java.io.Serializable
, Alignment
, AnnotationAlignment
, IdGroup
, Report
public class MultiLocusAnnotatedAlignment extends SimpleAlignment 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
|
DataType[] |
siteDataType |
provides datatype for each locus separately
|
float[] |
weightedPosition |
used to designate weighted position; accounts for gaps
|
idGroup, numSeqs, numSites
Constructor | Description |
---|---|
MultiLocusAnnotatedAlignment() |
null constructor.
|
MultiLocusAnnotatedAlignment(Alignment a) |
Basic constructor.
|
MultiLocusAnnotatedAlignment(AnnotationAlignment a) |
Clone constructor for Annotated alignment
|
MultiLocusAnnotatedAlignment(AnnotationAlignment a,
IdGroup newGroup) |
This constructor will subset the alignment based on the taxa in IdGroup
|
MultiLocusAnnotatedAlignment(Identifier[] ids,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt) |
|
MultiLocusAnnotatedAlignment(IdGroup group,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt) |
|
MultiLocusAnnotatedAlignment(IdGroup group,
java.lang.String[] sequences,
DataType dt) |
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)
|
protected void |
init(IdGroup group,
java.lang.String[] sequences) |
|
protected void |
initMatrices() |
|
void |
setChromosome(int chromosome,
int site) |
Sets chromosome
|
void |
setChromosomePosition(float position,
int site) |
Set the position along chromosome
|
void |
setLocusName(java.lang.String locusName,
int site) |
Sets the name of the locus
|
void |
setLocusPosition(int position,
int site) |
Set the position within the locus
|
void |
setPositionType(int site,
char posType) |
Set thes position type (eg.
|
void |
setWeightedLocusPosition(int site,
float weightedPos) |
Sets the weighted position along the gene (handles gaps)
|
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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
getAlignedSequenceString, getData
public float[] chromosomePosition
public int[] chromosome
public float[] weightedPosition
public int[] locusPosition
public char[] positionType
public java.lang.String[] locusName
public DataType[] siteDataType
public MultiLocusAnnotatedAlignment(Alignment a)
public MultiLocusAnnotatedAlignment()
public MultiLocusAnnotatedAlignment(AnnotationAlignment a)
public MultiLocusAnnotatedAlignment(Identifier[] ids, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
public MultiLocusAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, DataType dt)
public MultiLocusAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
public MultiLocusAnnotatedAlignment(AnnotationAlignment a, IdGroup newGroup)
protected void initMatrices()
protected void init(IdGroup group, java.lang.String[] sequences)
public float getChromosomePosition(int site)
getChromosomePosition
in interface AnnotationAlignment
public void setChromosomePosition(float position, int site)
public int getChromosome(int site)
getChromosome
in interface AnnotationAlignment
public void setChromosome(int chromosome, int site)
public float getWeightedLocusPosition(int site)
getWeightedLocusPosition
in interface AnnotationAlignment
public void setWeightedLocusPosition(int site, float weightedPos)
public int getLocusPosition(int site)
getLocusPosition
in interface AnnotationAlignment
public void setLocusPosition(int position, int site)
public char getPositionType(int site)
getPositionType
in interface AnnotationAlignment
public void setPositionType(int site, char posType)
public java.lang.String getLocusName(int site)
getLocusName
in interface AnnotationAlignment
public void setLocusName(java.lang.String locusName, int site)
public DataType getDataType(int site)
getDataType
in interface AnnotationAlignment