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

Field Summary

Fields inherited from class org.biojava.nbio.core.sequence.features.AbstractFeature

LENGTH, LOCATION_LENGTH, TYPE

Constructor Summary

Constructors

Constructor and Description
QualityFeature(String type, String source)

Method Summary

Modifier and Type	Method and Description
List<Number>	getQualities()
List<Number>	getQualities(int biostart, int bioend)
Number	getQualityAt(int bioindex)
void	setQualities(List<Number> qualities)

Methods inherited from class org.biojava.nbio.core.sequence.features.AbstractFeature

addQualifier, getChildrenFeatures, getDescription, getLocations, getParentFeature, getQualifiers, getShortDescription, getSource, getType, getUserObject, setChildrenFeatures, setDescription, setLocation, setParentFeature, setQualifiers, 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