From msouthern at exsar.com Mon Apr 4 15:26:15 2005 From: msouthern at exsar.com (Mark Southern) Date: Mon Apr 4 15:22:00 2005 Subject: [Biojava-l] Symbol / SymbolPropertyTable question Message-ID: <2C879FB52902524C85E8B616CF276F1A1CC57E@cartasrv.carta.local> I thought I would ask the list for advice before I embarked on something. I have some physiochemical properties of amino acids that I would like to access. (Milne Acid/Base Lambda/Rho) It includes values for modified amino acids, side groups and N and C termini. See below. I could of course do a very simple String -> value mapping. The question is: what would be the best way to implement this in biojava? I can imagine a setup similar to ProteinTools which reads in per-symbol properties from xml and creates SymbolPropertyTable instances but in this example I have modified amino acids and non-aa entities so I might need to create a new Alphabet? Cheers, Mark. ALANINE A ARGININE R ASPARTIC ACID D ASP COOH D+ ASPARAGINE N CYSTEIN C CYSTINE C2 GLYCINE G GLUTAMIC ACID E GLU COOH E+ GLUTAMINE Q HIS H ISOLEUCINE I LEUCINE L LYSINE K METHIONINE M PHENYLALANINE F PROLINE P PRO cis Pc SERINE S THREONINE T TRYPTOPHANE W TYROSINE Y VALINE V N-Term NT C-Term CT -NHMe NMe H3CCO- Ac From mark.schreiber at novartis.com Mon Apr 4 22:11:21 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Mon Apr 4 22:07:44 2005 Subject: [Biojava-l] Symbol / SymbolPropertyTable question Message-ID: It really depends on what you want to do with it but it would seems like a good target for an Alphabet - Mark "Mark Southern" Sent by: biojava-l-bounces@portal.open-bio.org 04/05/2005 03:26 AM To: cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] Symbol / SymbolPropertyTable question I thought I would ask the list for advice before I embarked on something. I have some physiochemical properties of amino acids that I would like to access. (Milne Acid/Base Lambda/Rho) It includes values for modified amino acids, side groups and N and C termini. See below. I could of course do a very simple String -> value mapping. The question is: what would be the best way to implement this in biojava? I can imagine a setup similar to ProteinTools which reads in per-symbol properties from xml and creates SymbolPropertyTable instances but in this example I have modified amino acids and non-aa entities so I might need to create a new Alphabet? Cheers, Mark. ALANINE A ARGININE R ASPARTIC ACID D ASP COOH D+ ASPARAGINE N CYSTEIN C CYSTINE C2 GLYCINE G GLUTAMIC ACID E GLU COOH E+ GLUTAMINE Q HIS H ISOLEUCINE I LEUCINE L LYSINE K METHIONINE M PHENYLALANINE F PROLINE P PRO cis Pc SERINE S THREONINE T TRYPTOPHANE W TYROSINE Y VALINE V N-Term NT C-Term CT -NHMe NMe H3CCO- Ac _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l ______________________________________________________________________ The Novartis email address format has changed to firstname.lastname@novartis.com. Please update your address book accordingly. ______________________________________________________________________ From msouthern at exsar.com Tue Apr 5 16:39:52 2005 From: msouthern at exsar.com (Mark Southern) Date: Tue Apr 5 16:34:04 2005 Subject: [Biojava-l] AlignmentRenderer works with TranslatedSequencePanel but not SequencePanel??? Message-ID: <2C879FB52902524C85E8B616CF276F1A1CC582@cartasrv.carta.local> The attached example code renders an alignment when used with a TranslatedSequencePanel but not with a SequencePanel - the SequencePanel remains blank. A diff of TranslatedSequencePanel and SequencePanel shows they are quite different. I am not sure what is going on. Can anyone give me some pointers as to how to get this to work in a SequencePanel? I would prefer this since SequencePanel can be scrolled in a JScrollPane and TranslatedSequencePanel cannot. Cheers, Mark. import java.awt.*; import java.io.*; import javax.swing.*; import java.util.*; import org.biojava.bio.*; import org.biojava.bio.seq.*; import org.biojava.bio.seq.impl.*; import org.biojava.bio.seq.io.*; import org.biojava.bio.symbol.*; public class Test{ /** Creates a new instance of Test */ private Test() { } public static void main(String[] args) throws Exception{ JFrame f = new JFrame(); f.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE); // doesn't work with a SequencePanel SequencePanel v = new SequencePanel(); v.setFont( new Font("Courier",Font.PLAIN, 12)); f.getContentPane().add(v, java.awt.BorderLayout.CENTER); BufferedReader br = new BufferedReader( new FileReader( new File( args[0] ) ) ); Alignment a = (Alignment)SeqIOTools.fileToBiojava( AlignIOConstants.MSF_AA, br); v.setSequence(a); MultiLineRenderer mlr = new MultiLineRenderer(); SymbolSequenceRenderer ssr = new SymbolSequenceRenderer(); for(Iterator it = a.getLabels().iterator(); it.hasNext(); ){ Object o = it.next(); AlignmentRenderer ar = new AlignmentRenderer(); ar.setLabel(o); ar.setRenderer(ssr); mlr.addRenderer(ar); } v.setRenderer(mlr); f.pack(); f.setVisible(true); } } From christoph.gille at charite.de Fri Apr 8 10:37:51 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Fri Apr 8 10:31:56 2005 Subject: [Biojava-l] (no subject) Message-ID: <50314.192.168.220.204.1112971071.squirrel@webmail.charite.de> Hi, I am currently working on an interface biojava <==> STRAP (http://www.charite.de/bioinf/strap/, http://www.charite.de/bioinf/strap/doc/index.pdf). First I create a GappedSequence object from a StrapProtein object. I include all STRAP anntotations and STRAP features. The features are subsets of the sequences with annotations like notes, URLs, TeXshade commands, Pymol commands, Rasmol commands. Second I create a converter the other way round. It makes a StrapProtein from a biojava Sequence with all its annotations and features. Does anybody has ideas, what tool could cooperate with STRAP using this interface ? The STRAP plugin technology alows even larger JAVA programs to be plugged in, simply by copying the jar-library into a special directory. Currently a few groups are creating plugins for STRAP. I hope that people will benefit from the biojava interface. Christoph From weelainy at hotmail.com Tue Apr 12 08:51:18 2005 From: weelainy at hotmail.com (Elaine Forbes) Date: Tue Apr 12 08:45:10 2005 Subject: [Biojava-l] Running a java program on mac Message-ID: Hi there- I am a geneticist who would like to run a java program to analyse some genomic sequences. So far i have downloaded Biojava 1.3 and my mac already has Java 1.4.2. Within 'Terminal' i can set my path so that it is looking in the directory which has my genomic seq files and the java program. I believe that firstly i have to compile the program therefore i am using the command javac followed by the name of the prog (ATcounter.java). unfortunately i am getting error messages (script attached below). Do i need to move my biojava folder to somewhere else. I have tried putting it in the same directory as the java prog- no difference. If anyone can help or suggest anything it would be much appreciated.... biosc171:~/desktop/documents/projects/transcript-slip-programs elaineforbes$ javac ATcounter.java ATcounter.java:17: package org.biojava.bio does not exist import org.biojava.bio.*; ^ ATcounter.java:18: package org.biojava.bio.seq does not exist import org.biojava.bio.seq.*; ^ ATcounter.java:19: package org.biojava.bio.seq.io does not exist import org.biojava.bio.seq.io.*; ^ ATcounter.java:20: package org.biojava.bio.symbol does not exist import org.biojava.bio.symbol.