Uses of Interface
net.sourceforge.cilib.bioinf.sequencealignment.ScoringMethod

Packages that use ScoringMethod

net.sourceforge.cilib.bioinf.sequencealignment

Uses of ScoringMethod in net.sourceforge.cilib.bioinf.sequencealignment

Classes in net.sourceforge.cilib.bioinf.sequencealignment that implement ScoringMethod

class	BestMatch A scoring function based on the highest number of matches per column.
class	BLOSUM62SoP This class implements the Sum Of Pairs scoring function that uses the BLOSUM62 substitutions matrices that give scores for proteins in a biologically meaningful manner.
class	MatchFogel A scoring function based on the overall score for the number of matched symbols over all columns.
class	PAM250SoP This class implements the Sum Of Pairs scoring function that uses PAM250 substitutions matrices that give scores for proteins in a biologically meaningful manner.
class	Similarity SIMILARITY SCORING FUNCTION Score all possible pairwise combinations in column Requires (N * (N-1))/2 comparisons for N sequences Total score = sum of score for each column SoP routine has been optimized for speed.

Methods in net.sourceforge.cilib.bioinf.sequencealignment that return ScoringMethod

ScoringMethod	BinaryAlignmentCreator.getTheMethod()
ScoringMethod	AlignmentCreator.getTheMethod()

Methods in net.sourceforge.cilib.bioinf.sequencealignment with parameters of type ScoringMethod

void	BinaryAlignmentCreator.setScoringMethod(ScoringMethod theMethod)
void	AlignmentCreator.setScoringMethod(ScoringMethod theMethod)