From aldaihani at hotmail.co.uk Wed Feb 2 20:53:22 2005 From: aldaihani at hotmail.co.uk (badr al-daihani) Date: Wed Feb 2 20:51:16 2005 Subject: [Biojava-dev] insufficient memory Message-ID: hi folks I use BlastParser to parse a big file (hundreds of mega) but I get insufficient memory error any idea to overcome this problem. best regards import java.io.*; import java.util.*; import org.biojava.bio.program.sax.*; import org.biojava.bio.program.ssbind.*; import org.biojava.bio.search.*; import org.biojava.bio.seq.db.*; import org.xml.sax.*; import org.biojava.bio.*; public class BlastParser { /** * args[0] is assumed to be the name of a Blast output file */ public static void main(String[] args) { try { //get the Blast input as a Stream InputStream is = new FileInputStream(args[0]); //make a BlastLikeSAXParser BlastLikeSAXParser parser = new BlastLikeSAXParser(); //make the SAX event adapter that will pass events to a Handler. SeqSimilarityAdapter adapter = new SeqSimilarityAdapter(); //set the parsers SAX event adapter parser.setContentHandler(adapter); //The list to hold the SeqSimilaritySearchResults List results = new ArrayList(); //create the SearchContentHandler that will build SeqSimilaritySearchResults //in the results List SearchContentHandler builder = new BlastLikeSearchBuilder(results, new DummySequenceDB("queries"), new DummySequenceDBInstallation()); //register builder with adapter adapter.setSearchContentHandler(builder); //parse the file, after this the result List will be populated with //SeqSimilaritySearchResults parser.parse(new InputSource(is)); //output some blast details for (Iterator i = results.iterator(); i.hasNext(); ) { SeqSimilaritySearchResult result = (SeqSimilaritySearchResult)i.next(); Annotation anno = result.getAnnotation(); for (Iterator j = anno.keys().iterator(); j.hasNext(); ) { Object key = j.next(); Object property = anno.getProperty(key); System.out.println(key+" : "+property); } System.out.println("Hits: "); //list the hits for (Iterator k = result.getHits().iterator(); k.hasNext(); ) { SeqSimilaritySearchHit hit = (SeqSimilaritySearchHit)k.next(); System.out.print("\tmatch: "+hit.getSubjectID()); System.out.println("\te score: "+hit.getEValue()); } System.out.println("\n"); } } catch (SAXException ex) { //XML problem ex.printStackTrace(); }catch (IOException ex) { //IO problem, possibly file not found ex.printStackTrace(); } } } _________________________________________________________________ It's fast, it's easy and it's free. Get MSN Messenger today! http://www.msn.co.uk/messenger From mark.schreiber at group.novartis.com Wed Feb 2 21:00:53 2005 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Wed Feb 2 20:56:45 2005 Subject: [Biojava-dev] insufficient memory Message-ID: Try increasing your stack (heap?) size using the -Xmx option on the command line. Or, take a look at http://www.biojava.org/docs/bj_in_anger/blastecho.htm "badr al-daihani" Sent by: biojava-dev-bounces@portal.open-bio.org 02/03/2005 09:53 AM To: biojava-dev@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] insufficient memory hi folks I use BlastParser to parse a big file (hundreds of mega) but I get insufficient memory error any idea to overcome this problem. best regards import java.io.*; import java.util.*; import org.biojava.bio.program.sax.*; import org.biojava.bio.program.ssbind.*; import org.biojava.bio.search.*; import org.biojava.bio.seq.db.*; import org.xml.sax.*; import org.biojava.bio.*; public class BlastParser { /** * args[0] is assumed to be the name of a Blast output file */ public static void main(String[] args) { try { //get the Blast input as a Stream InputStream is = new FileInputStream(args[0]); //make a BlastLikeSAXParser BlastLikeSAXParser parser = new BlastLikeSAXParser(); //make the SAX event adapter that will pass events to a Handler. SeqSimilarityAdapter adapter = new SeqSimilarityAdapter(); //set the parsers SAX event adapter parser.setContentHandler(adapter); //The list to hold the SeqSimilaritySearchResults List results = new ArrayList(); //create the SearchContentHandler that will build SeqSimilaritySearchResults //in the results List SearchContentHandler builder = new BlastLikeSearchBuilder(results, new DummySequenceDB("queries"), new DummySequenceDBInstallation()); //register builder with adapter adapter.setSearchContentHandler(builder); //parse the file, after this the result List will be populated with //SeqSimilaritySearchResults parser.parse(new