org.biojava3.alignment
Class SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound>
java.lang.Object
org.biojava3.alignment.template.AbstractScorer
org.biojava3.alignment.template.AbstractMatrixAligner<S,C>
org.biojava3.alignment.template.AbstractProfileProfileAligner<S,C>
org.biojava3.alignment.SimpleProfileProfileAligner<S,C>
- Type Parameters:
S
- each Sequence
in the pair of alignment Profile
s is of type SC
- each element of an AlignedSequence
is a Compound
of type C
- All Implemented Interfaces:
- Aligner<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>
Implements a simple (naive) 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.
- Author:
- Mark Chapman
Fields inherited from class org.biojava3.alignment.template.AbstractMatrixAligner |
anchors, cutsPerSection, gapPenalty, max, min, profile, score, scores, time, xyMax, xyStart |
Constructor Summary |
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(Future<ProfilePair<S,C>> query,
Future<ProfilePair<S,C>> target,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix)
Prepares for a profile-profile alignment run concurrently. |
SimpleProfileProfileAligner(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,
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. |
Methods inherited from class org.biojava3.alignment.template.AbstractProfileProfileAligner |
getCompoundSet, getCompoundsOfQuery, getCompoundsOfTarget, getPair, getQuery, getScoreMatrixDimensions, getSubstitutionScore, getTarget, isReady, reset, 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 java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
SimpleProfileProfileAligner
public 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
public SimpleProfileProfileAligner(Profile<S,C> query,
Profile<S,C> target,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix)
- Prepares for a profile-profile alignment.
- Parameters:
query
- the first Profile
of the pair to aligntarget
- the second Profile
of the pair to aligngapPenalty
- the gap penalties used during alignmentsubMatrix
- the set of substitution scores used during alignment
SimpleProfileProfileAligner
public SimpleProfileProfileAligner(Future<ProfilePair<S,C>> query,
Future<ProfilePair<S,C>> target,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix)
- Prepares for a profile-profile alignment run concurrently.
- Parameters:
query
- the first Profile
of the pair to align, still to be calculatedtarget
- the second Profile
of the pair to align, still to be calculatedgapPenalty
- the gap penalties used during alignmentsubMatrix
- the set of substitution scores used during alignment
SimpleProfileProfileAligner
public SimpleProfileProfileAligner(Profile<S,C> query,
Future<ProfilePair<S,C>> target,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix)
- Prepares for a profile-profile alignment run concurrently.
- Parameters:
query
- the first Profile
of the pair to aligntarget
- the second Profile
of the pair to align, still to be calculatedgapPenalty
- the gap penalties used during alignmentsubMatrix
- the set of substitution scores used during alignment
SimpleProfileProfileAligner
public SimpleProfileProfileAligner(Future<ProfilePair<S,C>> query,
Profile<S,C> target,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix)
- Prepares for a profile-profile alignment run concurrently.
- Parameters:
query
- the first Profile
of the pair to align, still to be calculatedtarget
- the second Profile
of the pair to aligngapPenalty
- the gap penalties used during alignmentsubMatrix
- the set of substitution scores used during alignment
setProfile
protected void setProfile(List<AlignedSequence.Step> sx,
List<AlignedSequence.Step> sy)
- Specified by:
setProfile
in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>