Package pal.alignment
Class IndelAnnotatedAlignment
- java.lang.Object
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- pal.alignment.AbstractAlignment
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- pal.alignment.IndelAlignment
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- pal.alignment.IndelAnnotatedAlignment
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- All Implemented Interfaces:
java.io.Serializable
,Alignment
,AnnotationAlignment
,IdGroup
,Report
public class IndelAnnotatedAlignment extends IndelAlignment implements AnnotationAlignment
an extension of the IndelAlignment that includes annotation. This should only extract indels from a single locus.- Version:
- $Id:
- Author:
- Ed Buckler
- See Also:
- Serialized Form
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
Fields Modifier and Type Field Description int
chromosome
used to designate chromosomefloat
chromosomePosition
used to designate position along chromosomejava.lang.String
locusName
used to designate locus nameint[]
locusPosition
used to designate position; do not account for gapschar[]
positionType
used to designate position Typefloat[]
weightedLocusPosition
used to designate weighted position; accounts for gaps-
Fields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
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Constructor Summary
Constructors Constructor Description IndelAnnotatedAlignment(AnnotationAlignment a, boolean anchored)
Basic constructor.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getChromosome(int site)
Returns chromosomefloat
getChromosomePosition(int site)
Return the position along chromosomeDataType
getDataType(int site)
Returns the datatypejava.lang.String
getLocusName(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(java.lang.String locusName)
Sets the name of the locus-
Methods inherited from class pal.alignment.IndelAlignment
getData
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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
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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Methods inherited from interface pal.alignment.Alignment
getAlignedSequenceString, getData, getDataType, getSequenceCount, getSiteCount
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Methods inherited from interface pal.alignment.AnnotationAlignment
report
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Methods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber
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Field Detail
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chromosomePosition
public float chromosomePosition
used to designate position along chromosome
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chromosome
public int chromosome
used to designate chromosome
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weightedLocusPosition
public float[] weightedLocusPosition
used to designate weighted position; accounts for gaps
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locusPosition
public int[] locusPosition
used to designate position; do not account for gaps
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positionType
public char[] positionType
used to designate position Type
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locusName
public java.lang.String locusName
used to designate locus name
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Constructor Detail
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IndelAnnotatedAlignment
public IndelAnnotatedAlignment(AnnotationAlignment a, boolean anchored)
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 Detail
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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
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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
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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
public java.lang.String getLocusName(int site)
Returns the name of the locus- Specified by:
getLocusName
in interfaceAnnotationAlignment
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setLocusName
public void setLocusName(java.lang.String locusName)
Sets the name of the locus
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getDataType
public DataType getDataType(int site)
Returns the datatype- Specified by:
getDataType
in interfaceAnnotationAlignment
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