Yes, the issue was also faced by me. I also highlighted the solution. The solution has also been uploaded/updated in SVN.
Muhammad Tariq Pervez PhD Scholar > From: [email protected] > Subject: Biojava-l Digest, Vol 105, Issue 2 > To: [email protected] > Date: Wed, 5 Oct 2011 12:00:04 -0400 > > Send Biojava-l mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.open-bio.org/mailman/listinfo/biojava-l > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Biojava-l digest..." > > > Today's Topics: > > 1. NullPointerException when using > Alignments.getMultipleSequenceAlignment (Hannes Brandst?tter-M?ller) > 2. Re: NullPointerException when using > Alignments.getMultipleSequenceAlignment (Hannes Brandst?tter-M?ller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 5 Oct 2011 09:41:57 +0200 > From: Hannes Brandst?tter-M?ller <[email protected]> > Subject: [Biojava-l] NullPointerException when using > Alignments.getMultipleSequenceAlignment > To: [email protected] > Message-ID: > <CAPXi2mnpLujT=dveqklxfpih1sv6pe_-vob2vjjd-axou4j...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hello! > > I tried to follow http://biojava.org/wiki/BioJava:CookBook3:MSA, but > when I run it, I get: > > java.util.concurrent.ExecutionException: java.lang.NullPointerException > at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222) > at java.util.concurrent.FutureTask.get(FutureTask.java:83) > at > org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282) > at > org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602) > at > org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:173) > > What could I be doing wrong? > > ( > on the cookbook page, there is also an import missing: > import org.biojava3.alignment.Alignments; > ) > -> then the cookbook runs, but my code does not > > private static void processFile(String filename) { > try { > FileInputStream inStream = new FileInputStream(filename); > FastaReader<DNASequence, NucleotideCompound> fastaReader = > new FastaReader<DNASequence, NucleotideCompound>( > inStream, > new GenericFastaHeaderParser<DNASequence, > NucleotideCompound>(), > new > DNASequenceCreator(DNACompoundSet.getDNACompoundSet())); > LinkedHashMap<String, DNASequence> b = fastaReader.process(); > > List<DNASequence> sequences = new ArrayList<DNASequence>(); > for (Entry<String, DNASequence> entry : b.entrySet()) { > if (sequences.size() < 5) { > sequences.add(entry.getValue()); > } > System.out.println(entry.getValue()); > } > > Profile<DNASequence, NucleotideCompound> profile = > Alignments.getMultipleSequenceAlignment(sequences); > System.out.printf("Clustalw:%n%s%n", profile); > > ConcurrencyTools.shutdown(); > } catch (Exception ex) { > Logger.getLogger(App.class.getName()).log(Level.SEVERE, null, ex); > } > } > > > ------------------------------ > > Message: 2 > Date: Wed, 5 Oct 2011 10:50:33 +0200 > From: Hannes Brandst?tter-M?ller <[email protected]> > Subject: Re: [Biojava-l] NullPointerException when using > Alignments.getMultipleSequenceAlignment > To: [email protected] > Message-ID: > <CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=q...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi! > > I read the sequence from a fasta file. > > FileInputStream inStream = new FileInputStream(filename); > FastaReader<DNASequence, NucleotideCompound> fastaReader = > new FastaReader<DNASequence, NucleotideCompound>( > inStream, > new GenericFastaHeaderParser<DNASequence, > NucleotideCompound>(), > new > DNASequenceCreator(DNACompoundSet.getDNACompoundSet())); > LinkedHashMap<String, DNASequence> b = fastaReader.process(); > > and then use > List<DNASequence> sequences = new ArrayList<DNASequence>(); > for (Entry<String, DNASequence> entry : b.entrySet()) { > sequences.add(entry.getValue()); > } > > to get the required list of DNA sequences. > > I noticed in an earlier discussion, there was some talk about this too > (3-4 months ago, perhaps) and something about a possible fix in SVN. > when will it be released on the maven server? > > Hannes > > On Wed, Oct 5, 2011 at 10:46, Hashem Koohy <[email protected]> wrote: > > Hi Hannes, > > It seems to me it doesn't like your ?dna Sequence! > > Is your sequence in the following format? > > > > Sequence dnaSeq = DNATools.createDNASequence("acccgggttttacagt", "id"); > > > > Good luck > > Hashem > > > > On 05/10/2011 08:41, "Hannes Brandst?tter-M?ller" <[email protected]> > > wrote: > > > >> Hello! > >> > >> I tried to follow http://biojava.org/wiki/BioJava:CookBook3:MSA, but > >> when I run it, I get: > >> > >> java.util.concurrent.ExecutionException: java.lang.NullPointerException > >> at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222) > >> at java.util.concurrent.FutureTask.get(FutureTask.java:83) > >> at > >> org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282) > >> at > >> org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602) > >> at > >> org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java > >> :173) > >> > >> ?What could I be doing wrong? > >> > >> ( > >> on the cookbook page, there is also an import missing: > >> import org.biojava3.alignment.Alignments; > >> ) > >> -> then the cookbook runs, but my code does not > >> > >> private static void processFile(String filename) { > >> ? ? ? ? try { > >> ? ? ? ? ? ? FileInputStream inStream = new FileInputStream(filename); > >> ? ? ? ? ? ? FastaReader<DNASequence, NucleotideCompound> fastaReader = > >> ? ? ? ? ? ? ? ? ? ? new FastaReader<DNASequence, NucleotideCompound>( > >> ? ? ? ? ? ? ? ? ? ? inStream, > >> ? ? ? ? ? ? ? ? ? ? new GenericFastaHeaderParser<DNASequence, > >> NucleotideCompound>(), > >> ? ? ? ? ? ? ? ? ? ? new > >> DNASequenceCreator(DNACompoundSet.getDNACompoundSet())); > >> ? ? ? ? ? ? LinkedHashMap<String, DNASequence> b = fastaReader.process(); > >> > >> ? ? ? ? ? ? List<DNASequence> sequences = new ArrayList<DNASequence>(); > >> ? ? ? ? ? ? for (Entry<String, DNASequence> entry : b.entrySet()) { > >> ? ? ? ? ? ? ? ? if (sequences.size() < 5) { > >> ? ? ? ? ? ? ? ? ? ? sequences.add(entry.getValue()); > >> ? ? ? ? ? ? ? ? } > >> ? ? ? ? ? ? ? ? System.out.println(entry.getValue()); > >> ? ? ? ? ? ? } > >> > >> ? ? ? ? ? ? Profile<DNASequence, NucleotideCompound> profile = > >> Alignments.getMultipleSequenceAlignment(sequences); > >> ? ? ? ? ? ? System.out.printf("Clustalw:%n%s%n", profile); > >> > >> ? ? ? ? ? ? ConcurrencyTools.shutdown(); > >> ? ? ? ? } catch (Exception ex) { > >> ? ? ? ? ? ? Logger.getLogger(App.class.getName()).log(Level.SEVERE, null, > >> ex); > >> ? ? ? ? } > >> ? ? } > >> _______________________________________________ > >> Biojava-l mailing list ?- [email protected] > >> http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > ------------------------------- > > Hashem Koohy > > PhD > > Postdoctoral Fellow, > > Sanger Institute, > > Cambridge > > Mobile: 07515425433 > > > > > > > > > > -- > > ?The Wellcome Trust Sanger Institute is operated by Genome Research > > ?Limited, a charity registered in England with number 1021457 and a > > ?company registered in England with number 2742969, whose registered > > ?office is 215 Euston Road, London, NW1 2BE. > > > > > > ------------------------------ > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > End of Biojava-l Digest, Vol 105, Issue 2 > ***************************************** _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
