T
- the token type used in the underlying alignment modelpublic interface IndexTranslator<T>
Modifier and Type | Method and Description |
---|---|
int |
getAlignedIndex(java.lang.String sequenceID,
int unalignedIndex)
Returns the column in the alignment, the specified token is contained in
|
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.
|
IndexRelation |
getUnalignedIndex(java.lang.String sequenceID,
int alignedIndex)
Returns the index of the sequence token at the specified alignment column.
|
int |
getUnalignedLength(java.lang.String sequenceID) |
AlignmentModel<T> getModel()
java.util.Set<T> getGapTokens()
IndexRelation getUnalignedIndex(java.lang.String sequenceID, int alignedIndex)
sequenceID
- the ID of the sequence which contains the token to be locatedalignedIndex
- the column index in the alignmentIndexRelation.getCorresponding()
will return IndexRelation.GAP
, and IndexRelation.getBefore()
and
{IndexRelation#getAfter()} the positions of the neighboring tokens, if present. If the specified
column contains a token, IndexRelation.getCorresponding()
will return the index of that
token in the unaligned sequence.)int getAlignedIndex(java.lang.String sequenceID, int unalignedIndex)
sequenceID
- the ID of the sequence which contains the token to be locatedunalignedIndex
- the index of the token in the unaligned sequenceint getUnalignedLength(java.lang.String sequenceID)