S
- each Sequence
in the pair of alignment Profile
s is of type SC
- each element of an AlignedSequence
is a Compound
of type CAligner<S,C>
, MatrixAligner<S,C>
, ProfileProfileAligner<S,C>
, ProfileProfileScorer<S,C>
, Scorer
public class SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound> extends AbstractProfileProfileAligner<S,C>
Aligner
for a pair of Profile
s. This is basically an extension of the
NeedlemanWunsch
pairwise sequence aligner to pairwise profile alignment using a sum-of-pairs score.anchors, cutsPerSection, gapPenalty, max, min, profile, score, scores, time, xyMax, xyStart
pair
Constructor | Description |
---|---|
SimpleProfileProfileAligner() |
Before running a profile-profile alignment, data must be sent in via calls to
AbstractProfileProfileAligner.setQuery(Profile) , AbstractProfileProfileAligner.setTarget(Profile) , AbstractMatrixAligner.setGapPenalty(GapPenalty) , and
AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix) . |
SimpleProfileProfileAligner(java.util.concurrent.Future<ProfilePair<S,C>> query,
java.util.concurrent.Future<ProfilePair<S,C>> target,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix) |
Prepares for a profile-profile alignment run concurrently.
|
SimpleProfileProfileAligner(java.util.concurrent.Future<ProfilePair<S,C>> query,
Profile<S,C> target,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix) |
Prepares for a profile-profile alignment run concurrently.
|
SimpleProfileProfileAligner(Profile<S,C> query,
java.util.concurrent.Future<ProfilePair<S,C>> target,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix) |
Prepares for a profile-profile alignment run concurrently.
|
SimpleProfileProfileAligner(Profile<S,C> query,
Profile<S,C> target,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix) |
Prepares for a profile-profile alignment.
|
Modifier and Type | Method | Description |
---|---|---|
protected void |
setProfile(java.util.List<AlignedSequence.Step> sx,
java.util.List<AlignedSequence.Step> sy) |
align, getComputationTime, getGapPenalty, getMaxScore, getMinScore, getProfile, getScore, getScoreMatrix, getScoreMatrixAsString, getSubstitutionMatrix, getSubstitutionScoreVector, getSubstitutionScoreVector, isLocal, isStoringScoreMatrix, setGapPenalty, setStoringScoreMatrix, setSubstitutionMatrix
getCompoundSet, getCompoundsOfQuery, getCompoundsOfTarget, getPair, getQuery, getScoreMatrixDimensions, getSubstitutionScore, getTarget, isReady, reset, setQuery, setTarget
getDistance, getDistance, getSimilarity, getSimilarity
getComputationTime, getProfile
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity
public SimpleProfileProfileAligner()
AbstractProfileProfileAligner.setQuery(Profile)
, AbstractProfileProfileAligner.setTarget(Profile)
, AbstractMatrixAligner.setGapPenalty(GapPenalty)
, and
AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
.public SimpleProfileProfileAligner(Profile<S,C> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
public SimpleProfileProfileAligner(java.util.concurrent.Future<ProfilePair<S,C>> query, java.util.concurrent.Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
public SimpleProfileProfileAligner(Profile<S,C> query, java.util.concurrent.Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
public SimpleProfileProfileAligner(java.util.concurrent.Future<ProfilePair<S,C>> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
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>