(CodeUtils.EMPTY_LIST); > [javac] ^ > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:482: >cannot resolve symbol > [javac] symbol : method make_checkcast >(org.biojava.utils.bytecode.CodeClass) > [javac] location: class >org.biojava.utils.bytecode.ByteCode > [javac] >revTIV.add(ByteCode.make_checkcast(c_FeatureTemplate)); > [javac] ^ > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:492: >cannot resolve symbol > [javac] symbol : method getFields () > [javac] location: interface >org.biojava.utils.bytecode.CodeClass > [javac] for(Iterator fi = >c_ourTemplate.getFields().iterator(); > [javac] ^ > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:522: >cannot resolve symbol > [javac] symbol : method make_checkcast >(org.biojava.utils.bytecode.CodeClass) > [javac] location: class >org.biojava.utils.bytecode.ByteCode > [javac] >revIV.add(ByteCode.make_checkcast(c_ourTemplate)); > [javac] ^ > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:524: >cannot resolve symbol > [javac] symbol : method make_checkcast >(org.biojava.utils.bytecode.CodeClass) > [javac] location: class >org.biojava.utils.bytecode.ByteCode > [javac] >revIV.add(ByteCode.make_checkcast(c_ourContext)); > [javac] ^ > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:526: >cannot resolve symbol > [javac] symbol : method make_checkcast >(org.biojava.utils.bytecode.CodeClass) > [javac] location: class >org.biojava.utils.bytecode.ByteCode > [javac] >revIV.add(ByteCode.make_checkcast(c_ourTemplate)); > [javac] ^ > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:198: >cannot resolve symbol > [javac] symbol : method make_checkcast >(org.biojava.utils.bytecode.CodeClass) > [javac] location: class >org.biojava.utils.bytecode.ByteCode > [javac] >walkIV.add(ByteCode.make_checkcast(c_ourVisitor)); > [javac] ^ > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:227: >cannot resolve symbol > [javac] symbol : method forMethod >(java.lang.reflect.Method) > [javac] location: class >org.biojava.utils.bytecode.IntrospectedCodeClass > [javac] CodeMethod m_getFilter = >IntrospectedCodeClass.forMethod(m); > [javac] > ^ > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:245: >cannot resolve symbol > [javac] symbol : method make_checkcast >(org.biojava.utils.bytecode.CodeClass) > [javac] location: class >org.biojava.utils.bytecode.ByteCode > [javac] >wfiv.add(ByteCode.make_checkcast(c_ourFilter)); > [javac] ^ > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:260: >cannot resolve symbol > [javac] symbol : method make_instanceof >(org.biojava.utils.bytecode.CodeClass) > [javac] location: class >org.biojava.utils.bytecode.ByteCode > [javac] >wrapperIV.add(ByteCode.make_instanceof(c_ourFilter)); > [javac] ^ > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:291: >cannot resolve symbol > [javac] symbol : method forMethod >(java.lang.reflect.Method) > [javac] location: class >org.biojava.utils.bytecode.IntrospectedCodeClass > [javac] CodeMethod ourMeth = >IntrospectedCodeClass.forMethod(meth); > [javac] > ^ > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:297: >cannot resolve symbol > [javac] symbol : method make_checkcast >(org.biojava.utils.bytecode.CodeClass) > [javac] location: class >org.biojava.utils.bytecode.ByteCode > [javac] >bodyIV.add(ByteCode.make_checkcast(c_thisFiltType)); > [javac] ^ > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:306: >cannot resolve symbol > [javac] symbol : method make_instanceof >(org.biojava.utils.bytecode.CodeClass) > [javac] location: class >org.biojava.utils.bytecode.ByteCode > [javac] >walkIV.add(ByteCode.make_instanceof(c_thisFiltType)); > [javac] ^ > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:328: >cannot resolve symbol > [javac] symbol : variable TYPE_OBJECT > [javac] location: class >org.biojava.utils.bytecode.CodeUtils > [javac] >CodeUtils.TYPE_OBJECT, > [javac] > ^ > [javac] >/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:358: >cannot resolve symbol > [javac] symbol : variable TYPE_OBJECT > [javac] location: class >org.biojava.utils.bytecode.CodeUtils > [javac] CodeUtils.TYPE_OBJECT, > [javac] ^ > [javac] 20 errors > >BUILD FAILED >file:/home/ahammer/downloads/biojava-live/build.xml:278: >Compile failed; see the compiler error output for >details. > >I think last time I bothered to build was around 1.3. >It has always worked in the past. . . >Any ideas would be appreciated. > >facemann > >__________________________________ >Do you Yahoo!? >Yahoo! SiteBuilder - Free, easy-to-use web site design software >http://sitebuilder.yahoo.com >_______________________________________________ >Biojava-l mailing list - Biojava-l@biojava.org >http://biojava.org/mailman/listinfo/biojava-l > > > From mark.schreiber at agresearch.co.nz Tue Sep 30 06:27:40 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Tue Sep 30 06:25:41 2003 Subject: [Biojava-l] RE: Sequence serialization exception - AlphabetManagerproblem? Message-ID: Hi - I was a bit thrown off at first cause I thought you meant there was an error in binary serialization. There seems to be a problem with SwissProt writing. I've commited an addition to SeqIOToolsTest in biojava live that replicates the error but I haven't got time to track it down just yet. If some one else doesn't get it I'll probably find it tommorrow. - Mark -----Original Message----- From: Mark Southern [mailto:msouthern@exsar.com] Sent: Tue 30/09/2003 10:45 a.m. To: biojava-l@biojava.org Cc: Subject: [Biojava-l] RE: Sequence serialization exception - AlphabetManagerproblem? Appologies for following up on my own post. What follows is a simpler test than the serialization I attempted before. Consider the bit of code below and corresponding error message; For some reason, the protein sequence is being treated as a dna sequence. Is there something I am missing with respect to how AlphabetManager treats dna and protein alphabets? Any explainations would be most welcome. Thanks again, Mark. //------------------------------------------------------------------------ public static void main(String[] args) throws Exception{ String seqFile = "c:\\temp\\KAP0_BOVIN.swiss"; SequenceIterator iter = (SequenceIterator) SeqIOTools.fileToBiojava(SeqIOConstants.SWISSPROT ,new BufferedReader( new FileReader( seqFile ) ) ); Sequence seq = iter.nextSequence(); SeqIOTools.biojavaToFile( SeqIOConstants.SWISSPROT, System.out, seq ); } org.biojava.bio.symbol.IllegalSymbolException: Symbol ALA not found in alphabet DNA at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:278) at org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper.val idate(AlphabetManager.java:1423) at org.biojava.bio.seq.io.CharacterTokenization._tokenizeSymbol(CharacterTokeni zation.java:178) at org.biojava.bio.seq.io.CharacterTokenization.tokenizeSymbol(CharacterTokeniz ation.java:191) at org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper.tokenize Symbol(AlphabetManager.java:1276) at org.biojava.bio.seq.io.AbstractGenEmblFileFormer.formatTokenBlock(AbstractGe nEmblFileFormer.java:337) at org.biojava.bio.seq.io.EmblFileFormer.addSymbols(EmblFileFormer.java:211) rethrown as org.biojava.bio.symbol.IllegalAlphabetException: DNA not tokenizing at org.biojava.bio.seq.io.EmblFileFormer.addSymbols(EmblFileFormer.java:224) at org.biojava.bio.seq.io.SeqIOEventEmitter.getSeqIOEvents(SeqIOEventEmitter.ja va:125) rethrown as org.biojava.bio.BioError: An internal error occurred processing symbols at org.biojava.bio.seq.io.SeqIOEventEmitter.getSeqIOEvents(SeqIOEventEmitter.ja va:137) at org.biojava.bio.seq.io.EmblLikeFormat.writeSequence(EmblLikeFormat.java:289) at org.biojava.bio.seq.io.EmblLikeFormat.writeSequence(EmblLikeFormat.java:253) at org.biojava.bio.seq.io.SeqIOTools.writeSwissprot(SeqIOTools.java:316) at org.biojava.bio.seq.io.SeqIOTools.seqToFile(SeqIOTools.java:1078) at org.biojava.bio.seq.io.SeqIOTools.biojavaToFile(SeqIOTools.java:870) at com.exsar.test.SerializeTest.main(SerializeTest.java:24) -----Original Message----- From: Mark Southern [mailto:msouthern@exsar.com] Sent: Monday, September 29, 2003 2:01 PM Cc: 'biojava-l@biojava.org' Subject: Sequence serialization exception I am getting the following exception when trying to serialize a protein sequence. I am using biojava 1.3. Can anyone please explain to me why? Many thanks, Mark. java.io.InvalidObjectException: Couldn't resolve symbol:SER at org.biojava.bio.symbol.AlphabetManager$WellKnownAtomicSymbol$OPH.readResolve (AlphabetManager.java:1441) 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:324) at java.io.ObjectStreamClass.invokeReadResolve(ObjectStreamClass.java:911) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1655) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.readArray(ObjectInputStream.java:1603) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1271) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.defaultReadObject(ObjectInputStream.java:452) at org.biojava.bio.seq.impl.SimpleSequence.readObject(SimpleSequence.java:119) 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:324) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.defaultReadObject(ObjectInputStream.java:452) at org.biojava.bio.seq.ViewSequence.readObject(ViewSequence.java:93) 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:324) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:324) at java.util.HashMap.readObject(HashMap.java:985) at sun.reflect.GeneratedMethodAccessor6.