From holland at ebi.ac.uk Wed Jan 2 06:52:12 2008 From: holland at ebi.ac.uk (Richard Holland) Date: Wed, 02 Jan 2008 11:52:12 +0000 Subject: [Biojava-l] BioJava 3 design discussion coming to an end Message-ID: <477B7AEC.9000401@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi all. At the end of January I will be taking the contents of our BioJava 3 discussion wiki page and compiling them into a more formal design proposal. If you have made any comments elsewhere (e.g. by email) which you would like to be considered in the final design proposal, then please add them to the wiki page (or its associated Talk page) before the end of the month. (I won't be trawling through email archives looking for comments so you really must copy your comments across to the wiki if you want them to be included!). The wiki address is: http://www.biojava.org/wiki/BioJava3_Proposal cheers, Richard - -- Richard Holland (BioMart) EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK Tel. +44 (0)1223 494416 http://www.biomart.org/ http://www.biojava.org/ -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHe3rs4C5LeMEKA/QRAgHqAJ0VR2utTbzjfPYNPXINv26yc1PRNgCZAUnX 978uKqgbePpnHm+3Ynfp7X4= =8nqF -----END PGP SIGNATURE----- From ayates at ebi.ac.uk Mon Jan 7 04:34:33 2008 From: ayates at ebi.ac.uk (Andy Yates) Date: Mon, 7 Jan 2008 09:34:33 +0000 Subject: [Biojava-l] [Biojava-dev] Error while reading byte data for creating a Trace. In-Reply-To: <2839.130.207.66.142.1194285555.squirrel@webmail.cc.gatech.edu> References: <6EDA8DA0-39B2-40A3-B3B3-DB5F3463DB51@sanger.ac.uk> <2839.130.207.66.142.1194285555.squirrel@webmail.cc.gatech.edu> Message-ID: <04BE1C71-B7CF-4428-86C7-300E4283DAE8@ebi.ac.uk> Hi, As far as I am aware there isn't a problem with the current ABI parser however if you could send a code snippit of reading in the byte array & the stack trace of the index out of bounds exception that would be most helpful Andy On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote: > Hi all, > I am having a byte array which is having the data from an .ab1 > file.The > biojava library provides a class called as ABITrace which takes as > input > either a byte[] array , a file or a url.If i use the later > parameters (the > file or the url )the program works but if I pass the byte array to the > constructor I get java.lang.arrayIndexOutOfBound.Exception.Is there a > problem with the ABITrace class or how can I bypass this particular > error. > I am printing the length of the byte array and it comes to > 144930...Can > that cause a problem in my code? > > Thanks in advance. > Abhinav > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev From ayates at ebi.ac.uk Mon Jan 7 04:43:24 2008 From: ayates at ebi.ac.uk (Andy Yates) Date: Mon, 7 Jan 2008 09:43:24 +0000 Subject: [Biojava-l] About ABITrace class In-Reply-To: <200712301004.05398.russ@kepler-eng.com> References: <1198832070.29755.0.camel@bioxpr-04.ct.fundp.ac.be> <200712301004.05398.russ@kepler-eng.com> Message-ID: <6A633935-18A9-4716-8C69-7F6FCC115A20@ebi.ac.uk> Yup Russ is on the ball with that one 100% :) A chromatogram is really a graph of 4 tracks where each scan index refers to an intensity of the 4 dyes used in Sanger Sequencing. There is no direct relation to the size of a chromatogram and the number of base pairs it will represent. If you require any changes to the rendering the options are controlled by ChromatogramGraphic.Option instances in conjunction with the