org.biojava.nbio.core.alignment.template

Interface AlignedSequence<S extends Sequence<C>,C extends Compound>

Type Parameters:

C - each element of the Sequence is a Compound of type C

All Superinterfaces:

Accessioned, Iterable<C>, Sequence<C>

All Known Subinterfaces:

MutableAlignedSequence<S,C>

All Known Implementing Classes:

SimpleAlignedSequence

public interface AlignedSequence<S extends Sequence<C>,C extends Compound>
extends Sequence<C>

Defines a data structure for a Sequence within an alignment.

Author:

Mark Chapman, Paolo Pavan

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	AlignedSequence.Step Defines an alignment step in order to pass alignment information from an Aligner to a constructor.

Method Summary

Modifier and Type	Method and Description
void	clearCache() Nullifies cached arrays/objects.
int[]	getAlignmentFromSequence() Returns the alignment.
int	getAlignmentIndexAt(int sequenceIndex) Returns the column index within an alignment corresponding to the given index in the original Sequence.
double	getCoverage() Returns the coverage, as a fraction between 0 and 1, of this AlignedSequence with respect to the original sequence.
Point	getEnd() Returns the Point within an alignment of the last element of the original Sequence.
Location	getLocationInAlignment() Returns the Location of the original Sequence within an alignment.
int	getNumGapPositions() Returns number of gap positions (gap openings and extensions) in the sequence.
int	getNumGaps() Returns number of gaps (gap openings) in the sequence.
S	getOriginalSequence() Returns the original Sequence before alignment.
int	getOverlapCount() Returns the maximum number of elements contributed to a column of an alignment by this Sequence.
int[]	getSequenceFromAlignment() Returns the sequence positions at each alignment index
int	getSequenceIndexAt(int alignmentIndex) Returns the index in the original Sequence corresponding to the given index within an alignment.
Point	getStart() Returns the Point within an alignment of the first element of the original Sequence.
boolean	isCircular() Returns true if this Sequence wraps around from the last alignment column back to the first.
boolean	isGap(int alignmentIndex) Returns true if this Sequence has a gap at a particular alignment column.

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

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

Methods inherited from interface java.lang.Iterable

forEach, iterator, spliterator

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

getAccession

Method Detail

clearCache

void clearCache()

Nullifies cached arrays/objects.

getAlignmentFromSequence

int[] getAlignmentFromSequence()

Returns the alignment.

Returns:

the alignment

getSequenceFromAlignment

int[] getSequenceFromAlignment()

Returns the sequence positions at each alignment index

Returns:

array of the sequence positions

getAlignmentIndexAt

int getAlignmentIndexAt(int sequenceIndex)

Returns the column index within an alignment corresponding to the given index in the original Sequence. Both indices are 1-indexed and inclusive.

Parameters:

sequenceIndex - index in the original Sequence

Returns:

column index within an alignment

Throws:

IndexOutOfBoundsException - if sequenceIndex < 1 or sequenceIndex > getOriginalSequence().Sequence.getLength()

getEnd

Point getEnd()

Returns the Point within an alignment of the last element of the original Sequence.

Returns:

position within an alignment of final original Sequence element

getLocationInAlignment

Location getLocationInAlignment()

Returns the Location of the original Sequence within an alignment. This provides access to additional substructure beyond start and end points.

Returns:

location within an alignment

getNumGaps

int getNumGaps()

Returns number of gaps (gap openings) in the sequence. This could be determined from the Location information or from gap Compounds, which may not necessarily result in the same number.

Returns:

number of gaps in the sequence

getNumGapPositions

int getNumGapPositions()

Returns number of gap positions (gap openings and extensions) in the sequence. This could be determined from the Location information or from gap Compounds, which may not necessarily result in the same number.

Returns:

number of gap positions in the sequence

getCoverage

double getCoverage()

Returns the coverage, as a fraction between 0 and 1, of this AlignedSequence with respect to the original sequence. This is equivalent to (Sequence.getLength() - getNumGapPositions()) / getOriginalSequence().getLength().

Returns:

coverage of the original sequence by the aligned sequence

getOriginalSequence

S getOriginalSequence()

Returns the original Sequence before alignment.

Returns:

the original sequence

getOverlapCount

int getOverlapCount()

Returns the maximum number of elements contributed to a column of an alignment by this Sequence. If this Sequence is circular, this number is >= 1. If not, this overlap count is definitely 1.

Returns:

the most elements contributed to any alignment column

getSequenceIndexAt

int getSequenceIndexAt(int alignmentIndex)

Returns the index in the original Sequence corresponding to the given index within an alignment. Both indices are 1-indexed and inclusive.

Parameters:

alignmentIndex - column index within an alignment

Returns:

index in the original Sequence

Throws:

IndexOutOfBoundsException - if alignmentIndex < 1 or alignmentIndex > Sequence.getLength()

getStart

Point getStart()

Returns the Point within an alignment of the first element of the original Sequence.

Returns:

position within an alignment of first original Sequence element

isCircular

boolean isCircular()

Returns true if this Sequence wraps around from the last alignment column back to the first. This makes overlap possible, but does not require an overlap count > 1.

Returns:

true for circular alignment elements

isGap

boolean isGap(int alignmentIndex)

Returns true if this Sequence has a gap at a particular alignment column.

Parameters:

alignmentIndex - column index within an alignment

Returns:

true if this column has a gap

Throws:

IndexOutOfBoundsException - if alignmentIndex < 1 or alignmentIndex > Sequence.getLength()