org.biojava3.alignment.template
Interface MutableAlignedSequence<S extends Sequence<C>,C extends Compound>
- Type Parameters:
C
- each element of the AlignedSequence
is a Compound
of type C
- All Superinterfaces:
- Accessioned, AlignedSequence<S,C>, Iterable<C>, Sequence<C>
public interface MutableAlignedSequence<S extends Sequence<C>,C extends Compound>
- extends AlignedSequence<S,C>
Defines a mutable (editable) data structure for an AlignedSequence
.
- Author:
- Mark Chapman
Methods inherited from interface org.biojava3.alignment.template.AlignedSequence |
clearCache, getAlignmentIndexAt, getEnd, getLocationInAlignment, getNumGaps, getOriginalSequence, getOverlapCount, getSequenceIndexAt, getStart, isCircular, isGap |
setLocationInAlignment
void setLocationInAlignment(Location location)
- Sets the position of the
AlignedSequence
to the given Location
(start, gaps, end).
- Parameters:
location
- new location for this sequence
- Throws:
IllegalArgumentException
- if location is invalid
shiftAtAlignmentLocation
void shiftAtAlignmentLocation(Location location,
int shift)
- Slides a part of the
AlignedSequence
.
- Parameters:
location
- portion of sequence moved in alignment coordinatesshift
- amount the alignment index changes for each contained element
- Throws:
IllegalArgumentException
- if location is invalid or the shift causes a collision with stationary elements
shiftAtSequenceLocation
void shiftAtSequenceLocation(Location location,
int shift)
- Slides a part of the
AlignedSequence
.
- Parameters:
location
- portion of sequence moved in sequence coordinatesshift
- amount the alignment index changes for each contained element
- Throws:
IllegalArgumentException
- if location is invalid or the shift causes a collision with stationary elements