[Biojava-dev] [Biojava-l] access to qualities

[Tony Power]

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 <HWillis at scripps.edu> 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" <power3d at gmail.com> 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 <power3d at gmail.com> 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));}
> >>
> >>
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>