pal.alignment
Class IndelAnnotatedAlignment

java.lang.Object
  pal.alignment.AbstractAlignment
      pal.alignment.IndelAlignment
          pal.alignment.IndelAnnotatedAlignment

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

Nested Class Summary

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

IdGroup.Utils

Field Summary

int	chromosome used to designate chromosome
float	chromosomePosition used to designate position along chromosome
java.lang.String	locusName used to designate locus name
int[]	locusPosition used to designate position; do not account for gaps
char[]	positionType used to designate position Type
float[]	weightedLocusPosition used to designate weighted position; accounts for gaps

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

IndelAnnotatedAlignment(AnnotationAlignment a, boolean anchored)
Basic constructor.

Method Summary

int	getChromosome(int site) Returns chromosome
float	getChromosomePosition(int site) Return the position along chromosome
DataType	getDataType(int site) Returns the datatype
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	setChromosome(int chromosome) Sets chromosome
void	setChromosomePosition(float position) Set the position along chromosome
void	setLocusName(java.lang.String locusName) Sets the name of the locus

Methods 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.AnnotationAlignment

report

Methods inherited from interface pal.alignment.Alignment

getAlignedSequenceString, getData, getDataType, getSequenceCount, getSiteCount

Methods inherited from interface pal.misc.IdGroup

getIdCount, getIdentifier, setIdentifier, whichIdNumber

Field Detail

chromosomePosition

public float chromosomePosition

used to designate position along chromosome

chromosome

public int chromosome

used to designate chromosome

weightedLocusPosition

public float[] weightedLocusPosition

used to designate weighted position; accounts for gaps

locusPosition

public int[] locusPosition

used to designate position; do not account for gaps

positionType

public char[] positionType

used to designate position Type

locusName

public java.lang.String locusName

used to designate locus name

Constructor Detail

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

Method Detail

getChromosomePosition

public float getChromosomePosition(int site)

Return the position along chromosome

Specified by:

getChromosomePosition in interface AnnotationAlignment

setChromosomePosition

public void setChromosomePosition(float position)

Set the position along chromosome

getChromosome

public int getChromosome(int site)

Returns chromosome

Specified by:

getChromosome in interface AnnotationAlignment

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 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

setLocusName

public void setLocusName(java.lang.String locusName)

Sets the name of the locus

getDataType

public DataType getDataType(int site)

Returns the datatype

Specified by:

getDataType in interface AnnotationAlignment