InputSource(is)); //output some blast details for (Iterator i = results.iterator(); i.hasNext(); ) { SeqSimilaritySearchResult result = (SeqSimilaritySearchResult)i.next(); Annotation anno = result.getAnnotation(); for (Iterator j = anno.keys().iterator(); j.hasNext(); ) { Object key = j.next(); Object property = anno.getProperty(key); System.out.println(key+" : "+property); } System.out.println("Hits: "); //list the hits for (Iterator k = result.getHits().iterator(); k.hasNext(); ) { SeqSimilaritySearchHit hit = (SeqSimilaritySearchHit)k.next(); System.out.print("\tmatch: "+hit.getSubjectID()); System.out.println("\te score: "+hit.getEValue()); } System.out.println("\n"); } } catch (SAXException ex) { //XML problem ex.printStackTrace(); }catch (IOException ex) { //IO problem, possibly file not found ex.printStackTrace(); } } } _________________________________________________________________ It's fast, it's easy and it's free. Get MSN Messenger today! http://www.msn.co.uk/messenger _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From mark.schreiber at group.novartis.com Thu Feb 3 03:47:22 2005 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Thu Feb 3 03:45:26 2005 Subject: [Biojava-dev] Ontology Triples names and discriptions Message-ID: Hello - In Ontology.Impl, the method: public Triple createTriple(Term subject, Term object, Term predicate, String name, String description) does nothing with the values of name and description. Is this intentional? Would anyone object if I made it so that the name and the description are actually stored in the triple? I know they are not critical but they are nice to have. - Mark From smh1008 at cam.ac.uk Thu Feb 3 03:03:54 2005 From: smh1008 at cam.ac.uk (Dr D.S-M. Huen) Date: Sun Feb 6 15:05:50 2005 Subject: [Biojava-dev] insufficient memory In-Reply-To: References: Message-ID: On Feb 3 2005, badr al-daihani wrote: > > hi folks > > I use BlastParser to parse a big file (hundreds of mega) but I get > insufficient memory error > any idea to overcome this problem. > The way your code is structured, you are accumulating all the results in-memory before printing them at the end which is why you run out of memory eventually. You can also prefilter your results as you go - this will solve your problem for arbitrary input size but it will also require to implement the required listener as your filter. Regards, David Huen From mark.schreiber at group.novartis.com Mon Feb 7 03:53:01 2005 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Mon Feb 7 21:42:40 2005 Subject: [Biojava-dev] ant docbuild failing Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/biojava-dev/attachments/20050207/1ca92909/attachment.htm From dirk.habighorst at epigenomics.com Mon Feb 7 08:23:27 2005 From: dirk.habighorst at epigenomics.com (Dirk Habighorst) Date: Mon Feb 7 21:42:42 2005 Subject: [Biojava-dev] bug in DASComponentFeature.iterator () ??? Message-ID: Hallo, Running the TestDAS demo from the head of biojava-live exits with a java.lang.StackOverflowError. As far as I have tracked it, the problem is: public Iterator features() { // System.err.println("Going to iterate over DASComponentFeature: " + getComponentSequenceName()); return getProjectedFeatures().features(); } getProjectedFeatures() returns a reference to the same DASComponentFeature that called the feature methode in the first place because the ReparentContext.feature() returns the an Iterator of its baseSet which is the DASComponentFeature. dirk -- Dirk Habighorst Software Engineer/ Bioinformatician Epigenomics AG Kleine Praesidentenstr. 1 10178 Berlin, Germany phone:+49-30-24345-372 fax:+49-30-24345-555 http://www.epigenomics.com dirk.habighorst@epigenomics.com From aldaihani at hotmail.co.uk Sun Feb 13 15:00:04 2005 From: aldaihani at hotmail.co.uk (badr al-daihani) Date: Sun Feb 13 14:56:52 2005 Subject: [Biojava-dev] help Message-ID: Hi folks I'm trying to install AcePerl in Windows and I get the following The problem I can not find Ace::RPC module although RPC folder is exist. any help C:\AcePerl-1.87>perl Makefile.pl What do you want to build? 