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java.lang.Objectorg.biojava3.alignment.template.AbstractScorer
org.biojava3.alignment.template.AbstractMatrixAligner<S,C>
S
- each element of the alignment Profile
is of type SC
- each element of an AlignedSequence
is a Compound
of type Cpublic abstract class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
Implements common code for an Aligner
which builds a score matrix during computation.
Field Summary | |
---|---|
protected int[] |
anchors
|
protected int |
cutsPerSection
|
protected GapPenalty |
gapPenalty
|
protected short |
max
|
protected short |
min
|
protected Profile<S,C> |
profile
|
protected short |
score
|
protected short[][][] |
scores
|
protected long |
time
|
protected int[] |
xyMax
|
protected int[] |
xyStart
|
Constructor Summary | |
---|---|
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 | |
---|---|
protected void |
align()
|
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. |
int |
getMaxScore()
Returns maximum possible score. |
int |
getMinScore()
Returns minimum possible score. |
Profile<S,C> |
getProfile()
Returns the alignment Profile produced by this alignment algorithm. |
int |
getScore()
Returns score resulting from algorithm. |
short[][][] |
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 short |
getSubstitutionScore(int queryColumn,
int targetColumn)
|
protected short[] |
getSubstitutionScoreVector(int queryColumn)
|
protected short[] |
getSubstitutionScoreVector(int queryColumn,
int[] subproblem)
|
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()
|
protected void |
resetAnchors()
|
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.biojava3.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.biojava3.alignment.template.Scorer |
---|
getDistance, getDistance, getSimilarity, getSimilarity |
Field Detail |
---|
protected GapPenalty gapPenalty
protected int[] anchors
protected int cutsPerSection
protected Profile<S extends Sequence<C>,C extends Compound> profile
protected int[] xyMax
protected int[] xyStart
protected short max
protected short min
protected short score
protected short[][][] scores
protected long time
Constructor Detail |
---|
protected AbstractMatrixAligner()
setGapPenalty(GapPenalty)
and
setSubstitutionMatrix(SubstitutionMatrix)
.
protected AbstractMatrixAligner(GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
gapPenalty
- the gap penalties used during alignmentsubMatrix
- the set of substitution scores used during alignmentprotected AbstractMatrixAligner(GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix, boolean local)
gapPenalty
- the gap penalties used during alignmentsubMatrix
- the set of substitution scores used during alignmentlocal
- if true, find a region of similarity rather than aligning every compoundMethod Detail |
---|
public GapPenalty getGapPenalty()
public SubstitutionMatrix<C> getSubstitutionMatrix()
public boolean isLocal()
public boolean isStoringScoreMatrix()
public void setGapPenalty(GapPenalty gapPenalty)
gapPenalty
- the gap penalties used during alignmentpublic void setSubstitutionMatrix(SubstitutionMatrix<C> subMatrix)
subMatrix
- the set of substitution scores used during alignmentpublic void setStoringScoreMatrix(boolean storingScoreMatrix)
storingScoreMatrix
- choice to cache the score matrixpublic short[][][] getScoreMatrix()
MatrixAligner
Sequence
.
getScoreMatrix
in interface MatrixAligner<S extends Sequence<C>,C extends Compound>
public String getScoreMatrixAsString()
MatrixAligner
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.
getScoreMatrixAsString
in interface MatrixAligner<S extends Sequence<C>,C extends Compound>
public long getComputationTime()
Aligner
getComputationTime
in interface Aligner<S extends Sequence<C>,C extends Compound>
public Profile<S,C> getProfile()
Aligner
Profile
produced by this alignment algorithm.
getProfile
in interface Aligner<S extends Sequence<C>,C extends Compound>
public int getMaxScore()
Scorer
getMaxScore
in interface Scorer
public int getMinScore()
Scorer
getMinScore
in interface Scorer
public int getScore()
Scorer
Scorer.getScore()
- Scorer.getMinScore()
) / (Scorer.getMaxScore()
- Scorer.getMinScore()
).
getScore
in interface Scorer
protected void align()
protected short[] getSubstitutionScoreVector(int queryColumn)
protected short[] getSubstitutionScoreVector(int queryColumn, int[] subproblem)
protected void reset()
protected void resetAnchors()
protected abstract CompoundSet<C> getCompoundSet()
protected abstract List<C> getCompoundsOfQuery()
protected abstract List<C> getCompoundsOfTarget()
protected abstract int[] getScoreMatrixDimensions()
protected abstract short getSubstitutionScore(int queryColumn, int targetColumn)
protected abstract boolean isReady()
protected abstract void setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
|
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