pal.alignment
Class IndelAnnotatedAlignment

java.lang.Object
  extended by pal.alignment.AbstractAlignment
      extended by pal.alignment.IndelAlignment
          extended by 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