[Biojava-l] access to qualities

[Tony Power]

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));}
>
>