*; ^ ATcounter.java:124: cannot resolve symbol symbol : class Symbol location: class ATcounter public void count(int[] theArray, Symbol sym){ ^ ATcounter.java:157: cannot resolve symbol symbol : class Sequence location: class ATcounter private Sequence seq; ^ ATcounter.java:158: cannot resolve symbol symbol : class Symbol location: class ATcounter private Symbol current; ^ ATcounter.java:61: cannot resolve symbol symbol : class SequenceIterator location: class ATcounter SequenceIterator si = SeqIOTools.readFastaDNA(br); ^ ATcounter.java:61: cannot resolve symbol symbol : variable SeqIOTools location: class ATcounter SequenceIterator si = SeqIOTools.readFastaDNA(br); ^ ATcounter.java:65: cannot resolve symbol symbol : class SequenceIterator location: class ATcounter SequenceIterator fnaSi = SeqIOTools.readFastaDNA(fnaBr); ^ ATcounter.java:65: cannot resolve symbol symbol : variable SeqIOTools location: class ATcounter SequenceIterator fnaSi = SeqIOTools.readFastaDNA(fnaBr); ^ ATcounter.java:79: cannot resolve symbol symbol : variable DNATools location: class ATcounter count(ffnAarray, DNATools.a()); ^ ATcounter.java:80: cannot resolve symbol symbol : variable DNATools location: class ATcounter count(ffnTarray, DNATools.t()); ^ ATcounter.java:91: cannot resolve symbol symbol : variable DNATools location: class ATcounter count(fnaAarray, DNATools.a()); ^ ATcounter.java:92: cannot resolve symbol symbol : variable DNATools location: class ATcounter count(fnaTarray, DNATools.t()); ^ 15 errors Thanks Weelainy From foisys at sympatico.ca Tue Apr 12 09:33:15 2005 From: foisys at sympatico.ca (Sylvain Foisy) Date: Tue Apr 12 09:26:17 2005 Subject: [Biojava-l] Running a java program on mac Message-ID: Hi Elaine, It looks that your path to the biojava.jar library is wrong. In Terminal, copy all the libraries from J into /Library/Java/Extensions and try again. Best regards Sylvain =================================================================== Sylvain Foisy, Ph. D. Directeur - operations / Project Manager BioneQ - Reseau quebecois de bio-informatique U. de Montreal / Genome-Quebec Adresse postale: Departement de biochimie Pavillon principal 2900, boul. ?douard-Montpetit Montr?al (Qu?bec) H3T 1J4 Tel: (514) 343-6111 x.2545 Fax: (514) 343-7759 Courriel: sylvain.foisy@bioneq.qc.ca =================================================================== From joel.bjorkman at gmail.com Tue Apr 12 10:17:23 2005 From: joel.bjorkman at gmail.com (=?ISO-8859-1?Q?Joel_Bj=F6rkman?=) Date: Tue Apr 12 10:11:34 2005 Subject: [Biojava-l] dasdsn.dtd Message-ID: Hello! I have a tiny question... I have a program that dies with the error message: "Can't build DAS url"... I'm 90% sure that the error comes from a dtd-URL-fault since it looks lite this in the XML file. I've tried to put the dtd in a couple of different locations with no result. Can I download the dtd and store it somewhere localy so that the program works? -- best regards Joel From douglas.hoen at mail.mcgill.ca Tue Apr 12 13:34:55 2005 From: douglas.hoen at mail.mcgill.ca (Douglas Hoen) Date: Tue Apr 12 13:29:16 2005 Subject: [Biojava-l] Can I modify a SeqSimilaritySearchSubHit? Message-ID: <1113327295.7441.95.camel@elegans> Hi, I want to modify the annotation of a SeqSimilaritySearchSubHit. (Specifically, I want to add the query ID, since I can't find a way to get at it from a SeqSimilaritySearchSubHit.) However, SeqSimilaritySearchSubHit appears to be immutable. Is there any way I can make this class mutable, or do I have to write my own class (e.g. a wrapper)? Thanks, Doug From christoph.gille at charite.de Tue Apr 12 18:40:23 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Tue Apr 12 18:33:57 2005 Subject: [Biojava-l] (no subject) Message-ID: <32841.217.86.170.155.1113345623.squirrel@webmail.charite.de> The following looks like a bug to me. It occured with jre (SUN) 1.4 and 1.5 on X-Windows: I loaded the example "How do I display Features" http://www.biojava.org/docs/bj_in_anger/featgui.htm The sequence and the associated feature are displayed in a JFrame without error as described in the tutorial. However, when I resize the JFrame with the mouse the end of the sequence is often not drawn. Only the 5' part (or N-terminus) is visible. The size of the part that is not drawn is different each time I resize the frame. It is also not redrawn when I hide the frame by another frame and unhide it subsequently even thought the paintComponent(Graphics) method is invoked; Hi everybody, The following looks like a bug to me but I am not completely sure. The paintComponent(Graphics g) method of SequencePanel is invoked each time as expected. I checked getPreferredSize() within the paintComponent(Graphics) and found that it returns correct Dimension values. If I place the SequencePanel directly to the JFrame.getContentPane() then drawing of the total sequence works fine. Only if I add it to an other JPanel and place this JPanel in the getContentPane() as explained in the example then the painting error occurs. seqPanel.setDirection(SequencePanel.VERTICAL) exhibits the same problem. When I place the SequencePanel into a JScrollPane than the scroll-bar size is incorrect and the scrollable area is too large. Christoph From td2 at sanger.ac.uk Wed Apr 13 04:01:24 2005 From: td2 at sanger.ac.uk (Thomas Down) Date: Wed Apr 13 03:55:00 2005 Subject: [Biojava-l] dasdsn.dtd In-Reply-To: References: Message-ID: <98184f5afa73b0aa98f86932e02c808b@sanger.ac.uk> On 12 Apr 2005, at 15:17, Joel Bj?rkman wrote: > Hello! > > I have a tiny question... > > I have a program that dies with the error message: "Can't build DAS > url"... > I'm 90% sure that the error comes from a dtd-URL-fault since it looks > lite > this in the XML file. The "Can't build DAS url" error isn't DTD related, as far as I can tell. The usual reason is that one or more DAS datasources has an invalid MAPMASTER URL, which causes problems when BioJava tries to parse it into a Java URL object. Which server were you trying to access? I know where was a configuration problem on the Sanger Institute DAS server yesterday, which could have caused errors like the one you report. I believe this has been fixed now, Thomas. From mark.schreiber at novartis.com Wed Apr 13 23:28:44 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Wed Apr 13 23:22:26 2005 Subject: [Biojava-l] (no subject) Message-ID: Hi Christoph, Not sure I understand the question. Presumably any programer developing with BioJava would be able to use the interface to allow STRAP compatable sevrves to be used direct from their biojava program? Could you possibly provide a simple example of how it might work that we could put on the "Biojava in Anger" page. I often find that providing such and example greatly increases the uptake of new (and old) features in biojava. - Mark "Dr. Christoph Gille" Sent by: biojava-l-bounces@portal.open-bio.org 04/08/2005 10:37 PM To: biojava-l@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] (no subject) Hi, I am currently working on an interface biojava <==> STRAP (http://www.charite.de/bioinf/strap/, http://www.charite.de/bioinf/strap/doc/index.pdf). First I create a GappedSequence object from a StrapProtein object. I include all STRAP anntotations and STRAP features. The features are subsets of the sequences with annotations like notes, URLs, TeXshade commands, Pymol commands, Rasmol commands. Second I create a converter the other way round. It makes a StrapProtein from a biojava Sequence with all its annotations and features. Does anybody has ideas, what tool could cooperate with STRAP using this interface ? The STRAP plugin technology alows even larger JAVA programs to be plugged in, simply by copying the jar-library into a special directory. Currently a few groups are creating plugins for STRAP. I hope that people will benefit from the biojava interface. Christoph _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From mark.schreiber at novartis.com Thu Apr 14 03:05:18 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Thu Apr 14 02:58:58 2005 Subject: [Biojava-l] Can I modify a SeqSimilaritySearchSubHit? Message-ID: Hello - They are immutable because the Annotation object (and others) throw ChangeVetoExceptions when altered. This is probably a good thing. The decision to not include the query ID is pretty contraversial and ran along the lines of ... you knew what it was when you did the search you should know it now. Probably not the best reason. I'm pretty sure the query is emmitted by the BLASTLikeSAXParser it's just not listened for by the subsequent SeqSimilarityAdapter or BlastLikeSearchBuilder (see http://www.biojava.org/docs/bj_in_anger/BlastParser.htm for a description of the Blast parsing pipeline). To check if the Query is emitted, and what type of event it generates, you could use the example here (http://www.biojava.org/docs/bj_in_anger/blastecho.htm). If the event is emitted then a simple