Re: Biojava-l Digest, Vol 105, Issue 2

Muhammad Tariq Pervez <[email protected]>
Newsgroups gmane.comp.java.bio.general
Message-ID <[email protected]> 
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
> 
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> 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-axOu4jr_w@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.
> >
> 
> 
> 
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> End of Biojava-l Digest, Vol 105, Issue 2
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