Uses of Class
jebl.evolution.align.scores.Scores

Packages that use Scores

jebl.evolution.align	Provides classes and interfaces for pairwise alignment of two sequences.
jebl.evolution.align.scores

Uses of Scores in jebl.evolution.align

Methods in jebl.evolution.align that return Scores

Scores

BartonSternberg.getEstimatedScores()

Methods in jebl.evolution.align with parameters of type Scores

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

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)

Uses of Scores in jebl.evolution.align.scores

Subclasses of Scores in jebl.evolution.align.scores

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

static Scores	Scores.duplicate(Scores scores)
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 matrices
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)

Methods in jebl.evolution.align.scores with parameters of type Scores

static Scores	Scores.duplicate(Scores 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

NucleotideScores(Scores scores, double percentmatches)