modification to SeqSimilarityAdapter of BlastLikeSearchBuilder should allow it to be included in the Annotation object of the SeqSimilaritySearchHit. - Mark Douglas Hoen Sent by: biojava-l-bounces@portal.open-bio.org 04/13/2005 01:34 AM To: biojava-l@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] Can I modify a SeqSimilaritySearchSubHit? Hi, I want to modify the annotation of a SeqSimilaritySearchSubHit. (Specifically, I want to add the query ID, since I can't find a way to get at it from a SeqSimilaritySearchSubHit.) However, SeqSimilaritySearchSubHit appears to be immutable. Is there any way I can make this class mutable, or do I have to write my own class (e.g. a wrapper)? Thanks, Doug _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From cs at is-analyse.de Thu Apr 14 04:40:42 2005 From: cs at is-analyse.de (Christian Storm) Date: Thu Apr 14 04:34:47 2005 Subject: [Biojava-l] Re: (no subject) In-Reply-To: <200504140702.j3E70wfa013856@portal.open-bio.org> Message-ID: <200504140840.j3E8eftk023796@post.webmailer.de> Hi Christoph, before you put in a lot of work, you might want to check the licenses. I think STRAP comes under GPL, and Biojava comes under lGPL. This might cause some problems, depending on what you plan to do. Christian > Message: 2 > Date: Fri, 8 Apr 2005 16:37:51 +0200 (CEST) > From: "Dr. Christoph Gille" > Subject: [Biojava-l] (no subject) > To: biojava-l@biojava.org > Message-ID: > <50314.192.168.220.204.1112971071.squirrel@webmail.charite.de> > Content-Type: text/plain;charset=iso-8859-1 > > Hi, > > I am currently working on an interface biojava <==> STRAP > (http://www.charite.de/bioinf/strap/, > http://www.charite.de/bioinf/strap/doc/index.pdf). > > First I create a GappedSequence object from a StrapProtein object. > I include all STRAP anntotations and STRAP features. > The features are subsets of the sequences with annotations like > notes, URLs, TeXshade commands, Pymol commands, Rasmol commands. > > Second I create a converter the other way round. > It makes a StrapProtein from a biojava Sequence with all its annotations > and features. > > Does anybody has ideas, what tool could > cooperate with STRAP using this interface ? > > The STRAP plugin technology alows even larger JAVA > programs to be plugged in, simply by copying the > jar-library into a special directory. > Currently a few groups are creating plugins for STRAP. > I hope that people will benefit from the biojava interface. > > Christoph From mmatilai at hytti.uku.fi Thu Apr 14 06:58:20 2005 From: mmatilai at hytti.uku.fi (mmatilai@hytti.uku.fi) Date: Thu Apr 14 06:52:18 2005 Subject: [Biojava-l] Location output Message-ID: <1113476300.425e4ccc1898e@maili.uku.fi> Hi! I have added features to a sequence file using StrandedFeature.Template as a template and RangeLocation class to define the locations. The sequence is saved in Genbank format after the addition of all features. I want to output the features later to a text file and this is how they look (type and location shown): ER9_rc [15276,15296] I would like to get rid of the [] brackets. I modified the toString method of the RangeLocation class and removed these brackets but after this I get an error message as the program tries to write the features added to the genbank file using GenbankFormat class method writeSequence. Does anyone have an explanation to this? Or a simple solution how I can simplify my text file output to leave out the brackets? Thanx, Merja Matilainen From td2 at sanger.ac.uk Thu Apr 14 08:16:43 2005 From: td2 at sanger.ac.uk (Thomas Down) Date: Thu Apr 14 08:10:39 2005 Subject: [Biojava-l] Location output In-Reply-To: <1113476300.425e4ccc1898e@maili.uku.fi> References: <1113476300.425e4ccc1898e@maili.uku.fi> Message-ID: On 14 Apr 2005, at 11:58, mmatilai@hytti.uku.fi wrote: > Hi! > > I have added features to a sequence file using > StrandedFeature.Template as a > template and RangeLocation class to define the locations. The sequence > is saved > in Genbank format after the addition of all features. I want to output > the > features later to a text file and this is how they look (type and > location shown): > > ER9_rc [15276,15296] > > I would like to get rid of the [] brackets. > > I modified the toString method of the RangeLocation class and removed > these > brackets but after this I get an error message as the program tries to > write the > features added to the genbank file using GenbankFormat class method > writeSequence. Does anyone have an explanation to this? Or a simple > solution how > I can simplify my text file output to leave out the brackets? Hi, In general, it's not a good idea to rely on "toString" methods returning any particular format -- they're really for debugging purposes, rather than day to day uses. The best solution here is to use code like: Feature f = ...; System.out.println( f.getType() + "\t" + f.getLocation().getMin() + "," + f.getLocation().getMax() ); This approach means you can have exactly the output format you want, and insulates you from any future changes to toString methods. I am, however, worried about why GenbankFormat is giving you an error -- it shouldn't be relying on toString methods at all. Could you send me a copy of the error stack trace? Thanks, Thomas. From mark.schreiber at novartis.com Mon Apr 18 05:08:23 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Mon Apr 18 05:02:15 2005 Subject: [Biojava-l] Re: [BioSQL-l] release preparation Message-ID: We tracked down the error to the fact that the Hilmar Oracle version (no assertion is made about the complexity) uses CLOBs to store sequence while the Len Oracle (no assertion about simplicity etc) version uses LONGs to store sequence. The biojava support code seems to assume LONGs and strangely until very recently the JDBC oracle dirver seems to let you write LONGs to CLOBs although the data that comes out again is completely munged. It would be possible to modify the biojava adapters to check for LONG or CLOB and behaive appropriately but this would cause lots of maintenance problems later. Given this situtation, unless some one complains very loudly, the biojava oracle adapters will be changed to assume CLOBs. Note: This means if you are using biojava and oracle and biosql now then it will break unless you adopts Hilmar's version. It will not cause any changes to biojava users of MySQL etc. - Mark Len Trigg 04/18/2005 04:58 PM To: Mark Schreiber/GP/Novartis@PH cc: Hilmar Lapp , Biosql Subject: Re: [BioSQL-l] release preparation Mark Schreiber wrote: > now, my bad! Agreed that from a SQL query perspective the schemas are the > same, one just has more complexity (if I can call it that) under the hood. Indeed, the complexity is more to do with the complexity of installing and understanding what's going on in all those files :-) (particularly if you are not an oracle expert and have only been looking at the BioSQL schemas for the other supported databases), and that's why I did the simple version. That's partly confirmed by the fact that the bjia description of how to use the original schema is about 8KB, while the description for the simple schema is about 1KB. I'm all for dumping the simple one if the barrier for entry for the original schema is lowered (maybe it already has been). > I would prefer to keep instructions for the less complex version up for > the time being as we are having difficulties getting biojava to work > seamlessly with the more complex version. This is almost certainly a > failing of biojava for which the oracle support seems to have been > compiled against the 'simple' schema not the 'complex schema'. It certainly was only tested against the simple version, because that's the only schema I had working when I wrote the Oracle support. I am a little surprised that you are having major difficulties though, since the original package has a compatibility layer that (supposedly) presents the same schema as the simple version. > I expect we will soon have biojava supporting your version and we can drop > the 'simple' schema. After all, there is not much point using oracle if > you don't make use of the features. In my case, it was a matter of using Oracle because that was what