Package pal.alignment
Class ConcatenatedAnnotatedAlignment
- java.lang.Object
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- pal.alignment.AbstractAlignment
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- pal.alignment.ConcatenatedAnnotatedAlignment
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- All Implemented Interfaces:
java.io.Serializable
,Alignment
,AnnotationAlignment
,IdGroup
,Report
public class ConcatenatedAnnotatedAlignment extends AbstractAlignment implements AnnotationAlignment
This is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences. It will merge by either union or intersection. Missing taxa will return missing values on getData.- 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
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Fields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
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Constructor Summary
Constructors Constructor Description ConcatenatedAnnotatedAlignment(AnnotationAlignment[] list, boolean mergeByID, boolean union)
concatenate alignments
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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 chromosomechar
getData(int seq, int site)
sequence alignment at (sequence, site)DataType
getDataType(int site)
Return the datatype for a given site, which can differ between source alignmentsjava.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
report(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model)void
sortSites()
sort the sites by chromosome, then by chromosomal location, and final locusPosition-
Methods inherited from class pal.alignment.AbstractAlignment
getAlignedSequenceString, getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, 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, getDataType, getSequenceCount, getSiteCount
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Methods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber
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Constructor Detail
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ConcatenatedAnnotatedAlignment
public ConcatenatedAnnotatedAlignment(AnnotationAlignment[] list, boolean mergeByID, boolean union) throws java.lang.IllegalArgumentException
concatenate alignments- Parameters:
list
- array with alignments to concatenatemergeByID
- if true it will be by ID nameunion
- if true it will create the union of the list, if false the intersection will be produced- Throws:
java.lang.IllegalArgumentException
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Method Detail
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getData
public char getData(int seq, int site)
sequence alignment at (sequence, site)- Specified by:
getData
in interfaceAlignment
- Specified by:
getData
in classAbstractAlignment
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getDataType
public DataType getDataType(int site)
Return the datatype for a given site, which can differ between source alignments- Specified by:
getDataType
in interfaceAnnotationAlignment
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getChromosomePosition
public float getChromosomePosition(int site)
Return the position along chromosome- Specified by:
getChromosomePosition
in interfaceAnnotationAlignment
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getChromosome
public int getChromosome(int site)
Returns chromosome- Specified by:
getChromosome
in interfaceAnnotationAlignment
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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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sortSites
public void sortSites()
sort the sites by chromosome, then by chromosomal location, and final locusPosition
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report
public void report(java.io.PrintWriter out)
Description copied from interface:Report
print human readable report (e.g., on parameters and associated model)- Specified by:
report
in interfaceAnnotationAlignment
- Specified by:
report
in interfaceReport
- Overrides:
report
in classAbstractAlignment
- Parameters:
out
- output stream
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