Uses of Class
jebl.evolution.align.scores.Scores
Packages that use Scores
Package
Description
Provides classes and interfaces for pairwise alignment of two sequences.
-
Uses of Scores in jebl.evolution.align
Methods in jebl.evolution.align that return ScoresMethods in jebl.evolution.align with parameters of type ScoresModifier and TypeMethodDescriptionstatic float
ProfileCharacter.score
(ProfileCharacter character1, ProfileCharacter character2, Scores scores) static float
ProfileCharacter.scoreSelf
(ProfileCharacter character, Scores scores) void
Constructors in jebl.evolution.align with parameters of type ScoresModifierConstructorDescriptionBartonSternberg
(Scores scores, float gapOpen, float gapExtend, int refinementIterations, boolean freeGapsAtEnds, boolean fastGuide) MaximalSegmentPair
(Scores sub) NeedlemanWunsch
(Scores sub, float d) NeedlemanWunschAffine
(Scores sub, float d, float e) NeedlemanWunschLinearSpace
(Scores sub, float d) NeedlemanWunschLinearSpaceAffine
(Scores sub, float openGapPenalty, float extendGapPenalty) NeedlemanWunschLinearSpaceAffine
(Scores sub, float d, float e, boolean freeGapsAtEnds) NeedlemanWunschLinearSpaceAffine
(Scores sub, float d, float e, boolean freeGapsAtEnds, boolean applyGapExtendCostToFirstGapResidue) NonOverlapMultipleLocalAffine
(Scores sub, float d, float e, int T) OldNeedlemanWunschAffine
(Scores sub, float d, float e) OverlapAlign
(Scores sub, float d) SmithWaterman
(Scores sub, float d) SmithWatermanLinearSpace
(Scores sub, float d) SmithWatermanLinearSpaceAffine
(Scores sub, float d, float e) -
Uses of Scores in jebl.evolution.align.scores
Subclasses of Scores in jebl.evolution.align.scoresModifier and TypeClassDescriptionclass
class
class
class
class
class
class
class
class
class
class
class
class
class
Jukes Cantor assumes equal substitution frequencies and equal nucleotide equilibrium frequencies.class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
Methods in jebl.evolution.align.scores that return ScoresModifier and TypeMethodDescriptionstatic Scores
static Scores
Scores.forMatrix
(ScoreMatrix scoreMatrix) static Scores
ScoresFactory.generateScores
(String nameVal) For any matrix.static Scores
ScoresFactory.generateScores
(String name, float val) For calculated nucleotide matrices.static Scores
ScoresFactory.generateScores
(String name, int val) For Blosum and Pam matricesstatic Scores
Scores.includeAdditionalCharacters
(Scores scores, String characters) includes additional characters in the score matrix which will all have scored zero when compared to other characters.static Scores
Scores.includeGaps
(Scores scores, float gapVersusResidueCost, float gapVersusGapCost) Methods in jebl.evolution.align.scores with parameters of type ScoresModifier and TypeMethodDescriptionstatic Scores
static Scores
Scores.includeAdditionalCharacters
(Scores scores, String characters) includes additional characters in the score matrix which will all have scored zero when compared to other characters.static Scores
Scores.includeGaps
(Scores scores, float gapVersusResidueCost, float gapVersusGapCost) Constructors in jebl.evolution.align.scores with parameters of type Scores