1) Interface to Ace socket server and local databases (pure Perl) 2) The above plus XS optimizations (requires C compiler) 3) The above plus RPC server interface (requires C compiler) Enter your choice: [1] 3 Do you want to install Ace::Browser? [n] Note (probably harmless): No library found for -lc Note (probably harmless): No library found for oldnames.lib Note (probably harmless): No library found for kernel32.lib Note (probably harmless): No library found for user32.lib Note (probably harmless): No library found for gdi32.lib Note (probably harmless): No library found for winspool.lib Note (probably harmless): No library found for comdlg32.lib Note (probably harmless): No library found for advapi32.lib Note (probably harmless): No library found for shell32.lib Note (probably harmless): No library found for ole32.lib Note (probably harmless): No library found for oleaut32.lib Note (probably harmless): No library found for netapi32.lib Note (probably harmless): No library found for uuid.lib Note (probably harmless): No library found for ws2_32.lib Note (probably harmless): No library found for mpr.lib Note (probably harmless): No library found for winmm.lib Note (probably harmless): No library found for version.lib Note (probably harmless): No library found for odbc32.lib Note (probably harmless): No library found for odbccp32.lib Note (probably harmless): No library found for msvcrt.lib Writing Makefile for Ace::Freesubs Note (probably harmless): No library found for -lc Note (probably harmless): No library found for oldnames.lib Note (probably harmless): No library found for kernel32.lib Note (probably harmless): No library found for user32.lib Note (probably harmless): No library found for gdi32.lib Note (probably harmless): No library found for winspool.lib Note (probably harmless): No library found for comdlg32.lib Note (probably harmless): No library found for advapi32.lib Note (probably harmless): No library found for shell32.lib Note (probably harmless): No library found for ole32.lib Note (probably harmless): No library found for oleaut32.lib Note (probably harmless): No library found for netapi32.lib Note (probably harmless): No library found for uuid.lib Note (probably harmless): No library found for ws2_32.lib Note (probably harmless): No library found for mpr.lib Note (probably harmless): No library found for winmm.lib Note (probably harmless): No library found for version.lib Note (probably harmless): No library found for odbc32.lib Note (probably harmless): No library found for odbccp32.lib Note (probably harmless): No library found for msvcrt.lib Using MSWIN32 definitions to build ace library. Writing Makefile for Ace::RPC Writing Makefile for Ace C:\AcePerl-1.87> _________________________________________________________________ It's fast, it's easy and it's free. Get MSN Messenger today! http://www.msn.co.uk/messenger From Robin.Emig at pioneer.com Wed Feb 16 16:17:30 2005 From: Robin.Emig at pioneer.com (Emig, Robin) Date: Thu Feb 17 18:02:07 2005 Subject: [Biojava-dev] MSFAlignment format fixes Message-ID: Attached contains fixes to the MSFAlignment format class 1) Round trip now works (ie you can read what you write) 2) dramatic speed improvements for large alignments can someone check this in for me and let me know that they have done so. thanks Robin <> This communication is for use by the intended recipient and contains information that may be privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html -------------- next part -------------- A non-text attachment was scrubbed... Name: MSFAlignmentFormat.java Type: application/octet-stream Size: 11717 bytes Desc: MSFAlignmentFormat.java Url : http://portal.open-bio.org/pipermail/biojava-dev/attachments/20050216/a5d1bbf5/MSFAlignmentFormat-0001.obj From td2 at sanger.ac.uk Fri Feb 18 04:11:01 2005 From: td2 at sanger.ac.uk (Thomas Down) Date: Fri Feb 18 04:07:44 2005 Subject: [Biojava-dev] MSFAlignment format fixes In-Reply-To: References: Message-ID: <9c966cdb9831cd6a7e3c3c1ec3a4dc23@sanger.ac.uk> On 16 Feb 2005, at 21:17, Emig, Robin wrote: > Attached contains fixes to the MSFAlignment format class > 1) Round trip now works (ie you can read what you write) > 2) dramatic speed improvements for large alignments > > can someone check this in for me and let me know that they have done > so. > thanks > Robin <> Done. Thomas. From smh1008 at cus.cam.ac.uk Sun Feb 20 06:25:20 2005 From: smh1008 at cus.cam.ac.uk (David Huen) Date: Sun Feb 20 06:24:18 2005 Subject: [Biojava-dev] Microarray code Message-ID: Dear colleagues, I am now finalising a body of code that does microarray quantitation with an algorithm of my own and also a program that simulates microarray images for pipeline validation. As the code appears to work both on simulated and real-world data, I would like to publish it and and make a public alpha release soon. I would like it to become part of Biojava but committed under another hierarchy than org.biojava.