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	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	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

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	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)
```

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

Field Summary

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

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

Field Detail

gapPenalty

anchors

cutsPerSection

profile

xyStart

xyMax

max

min

score

scores

time

Constructor Detail

AbstractMatrixAligner

AbstractMatrixAligner

AbstractMatrixAligner

Method Detail

getGapPenalty

getSubstitutionMatrix

isLocal

isStoringScoreMatrix

setGapPenalty

setSubstitutionMatrix

setStoringScoreMatrix

getScoreMatrix

getScoreMatrixAsString

getComputationTime

getProfile

getMaxScore

getMinScore

getScore

align

getSubstitutionScoreVector

getSubstitutionScoreVector

reset

getCompoundSet

getCompoundsOfQuery

getCompoundsOfTarget

getScoreMatrixDimensions

getSubstitutionScore

isReady

setProfile

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