org.biojava3.core.sequence.features
Class QualityFeature<S extends AbstractSequence<C>,C extends Compound>

java.lang.Object
  extended by org.biojava3.core.sequence.features.AbstractFeature<S,C>
      extended by 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

Field Summary
 
Fields inherited from class org.biojava3.core.sequence.features.AbstractFeature
LENGTH, LOCATION_LENGTH
 
Constructor Summary
QualityFeature(String type, String source)
           
 
Method Summary
 List<Number> getQualities()
           
 List<Number> getQualities(int biostart, int bioend)
           
 Number getQualityAt(int bioindex)
           
 void setQualities(List<Number> qualities)
           
 
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
 

Constructor Detail

QualityFeature

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

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