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl .java:25) at java.lang.reflect.Method.invoke(Method.java:324) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:324) at java.util.HashMap.readObject(HashMap.java:986) at sun.reflect.GeneratedMethodAccessor6.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl .java:25) at java.lang.reflect.Method.invoke(Method.java:324) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:324) at com.exsar.hdex.model.calc.Test.main(Test.java:104) _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From msouthern at exsar.com Tue Sep 30 09:30:37 2003 From: msouthern at exsar.com (Mark Southern) Date: Tue Sep 30 09:28:37 2003 Subject: [Biojava-l] RE: Sequence serialization exception - AlphabetManagerproblem? Message-ID: <2C879FB52902524C85E8B616CF276F1A0CA6B9@cartasrv.carta.local> Hi Mark, I did also have an error with binary serialization. I was just trying to approach to problem from a different direction. B/c that also was a problem with finding / determining a protein symbol, i wondered if was coming from AlphabetManager rather than the Swissprot writing. I include below the code fragment along with the serialization error. Best regards, Mark. public static void main(String[] args) throws Exception{ File file = new File("c:\\temp\\sequence.ser"); String seqFile = "c:\\temp\\KAP0_BOVIN.swiss"; SequenceIterator iter = (SequenceIterator) SeqIOTools.fileToBiojava( SeqIOConstants.SWISSPROT , new BufferedReader( new FileReader( seqFile ) ) ); Sequence seq = iter.nextSequence(); System.out.println("\nWriting Sequence object"); ObjectOutputStream out = new ObjectOutputStream( new FileOutputStream(file) ); out.writeObject( seq ); out.flush(); out.close(); System.out.println("\nReading Sequence object"); ObjectInputStream in = new ObjectInputStream( new FileInputStream(file) ); seq = (Sequence) in.readObject(); in.close(); } Writing Sequence object Reading Sequence object java.io.InvalidObjectException: Couldn't resolve symbol:ALA at org.biojava.bio.symbol.AlphabetManager$WellKnownAtomicSymbol$OPH.readResolve (AlphabetManager.java:1480) 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:324) at java.io.ObjectStreamClass.invokeReadResolve(ObjectStreamClass.java:911) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1655) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.readArray(ObjectInputStream.java:1603) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1271) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.defaultReadObject(ObjectInputStream.java:452) at org.biojava.bio.seq.impl.SimpleSequence.readObject(SimpleSequence.java:119) 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:324) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:324) at com.exsar.test.SerializeTest.main(SerializeTest.java:38) Exception in thread "main" -----Original Message----- From: Schreiber, Mark [mailto:mark.schreiber@agresearch.co.nz] Sent: Tuesday, September 30, 2003 6:28 AM To: msouthern@exsar.com; biojava-l@biojava.org Subject: RE: [Biojava-l] RE: Sequence serialization exception - AlphabetManagerproblem? Hi - I was a bit thrown off at first cause I thought you meant there was an error in binary serialization. There seems to be a problem with SwissProt writing. I've commited an addition to SeqIOToolsTest in biojava live that replicates the error but I haven't got time to track it down just yet. If some one else doesn't get it I'll probably find it tommorrow. - Mark -----Original Message----- From: Mark Southern [mailto:msouthern@exsar.com] Sent: Tue 30/09/2003 10:45 a.m. To: biojava-l@biojava.org Cc: Subject: [Biojava-l] RE: Sequence serialization exception - AlphabetManagerproblem? Appologies for following up on my own post. What follows is a simpler test than the serialization