was already installed :-) Cheers, Len. From hollandr at gis.a-star.edu.sg Mon Apr 18 05:08:41 2005 From: hollandr at gis.a-star.edu.sg (Richard HOLLAND) Date: Mon Apr 18 05:04:47 2005 Subject: [Biojava-l] RE: [BioSQL-l] release preparation Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D560195100A@BIONIC.biopolis.one-north.com> I looked into this in a bit more detail earlier today and found that, since some version of Oracle around the 9i point in time, the official Oracle JDBC driver API for accessing LOBs in changed. This means that whereas before the same code could be used in BioJava to access both Hilmar's and Len's versions of the database, since the 9i drivers this has no longer been possible, and BioJava only works with Len's version. The problem is due to the way in which Len's schema uses LONG values for biosequence.seq, but Hilmar's uses CLOBs. (The nitty gritty - before 9i, Oracle JDBC allowed you to access both LONG and CLOB columns using getString()/setString() methods to manipulate them. Now, these methods only work with LONG columns, and you have to do fancy tricks to get anything useful into/out of CLOBs). After discussing this with Mark earlier this afternoon, I am planning on changing BioJava to use the new Oracle CLOB API, at which point it will no longer work with schemas set up using Len's version. No change to BioSQL is required. This, from a BioJava point of view, would make the simple schema redundant. I am not sure if there are people in the other Bio* projects who use the simple schema though so we probably can't just drop it. Are there any objections? I have crossposted this to the BioJava list to make sure everyone who might be affected gets a say. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. --------------------------------------------- > -----Original Message----- > From: biosql-l-bounces@portal.open-bio.org > [mailto:biosql-l-bounces@portal.open-bio.org] On Behalf Of Len Trigg > Sent: Monday, April 18, 2005 4:58 PM > To: mark.schreiber@novartis.com > Cc: Hilmar Lapp; Biosql > Subject: Re: [BioSQL-l] release preparation > > > > Mark Schreiber wrote: > > now, my bad! Agreed that from a SQL query perspective the > schemas are the > > same, one just has more complexity (if I can call it that) > under the hood. > > Indeed, the complexity is more to do with the complexity of installing > and understanding what's going on in all those files :-) (particularly > if you are not an oracle expert and have only been looking at the > BioSQL schemas for the other supported databases), and that's why I > did the simple version. That's partly confirmed by the fact that the > bjia description of how to use the original schema is about 8KB, while > the description for the simple schema is about 1KB. I'm all for > dumping the simple one if the barrier for entry for the original > schema is lowered (maybe it already has been). > > > > I would prefer to keep instructions for the less complex > version up for > > the time being as we are having difficulties getting > biojava to work > > seamlessly with the more complex version. This is almost > certainly a > > failing of biojava for which the oracle support seems to have been > > compiled against the 'simple' schema not the 'complex schema'. > > It certainly was only tested against the simple version, because > that's the only schema I had working when I wrote the Oracle support. > I am a little surprised that you are having major difficulties though, > since the original package has a compatibility layer that (supposedly) > presents the same schema as the simple version. > > > > I expect we will soon have biojava supporting your version > and we can drop > > the 'simple' schema. After all, there is not much point > using oracle if > > you don't make use of the features. > > In my case, it was a matter of using Oracle because that was what was > already installed :-) > > > Cheers, > Len. > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > From hlapp at gmx.net Mon Apr 18 12:56:20 2005 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon Apr 18 12:50:02 2005 Subject: [Biojava-l] Re: [BioSQL-l] release preparation In-Reply-To: <6D9E9B9DF347EF4385F6271C64FB8D560195100A@BIONIC.biopolis.one-north.com> Message-ID: CLOB is IMHO actually easier to handle. Also, LONG is really odd to deal with in SQL whereas the Oracle server will nicely on-the-fly convert strings to CLOB and vice versa so long as they are shorter than 4000 chars. Some of the type-generic functions that come with Oracle will not accept LONG but do accept CLOB. Just as another anecdotal piece, the built-in BLAST searcher available in Oracle 10g expects a cursor returning CLOBs, not LONGs. With the java.sql.Clob interface to get at the full value as a string is as simple as Clob clob = resultSet.getClob(); String clobValue = clob.getSubString(0, clob.length()); Inserting a new value in reality is a two-step process: PreparedStatement pst = conn.prepareStatement("INSERT INTO Biosequence (Bioentry_Id, Seq) VALUES (?, EMPTY_CLOB())"); pst.executeUpdate(idValue); pst = conn.prepareStatement("SELECT Seq FROM Biosequence WHERE Bioentry_Id = ? FOR UPDATE", ResultSet.TYPE_FORWARD_ONLY, ResultSet.CONCUR_UPDATABLE); ResultSet rs = pst.executeQuery(idValue); Clob clob = rs.getClob(1); clob.setString(0, theSeq); // not sure this is necessary rs.updateClob(1, clob); rs.close(); // don't forget to release lock conn.commit(); I vaguely remember that Len or somebody else from the Biojava crowd had this all figured out? -hilmar On Monday, April 18, 2005, at 02:08 AM, Richard HOLLAND wrote: > I looked into this in a bit more detail earlier today and found that, > since some version of Oracle around the 9i point in time, the official > Oracle JDBC driver API for accessing LOBs in changed. This means that > whereas before the same code could be used in BioJava to access both > Hilmar's and Len's versions of the database, since the 9i drivers this > has no longer been possible, and BioJava only works with Len's version. > The problem is due to the way in which Len's schema uses LONG values > for > biosequence.seq, but Hilmar's uses CLOBs. > > (The nitty gritty - before 9i, Oracle JDBC allowed you to access both > LONG and CLOB columns using getString()/setString() methods to > manipulate them. Now, these methods only work with LONG columns, and > you > have to do fancy tricks to get anything useful into/out of CLOBs). > > After discussing this with Mark earlier this afternoon, I am planning > on > changing BioJava to use the new Oracle CLOB API, at which point it will > no longer work with schemas set up using Len's version. No change to > BioSQL is required. This, from a BioJava point of view, would make the > simple schema redundant. I am not sure if there are people in the other > Bio* projects who use the simple schema though so we probably can't > just > drop it. > > Are there any objections? I have crossposted this to the BioJava list > to > make sure everyone who might be affected gets a say. > > cheers, > Richard > > Richard Holland > Bioinformatics Specialist > GIS extension 8199 > --------------------------------------------- > This email is confidential and may be privileged. If you are not the > intended recipient, please delete it and notify us immediately. Please > do not copy or use it for any purpose, or disclose its content to any > other person. Thank you. > --------------------------------------------- > > >> -----Original Message----- >> From: biosql-l-bounces@portal.open-bio.org >> [mailto:biosql-l-bounces@portal.open-bio.org] On Behalf Of Len Trigg >> Sent: Monday, April 18, 2005 4:58 PM >> To: mark.schreiber@novartis.com >> Cc: Hilmar Lapp; Biosql >> Subject: Re: [BioSQL-l] release preparation >> >> >> >> Mark Schreiber wrote: >>> now, my bad! Agreed that from a SQL query perspective the >> schemas are the >>> same, one just has more complexity (if I can call it that) >> under the hood. >> >> Indeed, the complexity is more to do with the complexity of installing >> and understanding what's going on in all those files :-) (particularly >> if you are not an oracle expert and have only been looking at the >> BioSQL schemas for