|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.biojava3.alignment.template.AbstractScorer
org.biojava3.alignment.template.AbstractMatrixAligner<S,C>
org.biojava3.alignment.template.AbstractPairwiseSequenceAligner<S,C>
org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner<S,C>
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>
This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the
first until the last 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.
Field Summary |
---|
Fields inherited from class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner |
---|
pair |
Fields inherited from class org.biojava3.alignment.template.AbstractMatrixAligner |
---|
anchors, cutsPerSection, gapPenalty, max, min, profile, score, scores, time, xyMax, xyStart |
Constructor Summary | |
---|---|
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. |
Method Summary | |
---|---|
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(List<AlignedSequence.Step> sx,
List<AlignedSequence.Step> sy)
|
Methods inherited from class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner |
---|
getCompoundSet, getCompoundsOfQuery, getCompoundsOfTarget, getPair, getQuery, getScoreMatrixDimensions, getSubstitutionScore, getTarget, isReady, setQuery, setTarget |
Methods inherited from class org.biojava3.alignment.template.AbstractMatrixAligner |
---|
align, getComputationTime, getGapPenalty, getMaxScore, getMinScore, getProfile, getScore, getScoreMatrix, getScoreMatrixAsString, getSubstitutionMatrix, getSubstitutionScoreVector, getSubstitutionScoreVector, isLocal, isStoringScoreMatrix, resetAnchors, setGapPenalty, setStoringScoreMatrix, setSubstitutionMatrix |
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.Aligner |
---|
getComputationTime, getProfile |
Methods inherited from interface org.biojava3.alignment.template.Scorer |
---|
getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity |
Constructor Detail |
---|
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)
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 alignmentpublic AnchoredPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix, int cutsPerSection)
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 passpublic 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 anchorsMethod Detail |
---|
public 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()
reset
in class AbstractPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound>
protected void setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
setProfile
in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |