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java.lang.Objectpal.alignment.AbstractAlignment
pal.alignment.StrippedAlignment
pal.alignment.StrippedAnnotatedAlignment
public class StrippedAnnotatedAlignment
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.
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.misc.IdGroup |
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IdGroup.Utils |
Field Summary | |
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protected int |
firstSite
|
protected int |
lastSite
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protected int |
minimumCount
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protected double |
minimumProportion
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Fields inherited from class pal.alignment.StrippedAlignment |
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alias, notDropped |
Fields inherited from class pal.alignment.AbstractAlignment |
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idGroup, numSeqs, numSites |
Fields inherited from interface pal.alignment.Alignment |
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GAP, GAP_TLA, GAPS, UNKNOWN, UNKNOWN_TLA |
Constructor Summary | |
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StrippedAnnotatedAlignment(AnnotationAlignment a)
Simple constructor |
Method Summary | |
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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 |
void |
report(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model) |
Methods inherited from class pal.alignment.StrippedAlignment |
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dropSite, getData, removeConstantSites, removeGaps, removeNoninformativeSites, removeSites, removeUnknowns |
Methods inherited from class pal.alignment.AbstractAlignment |
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getAlignedSequenceString, getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, setDataType, setIdentifier, toString, whichIdNumber |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface pal.alignment.Alignment |
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getAlignedSequenceString, getData, getDataType, getSequenceCount, getSiteCount |
Methods inherited from interface pal.misc.IdGroup |
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getIdCount, getIdentifier, setIdentifier, whichIdNumber |
Field Detail |
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protected double minimumProportion
protected int minimumCount
protected int firstSite
protected int lastSite
Constructor Detail |
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public StrippedAnnotatedAlignment(AnnotationAlignment a)
Method Detail |
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public float getChromosomePosition(int site)
getChromosomePosition
in interface AnnotationAlignment
public int getChromosome(int site)
getChromosome
in interface AnnotationAlignment
public float getWeightedLocusPosition(int site)
getWeightedLocusPosition
in interface AnnotationAlignment
public int getLocusPosition(int site)
getLocusPosition
in interface AnnotationAlignment
public char getPositionType(int site)
getPositionType
in interface AnnotationAlignment
public java.lang.String getLocusName(int site)
getLocusName
in interface AnnotationAlignment
public DataType getDataType(int site)
getDataType
in interface AnnotationAlignment
public void removeSitesOutsideRange(int firstSite, int lastSite)
firstSite
- first site to keep in the rangelastSite
- last site to keep in the rangepublic void removeConstantSitesIgnoreGapsMissing()
public void removeSitesBasedOnFreqIgnoreGapsMissing(double minimumProportion, int minimumCount)
minimumProportion
- minimum proportion of sites different from the consensusminimumCount
- minimum number of sequences with a good bases (not - or ?)public void report(java.io.PrintWriter out)
Report
report
in interface AnnotationAlignment
report
in interface Report
report
in class AbstractAlignment
out
- output stream
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