setOption() method in ChromatogramGraphic. If you are rendering a processed ABI file and just want to see the base called sequences then the best option is to use the Chromatogram's getBaseCalls() method & look up the start & finish of the base calls. Use this to set where you want rendering to start & stop (again another ChromatogramGraphic.Option). Hope this helps, Andy On 30 Dec 2007, at 17:04, Russ Kepler wrote: > On Friday 28 December 2007 01:54:30 David Bourgais wrote: >> Hello BioJava users >> >> I am writing a little program using BioJava 1.5 and JFreeChart 1.0.8. >> My aim is to display with JFreeChart a chromatogram by reading an ab1 >> file with the BioJava help. >> Okay, I can display my chromatogram. But, my chromatogram size is >> 13301 >> (using getTrace(AtomicSymbol base)) when my sequence size is 1110 bp >> (according to the the BufferedImage produced with BioJava). >> Why this difference ? How can I correct my program in order to see >> correctly my chromatogram ? > > If I understand you correctly you're looking at the trace data > (multiple > points per peak) and comparing to the base calls (one call per > peak). In my > experience folks interested in the chromatogram would prefer to see > an image > with the chromatogram spaced properly, those primarily interested in > the base > calls prefer to have the chromatogram scaled around a fixed width > for the > basecall. There's code to do either in BioJava, but the former > might not be > setup to generate a BufferedImage (if you can't find it I might be > able to > help some). > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l From holland at ebi.ac.uk Mon Jan 7 07:01:55 2008 From: holland at ebi.ac.uk (Richard Holland) Date: Mon, 7 Jan 2008 12:01:55 -0000 (GMT) Subject: [Biojava-l] [Biojava-dev] Error while reading byte data for creating a Trace. In-Reply-To: <04BE1C71-B7CF-4428-86C7-300E4283DAE8@ebi.ac.uk> References: <6EDA8DA0-39B2-40A3-B3B3-DB5F3463DB51@sanger.ac.uk> <2839.130.207.66.142.1194285555.squirrel@webmail.cc.gatech.edu> <04BE1C71-B7CF-4428-86C7-300E4283DAE8@ebi.ac.uk> Message-ID: <50442.80.42.95.78.1199707315.squirrel@webmail.ebi.ac.uk> This problem was resolved back in November. For some reason during the last couple of weeks the BioJava mailing list has been sending out occasional duplicate copies of emails sent several months ago! This was one of them. cheers, Richard On Mon, January 7, 2008 9:34 am, Andy Yates wrote: > Hi, > > As far as I am aware there isn't a problem with the current ABI parser > however if you could send a code snippit of reading in the byte array > & the stack trace of the index out of bounds exception that would be > most helpful > > Andy > > On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote: > >> Hi all, >> I am having a byte array which is having the data from an .ab1 >> file.The >> biojava library provides a class called as ABITrace which takes as >> input >> either a byte[] array , a file or a url.If i use the later >> parameters (the >> file or the url )the program works but if I pass the byte array to the >> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is there a >> problem with the ABITrace class or how can I bypass this particular >> error. >> I am printing the length of the byte array and it comes to >> 144930...Can >> that cause a problem in my code? >> >> Thanks in advance. >> Abhinav >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -- Richard Holland BioMart (http://www.biomart.org/) EMBL-EBI Hinxton, Cambridgeshire CB10 1SD, UK From ayates at ebi.ac.uk Mon Jan 7 07:18:50 2008 From: ayates at ebi.ac.uk (Andy Yates) Date: Mon, 7 Jan 2008 12:18:50 +0000 Subject: [Biojava-l] [Biojava-dev] Error while reading byte data for creating a Trace. In-Reply-To: <50442.80.42.95.78.1199707315.squirrel@webmail.ebi.ac.uk> References: <6EDA8DA0-39B2-40A3-B3B3-DB5F3463DB51@sanger.ac.uk> <2839.130.207.66.142.1194285555.squirrel@webmail.cc.gatech.edu> <04BE1C71-B7CF-4428-86C7-300E4283DAE8@ebi.ac.uk> <50442.80.42.95.78.1199707315.squirrel@webmail.ebi.ac.uk> Message-ID: <065714BD-6D4F-4B5F-8AAE-E6C47C9405AB@ebi.ac.uk> Oh for ... :). Thought I'd seen this one before Andy On 7 Jan 2008, at 12:01, Richard Holland wrote: > This problem was resolved back in November. For some reason during the > last couple of weeks the BioJava mailing list has been sending out > occasional duplicate copies of emails sent several months ago! This > was > one of them. > > cheers, > Richard > > On Mon, January 7, 2008 9:34 am, Andy Yates wrote: >> Hi, >> >> As far as I am aware there isn't a problem with the current ABI >> parser >> however if you could send a code snippit of reading in the byte array >> & the stack trace of the index out of bounds exception that would be >> most helpful >> >> Andy >> >> On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote: >> >>> Hi all, >>> I am having a byte array which is having the data from an .ab1 >>> file.The >>> biojava library provides a class called as ABITrace which takes as >>> input >>> either a byte[] array , a file or a url.If i use the later >>> parameters (the >>> file or the url )the program works but if I pass the byte array to >>> the >>> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is >>> there a >>> problem with the ABITrace class or how can I bypass this particular >>> error. >>> I am printing the length of the byte array and it comes to >>> 144930...Can >>> that cause a problem in my code? >>> >>> Thanks in advance. >>> Abhinav >>> _______________________________________________ >>> biojava-dev mailing list >>> biojava-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > > > -- > Richard Holland > BioMart (http://www.biomart.org/) > EMBL-EBI > Hinxton, Cambridgeshire CB10 1SD, UK From david.bourgais at bioxpr.be Mon Jan 7 08:59:46 2008 From: david.bourgais at bioxpr.be (David Bourgais) Date: Mon, 07 Jan 2008 14:59:46 +0100 Subject: [Biojava-l] About ABITrace class In-Reply-To: <6A633935-18A9-4716-8C69-7F6FCC115A20@ebi.ac.uk> References: <1198832070.29755.0.camel@bioxpr-04.ct.fundp.ac.be> <200712301004.05398.russ@kepler-eng.com> <6A633935-18A9-4716-8C69-7F6FCC115A20@ebi.ac.uk> Message-ID: <1199714386.23005.17.camel@bioxpr-04.ct.fundp.ac.be> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From russ at kepler-eng.com Mon Jan 7 09:28:30 2008 From: russ at kepler-eng.com (Russ Kepler) Date: Mon, 7 Jan 2008 07:28:30 -0700 Subject: [Biojava-l] About ABITrace class In-Reply-To: <1199714386.23005.17.camel@bioxpr-04.ct.fundp.ac.be> References: <1198832070.29755.0.camel@bioxpr-04.ct.fundp.ac.be> <6A633935-18A9-4716-8C69-7F6FCC115A20@ebi.ac.uk> <1199714386.23005.17.camel@bioxpr-04.ct.fundp.ac.be> Message-ID: <200801070728.30528.russ@kepler-eng.com> On Monday 07 January 2008 06:59:46 David Bourgais wrote: > Hello Andy > > Thank you very much for your answer. > But, even if I have a ABIFChromatogram object and a ChromatogramGraphic > object, I do not