org.biojava3.core.sequence.features
Class QualityFeature<S extends AbstractSequence<C>,C extends Compound>
java.lang.Object
org.biojava3.core.sequence.features.AbstractFeature<S,C>
org.biojava3.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
Methods inherited from class org.biojava3.core.sequence.features.AbstractFeature |
getChildrenFeatures, getDescription, getLocations, getParentFeature, getShortDescription, getSource, getType, getUserObject, setChildrenFeatures, setDescription, setLocation, setParentFeature, setShortDescription, setSource, setType, setUserObject |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
QualityFeature
public QualityFeature(String type,
String source)
- Parameters:
type
- source
-
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