pal.alignment
Class ConcatenatedAnnotatedAlignment

java.lang.Object
  pal.alignment.AbstractAlignment
      pal.alignment.ConcatenatedAnnotatedAlignment

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

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.IdGroup

IdGroup.Utils

Field Summary

Fields inherited from class pal.alignment.AbstractAlignment

idGroup, numSeqs, numSites

Fields inherited from interface pal.alignment.Alignment

GAP, GAP_TLA, GAPS, UNKNOWN, UNKNOWN_TLA

Constructor Summary

ConcatenatedAnnotatedAlignment(AnnotationAlignment[] list, boolean mergeByID, boolean union)
concatenate alignments

Method Summary

int	getChromosome(int site) Returns chromosome
float	getChromosomePosition(int site) Return the position along chromosome
char	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 alignments
java.lang.String	getLocusName(int site) Returns the name of the locus
int	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

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, getDataType, getSequenceCount, getSiteCount

Methods inherited from interface pal.misc.IdGroup

getIdCount, getIdentifier, setIdentifier, whichIdNumber

Constructor Detail

ConcatenatedAnnotatedAlignment

public ConcatenatedAnnotatedAlignment(AnnotationAlignment[] list,
                                      boolean mergeByID,
                                      boolean union)
                               throws java.lang.IllegalArgumentException

concatenate alignments

Parameters:

list - array with alignments to concatenate

mergeByID - if true it will be by ID name

union - if true it will create the union of the list, if false the intersection will be produced

Throws:

java.lang.IllegalArgumentException

Method Detail

getData

public char getData(int seq,
                    int site)

sequence alignment at (sequence, site)

Specified by:

getData in interface Alignment

Specified by:

getData in class AbstractAlignment

getDataType

public DataType getDataType(int site)

Return the datatype for a given site, which can differ between source alignments

Specified by:

getDataType in interface AnnotationAlignment

getChromosomePosition

public float getChromosomePosition(int site)

Return the position along chromosome

Specified by:

getChromosomePosition in interface AnnotationAlignment

getChromosome

public int getChromosome(int site)

Returns chromosome

Specified by:

getChromosome in interface AnnotationAlignment

getWeightedLocusPosition

public float getWeightedLocusPosition(int site)

Return the weighted position along the gene (handles gaps)

Specified by:

getWeightedLocusPosition in interface AnnotationAlignment

getLocusPosition

public int getLocusPosition(int site)

Return the position along the locus (ignores gaps)

Specified by:

getLocusPosition in interface AnnotationAlignment

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 interface AnnotationAlignment

getLocusName

public java.lang.String getLocusName(int site)

Returns the name of the locus

Specified by:

getLocusName in interface AnnotationAlignment

sortSites

public void sortSites()

sort the sites by chromosome, then by chromosomal location, and final locusPosition

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 interface AnnotationAlignment

Specified by:

report in interface Report

Overrides:

report in class AbstractAlignment

Parameters:

out - output stream