Package pal.alignment
Class StrippedAnnotatedAlignment
java.lang.Object
pal.alignment.AbstractAlignment
pal.alignment.StrippedAlignment
pal.alignment.StrippedAnnotatedAlignment
- All Implemented Interfaces:
Serializable
,Alignment
,AnnotationAlignment
,IdGroup
,Report
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:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected int
protected int
protected int
protected double
Fields inherited from class pal.alignment.StrippedAlignment
alias, notDropped
Fields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionint
getChromosome
(int site) Returns chromosomefloat
getChromosomePosition
(int site) Return the position along chromosomegetDataType
(int site) Returns the datatypegetLocusName
(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
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
(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
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Field Details
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minimumProportion
protected double minimumProportion -
minimumCount
protected int minimumCount -
firstSite
protected int firstSite -
lastSite
protected int lastSite
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Constructor Details
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StrippedAnnotatedAlignment
Simple constructor
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Method Details
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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
Returns the name of the locus- Specified by:
getLocusName
in interfaceAnnotationAlignment
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getDataType
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 ?) -
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
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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