understand what you said about setting options. I see a > class Chromatogramgraphic.Option, but I do not know what can I do with > this. If you look inside the ChromatogramGraphic.Option class there is a bunch of static methods, these are the various options that you can set. I'd suggest setting the DRAW_CALL and DRAW_TRACE options for all the nucleotides and FROM_TRACE_SAMPLE and TO_TRACE_SAMPLE and one of WIDTH_IS_AUTHORITATIVE and HEIGHT_IS_AUTHORITATIVE as a starting point. I suspect that you haven't been telling your ChromatorgramObject that you want anything displayed or how. From ayates at ebi.ac.uk Mon Jan 7 09:36:26 2008 From: ayates at ebi.ac.uk (Andy Yates) Date: Mon, 07 Jan 2008 14:36:26 +0000 Subject: [Biojava-l] About ABITrace class In-Reply-To: <1199714386.23005.17.camel@bioxpr-04.ct.fundp.ac.be> References: <1198832070.29755.0.camel@bioxpr-04.ct.fundp.ac.be> <200712301004.05398.russ@kepler-eng.com> <6A633935-18A9-4716-8C69-7F6FCC115A20@ebi.ac.uk> <1199714386.23005.17.camel@bioxpr-04.ct.fundp.ac.be> Message-ID: <478238EA.9060106@ebi.ac.uk> Hi David, Not to worry it's quite confusing at first. ChromatogramGraphic.Option is a pre Java 1.5 enum (where a restricted vocab is specified by class type rather than accepting plain Strings or ints which can be abused). Your code should look something like: Chromatogram c = getChromatogram(); Alignment baseCalls = c.getBaseCalls(); //Of course you've got to check if you've got an alignment, base pairs //and that these values are going to make sense when rendering (nothing //beats attempting to render a chromatogram from & to the same position) int start = getIndex(0, baseCalls); int end = getIndex(baseCalls.length); ChromatogramGraphic cg = new ChromatogramGraphic(c); cg.setOption(ChromatogramGraphic.Option.FROM_TRACE_SAMPLE, start); cg.setOption(ChromatogramGraphic.Option.TO_TRACE_SAMPLE, end); private int getIndex(int pos, Alignment baseCalls) { Symbol sym = baseCalls.symbolAt(Chromatogram.OFFSETS, pos); return ((IntegerAlphabet.IntegerSymbol)sym).intValue(); } It's been a long time since I've used this library in anger (and to be honest I wrote a wrapper around it for my particular usage) but hopefully it should give you a point in the right direction (also the above code is in Java 5 so that will probably have an impact on it working for you). Hope that helps Andy David Bourgais wrote: > Hello Andy > > Thank you very much for your answer. > But, even if I have a ABIFChromatogram object and a ChromatogramGraphic > object, I do not understand what you said about setting options. I see a > class Chromatogramgraphic.Option, but I do not know what can I do with this. > > Thank you very much for your help. > > Best regards. >> Yup Russ is on the ball with that one 100% :) >> >> A chromatogram is really a graph of 4 tracks where each scan index >> refers to an intensity of the 4 dyes used in Sanger Sequencing. There >> is no direct relation to the size of a chromatogram and the number of >> base pairs it will represent. If you require any changes to the >> rendering the options are controlled by ChromatogramGraphic.Option >> instances in conjunction with the setOption() method in >> ChromatogramGraphic. >> >> If you are rendering a processed ABI file and just want to see the >> base called sequences then the best option is to use the >> Chromatogram's getBaseCalls() method & look up the start & finish of >> the base calls. Use this to set where you want