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

Packages that use GapPenaltiesMethod

net.sourceforge.cilib.bioinf.sequencealignment

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

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

class	GapFogel Method that calculates a gap score by linearly or not scale the number of gaps over all columns.
class	GapFourFour Method that penalises gaps.
class	GapOpeningAndExtensionPenalty Method that penalises indels as gap groups.

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

GapPenaltiesMethod	BinaryMSAProblem.getGapPenaltyMethod() Get the current gap penelization method.
GapPenaltiesMethod	MSAProblem.getGapPenaltyMethod()

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

void	BinaryMSAProblem.setGapPenaltyMethod(GapPenaltiesMethod gapPenaltyMethod) Set the strategy to penalize gaps.
void	MSAProblem.setGapPenaltyMethod(GapPenaltiesMethod gapPenaltyMethod)