pal.alignment
public interface AnnotationAlignment extends Alignment, Report
IdGroup.Utils
Modifier and Type | Method and Description |
---|---|
int |
getChromosome(int site)
Returns chromosome
|
float |
getChromosomePosition(int site)
Return the position along chromosome
|
DataType |
getDataType(int site)
Returns the datatype for a specific site, which could differ by site in complex alignments
|
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 locus (handles gaps)
|
void |
report(java.io.PrintWriter out)
Returns a report for the alignment
|
getAlignedSequenceString, getData, getDataType, getSequenceCount, getSiteCount
getIdCount, getIdentifier, setIdentifier, whichIdNumber
float getChromosomePosition(int site)
int getChromosome(int site)
float getWeightedLocusPosition(int site)
int getLocusPosition(int site)
char getPositionType(int site)
java.lang.String getLocusName(int site)
DataType getDataType(int site)