Uses of Class jebl.evolution.align.scores.Scores (JEBL2 lib API)

Packages that use Scores
Package	Description
jebl.evolution.align	Provides classes and interfaces for pairwise alignment of two sequences.
jebl.evolution.align.scores

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)`

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 matrices
`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)`

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)`

Uses of Classjebl.evolution.align.scores.Scores