org.biojava3.alignment.routines
Class GuanUberbacher<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.AbstractPairwiseSequenceAligner<S,C>
              extended by org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner<S,C>
                  extended by org.biojava3.alignment.routines.GuanUberbacher<S,C>
Type Parameters:
S - each Sequence of the alignment pair 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>, PairwiseSequenceAligner<S,C>, PairwiseSequenceScorer<S,C>, Scorer

public class GuanUberbacher<S extends Sequence<C>,C extends Compound>
extends AnchoredPairwiseSequenceAligner<S,C>

Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence). 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.

Author:
Mark Chapman

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
GuanUberbacher()
          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).
GuanUberbacher(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
          Prepares for a pairwise global sequence alignment.
GuanUberbacher(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix, int cutsPerSection)
          Prepares for a pairwise global sequence alignment.
 
Method Summary
 
Methods inherited from class org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner
getAnchors, getCutsPerSection, reset, setAnchors, setCutsPerSection, setDefaultCutsPerSection, setProfile
 
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

GuanUberbacher

public GuanUberbacher()
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).


GuanUberbacher

public GuanUberbacher(S query,
                      S target,
                      GapPenalty gapPenalty,
                      SubstitutionMatrix<C> subMatrix)
Prepares for a pairwise global sequence alignment.

Parameters:
query - the first Sequence of the pair to align
target - the second Sequence of the pair to align
gapPenalty - the gap penalties used during alignment
subMatrix - the set of substitution scores used during alignment

GuanUberbacher

public GuanUberbacher(S query,
                      S target,
                      GapPenalty gapPenalty,
                      SubstitutionMatrix<C> subMatrix,
                      int cutsPerSection)
Prepares for a pairwise global sequence alignment.

Parameters:
query - the first Sequence of the pair to align
target - the second Sequence of the pair to align
gapPenalty - the gap penalties used during alignment
subMatrix - the set of substitution scores used during alignment
cutsPerSection - the number of cuts added to each section during each pass