C - each element of the AlignedSequence is a Compound of type CAccessioned, AlignedSequence<S,C>, java.lang.Iterable<S>, Sequence<S>public interface MutableAlignedSequence<S extends Sequence<C>,C extends Compound> extends AlignedSequence<S,C>
AlignedSequence.AlignedSequence.Step| Modifier and Type | Method | Description |
|---|---|---|
void |
setLocationInAlignment(Location location) |
Sets the position of the
AlignedSequence to the given Location (start, gaps, end). |
void |
shiftAtAlignmentLocation(Location location,
int shift) |
Slides a part of the
AlignedSequence. |
void |
shiftAtSequenceLocation(Location location,
int shift) |
Slides a part of the
AlignedSequence. |
getAccessionclearCache, getAlignmentIndexAt, getEnd, getLocationInAlignment, getNumGaps, getOriginalSequence, getOverlapCount, getSequenceIndexAt, getStart, isCircular, isGapcountCompounds, getAsList, getCompoundAt, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getLength, getSequenceAsString, getSubSequencevoid setLocationInAlignment(Location location)
AlignedSequence to the given Location (start, gaps, end).location - new location for this sequencejava.lang.IllegalArgumentException - if location is invalidvoid shiftAtAlignmentLocation(Location location, int shift)
AlignedSequence.location - portion of sequence moved in alignment coordinatesshift - amount the alignment index changes for each contained elementjava.lang.IllegalArgumentException - if location is invalid or the shift causes a collision with stationary elementsvoid shiftAtSequenceLocation(Location location, int shift)
AlignedSequence.location - portion of sequence moved in sequence coordinatesshift - amount the alignment index changes for each contained elementjava.lang.IllegalArgumentException - if location is invalid or the shift causes a collision with stationary elements