S
- each Sequence
of the alignment pair is of type SC
- each element of an AlignedSequence
is a Compound
of type Cpublic class AnchoredPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> extends AbstractPairwiseSequenceAligner<S,C>
Compound
of each Sequence
) with the restriction that any alignment produced
will connect the query sequence to the target sequence at the anchors. This class performs such global
sequence comparisons efficiently by dynamic programming with a space requirement reduced from quadratic (a multiple
of query sequence length times target sequence length) to only linear (a multiple of query sequence length). The
counterpoint to this reduction in space complexity is a modest (a multiple < 2) increase in time.pair
anchors, cutsPerSection, gapPenalty, max, min, profile, score, scores, time, xyMax, xyStart
Constructor and Description |
---|
AnchoredPairwiseSequenceAligner()
Before running a pairwise global sequence alignment, data must be sent in via calls to
AbstractPairwiseSequenceAligner.setQuery(Sequence) , AbstractPairwiseSequenceAligner.setTarget(Sequence) , AbstractMatrixAligner.setGapPenalty(GapPenalty) , and
AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix) . |
AnchoredPairwiseSequenceAligner(S query,
S target,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix)
Prepares for a pairwise global sequence alignment.
|
AnchoredPairwiseSequenceAligner(S query,
S target,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix,
int cutsPerSection)
Prepares for a pairwise global sequence alignment.
|
AnchoredPairwiseSequenceAligner(S query,
S target,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix,
int cutsPerSection,
int[] anchors)
Prepares for a pairwise global sequence alignment.
|
Modifier and Type | Method and Description |
---|---|
int[] |
getAnchors()
Returns the list of anchors.
|
int |
getCutsPerSection()
Returns the number of cuts added to each section during each pass.
|
protected void |
reset() |
void |
setAnchors(int[] anchors)
Sets the starting list of anchors before running the alignment routine.
|
void |
setCutsPerSection(int cutsPerSection)
Sets the number of cuts added to each section during each pass.
|
static void |
setDefaultCutsPerSection(int defaultCutsPerSection)
Sets the default number of cuts added to each section during each pass.
|
protected void |
setProfile(java.util.List<AlignedSequence.Step> sx,
java.util.List<AlignedSequence.Step> sy) |
getCompoundSet, getCompoundsOfQuery, getCompoundsOfTarget, getPair, getQuery, getScoreMatrixDimensions, getSubstitutionScore, getTarget, isReady, setQuery, setTarget
align, getComputationTime, getGapPenalty, getMaxScore, getMinScore, getProfile, getScore, getScoreMatrix, getScoreMatrixAsString, getSubstitutionMatrix, getSubstitutionScoreVector, getSubstitutionScoreVector, isLocal, isStoringScoreMatrix, resetAnchors, setGapPenalty, setStoringScoreMatrix, setSubstitutionMatrix
getDistance, getDistance, getSimilarity, getSimilarity
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getComputationTime, getProfile
getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity
public AnchoredPairwiseSequenceAligner()
AbstractPairwiseSequenceAligner.setQuery(Sequence)
, AbstractPairwiseSequenceAligner.setTarget(Sequence)
, AbstractMatrixAligner.setGapPenalty(GapPenalty)
, and
AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
.public AnchoredPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
public AnchoredPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix, int cutsPerSection)
public AnchoredPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix, int cutsPerSection, int[] anchors)
query
- the first Sequence
of the pair to aligntarget
- the second Sequence
of the pair to aligngapPenalty
- the gap penalties used during alignmentsubMatrix
- the set of substitution scores used during alignmentcutsPerSection
- the number of cuts added to each section during each passanchors
- the initial list of anchorspublic static void setDefaultCutsPerSection(int defaultCutsPerSection)
defaultCutsPerSection
- the default number of cuts added to each section during each passpublic int[] getAnchors()
public int getCutsPerSection()
public void setAnchors(int[] anchors)
anchors
- list of points that are tied to the given indices in the targetpublic void setCutsPerSection(int cutsPerSection)
cutsPerSection
- the number of cuts added to each section during each passprotected void reset()
protected void setProfile(java.util.List<AlignedSequence.Step> sx, java.util.List<AlignedSequence.Step> sy)
setProfile
in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>