rendering to start & >> stop (again another ChromatogramGraphic.Option). >> >> Hope this helps, >> >> Andy > > -- > David Bourgais > Bioinformatician > BioXpr SA/NV > http://www.bioxpr.com > Rue du Seminaire, 22 > 5000, Namur, Belgium > Phone: +32(0)81 72 51 58 > From mheusel at gmail.com Fri Jan 11 17:27:53 2008 From: mheusel at gmail.com (Martin Heusel) Date: Fri, 11 Jan 2008 23:27:53 +0100 Subject: [Biojava-l] Question about StructureTools and PDBFileReader Message-ID: <6127fc200801111427n6464caf5g4113ac071e44b6ef@mail.gmail.com> Hi, i read a PDB file with PDBFileReader.getStructure and want to extract the backbone of a chain with StructureTools. Now i have seen that for entries e.g. ATOM 3505 N GLN A 27 32.144 27.054 0.696 1.00 47.70 N ATOM 3506 CA GLN A 27 32.507 26.162 -0.401 1.00 42.73 C ATOM 3507 C GLN A 27 31.388 26.137 -1.437 1.00 40.44 C ATOM 3508 O GLN A 27 30.205 26.248 -1.096 1.00 41.47 O ATOM 3509 CB GLN A 27 32.729 24.738 0.121 1.00 42.51 C ATOM 3510 CG GLN A 27 34.124 24.449 0.611 1.00 39.02 C ATOM 3511 CD GLN A 27 34.158 23.301 1.593 1.00 41.90 C ATOM 3512 OE1 GLN A 27 33.982 22.143 1.214 1.00 39.58 O ATOM 3513 NE2 GLN A 27 34.386 23.615 2.869 1.00 43.85 N ATOM 3514 N SER A1027 31.762 25.988 -2.703 1.00 33.42 N ATOM 3515 CA SER A1027 30.776 25.929 -3.769 1.00 31.11 C ATOM 3516 C SER A1027 29.915 24.723 -3.462 1.00 27.99 C ATOM 3517 O SER A1027 30.418 23.706 -2.991 1.00 29.25 O ATOM 3518 CB SER A1027 31.449 25.746 -5.130 1.00 22.71 C ATOM 3519 OG SER A1027 30.542 25.185 -6.056 1.00 28.95 O ATOM 3520 N LEU A2027 28.619 24.838 -3.718 1.00 25.68 N ATOM 3521 CA LEU A2027 27.714 23.743 -3.444 1.00 23.42 C ATOM 3522 C LEU A2027 27.489 22.933 -4.694 1.00 24.27 C ATOM 3523 O LEU A2027 26.750 21.950 -4.675 1.00 28.95 O ATOM 3524 CB LEU A2027 26.391 24.278 -2.906 1.00 23.54 C ATOM 3525 CG LEU A2027 26.547 25.090 -1.619 1.00 22.93 C ATOM 3526 CD1 LEU A2027 25.179 25.430 -1.056 1.00 26.74 C ATOM 3527 CD2 LEU A2027 27.361 24.285 -0.603 1.00 19.54 C the two residues SER and LEU are not counted. However, the fasta file from pdb.org website shows both residues for that chain. I wonder how the two entries A1027 and A2027 are interpreted by StructureTools. Thanks for any hints Martin From ap3 at sanger.ac.uk Fri Jan 11 19:32:30 2008 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Sat, 12 Jan 2008 00:32:30 +0000 (GMT) Subject: [Biojava-l] Question about StructureTools and PDBFileReader In-Reply-To: <6127fc200801111427n6464caf5g4113ac071e44b6ef@mail.gmail.com> References: <6127fc200801111427n6464caf5g4113ac071e44b6ef@mail.gmail.com> Message-ID: Hi Martin, I am not sure what you mean with "not counted". When I test the PDB file you posted below it parses all the 3 amino acids into Groups, which is the intended behaviour. PDBFileParser pdbpars = new PDBFileParser(); Structure structure = pdbpars.parsePDBFile(inStream) ; System.out.println(structure); Chain c = structure.getChainByPDB("A"); List groups = c.getAtomGroups(); for (Group g: groups){ System.out.println(g); } System.out.println("sequence: " + c.getAtomSequence()); gives an output of: structure null DepDate: Thu Jan 01 01:00:00 GMT 1970 Resolution: 0.0 ModDate: Thu Jan 01 01:00:00 GMT 1970 chains: chain: >A< length SEQRES: 0 length ATOM: 3 aminos: 3 hetatms: 0 nucleotides: 0 DBRefs: 0 Molecules: AminoAcid ATOM:GLN Q 27 true ATOMatoms: 7 AminoAcid ATOM:SER S 1027 true ATOMatoms: 6 AminoAcid ATOM:LEU L 2027 true ATOMatoms: 8 sequence: QSL In case you