* (I have my own stupidly snazzy name for it but hey, that's half the fun of doing code :-). It shares almost nothing with the existing codebase. It runs under Java 1.4 and uses JAI and some Jakarta code and the backported Java 5 synchronisation library. Parts of it are also rather hacked to take data from our internal pipeline and will probably need work to make it suitable for other pipelines but as I don't know how others do this kind of thang, I would not even know where to start on that. It will probably not work out of the box for you but could be beaten into shape in a week or two of hacking and scripting. Could I have a decision on your willingness to host this codebase post-publication? Regards, David Huen ----- David Huen, Ph.D. Email: smh1008@cus.cam.ac.uk Dept. of Genetics Fax : +44 1223 333992 University of Cambridge Phone: +44 1223 766748/333982 Cambridge, CB2 3EH U.K. From heuermh at acm.org Mon Feb 21 12:24:01 2005 From: heuermh at acm.org (Michael Heuer) Date: Mon Feb 21 12:18:44 2005 Subject: [Biojava-dev] Microarray code In-Reply-To: Message-ID: Hello David, There is a wiki up at > http://hume.ccgb.umn.edu:8668/space/BiojavaExpr and a page on the MAGE wiki at > https://www.cbil.upenn.edu/magewiki/index.php/MGED%20and%20biojava to discuss gene expression support in biojava. The former would probably be a good place to document what you've built. I have started committing to the subversion repository at > http://www.derkholm.net/svn/repos/biojava-expr/ but to be honest the only thing there so far is a library for source code generation. I would suggest committing to a separate project in the subversion repository then hopefully over time as I start committing more useful bits to biojava-expr we can merge things there. For what it's worth, the open-bio folks are open to creating a subversion repository on the open-bio hardware as part of the new hardware migration you may have recently received a notice about, so whatever gets committed to derkholm.net should be easily migrate-able to open-bio hardware when it is ready. michael On Sun, 20 Feb 2005, David Huen wrote: > Dear colleagues, > I am now finalising a body of code that does microarray quantitation > with an algorithm of my own and also a program that simulates microarray > images for pipeline validation. As the code appears to work both on > simulated and real-world data, I would like to publish it and and make a > public alpha release soon. > > I would like it to become part of Biojava but committed under another > hierarchy than org.biojava.* (I have my own stupidly snazzy name for it > but hey, that's half the fun of doing code :-). It shares almost nothing > with the existing codebase. It runs under Java 1.4 and uses JAI and some > Jakarta code and the backported Java 5 synchronisation library. Parts of > it are also rather hacked to take data from our internal pipeline and will > probably need work to make it suitable for other pipelines but as I don't > know how others do this kind of thang, I would not even know where to > start on that. It will probably not work out of the box for you but could > be beaten into shape in a week or two of hacking and scripting. > > Could I have a decision on your willingness to host this codebase > post-publication? > > Regards, > David Huen > > ----- > > David Huen, Ph.D. Email: smh1008@cus.cam.ac.uk > Dept. of Genetics Fax : +44 1223 333992 > University of Cambridge Phone: +44 1223 766748/333982 > Cambridge, CB2 3EH > U.K. > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > From heuermh at acm.org Thu Feb 24 15:09:13 2005 From: heuermh at acm.org (Michael Heuer) Date: Thu Feb 24 15:57:56 2005 Subject: [Biojava-dev] SourceForge StAX version 1.0 finally released Message-ID: SourceForge StAX version 1.0 finally released In the summer of 2001 the package org.biojava.utils.stax was migrated to a project on SourceForge to allow it to have a life of its own outside of biojava. Although some documentation and features were added, a proper release was never made and the project languished in cvs. Stack API for XML (StAX) is an event-based interface for XML parsing, very similar to Simple API for XML (SAX). However, instead of passing parse events for a whole document to a single ContentHandler, sub-trees can easily be delegated to other handlers. StAX also provides an event-based interface for the process