Package org.biojava.nbio.core.sequence.features

Class QualityFeature<S extends AbstractSequence<C>,C extends Compound>

java.lang.Object
org.biojava.nbio.core.sequence.features.AbstractFeature<S,C>
org.biojava.nbio.core.sequence.features.QualityFeature<S,C>
All Implemented Interfaces:
FeatureInterface<S,C>
public class QualityFeature<S extends AbstractSequence<C>,C extends Compound> extends AbstractFeature<S,C>
DNA Sequences produced by modern sequencers usually have quality informaion attached to them. This feature allows to store the information directly in the DNASequence
Since:
3.0.3
Author:
brandstaetter

  • Constructor Details

    • QualityFeature

      public QualityFeature(String type, String source)
      Parameters:
      type -
      source -

  • Method Details

    • getQualities

      public List<Number> getQualities()
      Returns:
      the qualities

    • setQualities

      public void setQualities(List<Number> qualities)
      Parameters:
      qualities - the qualities to set

    • getQualityAt

      public Number getQualityAt(int bioindex)
      Parameters:
      bioindex - the biological index (starts with 1)
      Returns:
      the quality value at the given biological index (starts with 1)

    • getQualities

      public List<Number> getQualities(int biostart, int bioend)
      Parameters:
      biostart - biological start index (starts with 1)
      bioend - biological end index (starts with 1)
      Returns:
      a sublist of the qualities between the given biological indices