org.biojava.nbio.alignment.template

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

java.lang.Object

org.biojava.nbio.alignment.template.AbstractScorer

org.biojava.nbio.alignment.template.AbstractMatrixAligner<S,C>

Type Parameters:

S - each element of the alignment Profile is of type S

C - each element of an AlignedSequence is a Compound of type C

All Implemented Interfaces:

Aligner<S,C>, MatrixAligner<S,C>, Scorer

Direct Known Subclasses:

AbstractPairwiseSequenceAligner, AbstractProfileProfileAligner

public abstract class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
extends AbstractScorer
implements MatrixAligner<S,C>

Implements common code for an Aligner which builds a score matrix during computation.

Author:

Mark Chapman, Daniel Cameron

Field Summary

Fields

Modifier and Type	Field and Description
protected List<AlignerHelper.Anchor>	anchors
protected int	cutsPerSection
protected GapPenalty	gapPenalty
protected int	max
protected int	min
protected Profile<S,C>	profile
protected int	score
protected int[][][]	scores Dynamic programming score matrix The first dimension has the length of the first (query) sequence + 1 The second has the length of the second (target) sequence + 1 The third has length 1 for linear gap penalty and 3 for affine/constant gap (one each for match/substitution, deletion, insertion)
protected long	time
protected int[]	xyMax End position of the aligned sequence in the query and target respectively
protected int[]	xyStart Start position of the aligned sequence in the query and target respectively

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractMatrixAligner() Before running an alignment, data must be sent in via calls to setGapPenalty(GapPenalty) and setSubstitutionMatrix(SubstitutionMatrix).
protected	AbstractMatrixAligner(GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) Prepares for an alignment.
protected	AbstractMatrixAligner(GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix, boolean local) Prepares for an alignment.

Method Summary

Modifier and Type	Method and Description
protected void	align() Performs alignment
protected abstract CompoundSet<C>	getCompoundSet()
protected abstract List<C>	getCompoundsOfQuery()
protected abstract List<C>	getCompoundsOfTarget()
long	getComputationTime() Returns the computation time needed for an alignment computed in nanoseconds.
GapPenalty	getGapPenalty() Returns the gap penalties.
double	getMaxScore() Returns maximum possible score.
double	getMinScore() Returns minimum possible score.
Profile<S,C>	getProfile() Returns the alignment Profile produced by this alignment algorithm.
double	getScore() Returns score resulting from algorithm.
int[][][]	getScoreMatrix() Returns the entire score matrix built during alignment.
String	getScoreMatrixAsString() Returns a depiction of the score matrix as a String.
protected abstract int[]	getScoreMatrixDimensions()
SubstitutionMatrix<C>	getSubstitutionMatrix() Returns the substitution matrix.
protected abstract int	getSubstitutionScore(int queryColumn, int targetColumn)
protected int[]	getSubstitutionScoreVector(int queryColumn) Returns score for the alignment of the query column to all target columns
protected int[]	getSubstitutionScoreVector(int queryColumn, AlignerHelper.Subproblem subproblem) Returns score for the alignment of the query column to all target columns
boolean	isLocal() Returns whether alignment finds a region of similarity rather than aligning every compound.
protected abstract boolean	isReady()
boolean	isStoringScoreMatrix() Returns choice to cache the score matrix or to save memory by deleting score matrix after alignment.
protected void	reset() Resets output fields; should be overridden to set max and min
void	setGapPenalty(GapPenalty gapPenalty) Sets the gap penalties.
protected abstract void	setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
void	setStoringScoreMatrix(boolean storingScoreMatrix) Sets choice to cache the score matrix or to save memory by deleting score matrix after alignment.
void	setSubstitutionMatrix(SubstitutionMatrix<C> subMatrix) Sets the substitution matrix.

Methods inherited from class org.biojava.nbio.alignment.template.AbstractScorer

getDistance, getDistance, getSimilarity, getSimilarity

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.nbio.alignment.template.Scorer

getDistance, getDistance, getSimilarity, getSimilarity

Field Detail

gapPenalty

protected GapPenalty gapPenalty

anchors

protected List<AlignerHelper.Anchor> anchors

cutsPerSection

protected int cutsPerSection

profile

protected Profile<S extends Sequence<C>,C extends Compound> profile

xyStart

protected int[] xyStart

Start position of the aligned sequence in the query and target respectively

xyMax

protected int[] xyMax

End position of the aligned sequence in the query and target respectively

max

protected int max

min

protected int min

score

protected int score

scores

protected int[][][] scores

Dynamic programming score matrix The first dimension has the length of the first (query) sequence + 1 The second has the length of the second (target) sequence + 1 The third has length 1 for linear gap penalty and 3 for affine/constant gap (one each for match/substitution, deletion, insertion)

time

protected long time

Constructor Detail

AbstractMatrixAligner

protected AbstractMatrixAligner()

Before running an alignment, data must be sent in via calls to setGapPenalty(GapPenalty) and setSubstitutionMatrix(SubstitutionMatrix).

AbstractMatrixAligner

protected AbstractMatrixAligner(GapPenalty gapPenalty,
                                SubstitutionMatrix<C> subMatrix)

Prepares for an alignment.