of mapping XML ids to java objects. After a bit of refactoring, documentation, and unit testing, a version 1.0 release of the SourceForge StAX has been made and a new web site has been created at > http://stax.sourceforge.net Changes made since the migration from biojava: DelegationManager replaced by StAXContext and StAXDelegationContext Added IdMapper and IdListener, support for mapping XML ids to objects Built-in handlers return value in endTree instead of requiring subclassing Added convenience delegators DispatchForChild and DispatchOnElement Changes made to prepare the sf StAX for release: Created maven build and web site Added simple unit test cases Built-in handlers are reusable Refactored IDMapper --> IdMapper and similar Source code cleanup and documentation Refactored from biojava to net.sf.stax package The 1.0 release has been thoroughly documented and has nearly complete unit test coverage. The javadoc for each class has an example of how to use that class in a handler, and each unit test contains complete examples of handlers for test xml files. Thank yous to StAX developers Matthew Pocock and Thomas Down, and to Mark Schreiber for unintentionally providing the motivation to get a release done. michael From Lukas.Kall at cgb.ki.se Tue Feb 22 10:04:30 2005 From: Lukas.Kall at cgb.ki.se (Lukas Kall) Date: Sun Apr 10 22:11:44 2005 Subject: [Biojava-dev] Inheriting from the HMM classes Message-ID: <1109084947.19126.24.camel@aquarius.cgb.ki.se> Hi, I have tried to use the BioJava library for implementing some HMM decoding algorithms. It was fairly convenient to do so, apart from that many of the declarations in your classes are private, when I would prefer them to be public. Any chance that you could change the declarations in future versions? I have attached a diff to my sources beneath. Meanwhile I have put my version under GPL (See http://phobius.cgb.ki.se/data.html). I hope that this suites you. BRs -Lukas K?ll Center for Genomics and Bioinformatics Karolinska Institutet S-171 77 Stockholm, Sweden Tel: +46 (0)8 52 48 66 88 Fax: +46 (0)8 33 79 83 http://phobius.cgb.ki.se/ diff -r biojava-1.30/src/org/biojava/bio/dp/onehead/DPCursor.java orig/biojava-1.30/src/org/biojava/bio/dp/onehead/DPCursor.java 33c33 < public interface DPCursor { --- > interface DPCursor { diff -r biojava-1.30/src/org/biojava/bio/dp/onehead/SingleDP.java orig/biojava-1.30/src/org/biojava/bio/dp/onehead/SingleDP.java 42,44c42,44 < protected final HashMap emissionsProb; < protected final HashMap emissionsOdds; < protected final HashMap emissionsNull; --- > private final HashMap emissionsProb; > private final HashMap emissionsOdds; > private final HashMap emissionsNull; 100,105c100 < double emS = scoreType.calculateScore(dis, sym); < if (emS>0.0) { < em[i] = Math.log(emS); < } else { < em[i] = Double.NEGATIVE_INFINITY; < } --- > em[i] = Math.log(scoreType.calculateScore(dis, sym)); 212c207 < protected double forward(DPCursor dpCursor, ScoreType scoreType) --- > private double forward(DPCursor dpCursor, ScoreType scoreType) 219c214 < protected double backward(DPCursor dpCursor, ScoreType scoreType) --- > private double backward(DPCursor dpCursor, ScoreType scoreType) 226c221 < protected void forward_initialize(DPCursor dpCursor, ScoreType scoreType) --- > private void forward_initialize(DPCursor dpCursor, ScoreType scoreType) 276d270 < // System.out.println("currentCol[" + states[l].getName() + "]=" + currentCol[l]); 280c274 < protected void backward_initialize(DPCursor dpCursor, ScoreType scoreType) --- > private void backward_initialize(DPCursor dpCursor, ScoreType scoreType) 294c288 < protected void forward_recurse(DPCursor dpCursor, ScoreType scoreType) --- > private void forward_recurse(DPCursor dpCursor, ScoreType scoreType) 308c302 < // System.out.println("Consuming " + sym.getName()); --- > // System.out.println("Consuming " + sym.getName()); 314c308 < // System.out.println("* at " + states[l].getName()); --- > // System.out.println("*"); 335,336c329 < if (lastCol[k] != Double.NEGATIVE_INFINITY && < lastCol[k] != Double.NaN) { --- > if (lastCol[k] != Double.NEGATIVE_INFINITY) { 339,342c332,335 < // if(states[l]== getModel().magicalState()) { < // System.out.print("magic " + "lastCol["+states[k].getName()+"]=" + lastCol[k] + " , "); < // System.out.println("t=" + t); < // } --- > if(states[l]== getModel().magicalState()) { > // System.out.print("magic " + "lastCol[k]=" + lastCol[k] + " , "); > // System.out.println("t=" + t); > } 