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 . |
getAccession
clearCache, getAlignmentIndexAt, getEnd, getLocationInAlignment, getNumGaps, getOriginalSequence, getOverlapCount, getSequenceIndexAt, getStart, isCircular, isGap
countCompounds, getAsList, getCompoundAt, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getLength, getSequenceAsString, getSubSequence
void 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