Package pal.alignment
Class StrippedAnnotatedAlignment
- java.lang.Object
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- pal.alignment.AbstractAlignment
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- pal.alignment.StrippedAlignment
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- pal.alignment.StrippedAnnotatedAlignment
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- 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
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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
Fields Modifier and Type Field Description protected int
firstSite
protected int
lastSite
protected int
minimumCount
protected double
minimumProportion
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Fields inherited from class pal.alignment.StrippedAlignment
alias, notDropped
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Fields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
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Constructor Summary
Constructors Constructor Description StrippedAnnotatedAlignment(AnnotationAlignment a)
Simple constructor
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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 chromosomeDataType
getDataType(int site)
Returns the datatypejava.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
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 consensusvoid
removeSitesOutsideRange(int firstSite, int lastSite)
Remove sites based on site position (excluded sites arelastSite) 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
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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, getData, 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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StrippedAnnotatedAlignment
public StrippedAnnotatedAlignment(AnnotationAlignment a)
Simple constructor
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Method Detail
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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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getDataType
public DataType getDataType(int site)
Returns the datatype- Specified by:
getDataType
in interfaceAnnotationAlignment
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removeSitesOutsideRange
public void removeSitesOutsideRange(int firstSite, int lastSite)
Remove sites based on site position (excluded sites arelastSite) This not effect any prior exclusions. - Parameters:
firstSite
- first site to keep in the rangelastSite
- last site to keep in the range
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removeConstantSitesIgnoreGapsMissing
public void removeConstantSitesIgnoreGapsMissing()
remove constant sites but ignore gaps and missing data (- and ?)
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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 consensusminimumCount
- minimum number of sequences with a good bases (not - or ?)
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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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