org.biojava3.alignment
Class SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound>

java.lang.Object
  extended by org.biojava3.alignment.template.AbstractScorer
      extended by org.biojava3.alignment.template.AbstractMatrixAligner<S,C>
          extended by org.biojava3.alignment.template.AbstractProfileProfileAligner<S,C>
              extended by org.biojava3.alignment.SimpleProfileProfileAligner<S,C>
Type Parameters:
S - each Sequence in the pair of alignment Profiles is of type S
C - 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 Profiles. This is basically an extension of the NeedlemanWunsch pairwise sequence aligner to pairwise profile alignment using a sum-of-pairs score.

Author:
Mark Chapman

Field Summary
 
Fields inherited from class org.biojava3.alignment.template.AbstractProfileProfileAligner
pair
 
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.
 
Method Summary
protected  void setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
           
 
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 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

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 align
target - the second Profile of the pair to align
gapPenalty - the gap penalties used during alignment
subMatrix - 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 calculated
target - the second Profile of the pair to align, still to be calculated
gapPenalty - the gap penalties used during alignment
subMatrix - 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 align
target - the second Profile of the pair to align, still to be calculated
gapPenalty - the gap penalties used during alignment
subMatrix - 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 calculated
target - the second Profile of the pair to align
gapPenalty - the gap penalties used during alignment
subMatrix - the set of substitution scores used during alignment
Method Detail

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>