Uses of Class
jebl.evolution.align.scores.Scores
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Packages that use Scores Package Description jebl.evolution.align Provides classes and interfaces for pairwise alignment of two sequences.jebl.evolution.align.scores -
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Uses of Scores in jebl.evolution.align
Methods in jebl.evolution.align that return Scores Modifier and Type Method Description Scores
BartonSternberg. getEstimatedScores()
Methods in jebl.evolution.align with parameters of type Scores Modifier and Type Method Description static float
ProfileCharacter. score(ProfileCharacter character1, ProfileCharacter character2, Scores scores)
static float
ProfileCharacter. scoreSelf(ProfileCharacter character, Scores scores)
void
Align. setScores(Scores sub)
Constructors in jebl.evolution.align with parameters of type Scores Constructor Description Align(Scores sub, float d)
BartonSternberg(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)
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Uses of Scores in jebl.evolution.align.scores
Subclasses of Scores in jebl.evolution.align.scores Modifier and Type Class Description class
AminoAcidScores
class
Blosum45
class
Blosum50
class
Blosum55
class
Blosum60
class
Blosum62
class
Blosum65
class
Blosum70
class
Blosum75
class
Blosum80
class
Blosum85
class
Blosum90
class
Hamming
class
JukesCantor
Jukes Cantor assumes equal substitution frequencies and equal nucleotide equilibrium frequencies.class
NucleotideScores
class
Pam100
class
Pam110
class
Pam120
class
Pam130
class
Pam140
class
Pam150
class
Pam160
class
Pam170
class
Pam180
class
Pam190
class
Pam200
class
Pam210
class
Pam220
class
Pam230
class
Pam240
class
Pam250
class
SubstScoreMatrix
Methods in jebl.evolution.align.scores that return Scores Modifier and Type Method Description static Scores
Scores. duplicate(Scores scores)
static Scores
Scores. forMatrix(ScoreMatrix scoreMatrix)
static Scores
ScoresFactory. generateScores(java.lang.String nameVal)
For any matrix.static Scores
ScoresFactory. generateScores(java.lang.String name, float val)
For calculated nucleotide matrices.static Scores
ScoresFactory. generateScores(java.lang.String name, int val)
For Blosum and Pam matricesstatic Scores
Scores. includeAdditionalCharacters(Scores scores, java.lang.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 Scores Modifier and Type Method Description static Scores
Scores. duplicate(Scores scores)
static Scores
Scores. includeAdditionalCharacters(Scores scores, java.lang.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 Constructor Description NucleotideScores(Scores scores, double percentmatches)
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