org.biojava.nbio.alignment

Class SimpleAlignedSequence<S extends Sequence<C>,C extends Compound>

java.lang.Object

org.biojava.nbio.alignment.SimpleAlignedSequence<S,C>

Type Parameters:

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

All Implemented Interfaces:

Iterable<C>, AlignedSequence<S,C>, Accessioned, Sequence<C>

public class SimpleAlignedSequence<S extends Sequence<C>,C extends Compound>
extends Object
implements AlignedSequence<S,C>

Implements a data structure for a Sequence within an alignment.

Author:

Mark Chapman

Nested Class Summary

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

AlignedSequence.Step

Constructor Summary

Constructors

Constructor and Description
SimpleAlignedSequence(AlignedSequence<S,C> prev, List<AlignedSequence.Step> steps) Creates a new AlignedSequence for the given AlignedSequence in a global alignment.
SimpleAlignedSequence(AlignedSequence<S,C> prev, List<AlignedSequence.Step> steps, int numBefore, int numAfter) Creates a new AlignedSequence for the given AlignedSequence in a local alignment.
SimpleAlignedSequence(S original, List<AlignedSequence.Step> steps) Creates an AlignedSequence for the given Sequence in a global alignment.
SimpleAlignedSequence(S original, List<AlignedSequence.Step> steps, int numBefore, int numAfter) Creates an AlignedSequence for the given Sequence in a local alignment.

Method Summary

Methods

Modifier and Type	Method and Description
void	clearCache() Nullifies cached arrays/objects.
int	countCompounds(C... compounds)
AccessionID	getAccession()
int	getAlignmentIndexAt(int sequenceIndex) Returns the column index within an alignment corresponding to the given index in the original Sequence.
List<C>	getAsList()
C	getCompoundAt(int alignmentIndex)
CompoundSet<C>	getCompoundSet()
Point	getEnd() Returns the Point within an alignment of the last element of the original Sequence.
int	getIndexOf(C compound)
SequenceView<C>	getInverse()
int	getLastIndexOf(C compound)
int	getLength()
Location	getLocationInAlignment() Returns the Location of the original Sequence within an alignment.
int	getNumGaps() Returns number of gaps 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.
String	getSequenceAsString()
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.
SequenceView<C>	getSubSequence(Integer start, Integer end)
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.
Iterator<C>	iterator()
String	toString() Provides standard Java language access to results of getSequenceAsString().

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

SimpleAlignedSequence

public SimpleAlignedSequence(S original,
                     List<AlignedSequence.Step> steps)

Creates an AlignedSequence for the given Sequence in a global alignment.

Parameters:

original - the original Sequence before alignment

steps - lists whether the sequence aligns a Compound or gap at each index of the alignment

Throws:

IllegalArgumentException - if given sequence does not fit in alignment

SimpleAlignedSequence

public SimpleAlignedSequence(S original,
                     List<AlignedSequence.Step> steps,
                     int numBefore,
                     int numAfter)

Creates an AlignedSequence for the given Sequence in a local alignment.

Parameters:

original - the original Sequence before alignment

steps - lists whether the sequence aligns a Compound or gap at each index of the alignment

numBefore - number of Compounds before a local alignment

numAfter - number of Compounds after a local alignment

Throws:

IllegalArgumentException - if given sequence does not fit in alignment

SimpleAlignedSequence

public SimpleAlignedSequence(AlignedSequence<S,C> prev,
                     List<AlignedSequence.Step> steps)

Creates a new AlignedSequence for the given AlignedSequence in a global alignment.

Parameters:

prev - the previous AlignedSequence before this alignment

steps - lists whether the sequence aligns a Compound or gap at each index of the alignment

Throws:

IllegalArgumentException - if given sequence does not fit in alignment

SimpleAlignedSequence

public SimpleAlignedSequence(AlignedSequence<S,C> prev,
                     List<AlignedSequence.Step> steps,
                     int numBefore,
                     int numAfter)

Creates a new AlignedSequence for the given AlignedSequence in a local alignment.

Parameters:

prev - the previous AlignedSequence before this alignment

steps - lists whether the sequence aligns a Compound or gap at each index of the alignment

numBefore - number of Compounds before a local alignment

numAfter - number of Compounds after a local alignment

Throws:

IllegalArgumentException - if given sequence does not fit in alignment

Method Detail

clearCache

public void clearCache()

Description copied from interface: AlignedSequence

Nullifies cached arrays/objects.