346,349c339 < if (lastCol[k] == Double.NaN) { < System.out.println("k=" + states[k].getName() + "->l=" + states[l].getName()); < System.out.println("-"); < } --- > // System.out.println("-"); 354,359d343 < if ((new Double(currentCol[l])).isNaN()) { < System.out.println("currentCol[" + states[l].getName() + "]=" + currentCol[l]); < System.out.println("weight="+weight+", score="+score+ < ", constant="+constant); < currentCol[l]=Double.NEGATIVE_INFINITY; < } 362d345 < // System.out.println("currentCol[" + states[l].getName() + "]=" +currentCol[l]+" NaN=" + ( (new Double(currentCol[l])).isNaN())); 364,369c347,352 < /* if(states[l] == getModel().magicalState()) { < System.out.print("magic\t"); < System.out.print("Weight " + weight + "\t"); < System.out.print(", score " + score + " = " + Math.log(score) + "\t"); < System.out.println(", constant " + constant); < } */ --- > if(states[l] == getModel().magicalState()) { > // System.out.print("magic\t"); > //System.out.print("Weight " + weight + "\t"); > // System.out.print(", score " + score + " = " + Math.log(score) + "\t"); > // System.out.println(", constant " + constant); > } 393c376 < && currentCol[k] != Double.NaN --- > && currentCol[k] !=Double.NaN 398,400d380 < if (currentCol[k] == Double.NaN) { < System.out.println("k=" + states[k].getName() + "->l=" + states[l].getName()); < } 403,408c383,384 < if (score>=0.0 && score != Double.NaN) { < currentCol[l] = Math.log(score) + constant; < } else { < currentCol[l] = Double.NEGATIVE_INFINITY; < } < // System.out.println("currentCol[" + states[l].getName() + "]=" + currentCol[l]); --- > currentCol[l] = Math.log(score) + constant; > //System.out.println("currentCol[" + states[l].getName() + "]=" + currentCol[l]); 413c389 < protected void backward_recurse(DPCursor dpCursor, ScoreType scoreType) --- > private void backward_recurse(DPCursor dpCursor, ScoreType scoreType) 484c460 < protected double forward_termination(DPCursor dpCursor, ScoreType scoreType) --- > private double forward_termination(DPCursor dpCursor, ScoreType scoreType) 496c472 < protected double backward_termination(DPCursor dpCursor, ScoreType scoreType) --- > private double backward_termination(DPCursor dpCursor, ScoreType scoreType) 515c491 < protected StatePath viterbi(DPCursor dpCursor, ScoreType scoreType) --- > private StatePath viterbi(DPCursor dpCursor, ScoreType scoreType) diff -r biojava-1.30/src/org/biojava/bio/dp/onehead/SingleDPMatrix.java orig/biojava-1.30/src/org/biojava/bio/dp/onehead/SingleDPMatrix.java 36,40c36,40 < protected final State [] states; < protected final MarkovModel model; < protected final SymbolList [] symList; < public final double [][] scores; // [symbol][state] < protected double score; --- > private final State [] states; > private final MarkovModel model; > private final SymbolList [] symList; > public final double [][] scores; // [symbol][state] > private double score; 58c58 < public void setScore(double score) { --- > void setScore(double score) { diff -r biojava-1.30/src/org/biojava/bio/dp/onehead/SmallCursor.java orig/biojava-1.30/src/org/biojava/bio/dp/onehead/SmallCursor.java 34c34 < public class SmallCursor extends AbstractCursor { --- > class SmallCursor extends AbstractCursor { diff -r biojava-1.30/src/org/biojava/bio/seq/io/FastaFormat.java orig/biojava-1.30/src/org/biojava/bio/seq/io/FastaFormat.java 61c61 < protected Vector mListeners = new Vector(); --- > private Vector mListeners = new Vector(); 66c66 < protected int lineWidth = 60; --- > private int lineWidth = 60; From tiagojab at yahoo.com.br Wed Feb 23 10:21:05 2005 From: tiagojab at yahoo.com.br (Tiago Lopes) Date: Sun Apr 10 22:11:46 2005 Subject: [Biojava-dev] Microarray modules Message-ID: <20050223152605.83814.qmail@web54307.mail.yahoo.com> Hello, I hope everything is okay with you and your projects. Well, I have developes java classes for microarray analysis, and the modules are for background correction, normalization (global), and analysis by the SAM (Significance Analysis of Microarray - Tusher et al.). I want to make this classes avaliable, and I would be proud to help in the development of Biojava.org. I have wrote once, but had no answer if I could join the project or not. So, I'm writing again ! Thanks ! "Publish or perish !" ========================= Tiago Jos? da Silva Lopes ICQ: 195209391 ========================= --------------------------------- Yahoo! Acesso Gr?tis - Internet r?pida e gr?tis. Instale o discador do Yahoo! agora.