org.biojava.bio.program.phred

Class PhredSequence

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.seq.impl.SimpleSequence

org.biojava.bio.program.phred.PhredSequence

All Implemented Interfaces:

Serializable, Annotatable, Qualitative, FeatureHolder, RealizingFeatureHolder, Sequence, SymbolList, Changeable

public class PhredSequence
extends SimpleSequence
implements Qualitative

PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores.

Copyright: Copyright (c) 2001

Company: AgResearch

Since:

1.1

Author:

Mark Schreiber

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder

FeatureHolder.EmptyFeatureHolder

Field Summary

Fields inherited from interface org.biojava.bio.symbol.SymbolList

EDIT, EMPTY_LIST

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Fields inherited from interface org.biojava.bio.seq.FeatureHolder

EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA

Constructor Summary

Constructors

Constructor and Description
PhredSequence(SymbolList phredSequence, String name, String urn, Annotation anno) Constructs a new PhredSequence.

Method Summary

Modifier and Type	Method and Description
SymbolList	getDNA() Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolList
Symbol	getDNAAt(int index)
SymbolList	getQuality() Extracts the quality part if the Phred Alphabet and returns it as a SymbolList over the Integer SubAlphabet from 0..99.
Symbol	getQualityAt(int index) Retreives the quality symbol for the specified index.

Methods inherited from class org.biojava.bio.seq.impl.SimpleSequence

containsFeature, countFeatures, createFeature, createFeature, edit, featureHolderAllocated, features, filter, filter, getAlphabet, getAnnotation, getChangeSupport, getFeatureHolder, getName, getSchema, getURN, iterator, length, realizeFeature, removeFeature, seqString, setName, setURN, subList, subStr, symbolAt, toList, toString

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

PhredSequence

public PhredSequence(SymbolList phredSequence,
                     String name,
                     String urn,
                     Annotation anno)
              throws IllegalAlphabetException

Constructs a new PhredSequence.

Parameters:

phredSequence - - a SymbolList over the Phred Alphabet.

name - - the name for the sequence.

urn - - the URN for the sequence.

anno - - the Annotation object for the sequence.

Throws:

IllegalAlphabetException

Method Detail

getQuality

public SymbolList getQuality()

Extracts the quality part if the Phred Alphabet and returns it as a SymbolList over the Integer SubAlphabet from 0..99.

Specified by:

getQuality in interface Qualitative

getDNA

public SymbolList getDNA()

Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolList

getQualityAt

public Symbol getQualityAt(int index)
                    throws IndexOutOfBoundsException

Description copied from interface: Qualitative

Retreives the quality symbol for the specified index.

Specified by:

getQualityAt in interface Qualitative

Parameters:

index - - Must be greater than zero.

Throws:

IndexOutOfBoundsException - if index is outside of the quality symbol list.

getDNAAt

public Symbol getDNAAt(int index)
                throws IndexOutOfBoundsException

Throws:

IndexOutOfBoundsException