pal.alignment
Class StrippedAnnotatedAlignment

java.lang.Object
  pal.alignment.AbstractAlignment
      pal.alignment.StrippedAlignment
          pal.alignment.StrippedAnnotatedAlignment

All Implemented Interfaces:

java.io.Serializable, Alignment, AnnotationAlignment, IdGroup, Report

public class StrippedAnnotatedAlignment
extends StrippedAlignment
implements AnnotationAlignment

This is the stripped implementation of the Annotation interface, which is designed to provide stripped and annotated alignments. This annotation can include information on chromosomal location, site positions, locus name, and the type of position (exon, intron, etc.) This class also add some methods for stripping sites based on frequency, count, and a range of positions.

Version:

$Id: StrippedAnnotatedAlignment.java,v 1

Author:

Ed Buckler

See Also:

Serialized Form

Nested Class Summary

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

IdGroup.Utils

Field Summary

protected int	firstSite
protected int	lastSite
protected int	minimumCount
protected double	minimumProportion

Fields inherited from class pal.alignment.StrippedAlignment

alias, notDropped

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

StrippedAnnotatedAlignment(AnnotationAlignment a)
Simple 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	removeConstantSitesIgnoreGapsMissing() remove constant sites but ignore gaps and missing data (- and ?)
void	removeSitesBasedOnFreqIgnoreGapsMissing(double minimumProportion, int minimumCount) remove sites based on minimum frequency (the count of good bases) and based on the proportion of good sites different from consensus
void	removeSitesOutsideRange(int firstSite, int lastSite) Remove sites based on site position (excluded sites are lastSite) This not effect any prior exclusions.
void	report(java.io.PrintWriter out) print human readable report (e.g., on parameters and associated model)

Methods inherited from class pal.alignment.StrippedAlignment

dropSite, getData, removeConstantSites, removeGaps, removeNoninformativeSites, removeSites, removeUnknowns

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, getData, getDataType, getSequenceCount, getSiteCount

Methods inherited from interface pal.misc.IdGroup

getIdCount, getIdentifier, setIdentifier, whichIdNumber

Field Detail

minimumProportion

protected double minimumProportion

minimumCount

protected int minimumCount

firstSite

protected int firstSite

lastSite

protected int lastSite

Constructor Detail

StrippedAnnotatedAlignment

public StrippedAnnotatedAlignment(AnnotationAlignment a)

Simple constructor

Method Detail

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

getDataType

public DataType getDataType(int site)

Returns the datatype

Specified by:

getDataType in interface AnnotationAlignment

removeSitesOutsideRange

public void removeSitesOutsideRange(int firstSite,
                                    int lastSite)

Remove sites based on site position (excluded sites are lastSite) This not effect any prior exclusions.

Parameters:

firstSite - first site to keep in the range

lastSite - last site to keep in the range

removeConstantSitesIgnoreGapsMissing

public void removeConstantSitesIgnoreGapsMissing()

remove constant sites but ignore gaps and missing data (- and ?)

removeSitesBasedOnFreqIgnoreGapsMissing

public void removeSitesBasedOnFreqIgnoreGapsMissing(double minimumProportion,
                                                    int minimumCount)

remove sites based on minimum frequency (the count of good bases) and based on the proportion of good sites different from consensus

Parameters:

minimumProportion - minimum proportion of sites different from the consensus

minimumCount - minimum number of sequences with a good bases (not - or ?)

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