Package org.biojava.nbio.core.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, Paolo Pavan

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.nbio.core.alignment.template.AlignedSequence

AlignedSequence.Step

Method Summary

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.

Methods inherited from interface org.biojava.nbio.core.sequence.template.Accessioned

getAccession

Methods inherited from interface org.biojava.nbio.core.alignment.template.AlignedSequence

clearCache, getAlignmentFromSequence, getAlignmentIndexAt, getCoverage, getEnd, getLocationInAlignment, getNumGapPositions, getNumGaps, getOriginalSequence, getOverlapCount, getSequenceFromAlignment, getSequenceIndexAt, getStart, isCircular, isGap

Methods inherited from interface java.lang.Iterable

forEach, iterator, spliterator

Methods inherited from interface org.biojava.nbio.core.sequence.template.Sequence

countCompounds, getAsList, getCompoundAt, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getLength, getSequenceAsString, getSubSequence

Method Detail

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 coordinates

shift - 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 coordinates

shift - amount the alignment index changes for each contained element

Throws:

IllegalArgumentException - if location is invalid or the shift causes a collision with stationary elements