java.io.Serializable
, Alignment
, AnnotationAlignment
, IdGroup
, Report
public class IndelAnnotatedAlignment extends IndelAlignment implements AnnotationAlignment
IdGroup.Utils
Modifier and Type | Field | Description |
---|---|---|
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
|
idGroup, numSeqs, numSites
Constructor | Description |
---|---|
IndelAnnotatedAlignment(AnnotationAlignment a,
boolean anchored) |
Basic constructor.
|
Modifier and Type | Method | Description |
---|---|---|
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
|
getAlignedSequenceString, getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, setDataType, setIdentifier, toString, whichIdNumber
getAlignedSequenceString, getData, getDataType, getSequenceCount, getSiteCount
report
getIdCount, getIdentifier, setIdentifier, whichIdNumber
getData
public float chromosomePosition
public int chromosome
public float[] weightedLocusPosition
public int[] locusPosition
public char[] positionType
public java.lang.String locusName
public IndelAnnotatedAlignment(AnnotationAlignment a, boolean anchored)
anchored
- sets to score anchored indels as same positionpublic 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