Package pal.alignment
Class IndelAnnotatedAlignment
java.lang.Object
pal.alignment.AbstractAlignment
pal.alignment.IndelAlignment
pal.alignment.IndelAnnotatedAlignment
- All Implemented Interfaces:
Serializable
,Alignment
,AnnotationAlignment
,IdGroup
,Report
an extension of the IndelAlignment that includes annotation. This should only extract
indels from a single locus.
- Version:
- $Id:
- Author:
- Ed Buckler
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
FieldsModifier and TypeFieldDescriptionint
used to designate chromosomefloat
used to designate position along chromosomeused to designate locus nameint[]
used to designate position; do not account for gapschar[]
used to designate position Typefloat[]
used to designate weighted position; accounts for gapsFields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
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Constructor Summary
ConstructorsConstructorDescriptionIndelAnnotatedAlignment
(AnnotationAlignment a, boolean anchored) Basic constructor. -
Method Summary
Modifier and TypeMethodDescriptionint
getChromosome
(int site) Returns chromosomefloat
getChromosomePosition
(int site) Return the position along chromosomegetDataType
(int site) Returns the datatypegetLocusName
(int site) Returns the name of the locusint
getLocusPosition
(int site) Return the position along the locus (ignores gaps)char
getPositionType
(int site) Returns position type (eg.float
getWeightedLocusPosition
(int site) Return the weighted position along the gene (handles gaps)void
setChromosome
(int chromosome) Sets chromosomevoid
setChromosomePosition
(float position) Set the position along chromosomevoid
setLocusName
(String locusName) Sets the name of the locusMethods inherited from class pal.alignment.IndelAlignment
getData
Methods inherited from class pal.alignment.AbstractAlignment
getAlignedSequenceString, getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, setDataType, setIdentifier, toString, whichIdNumber
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface pal.alignment.Alignment
getAlignedSequenceString, getData, getDataType, getSequenceCount, getSiteCount
Methods inherited from interface pal.alignment.AnnotationAlignment
report
Methods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber
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Field Details
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chromosomePosition
public float chromosomePositionused to designate position along chromosome -
chromosome
public int chromosomeused to designate chromosome -
weightedLocusPosition
public float[] weightedLocusPositionused to designate weighted position; accounts for gaps -
locusPosition
public int[] locusPositionused to designate position; do not account for gaps -
positionType
public char[] positionTypeused to designate position Type -
locusName
used to designate locus name
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Constructor Details
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IndelAnnotatedAlignment
Basic constructor. All annotation is based off the first site in the AnnotationAlignment. This Alignment should not span multiple loci.- Parameters:
anchored
- sets to score anchored indels as same position
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Method Details
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getChromosomePosition
public float getChromosomePosition(int site) Return the position along chromosome- Specified by:
getChromosomePosition
in interfaceAnnotationAlignment
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setChromosomePosition
public void setChromosomePosition(float position) Set the position along chromosome -
getChromosome
public int getChromosome(int site) Returns chromosome- Specified by:
getChromosome
in interfaceAnnotationAlignment
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setChromosome
public void setChromosome(int chromosome) Sets chromosome -
getWeightedLocusPosition
public float getWeightedLocusPosition(int site) Return the weighted position along the gene (handles gaps)- Specified by:
getWeightedLocusPosition
in interfaceAnnotationAlignment
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getLocusPosition
public int getLocusPosition(int site) Return the position along the locus (ignores gaps)- Specified by:
getLocusPosition
in interfaceAnnotationAlignment
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getPositionType
public char getPositionType(int site) Returns position type (eg. I=intron, E-exon, P=promoter, 1=first, 2=second, 3=third, etc.- Specified by:
getPositionType
in interfaceAnnotationAlignment
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getLocusName
Returns the name of the locus- Specified by:
getLocusName
in interfaceAnnotationAlignment
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setLocusName
Sets the name of the locus -
getDataType
Returns the datatype- Specified by:
getDataType
in interfaceAnnotationAlignment
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