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java.lang.Objectpal.alignment.AbstractAlignment
pal.alignment.IndelAlignment
pal.alignment.IndelAnnotatedAlignment
public class IndelAnnotatedAlignment
an extension of the IndelAlignment that includes annotation. This should only extract indels from a single locus.
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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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 |
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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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IndelAnnotatedAlignment(AnnotationAlignment a,
boolean anchored)
Basic 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 |
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 |
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getData |
Methods inherited from class pal.alignment.AbstractAlignment |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface pal.alignment.AnnotationAlignment |
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report |
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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public float chromosomePosition
public int chromosome
public float[] weightedLocusPosition
public int[] locusPosition
public char[] positionType
public java.lang.String locusName
Constructor Detail |
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public IndelAnnotatedAlignment(AnnotationAlignment a, boolean anchored)
anchored
- sets to score anchored indels as same positionMethod Detail |
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public float getChromosomePosition(int site)
getChromosomePosition
in interface AnnotationAlignment
public void setChromosomePosition(float position)
public int getChromosome(int site)
getChromosome
in interface AnnotationAlignment
public void setChromosome(int chromosome)
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 void setLocusName(java.lang.String locusName)
public DataType getDataType(int site)
getDataType
in interface AnnotationAlignment
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