I attempted before. Consider the bit of code below and corresponding error message; For some reason, the protein sequence is being treated as a dna sequence. Is there something I am missing with respect to how AlphabetManager treats dna and protein alphabets? Any explainations would be most welcome. Thanks again, Mark. //------------------------------------------------------------------------ public static void main(String[] args) throws Exception{ String seqFile = "c:\\temp\\KAP0_BOVIN.swiss"; SequenceIterator iter = (SequenceIterator) SeqIOTools.fileToBiojava(SeqIOConstants.SWISSPROT ,new BufferedReader( new FileReader( seqFile ) ) ); Sequence seq = iter.nextSequence(); SeqIOTools.biojavaToFile( SeqIOConstants.SWISSPROT, System.out, seq ); } org.biojava.bio.symbol.IllegalSymbolException: Symbol ALA not found in alphabet DNA at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:278) at org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper.val idate(AlphabetManager.java:1423) at org.biojava.bio.seq.io.CharacterTokenization._tokenizeSymbol(CharacterTokeni zation.java:178) at org.biojava.bio.seq.io.CharacterTokenization.tokenizeSymbol(CharacterTokeniz ation.java:191) at org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper.tokenize Symbol(AlphabetManager.java:1276) at org.biojava.bio.seq.io.AbstractGenEmblFileFormer.formatTokenBlock(AbstractGe nEmblFileFormer.java:337) at org.biojava.bio.seq.io.EmblFileFormer.addSymbols(EmblFileFormer.java:211) rethrown as org.biojava.bio.symbol.IllegalAlphabetException: DNA not tokenizing at org.biojava.bio.seq.io.EmblFileFormer.addSymbols(EmblFileFormer.java:224) at org.biojava.bio.seq.io.SeqIOEventEmitter.getSeqIOEvents(SeqIOEventEmitter.ja va:125) rethrown as org.biojava.bio.BioError: An internal error occurred processing symbols at org.biojava.bio.seq.io.SeqIOEventEmitter.getSeqIOEvents(SeqIOEventEmitter.ja va:137) at org.biojava.bio.seq.io.EmblLikeFormat.writeSequence(EmblLikeFormat.java:289) at org.biojava.bio.seq.io.EmblLikeFormat.writeSequence(EmblLikeFormat.java:253) at org.biojava.bio.seq.io.SeqIOTools.writeSwissprot(SeqIOTools.java:316) at org.biojava.bio.seq.io.SeqIOTools.seqToFile(SeqIOTools.java:1078) at org.biojava.bio.seq.io.SeqIOTools.biojavaToFile(SeqIOTools.java:870) at com.exsar.test.SerializeTest.main(SerializeTest.java:24) -----Original Message----- From: Mark Southern [mailto:msouthern@exsar.com] Sent: Monday, September 29, 2003 2:01 PM Cc: 'biojava-l@biojava.org' Subject: Sequence serialization exception I am getting the following exception when trying to serialize a protein sequence. I am using biojava 1.3. Can anyone please explain to me why? Many thanks, Mark. java.io.InvalidObjectException: Couldn't resolve symbol:SER at org.biojava.bio.symbol.AlphabetManager$WellKnownAtomicSymbol$OPH.readResolve (AlphabetManager.java:1441) 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:324) at java.io.ObjectStreamClass.invokeReadResolve(ObjectStreamClass.java:911) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1655) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.readArray(ObjectInputStream.java:1603) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1271) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.defaultReadObject(ObjectInputStream.java:452) at org.biojava.bio.seq.impl.SimpleSequence.readObject(SimpleSequence.java:119) 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:324) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.defaultReadObject(ObjectInputStream.java:452) at org.biojava.bio.seq.ViewSequence.readObject(ViewSequence.java:93) 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:324) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:324) at java.util.HashMap.readObject(HashMap.java:985) at sun.reflect.GeneratedMethodAccessor6.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl .java:25) at java.lang.reflect.Method.invoke(Method.java:324) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:324) at java.util.HashMap.readObject(HashMap.java:986) at sun.reflect.GeneratedMethodAccessor6.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl .java:25) at java.lang.reflect.Method.invoke(Method.java:324) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:324) at com.exsar.hdex.model.calc.Test.main(Test.java:104) _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. 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