the other supported databases), and that's why I >> did the simple version. That's partly confirmed by the fact that the >> bjia description of how to use the original schema is about 8KB, while >> the description for the simple schema is about 1KB. I'm all for >> dumping the simple one if the barrier for entry for the original >> schema is lowered (maybe it already has been). >> >> >>> I would prefer to keep instructions for the less complex >> version up for >>> the time being as we are having difficulties getting >> biojava to work >>> seamlessly with the more complex version. This is almost >> certainly a >>> failing of biojava for which the oracle support seems to have been >>> compiled against the 'simple' schema not the 'complex schema'. >> >> It certainly was only tested against the simple version, because >> that's the only schema I had working when I wrote the Oracle support. >> I am a little surprised that you are having major difficulties though, >> since the original package has a compatibility layer that (supposedly) >> presents the same schema as the simple version. >> >> >>> I expect we will soon have biojava supporting your version >> and we can drop >>> the 'simple' schema. After all, there is not much point >> using oracle if >>> you don't make use of the features. >> >> In my case, it was a matter of using Oracle because that was what was >> already installed :-) >> >> >> Cheers, >> Len. >> >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l@open-bio.org >> http://open-bio.org/mailman/listinfo/biosql-l >> > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From len at reeltwo.com Mon Apr 18 17:50:54 2005 From: len at reeltwo.com (Len Trigg) Date: Mon Apr 18 17:44:40 2005 Subject: [Biojava-l] Re: [BioSQL-l] release preparation In-Reply-To: References: Message-ID: Mark Schreiber wrote: > store sequence. The biojava support code seems to assume LONGs and > strangely until very recently the JDBC oracle dirver seems to let you > write LONGs to CLOBs although the data that comes out again is completely > munged. > > It would be possible to modify the biojava adapters to check for LONG or > CLOB and behaive appropriately but this would cause lots of maintenance > problems later. OK, I see. That sequence insertion code isn't in the database-specific helper classes, but sounds like it'll have to move there (since some of the databases won't support CLOBs). You could have the abstract helper look at the tables to see which version to use, and that way you'd have backward compatibility with the existing databases too. Cheers, Len. From hollandr at gis.a-star.edu.sg Mon Apr 18 21:45:33 2005 From: hollandr at gis.a-star.edu.sg (Richard HOLLAND) Date: Mon Apr 18 21:41:00 2005 Subject: [Biojava-l] RE: [BioSQL-l] release preparation Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D5601951039@BIONIC.biopolis.one-north.com> Don't worry, I do know how to do it, it's just that in the existing BioJava-live code it hasn't been done, and I'll need to be careful to add the usual checks to see if we're using Oracle or not before choosing the appropriate SQL to update biosequence with. CLOBs under 4000 chars are certainly easier, but over 4000 you have to be careful, and there is a bug which prevents clob.getSubstring() working for any position greater than can be described in 16 bits (although I know I experienced this one before, I can't find a reference to it now....). You then have to use the clob's Stream accessors instead, but it's not a problem really. Yes, I know 16-bits (65k bases or so) is huge, but in our current BioSQL all our sequences are around the 10000 base length so the 4000-char limited accessor methods are not an option. Len's suggestion of having table helpers in BioJava to check which version to use and therefore maintain backwards compatibility is a good one. It's slightly more work, but not too much to warrant a major panic attack. I'll let you know when biojava-live has been updated. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. --------------------------------------------- > -----Original Message----- > From: Hilmar Lapp [mailto:hlapp@gmx.net] > Sent: Tuesday, April 19, 2005 12:56 AM > To: Richard HOLLAND > Cc: Len Trigg; mark.schreiber@novartis.com; Biosql; biojava-list List > Subject: Re: [BioSQL-l] release preparation > > > CLOB is IMHO actually easier to handle. Also, LONG is really odd to > deal with in SQL whereas the Oracle server will nicely on-the-fly > convert strings to CLOB and vice versa so long as they are > shorter than > 4000 chars. Some of the type-generic functions that come with Oracle > will not accept LONG but do accept CLOB. Just as another anecdotal > piece, the built-in BLAST searcher available in Oracle 10g expects a > cursor returning CLOBs, not LONGs. > > With the java.sql.Clob interface to get at the full value as a string > is as simple as > > Clob clob = resultSet.getClob(); > String clobValue = clob.getSubString(0, clob.length()); > > Inserting a new value in reality is a two-step process: > > PreparedStatement pst = conn.prepareStatement("INSERT > INTO Biosequence > (Bioentry_Id, Seq) VALUES (?, EMPTY_CLOB())"); > pst.executeUpdate(idValue); > pst = conn.prepareStatement("SELECT Seq FROM Biosequence WHERE > Bioentry_Id = ? FOR UPDATE", ResultSet.TYPE_FORWARD_ONLY, > ResultSet.CONCUR_UPDATABLE); > > ResultSet rs = pst.executeQuery(idValue); > Clob clob = rs.getClob(1); > clob.setString(0, theSeq); > // not sure this is necessary > rs.updateClob(1, clob); > rs.close(); > // don't forget to release lock > conn.commit(); > > I vaguely remember that Len or somebody else from the Biojava > crowd had > this all figured out? > > -hilmar > > On Monday, April 18, 2005, at 02:08 AM, Richard HOLLAND wrote: > > > I looked into this in a bit more detail earlier today and > found that, > > since some version of Oracle around the 9i point in time, > the official > > Oracle JDBC driver API for accessing LOBs in changed. This > means that > > whereas before the same code could be used in BioJava to access both > > Hilmar's and Len's versions of the database, since the 9i > drivers this > > has no longer been possible, and BioJava only works with > Len's version. > > The problem is due to the way in which Len's schema uses > LONG values > > for > > biosequence.seq, but Hilmar's uses CLOBs. > > > > (The nitty gritty - before 9i, Oracle JDBC allowed you to > access both > > LONG and CLOB columns using getString()/setString() methods to > > manipulate them. Now, these methods only work with LONG > columns, and > > you > > have to do fancy tricks to get anything useful into/out of CLOBs). > > > > After discussing this with Mark earlier this afternoon, I > am planning > > on > > changing BioJava to use the new Oracle CLOB API, at which > point it will > > no longer work with schemas set up using Len's version. No change to > > BioSQL is required. This, from a BioJava point of view, > would make the > > simple schema redundant. I am not sure if there are people > in the other > > Bio* projects who use the simple schema though so we probably can't > > just > > drop it. > > > > Are there any objections? I have crossposted this to the > BioJava list > > to > > make sure everyone who might be affected gets a say. > > > > cheers, > > Richard > > > > Richard Holland > > Bioinformatics Specialist > > GIS extension 8199 > > --------------------------------------------- > > This email is confidential and may be privileged. If you are not the > > intended recipient, please delete it and notify us > immediately. Please > > do not copy or use it for any purpose, or disclose its > content to any > > other person. Thank you. > > --------------------------------------------- > > > > > >> -----Original Message----- > >> From: biosql-l-bounces@portal.open-bio.org > >> [mailto:biosql-l-bounces@portal.open-bio.org] On Behalf Of > Len Trigg > >> Sent: Monday, April 18, 2005 4:58 PM > >> To: mark.schreiber@novartis.com > >> Cc: Hilmar Lapp; Biosql > >> Subject: Re: [BioSQL-l] release preparation > >> > >> > >> > >> Mark Schreiber wrote: > >>> now, my bad! Agreed that from a SQL query perspective the > >> schemas are the > >>> same, one just