Specified by:

clearCache in interface AlignedSequence<S extends Sequence<C>,C extends Compound>

getAlignmentIndexAt

public int getAlignmentIndexAt(int sequenceIndex)

Description copied from interface: AlignedSequence

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

Specified by:

getAlignmentIndexAt in interface AlignedSequence<S extends Sequence<C>,C extends Compound>

Parameters:

sequenceIndex - index in the original Sequence

Returns:

column index within an alignment

getEnd

public Point getEnd()

Description copied from interface: AlignedSequence

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

Specified by:

getEnd in interface AlignedSequence<S extends Sequence<C>,C extends Compound>

Returns:

position within an alignment of final original Sequence element

getLocationInAlignment

public Location getLocationInAlignment()

Description copied from interface: AlignedSequence

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

Specified by:

getLocationInAlignment in interface AlignedSequence<S extends Sequence<C>,C extends Compound>

Returns:

location within an alignment

getNumGaps

public int getNumGaps()

Description copied from interface: AlignedSequence

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

Specified by:

getNumGaps in interface AlignedSequence<S extends Sequence<C>,C extends Compound>

Returns:

number of gaps in the sequence

getOriginalSequence

public S getOriginalSequence()

Description copied from interface: AlignedSequence

Returns the original Sequence before alignment.

Specified by:

getOriginalSequence in interface AlignedSequence<S extends Sequence<C>,C extends Compound>

Returns:

the original sequence

getOverlapCount

public int getOverlapCount()

Description copied from interface: AlignedSequence

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.

Specified by:

getOverlapCount in interface AlignedSequence<S extends Sequence<C>,C extends Compound>

Returns:

the most elements contributed to any alignment column

getSequenceIndexAt

public int getSequenceIndexAt(int alignmentIndex)

Description copied from interface: AlignedSequence

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

Specified by:

getSequenceIndexAt in interface AlignedSequence<S extends Sequence<C>,C extends Compound>

Parameters:

alignmentIndex - column index within an alignment

Returns:

index in the original Sequence

getStart

public Point getStart()

Description copied from interface: AlignedSequence

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

Specified by:

getStart in interface AlignedSequence<S extends Sequence<C>,C extends Compound>

Returns:

position within an alignment of first original Sequence element

isCircular

public boolean isCircular()

Description copied from interface: AlignedSequence

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.

Specified by:

isCircular in interface AlignedSequence<S extends Sequence<C>,C extends Compound>

Returns:

true for circular alignment elements

isGap

public boolean isGap(int alignmentIndex)

Description copied from interface: AlignedSequence

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

Specified by:

isGap in interface AlignedSequence<S extends Sequence<C>,C extends Compound>

Parameters:

alignmentIndex - column index within an alignment

Returns:

true if this column has a gap

countCompounds

public int countCompounds(C... compounds)

Specified by:

countCompounds in interface Sequence<C extends Compound>

getAccession

public AccessionID getAccession()

Specified by:

getAccession in interface Accessioned

getAsList

public List<C> getAsList()

Specified by:

getAsList in interface Sequence<C extends Compound>

getCompoundAt

public C getCompoundAt(int alignmentIndex)

Specified by:

getCompoundAt in interface Sequence<C extends Compound>

getCompoundSet

public CompoundSet<C> getCompoundSet()

Specified by:

getCompoundSet in interface Sequence<C extends Compound>

getIndexOf

public int getIndexOf(C compound)

Specified by:

getIndexOf in interface Sequence<C extends Compound>

getLastIndexOf

public int getLastIndexOf(C compound)

Specified by:

getLastIndexOf in interface Sequence<C extends Compound>

getLength

public int getLength()

Specified by:

getLength in interface Sequence<C extends Compound>

getSequenceAsString

public String getSequenceAsString()

Specified by:

getSequenceAsString in interface Sequence<C extends Compound>

getSubSequence

public SequenceView<C> getSubSequence(Integer start,
                             Integer end)

Specified by:

getSubSequence in interface Sequence<C extends Compound>

iterator

public Iterator<C> iterator()

Specified by:

iterator in interface Iterable<C extends Compound>

toString

public String toString()

Provides standard Java language access to results of getSequenceAsString().

Overrides:

toString in class Object

getInverse

public SequenceView<C> getInverse()

Specified by:

getInverse in interface Sequence<C extends Compound>