would want to access the groups as SEQRES groups then these residues need to be specified in the the corresponding header line in the file. see also http://biojava.org/wiki/BioJava:CookBook:PDB:seqres Does that help? Andreas -------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK On Fri, 11 Jan 2008, Martin Heusel wrote: > Hi, > > i read a PDB file with PDBFileReader.getStructure and want to extract > the backbone of a chain with StructureTools. Now i have seen that for > entries e.g. > > ATOM 3505 N GLN A 27 32.144 27.054 0.696 1.00 47.70 N > ATOM 3506 CA GLN A 27 32.507 26.162 -0.401 1.00 42.73 C > ATOM 3507 C GLN A 27 31.388 26.137 -1.437 1.00 40.44 C > ATOM 3508 O GLN A 27 30.205 26.248 -1.096 1.00 41.47 O > ATOM 3509 CB GLN A 27 32.729 24.738 0.121 1.00 42.51 C > ATOM 3510 CG GLN A 27 34.124 24.449 0.611 1.00 39.02 C > ATOM 3511 CD GLN A 27 34.158 23.301 1.593 1.00 41.90 C > ATOM 3512 OE1 GLN A 27 33.982 22.143 1.214 1.00 39.58 O > ATOM 3513 NE2 GLN A 27 34.386 23.615 2.869 1.00 43.85 N > ATOM 3514 N SER A1027 31.762 25.988 -2.703 1.00 33.42 N > ATOM 3515 CA SER A1027 30.776 25.929 -3.769 1.00 31.11 C > ATOM 3516 C SER A1027 29.915 24.723 -3.462 1.00 27.99 C > ATOM 3517 O SER A1027 30.418 23.706 -2.991 1.00 29.25 O > ATOM 3518 CB SER A1027 31.449 25.746 -5.130 1.00 22.71 C > ATOM 3519 OG SER A1027 30.542 25.185 -6.056 1.00 28.95 O > ATOM 3520 N LEU A2027 28.619 24.838 -3.718 1.00 25.68 N > ATOM 3521 CA LEU A2027 27.714 23.743 -3.444 1.00 23.42 C > ATOM 3522 C LEU A2027 27.489 22.933 -4.694 1.00 24.27 C > ATOM 3523 O LEU A2027 26.750 21.950 -4.675 1.00 28.95 O > ATOM 3524 CB LEU A2027 26.391 24.278 -2.906 1.00 23.54 C > ATOM 3525 CG LEU A2027 26.547 25.090 -1.619 1.00 22.93 C > ATOM 3526 CD1 LEU A2027 25.179 25.430 -1.056 1.00 26.74 C > ATOM 3527 CD2 LEU A2027 27.361 24.285 -0.603 1.00 19.54 C > > the two residues SER and LEU are not counted. However, the fasta file > from pdb.org website shows both residues for that chain. I wonder how > the two entries A1027 and A2027 are interpreted by StructureTools. > > Thanks for any hints > > Martin > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From mheusel at gmail.com Sat Jan 12 08:16:48 2008 From: mheusel at gmail.com (Martin Heusel) Date: Sat, 12 Jan 2008 14:16:48 +0100 Subject: [Biojava-l] Question about StructureTools and PDBFileReader In-Reply-To: References: <6127fc200801111427n6464caf5g4113ac071e44b6ef@mail.gmail.com> Message-ID: <6127fc200801120516n2b4e8377ja041611614516100@mail.gmail.com> Hi Andreas, thanks for your fast help. Sorry it was my fault, i was irritated by a SCOP sequence: >d1a4ka1 b.1.1.1 (A:1-112) Immunoglobulin light chain kappa variable domain, VL-kappa {Mouse (Mus musculus), cluster 1.1} ELVMTQTPLSLPVSLGDQASISCRSSQSLLHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQVTHVPPTFGGGTKLEIKRTVAA it says chain A sequence numbers 1-112 but the sequence is 117 long. At sequence number 27 there is ATOM 3506 CA GLN A 27 32.507 26.162 -0.401 1.00 42.73 C and five additional residues afterwards (only CA) ATOM 3515 CA SER A1027 30.776 25.929 -3.769 1.00 31.11 C ATOM 3521 CA LEU A2027 27.714 23.743 -3.444 1.00 23.42 C ATOM 3529 CA LEU A3027 28.008 22.622 -7.045 1.00 26.03 C ATOM 3537 CA HIS A4027 28.614 18.875 -6.927 1.00 27.10 C ATOM 3547 CA SER A5027 31.052 17.066 -9.205 1.00 31.92 C so there is a sequence number 27 and five additional numbers 1027 - 5027 Then it goes further with 28 ATOM 3553 CA ASN A 28 27.957 15.242 -10.411 