Package pal.alignment
Class MultiLocusAnnotatedAlignment
- java.lang.Object
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- pal.alignment.AbstractAlignment
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- pal.alignment.SimpleAlignment
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- pal.alignment.MultiLocusAnnotatedAlignment
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- All Implemented Interfaces:
java.io.Serializable
,Alignment
,AnnotationAlignment
,IdGroup
,Report
public class MultiLocusAnnotatedAlignment extends SimpleAlignment implements AnnotationAlignment
MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci. Separate annotation information is stored from each sites. This would be good SNP SSR type of data, but it would be inefficient for single gene data.- 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 TypeDataType[]
siteDataType
provides datatype for each locus separatelyfloat[]
weightedPosition
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 MultiLocusAnnotatedAlignment()
null constructor.MultiLocusAnnotatedAlignment(Alignment a)
Basic constructor.MultiLocusAnnotatedAlignment(AnnotationAlignment a)
Clone constructor for Annotated alignmentMultiLocusAnnotatedAlignment(AnnotationAlignment a, IdGroup newGroup)
This constructor will subset the alignment based on the taxa in IdGroupMultiLocusAnnotatedAlignment(Identifier[] ids, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
MultiLocusAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
MultiLocusAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, DataType dt)
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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)protected void
init(IdGroup group, java.lang.String[] sequences)
protected void
initMatrices()
void
setChromosome(int chromosome, int site)
Sets chromosomevoid
setChromosomePosition(float position, int site)
Set the position along chromosomevoid
setLocusName(java.lang.String locusName, int site)
Sets the name of the locusvoid
setLocusPosition(int position, int site)
Set the position within the locusvoid
setPositionType(int site, char posType)
Set thes position type (eg.void
setWeightedLocusPosition(int site, float weightedPos)
Sets the weighted position along the gene (handles gaps)-
Methods inherited from class pal.alignment.SimpleAlignment
getAlignedSequenceString, getData
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Methods inherited from class pal.alignment.AbstractAlignment
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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weightedPosition
public float[] weightedPosition
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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siteDataType
public DataType[] siteDataType
provides datatype for each locus separately
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Constructor Detail
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MultiLocusAnnotatedAlignment
public MultiLocusAnnotatedAlignment(Alignment a)
Basic constructor.
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MultiLocusAnnotatedAlignment
public MultiLocusAnnotatedAlignment()
null constructor.
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MultiLocusAnnotatedAlignment
public MultiLocusAnnotatedAlignment(AnnotationAlignment a)
Clone constructor for Annotated alignment
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MultiLocusAnnotatedAlignment
public MultiLocusAnnotatedAlignment(Identifier[] ids, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
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MultiLocusAnnotatedAlignment
public MultiLocusAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, DataType dt)
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MultiLocusAnnotatedAlignment
public MultiLocusAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
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MultiLocusAnnotatedAlignment
public MultiLocusAnnotatedAlignment(AnnotationAlignment a, IdGroup newGroup)
This constructor will subset the alignment based on the taxa in IdGroup
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Method Detail
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initMatrices
protected void initMatrices()
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init
protected void init(IdGroup group, java.lang.String[] sequences)
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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, int site)
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, int site)
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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setWeightedLocusPosition
public void setWeightedLocusPosition(int site, float weightedPos)
Sets the weighted position along the gene (handles gaps)
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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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setLocusPosition
public void setLocusPosition(int position, int site)
Set the position within the locus
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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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setPositionType
public void setPositionType(int site, char posType)
Set thes position type (eg. I=intron, E-exon, P=promoter, 1=first, 2=second, 3=third, etc.
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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, int site)
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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