has more complexity (if I can call it that) > >> under the hood. > >> > >> Indeed, the complexity is more to do with the complexity > of installing > >> and understanding what's going on in all those files :-) > (particularly > >> if you are not an oracle expert and have only been looking at the > >> BioSQL schemas for the other supported databases), and that's why I > >> did the simple version. That's partly confirmed by the > fact that the > >> bjia description of how to use the original schema is > about 8KB, while > >> the description for the simple schema is about 1KB. I'm all for > >> dumping the simple one if the barrier for entry for the original > >> schema is lowered (maybe it already has been). > >> > >> > >>> I would prefer to keep instructions for the less complex > >> version up for > >>> the time being as we are having difficulties getting > >> biojava to work > >>> seamlessly with the more complex version. This is almost > >> certainly a > >>> failing of biojava for which the oracle support seems to have been > >>> compiled against the 'simple' schema not the 'complex schema'. > >> > >> It certainly was only tested against the simple version, because > >> that's the only schema I had working when I wrote the > Oracle support. > >> I am a little surprised that you are having major > difficulties though, > >> since the original package has a compatibility layer that > (supposedly) > >> presents the same schema as the simple version. > >> > >> > >>> I expect we will soon have biojava supporting your version > >> and we can drop > >>> the 'simple' schema. After all, there is not much point > >> using oracle if > >>> you don't make use of the features. > >> > >> In my case, it was a matter of using Oracle because that > was what was > >> already installed :-) > >> > >> > >> Cheers, > >> Len. > >> > >> _______________________________________________ > >> BioSQL-l mailing list > >> BioSQL-l@open-bio.org > >> http://open-bio.org/mailman/listinfo/biosql-l > >> > > > > > -- > ------------------------------------------------------------- > Hilmar Lapp email: lapp at gnf.org > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 > ------------------------------------------------------------- > > > From mark.schreiber at novartis.com Mon Apr 18 22:55:17 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Mon Apr 18 22:48:42 2005 Subject: [Biojava-l] Re: [Biojava-dev] XML format Message-ID: You can use NCBI's eutils to get GenBank in XML format. BioJava has a GenBankXML parser. Robin XML Sent by: biojava-dev-bounces@portal.open-bio.org 04/16/2005 07:23 PM To: biojava-l@biojava.org cc: biojava-dev@biojava.org, (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] XML format Dear All, Please help! I am a beginner in bioJava. Is it possible to retrieve data from GenBank or SwissProt by access ID, and then transfer to XML format? Thank you!!!!!! Best regards, Robin > __________________________________ Do you Yahoo!? Yahoo! Mail - now with 250MB free storage. Learn more. http://info.mail.yahoo.com/mail_250 _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From Russell.Smithies at agresearch.co.nz Mon Apr 18 22:58:25 2005 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon Apr 18 22:51:45 2005 Subject: [Biojava-l] RE: [Biojava-dev] XML format Message-ID: Use eutils Here's an example: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&i d=NM_003234&report=docsum&rettype=xml Russell -----Original Message----- From: biojava-dev-bounces@portal.open-bio.org [mailto:biojava-dev-bounces@portal.open-bio.org] On Behalf Of Robin XML Sent: Saturday, 16 April 2005 11:23 p.m. To: biojava-l@biojava.org Cc: biojava-dev@biojava.org Subject: [Biojava-dev] XML format Dear All, Please help! I am a beginner in bioJava. Is it possible to retrieve data from GenBank or SwissProt by access ID, and then transfer to XML format? Thank you!!!!!! Best regards, Robin > __________________________________ Do you Yahoo!? Yahoo! Mail - now with 250MB free storage. Learn more. http://info.mail.yahoo.com/mail_250 _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev ======================================================================= 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 Russell.Smithies at agresearch.co.nz Mon Apr 18 23:00:34 2005 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon Apr 18 22:53:50 2005 Subject: [Biojava-l] RE: [Biojava-dev] XML format Message-ID: Sorry, here's the XML version: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&i d=NM_003234&rettype=gb&retmode=text -----Original Message----- From: biojava-dev-bounces@portal.open-bio.org [mailto:biojava-dev-bounces@portal.open-bio.org] On Behalf Of Robin XML Sent: Saturday, 16 April 2005 11:23 p.m. To: biojava-l@biojava.org Cc: biojava-dev@biojava.org Subject: [Biojava-dev] XML format Dear All, Please help! I am a beginner in bioJava. Is it possible to retrieve data from GenBank or SwissProt by access ID, and then transfer to XML format? Thank you!!!!!! Best regards, Robin > __________________________________ Do you Yahoo!? Yahoo! Mail - now with 250MB free storage. Learn more. http://info.mail.yahoo.com/mail_250 _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev ======================================================================= 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 dlondon at ebi.ac.uk Tue Apr 19 05:16:30 2005 From: dlondon at ebi.ac.uk (Darin London) Date: Tue Apr 19 07:05:11 2005 Subject: [Biojava-l] Re: BOSC 2005 In-Reply-To: <20050120175859.GA7254@parrot.ebi.ac.uk> References: <20050120175859.GA7254@parrot.ebi.ac.uk> Message-ID: <20050419091628.GN17377@parrot.ebi.ac.uk> {Please pass the word!} SECOND CALL FOR SPEAKERS The 6th annual Bioinformatics Open Source Conference (BOSC'2005) is organized by the not-for-profit Open Bioinformatics Foundation. The meeting will take place June 23-24, 2005 in Detroit, Michigan, USA, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 13th International Conference on Intelligent Systems for Molecular Biology. see http://www.iscb.org/ismb2005 for more information. Because of the power of many Open Source bioinformatics packages in use by the Research Community today, it is not too presumptuous to say that the work of the Open Source Bioinformatics Community represents the cutting edge of Bioinformatics in general. This has been repeatedly demonstrated by the quality of presentations at previous BOSC conferences. This year, at BOSC 2005, we want to continue this tradition of excellence, while presenting this message to a wider part of the Research Community. Please, pass this message on to anyone you know that is interested in Bioinformatics software. BOSC PROGRAM & CONTACT INFO * Web: http://www.open-bio.org/bosc2005/ * Online Registration: https://www.cteusa.com/iscb4/ * Email: bosc@open-bio.org FEES * Corporate : $195 ($245 after May 16th) * Academic : $170 ($220 after May 16th) * Student : $145 ($195 after May 16th) SPEAKERS & ABSTRACTS WANTED The program committee is currently seeking abstracts for talks at BOSC 2005. BOSC is a great opportunity for you to tell the community about your use, development, or philosophy of open source software development in bioinformatics. The committee will select several submitted abstracts for 25-minute talks and others for shorter "lightning" talks. Accepted abstracts will be published on the BOSC web site. If you are interested in speaking at BOSC 2005, please send us before April 26, 2005: * an abstract (no more than a few paragraphs) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. Abstracts will be accepted for submission until April 26, 2005. Abstracts chosen for presentation will be announced May 12, 2005 (before the ISMB Early Registration Deadline). LIGHTNING-TALK SPEAKERS WANTED! The program committee is currently seeking speakers for the lightning talks at BOSC 2005. Lightning talks are quick - only five minutes long - and a great opportunity for you to give people a quick summary of your open source project, code, idea, or vision of the future. If you are interested in giving a lightning talk at BOSC 2005, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. We will accept entries on-line until BOSC starts, but space for demos and lightning talks is limited.
