Thanks for the feedback. So, from the example I provided, how would you print the quality features?
On Thu, Nov 15, 2012 at 2:46 PM, Scooter Willis <[email protected]> wrote: > Tony > > The features get added as a named string to support any number of feature > types. If you look in the FastqTools code should be able to find the > string that is used to denote the quality score and then use the > corresponding get method to return the value. > > Scooter > > On 11/15/12 9:23 AM, "Tony Power" <[email protected]> wrote: > > >Sorry, the message went before I finish it. > > > >How can I access the qualities of each sequence? > > > >I am trying like this: > >List<FeatureInterface<AbstractSequence<NucleotideCompound>, > >NucleotideCompound>> features = s.getFeaturesByType("qualityScores"); > >for (int i = 0; i < features.size(); i++){ > > System.out.println(": " + features.get(i).toString()); > >} > > > >How can I access the qualities? > > > >Thanks for your help, > >Tony > > > > > >On Thu, Nov 15, 2012 at 2:15 PM, Tony Power <[email protected]> wrote: > > > >> Hi, > >> > >> I am trying to access to the qualities created with the example: > >> > >> FastqReader fastqReader = new SangerFastqReader(); > >> List<DNASequence> sequences = new LinkedList<DNASequence>(); > >> for (Fastq fastq : fastqReader.read(new File > >>< > http://www.google.com/search?hl=en&q=allinurl%3Afile+java.sun.com&btnI=I > >>%27m%20Feeling%20Lucky>("sanger.fastq"))){ > >> sequences.add(FastqTools.createDNASequenceWithQualityScores(fastq));} > >> > >> > >_______________________________________________ > >Biojava-l mailing list - [email protected] > >http://lists.open-bio.org/mailman/listinfo/biojava-l > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