Parameters:

gapPenalty - the gap penalties used during alignment

subMatrix - the set of substitution scores used during alignment

AbstractMatrixAligner

protected AbstractMatrixAligner(GapPenalty gapPenalty,
                                SubstitutionMatrix<C> subMatrix,
                                boolean local)

Prepares for an alignment.

Parameters:

gapPenalty - the gap penalties used during alignment

subMatrix - the set of substitution scores used during alignment

local - if true, find a region of similarity rather than aligning every compound

Method Detail

getGapPenalty

public GapPenalty getGapPenalty()

Returns the gap penalties.

Returns:

the gap penalties used during alignment

getSubstitutionMatrix

public SubstitutionMatrix<C> getSubstitutionMatrix()

Returns the substitution matrix.

Returns:

the set of substitution scores used during alignment

isLocal

public boolean isLocal()

Returns whether alignment finds a region of similarity rather than aligning every compound.

Returns:

true if alignment finds a region of similarity rather than aligning every compound

isStoringScoreMatrix

public boolean isStoringScoreMatrix()

Returns choice to cache the score matrix or to save memory by deleting score matrix after alignment.

Returns:

choice to cache the score matrix

setGapPenalty

public void setGapPenalty(GapPenalty gapPenalty)

Sets the gap penalties.

Parameters:

gapPenalty - the gap penalties used during alignment

setSubstitutionMatrix

public void setSubstitutionMatrix(SubstitutionMatrix<C> subMatrix)

Sets the substitution matrix.

Parameters:

subMatrix - the set of substitution scores used during alignment

setStoringScoreMatrix

public void setStoringScoreMatrix(boolean storingScoreMatrix)

Sets choice to cache the score matrix or to save memory by deleting score matrix after alignment.

Parameters:

storingScoreMatrix - choice to cache the score matrix

getScoreMatrix

public int[][][] getScoreMatrix()

Description copied from interface: MatrixAligner

Returns the entire score matrix built during alignment. The first dimension has the length of the first (query) sequence + 1; the second has the length of the second (target) sequence + 1; the third has length equal to the number of scores stored per pairing of an element from each Sequence.

Specified by:

getScoreMatrix in interface MatrixAligner<S extends Sequence<C>,C extends Compound>

Returns:

the score matrix

getScoreMatrixAsString

public String getScoreMatrixAsString()

Description copied from interface: MatrixAligner

Returns a depiction of the score matrix as a String. This may include additional description such as labels for each dimension: element from query sequence, element from target sequence, and meaning of each score.

Specified by:

getScoreMatrixAsString in interface MatrixAligner<S extends Sequence<C>,C extends Compound>

Returns:

the score matrix as a character sequence

getComputationTime

public long getComputationTime()

Description copied from interface: Aligner

Returns the computation time needed for an alignment computed in nanoseconds.

Specified by:

getComputationTime in interface Aligner<S extends Sequence<C>,C extends Compound>

Returns:

the computation time in nanoseconds

getProfile

public Profile<S,C> getProfile()

Description copied from interface: Aligner

Returns the alignment Profile produced by this alignment algorithm.

Specified by:

getProfile in interface Aligner<S extends Sequence<C>,C extends Compound>

Returns:

the alignment profile

getMaxScore

public double getMaxScore()

Description copied from interface: Scorer

Returns maximum possible score.

Specified by:

getMaxScore in interface Scorer

Returns:

maximum possible score

getMinScore

public double getMinScore()

Description copied from interface: Scorer

Returns minimum possible score.

Specified by:

getMinScore in interface Scorer

Returns:

minimum possible score

getScore

public double getScore()

Description copied from interface: Scorer

Returns score resulting from algorithm. This should normalize between 0 and 1 by calculating (Scorer.getScore() - Scorer.getMinScore()) / (Scorer.getMaxScore() - Scorer.getMinScore()).

Specified by:

getScore in interface Scorer

Returns:

score resulting from algorithm

align

protected void align()

Performs alignment

getSubstitutionScoreVector

protected int[] getSubstitutionScoreVector(int queryColumn)

Returns score for the alignment of the query column to all target columns

Parameters:

queryColumn -

Returns:

getSubstitutionScoreVector

protected int[] getSubstitutionScoreVector(int queryColumn,
                                           AlignerHelper.Subproblem subproblem)

Returns score for the alignment of the query column to all target columns

Parameters:

queryColumn -

subproblem -

Returns:

reset

protected void reset()

Resets output fields; should be overridden to set max and min

getCompoundSet

protected abstract CompoundSet<C> getCompoundSet()

getCompoundsOfQuery

protected abstract List<C> getCompoundsOfQuery()

getCompoundsOfTarget

protected abstract List<C> getCompoundsOfTarget()

getScoreMatrixDimensions

protected abstract int[] getScoreMatrixDimensions()

getSubstitutionScore

protected abstract int getSubstitutionScore(int queryColumn,
                                            int targetColumn)

isReady

protected abstract boolean isReady()

setProfile

protected abstract void setProfile(List<AlignedSequence.Step> sx,
                                   List<AlignedSequence.Step> sy)