public abstract class AbstractIndexTranslator<T,D> extends java.lang.Object
Constructor and Description |
---|
AbstractIndexTranslator(AlignmentModel<T> model,
java.util.Set<T> gapTokens) |
Modifier and Type | Method and Description |
---|---|
protected abstract D |
createSequenceData(java.lang.String sequenceID) |
protected void |
finalize() |
abstract int |
getAlignedIndex(java.lang.String sequenceID,
int unalignedIndex) |
java.util.Set<T> |
getGapTokens()
Returns the set of gap tokens used by this instance.
|
AlignmentModel<T> |
getModel()
Returns the alignment model this instance works on.
|
protected D |
getSequenceData(java.lang.String sequenceID) |
abstract IndexRelation |
getUnalignedIndex(java.lang.String sequenceID,
int alignedIndex) |
public AbstractIndexTranslator(AlignmentModel<T> model, java.util.Set<T> gapTokens)
public AlignmentModel<T> getModel()
public java.util.Set<T> getGapTokens()
public abstract IndexRelation getUnalignedIndex(java.lang.String sequenceID, int alignedIndex)
public abstract int getAlignedIndex(java.lang.String sequenceID, int unalignedIndex)
protected abstract D createSequenceData(java.lang.String sequenceID)
protected D getSequenceData(java.lang.String sequenceID)
protected void finalize() throws java.lang.Throwable
finalize
in class java.lang.Object
java.lang.Throwable