Hi, I am trying to show an alignment. I saw there is the class AlignmentRenderer but I couldn't figure out how to use it. Does someone know? Thanks, Tal Blum From meena_hariharan at hotmail.com Mon Apr 25 02:05:36 2005 From: meena_hariharan at hotmail.com (MEENA HARIHARAN) Date: Mon Apr 25 01:58:59 2005 Subject: [Biojava-l] setting up biojava and running a program for translate Message-ID: Hi I installed jdk1.3.1_15 in c:\jdk1.3.1_15. I also downloaded xerces.jar, bytecode-0.91.jar, biojava-1.3.1, and jakarta-regexp.jar in C:\biojava\downloads When I try to run c:\biojava\Translate.java I get the following errors "C:\biojava\Translate.java:1: package org.biojava.bio.symbol does not exist import org.biojava.bio.symbol.*; C:\biojava\Translate.java:2: package org.biojava.bio.seq does not exist import org.biojava.bio.seq.*; etc. I do I handle import in biojava so that I correct these errors. meena From hollandr at gis.a-star.edu.sg Mon Apr 25 02:16:18 2005 From: hollandr at gis.a-star.edu.sg (Richard HOLLAND) Date: Mon Apr 25 02:11:52 2005 Subject: [Biojava-l] setting up biojava and running a program for translate Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D56019512AA@BIONIC.biopolis.one-north.com> Include the downloaded jar files on your classpath when running any programs using them. Otherwise you will get exactly the errors you mention below. Richard Holland Bioinformatics Specialist GIS extension 8199 --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. --------------------------------------------- > -----Original Message----- > From: biojava-l-bounces@portal.open-bio.org > [mailto:biojava-l-bounces@portal.open-bio.org] On Behalf Of > MEENA HARIHARAN > Sent: Monday, April 25, 2005 2:06 PM > To: Biojava-l@biojava.org > Subject: [Biojava-l] setting up biojava and running a program > for translate > > > Hi > > I installed jdk1.3.1_15 in c:\jdk1.3.1_15. > I also downloaded xerces.jar, bytecode-0.91.jar, biojava-1.3.1, and > jakarta-regexp.jar > in C:\biojava\downloads > > When I try to run c:\biojava\Translate.java I get the following errors > "C:\biojava\Translate.java:1: package org.biojava.bio.symbol > does not exist > import org.biojava.bio.symbol.*; > > C:\biojava\Translate.java:2: package org.biojava.bio.seq does > not exist > import org.biojava.bio.seq.*; > > etc. > > I do I handle import in biojava so that I correct these errors. > > meena > > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > From mark.schreiber at novartis.com Mon Apr 25 02:21:45 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Mon Apr 25 02:15:54 2005 Subject: [Biojava-l] setting up biojava and running a program for translate Message-ID: There is help on setting your classpath here: http://www.biojava.org/started.html "Richard HOLLAND" Sent by: biojava-l-bounces@portal.open-bio.org 04/25/2005 02:16 PM To: "MEENA HARIHARAN" , cc: (bcc: Mark Schreiber/GP/Novartis) Subject: RE: [Biojava-l] setting up biojava and running a program for translate Include the downloaded jar files on your classpath when running any programs using them. Otherwise you will get exactly the errors you mention below. Richard Holland Bioinformatics Specialist GIS extension 8199 --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. --------------------------------------------- > -----Original Message----- > From: biojava-l-bounces@portal.open-bio.org > [mailto:biojava-l-bounces@portal.open-bio.org] On Behalf Of > MEENA HARIHARAN > Sent: Monday, April 25, 2005 2:06 PM > To: Biojava-l@biojava.org > Subject: [Biojava-l] setting up biojava and running a program > for translate > > > Hi > > I installed jdk1.3.1_15 in c:\jdk1.3.1_15. > I also downloaded xerces.jar, bytecode-0.91.jar, biojava-1.3.1, and > jakarta-regexp.jar > in C:\biojava\downloads > > When I try to run c:\biojava\Translate.java I get the following errors > "C:\biojava\Translate.java:1: package org.biojava.bio.symbol > does not exist > import org.biojava.bio.symbol.*; > > C:\biojava\Translate.java:2: package org.biojava.bio.seq does > not exist > import org.biojava.bio.seq.*; > > etc. > > I do I handle import in biojava so that I correct these errors. > > meena > > > _______________________________________________ > 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 hollandr at gis.a-star.edu.sg Mon Apr 25 02:41:44 2005 From: hollandr at gis.a-star.edu.sg (Richard HOLLAND) Date: Mon Apr 25 02:36:59 2005 Subject: [Biojava-l] BioJava/BioSQL on Oracle Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D56019512B1@BIONIC.biopolis.one-north.com> I've committed some changes to biojava-live which make BioJava compatible with BioSQL when the latter is running on Oracle 9i or greater and using the official schema as per the biosql-schema CVS. This involved adding an autodetect function to detect whether Clobs were used in biosequence or not, and then creating code to work with Clobs where necessary. Two extensions to OracleDBHelper might be useful in other tasks - stringToClob() and clobToString(). I also made some changes to the Ontology part of the BioJava/BioSQL interface, which was not persisting Triples correctly. It would attempt to reference the triple by its unique ID before actually giving it one, which of course fails. This should now be fixed. cheers, Richard Richard Holland Bioinformatics Specialist Genome Institute of Singapore 60 Biopolis Street, #02-01 Genome, Singapore 138672 Tel: (65) 6478 8000 DID: (65) 6478 8199 Email: hollandr@gis.a-star.edu.sg --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. --------------------------------------------- From hollandr at gis.a-star.edu.sg Wed Apr 27 23:41:42 2005 From: hollandr at gis.a-star.edu.sg (Richard HOLLAND) Date: Wed Apr 27 23:36:22 2005 Subject: [Biojava-l] RE: [BioSQL-l] location in features Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D5601951467@BIONIC.biopolis.one-north.com> Hullo Martina. I must admit I am confused. I have been using BioJava+BioSQL to load Genbank records with features with no trouble, they always come out again with no exceptions raised and none missing. I am using Oracle, but this shouldn't make a difference as the SQL code that looks for features is the same for all database types at present. Can I ask what database type you are using (MySQL, Oracle etc.), and the versions of BioJava and BioSQL you have? I'd also suggest downloading biojava-live from CVS, if you haven't done so already, and trying that to see if someone has already fixed your problem. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. --------------------------------------------- > -----Original Message----- > From: Hilmar Lapp [mailto:hlapp@gnf.org] > Sent: Thursday, April 28, 2005 2:51 AM > To: Martina > Cc: OBDA BioSQL; BioJava; Richard HOLLAND; Mark Schreiber > Subject: Re: [BioSQL-l] location in features > > > Hi Martina, people on the biojava mailing list will probably > be better > able to help you out. Also, Richard and Mark have been working on > getting Biojava interoperate better with the standard biosql schema. > They may know better where your issue is coming from. > > -hilmar > > On Apr 27, 2005, at 8:27 AM, Martina wrote: > > > Hi, > > I can't get rid of this exception: > > org.biojava.bio.BioRuntimeException: BioSQL SeqFeature doesn't have > > any associated location spans. seqfeature_id=148 > > > > Can anybody help me? > > > > put the sequence in: > > > > Sequence seq = DNATools.createDNASequence(sequence, "AF100928"); > > Feature.Template templSeq = new Feature.Template(); > > templSeq.source = "ncbi"; > > templSeq.type = "gen"; > > templSeq.location = Location.empty; > > seq.createFeature(templSeq); > > db.addSequence(seq); > > > > get it out: > > seq = db.getSequence("AF100928"); > > System.out.println(seq.getName() + " contains " + > seq.countFeatures() > > + " features"); > > > > seq.getName() works fine, but the seq doesn't have any > features, but I > > can see them in the db. > > > > What am I missing here? > > > > Martina > > > > _______________________________________________ > > BioSQL-l mailing list > > BioSQL-l@open-bio.org > > http://open-bio.org/mailman/listinfo/biosql-l > > > -- > ------------------------------------------------------------- > Hilmar Lapp email: lapp at gnf.org > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 > ------------------------------------------------------------- > > From boehme at mpiib-berlin.mpg.de Thu Apr 28 05:03:39 2005 From: boehme at mpiib-berlin.mpg.de (Martina) Date: Thu Apr 28 04:56:49 2005 Subject: [Biojava-l] Re: [BioSQL-l] location in features In-Reply-To: <6D9E9B9DF347EF4385F6271C64FB8D5601951467@BIONIC.biopolis.one-north.com> References: <6D9E9B9DF347EF4385F6271C64FB8D5601951467@BIONIC.biopolis.one-north.com> Message-ID: <4270A6EB.1030006@mpiib-berlin.mpg.de> I'm using MySQL, biojava-1.4pre1, biosql,v 1.40 Richard HOLLAND wrote: > Hullo Martina. > > I must admit I am confused. I have been using BioJava+BioSQL to load > Genbank records with features with no trouble, they always come out > again with no exceptions raised and none missing. I am using Oracle, but > this shouldn't make a difference as the SQL code that looks for features > is the same for all database types at present. > > Can I ask what database type you are using (MySQL, Oracle etc.), and the > versions of BioJava and BioSQL you have? > > I'd also suggest downloading biojava-live from CVS, if you haven't done > so already, and trying that to see if someone has already fixed your > problem. > > cheers, > Richard > > Richard Holland > Bioinformatics Specialist > GIS extension 8199 > --------------------------------------------- > This email is confidential and may be privileged. If you are not the > intended recipient, please delete it and notify us immediately. Please > do not copy or use it for any purpose, or disclose its content to any > other person. Thank you. > --------------------------------------------- > > > >>-----Original Message----- >>From: Hilmar Lapp [mailto:hlapp@gnf.org] >>Sent: Thursday, April 28, 2005 2:51 AM >>To: Martina >>Cc: OBDA BioSQL; BioJava; Richard HOLLAND; Mark Schreiber >>Subject: Re: [BioSQL-l] location in features >> >> >>Hi Martina, people on the biojava mailing list will probably >>be better >>able to help you out. Also, Richard and Mark have been working on >>getting Biojava interoperate better with the standard biosql schema. >>They may know better where your issue is coming from. >> >> -hilmar >> >>On Apr 27, 2005, at 8:27 AM, Martina wrote: >> >> >>>Hi, >>>I can't get rid of this exception: >>>org.biojava.bio.BioRuntimeException: BioSQL SeqFeature doesn't have >>>any associated location spans. seqfeature_id=148 >>> >>>Can anybody help me? >>> >>>put the sequence in: >>> >>>Sequence seq = DNATools.createDNASequence(sequence, "AF100928"); >>>Feature.Template templSeq = new Feature.Template(); >>> templSeq.source = "ncbi"; >>> templSeq.type = "gen"; >>> templSeq.location = Location.empty; >>> seq.createFeature(templSeq); >>>db.addSequence(seq); >>> >>>get it out: >>>seq = db.getSequence("AF100928"); >>>System.out.println(seq.getName() + " contains " + >> >>seq.countFeatures() >> >>> + " features"); >>> >>>seq.getName() works fine, but the seq doesn't have any >> >>features, but I >> >>>can see them in the db. >>> >>>What am I missing here? >>> >>>Martina >>> >>>_______________________________________________ >>>BioSQL-l mailing list >>>BioSQL-l@open-bio.org >>>http://open-bio.org/mailman/listinfo/biosql-l >>> >> >>-- >>------------------------------------------------------------- >>Hilmar Lapp email: lapp at gnf.org >>GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 >>------------------------------------------------------------- >> > > From hollandr at gis.a-star.edu.sg Thu Apr 28 05:52:22 2005 From: hollandr at gis.a-star.edu.sg (Richard HOLLAND) Date: Thu Apr 28 05:46:58 2005 Subject: [Biojava-l] RE: [BioSQL-l] location in features Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D56019514BC@BIONIC.biopolis.one-north.com> OK. I ran your code against biojava-live and my Oracle db and got the same errors as you report. On further analysis I found that, as your feature should have no location (Location.empty), if you look in the database it doesn't have any there either, which is correct. However the code that extracts features from BioSQL expects all features to have locations and throws the exception that you are seeing if it can't find at least one per feature. I altered org.biojava.bio.seq.db.biosql.FeaturesSQL so that if it could not find a location for a feature at read-time, it would set the feature object location to Location.empty. I have committed this change to biojava-live, so you will need to use CVS to check out a copy of biojava-live to see if this has solved your problem. For the copy of your code which I have here, it works fine. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. --------------------------------------------- > -----Original Message----- > From: Martina [mailto:boehme@mpiib-berlin.mpg.de] > Sent: Thursday, April 28, 2005 5:04 PM > To: Richard HOLLAND > Cc: BioJava; Mark Schreiber > Subject: Re: [BioSQL-l] location in features > > > I'm using MySQL, biojava-1.4pre1, biosql,v 1.40 > > Richard HOLLAND wrote: > > > Hullo Martina. > > > > I must admit I am confused. I have been using BioJava+BioSQL to load > > Genbank records with features with no trouble, they always come out > > again with no exceptions raised and none missing. I am > using Oracle, but > > this shouldn't make a difference as the SQL code that looks > for features > > is the same for all database types at present. > > > > Can I ask what database type you are using (MySQL, Oracle > etc.), and the > > versions of BioJava and BioSQL you have? > > > > I'd also suggest downloading biojava-live from CVS, if you > haven't done > > so already, and trying that to see if someone has already fixed your > > problem. > > > > cheers, > > Richard > > > > Richard Holland > > Bioinformatics Specialist > > GIS extension 8199 > > --------------------------------------------- > > This email is confidential and may be privileged. If you are not the > > intended recipient, please delete it and notify us > immediately. Please > > do not copy or use it for any purpose, or disclose its > content to any > > other person. Thank you. > > --------------------------------------------- > > > > > > > >>-----Original Message----- > >>From: Hilmar Lapp [mailto:hlapp@gnf.org] > >>Sent: Thursday, April 28, 2005 2:51 AM > >>To: Martina > >>Cc: OBDA BioSQL; BioJava; Richard HOLLAND; Mark Schreiber > >>Subject: Re: [BioSQL-l] location in features > >> > >> > >>Hi Martina, people on the biojava mailing list will probably > >>be better > >>able to help you out. Also, Richard and Mark have been working on > >>getting Biojava interoperate better with the standard > biosql schema. > >>They may know better where your issue is coming from. > >> > >> -hilmar > >> > >>On Apr 27, 2005, at 8:27 AM, Martina wrote: > >> > >> > >>>Hi, > >>>I can't get rid of this exception: > >>>org.biojava.bio.BioRuntimeException: BioSQL SeqFeature > doesn't have > >>>any associated location spans. seqfeature_id=148 > >>> > >>>Can anybody help me? > >>> > >>>put the sequence in: > >>> > >>>Sequence seq = DNATools.createDNASequence(sequence, "AF100928"); > >>>Feature.Template templSeq = new Feature.Template(); > >>> templSeq.source = "ncbi"; > >>> templSeq.type = "gen"; > >>> templSeq.location = Location.empty; > >>> seq.createFeature(templSeq); > >>>db.addSequence(seq); > >>> > >>>get it out: > >>>seq = db.getSequence("AF100928"); > >>>System.out.println(seq.getName() + " contains " + > >> > >>seq.countFeatures() > >> > >>> + " features"); > >>> > >>>seq.getName() works fine, but the seq doesn't have any > >> > >>features, but I > >> > >>>can see them in the db. > >>> > >>>What am I missing here? > >>> > >>>Martina > >>> > >>>_______________________________________________ > >>>BioSQL-l mailing list > >>>BioSQL-l@open-bio.org > >>>http://open-bio.org/mailman/listinfo/biosql-l > >>> > >> > >>-- > >>------------------------------------------------------------- > >>Hilmar Lapp email: lapp at gnf.org > >>GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 > >>------------------------------------------------------------- > >> > > > > >