Package 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
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:
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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
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Field Summary
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
Fields inherited from interface org.biojava.bio.seq.FeatureHolder
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA
Fields inherited from interface org.biojava.bio.symbol.SymbolList
EDIT, EMPTY_LIST
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Constructor Summary
ConstructorsConstructorDescriptionPhredSequence
(SymbolList phredSequence, String name, String urn, Annotation anno) Constructs a new PhredSequence. -
Method Summary
Modifier and TypeMethodDescriptiongetDNA()
Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolListgetDNAAt
(int index) Extracts the quality part if the Phred Alphabet and returns it as a SymbolList over the Integer SubAlphabet from 0..99.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
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Constructor Details
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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
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Method Details
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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 interfaceQualitative
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getDNA
Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolList -
getQualityAt
Description copied from interface:Qualitative
Retreives the quality symbol for the specified index.- Specified by:
getQualityAt
in interfaceQualitative
- Parameters:
index
- - Must be greater than zero.- Throws:
IndexOutOfBoundsException
- if index is outside of the quality symbol list.
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getDNAAt
- Throws:
IndexOutOfBoundsException
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