Package org.biojava.nbio.core.alignment

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

java.lang.Object

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

Type Parameters:

S - the sequence type

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

All Implemented Interfaces:

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

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

Implements a data structure for a Sequence within an alignment.

Author:

Mark Chapman

See Also:

• Serialized Form

Nested Class Summary

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

AlignedSequence.Step

Constructor Summary

Constructors

Constructor	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

Modifier and Type	Method	Description
void	clearCache()	Nullifies cached arrays/objects.
int	countCompounds(C... compounds)	Returns the number of times we found a compound in the Sequence
boolean	equals(Object o)
AccessionID	getAccession()	Returns the AccessionID this location is currently bound with
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.
List<C>	getAsList()	Returns the Sequence as a List of compounds
C	getCompoundAt(int alignmentIndex)	Returns the Compound at the given biological index
CompoundSet<C>	getCompoundSet()	Gets the compound set used to back this 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.
int	getIndexOf(C compound)	Scans through the Sequence looking for the first occurrence of the given compound
SequenceView<C>	getInverse()	Does the right thing to get the inverse of the current Sequence.
int	getLastIndexOf(C compound)	Scans through the Sequence looking for the last occurrence of the given compound
int	getLength()	Returns the length of the 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.
String	getSequenceAsString()	Returns the String representation of the 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.
SequenceView<C>	getSubSequence(Integer start, Integer end)	Returns a portion of the sequence from the different positions.
int	hashCode()
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, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Details

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 Details

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>

getAlignmentFromSequence

public int[] getAlignmentFromSequence()

Description copied from interface: AlignedSequence

Returns the alignment.

Specified by:

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

Returns:

the alignment

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 (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.

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

getSequenceFromAlignment

public int[] getSequenceFromAlignment()

Description copied from interface: AlignedSequence

Returns the sequence positions at each alignment index

Specified by:

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

Returns:

array of the sequence positions

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)

Description copied from interface: Sequence

Returns the number of times we found a compound in the Sequence

Specified by:

countCompounds in interface Sequence<S extends Sequence<C>>

Parameters:

compounds - Vargs of the compounds to count

Returns:

Number of times a compound was found

getAccession

public AccessionID getAccession()

Description copied from interface: Accessioned

Returns the AccessionID this location is currently bound with

Specified by:

getAccession in interface Accessioned

getAsList

public List<C> getAsList()

Description copied from interface: Sequence

Returns the Sequence as a List of compounds

Specified by:

getAsList in interface Sequence<S extends Sequence<C>>

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

getCompoundAt

public C getCompoundAt(int alignmentIndex)

Description copied from interface: Sequence

Returns the Compound at the given biological index

Specified by:

getCompoundAt in interface Sequence<S extends Sequence<C>>

Parameters:

alignmentIndex - Biological index (1 to n)

Returns:

Compound at the specified position

getCompoundSet

public CompoundSet<C> getCompoundSet()

Description copied from interface: Sequence

Gets the compound set used to back this Sequence

Specified by:

getCompoundSet in interface Sequence<S extends Sequence<C>>

getIndexOf

public int getIndexOf(C compound)

Description copied from interface: Sequence

Scans through the Sequence looking for the first occurrence of the given compound

Specified by:

getIndexOf in interface Sequence<S extends Sequence<C>>

Parameters:

compound - Compounds to look for

Returns:

Index of the first position of the compound in the sequence (1 to n)

getLastIndexOf

public int getLastIndexOf(C compound)

Description copied from interface: Sequence

Scans through the Sequence looking for the last occurrence of the given compound

Specified by:

getLastIndexOf in interface Sequence<S extends Sequence<C>>

Parameters:

compound - Compounds to look for

Returns:

Index of the last position of the compound in the sequence (1 to n)

getLength

public int getLength()

Description copied from interface: Sequence

Returns the length of the Sequence

Specified by:

getLength in interface Sequence<S extends Sequence<C>>

getSequenceAsString

public String getSequenceAsString()

Description copied from interface: Sequence

Returns the String representation of the Sequence

Specified by:

getSequenceAsString in interface Sequence<S extends Sequence<C>>

getSubSequence

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

Description copied from interface: Sequence

Returns a portion of the sequence from the different positions. This is indexed from 1

Specified by:

getSubSequence in interface Sequence<S extends Sequence<C>>

Parameters:

start - Biological index start; must be greater than 0

end - Biological end; must be less than length + 1

Returns:

A SequenceView of the offset

iterator

public Iterator<C> iterator()

Specified by:

iterator in interface Iterable<S extends Sequence<C>>

toString

public String toString()

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

Overrides:

toString in class Object

getInverse

public SequenceView<C> getInverse()

Description copied from interface: Sequence

Does the right thing to get the inverse of the current Sequence. This means either reversing the Sequence and optionally complementing the Sequence.

Specified by:

getInverse in interface Sequence<S extends Sequence<C>>

getNumGapPositions

public int getNumGapPositions()

Description copied from interface: AlignedSequence

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.

Specified by:

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

Returns:

number of gap positions in the sequence

getCoverage

public double getCoverage()

Description copied from interface: AlignedSequence

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() - AlignedSequence.getNumGapPositions()) / getOriginalSequence().getLength().

Specified by:

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

Returns:

coverage of the original sequence by the aligned sequence