1.00 26.69 C So if i iterate over a CA Atom array from 1 to 28 in this case, i correctly get the first 28 CAs. So my assumption that i don't get these additional CAs was not correct, i missed the last five. I'm sorry i should have debugged more closely. My question is now if it's possible to get the CAs or groups in a sequence number interval? Also i wonder what these additional groups between 27 and 28 are. best regards Martin From ap3 at sanger.ac.uk Sat Jan 12 11:24:15 2008 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Sat, 12 Jan 2008 16:24:15 +0000 (GMT) Subject: [Biojava-l] Question about StructureTools and PDBFileReader In-Reply-To: <6127fc200801120516n2b4e8377ja041611614516100@mail.gmail.com> References: <6127fc200801111427n6464caf5g4113ac071e44b6ef@mail.gmail.com> <6127fc200801120516n2b4e8377ja041611614516100@mail.gmail.com> Message-ID: > My question is now if it's possible to get the CAs or groups in a > sequence number interval? you can access them either by their index position or PDB residue number. I recommend consulting the javadocs for the Chain class. http://www.biojava.org/docs/api16/org/biojava/bio/structure/package-summary.html > Also i wonder what these additional groups between 27 and 28 are. There are many differences between PDB files, please see either the header of the file, or go back to the original paper that describes the structure to find out what it means. Andreas -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From mheusel at gmail.com Sat Jan 12 11:37:30 2008 From: mheusel at gmail.com (Martin Heusel) Date: Sat, 12 Jan 2008 17:37:30 +0100 Subject: [Biojava-l] Question about StructureTools and PDBFileReader In-Reply-To: References: <6127fc200801111427n6464caf5g4113ac071e44b6ef@mail.gmail.com> <6127fc200801120516n2b4e8377ja041611614516100@mail.gmail.com> Message-ID: <6127fc200801120837p40cf59aek4d03aa4654d79c56@mail.gmail.com> > you can access them either by their index position or PDB residue number. > > I recommend consulting the javadocs for the Chain class. > http://www.biojava.org/docs/api16/org/biojava/bio/structure/package-summary.html Yes, i already found getGroupsByPDB() and stuff. That looks for something what i need. Thank you. > > Also i wonder what these additional groups between 27 and 28 are. > > There are many differences between PDB files, please see either the header > of the file, or go back to the original paper that describes the > structure to find out what it means. Okay. The important thing for me was if these groups all belong to the sequence or if they are alternatives or something. Thanks again and regards Martin From markjschreiber at gmail.com Sun Jan 13 17:59:59 2008 From: markjschreiber at gmail.com (Mark Schreiber) Date: Mon, 14 Jan 2008 06:59:59 +0800 Subject: [Biojava-l] toProtein method in DNAtools Message-ID: <93b45ca50801131459n72822471k9f7bf27455ea2079@mail.gmail.com> Hi - I have added a toProtein() method to DNATools. This method and it's overloaded variants gives you a very quick way to turn a DNA SymbolList into a Protein SymbolList without having to convert to RNA and set up the codon view etc. It still does all those things but you don't need to see them. Hopefully this will make it into the 1.6 release. - Mark From ap3 at sanger.ac.uk Mon Jan 14 12:26:30 2008 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Mon, 14 Jan 2008 17:26:30 +0000 Subject: [Biojava-l] biojava svn migration complete Message-ID: <1B7EE4F0-142D-47BC-8143-677627AAC1AC@sanger.ac.uk> Hi! The BioJava SVN migration has been completed. Thanks a lot to everyone who has made contributions to this!! The new anonymous checkout of BioJava is now possible via svn co svn://code.open-bio.org/biojava/biojava-live/trunk biojava-live Developers can obtain a checkout from svn co svn+ssh://dev.open-bio.org/home/svn-repositories/biojava/ biojava-live/trunk/ ./biojava-live and it is possible to browse the repository online at http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/ trunk Also the automated builds have been updated http://www.spice-3d.org/cruise/ see http://biojava.org/wiki/CVS_to_SVN_Migration for more details. Andreas ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From bluky999 at 163.com Thu Jan 17 08:56:52 2008 From: bluky999 at 163.com (yang) Date: Thu, 17 Jan 2008 21:56:52 +0800 Subject: [Biojava-l] Hi_test Message-ID: <478F5EA4.2080200@163.com> Just test this mailing list :-) From ap3 at sanger.ac.uk Tue Jan 22 03:25:49 2008 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Tue, 22 Jan 2008 08:25:49 +0000 Subject: [Biojava-l] biojava looking for maintainers Message-ID: <20765D52-2C0E-40C6-A769-7D13CF1DB489@sanger.ac.uk> Hi, BioJava is a widely used Java library that provides standard APIs, parsers, and solutions for common bioinformatics problems. It is used in a number of applications and referenced in many scientific publications. See here for an overview of these: http://biojava.org/wiki/ BioJava:BioJavaInside In order to continue our first class efforts to serve the community and to further the quality of our source code we are looking for motivated individuals who want to claim responsibility for some of the core libraries and take over maintenance of these. Please see here for a list of modules for which we are currently looking for maintainers: http://biojava.org/wiki/Maintainers_wanted If you want to become a BioJava maintainer, please post to the biojava-dev mailing list. As always - happy biojavaing, Andreas ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From ola.spjuth at farmbio.uu.se Wed Jan 23 04:12:41 2008 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Wed, 23 Jan 2008 10:12:41 +0100 Subject: [Biojava-l] RNA I/O Message-ID: <3518D616-E30E-43E2-B8E5-89012D017AC1@farmbio.uu.se> Hi, I have a question regarding I/O of RNA. RichSequence.IOTools.readStream(bufferedStream, ns); fails for the fasta file: >sequence1 CCCUCGGCUUC Could it be that RNA is not supported in the RichSequence.IOTools, or am I doing something wrong here? Cheers, .../Ola From ayates at ebi.ac.uk Wed Jan 23 04:48:33 2008 From: ayates at ebi.ac.uk (Andy Yates) Date: Wed, 23 Jan 2008 09:48:33 +0000 Subject: [Biojava-l] RNA I/O In-Reply-To: <3518D616-E30E-43E2-B8E5-89012D017AC1@farmbio.uu.se> References: <3518D616-E30E-43E2-B8E5-89012D017AC1@farmbio.uu.se> Message-ID: <47970D71.4050202@ebi.ac.uk> Hi Ola, RNA is supported in the IOTools class as can be seen from the method readFastaRNA(BufferedReader br, Namespace ns). What is the exception trace you're receiving from BioJava? Andy Ola Spjuth wrote: > Hi, > > I have a question regarding I/O of RNA. > > RichSequence.IOTools.readStream(bufferedStream, ns); > > fails for the fasta file: > > >sequence1 > CCCUCGGCUUC > > Could it be that RNA is not supported in the RichSequence.IOTools, or am > I doing something wrong here? > > Cheers, > > .../Ola > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l