Uses of Package
net.sourceforge.cilib.bioinf.sequencealignment

Packages that use net.sourceforge.cilib.bioinf.sequencealignment

net.sourceforge.cilib.bioinf.sequencealignment

Classes in net.sourceforge.cilib.bioinf.sequencealignment used by net.sourceforge.cilib.bioinf.sequencealignment

AlignmentCreator
This class is responsible for creating an output alignment by populating the input alignment with gaps at positions given by the discretization of the particles positions.

AlignmentVisualizer
This class serves as a measurement, its puspose is to display the output alignment.

BinaryAlignmentCreator
This class is responsible for creating an output alignment by populating the input alignment with gaps at positions given by the discretization of the particles positions.

DesiredMaximizationFitness
This class serves as a crude implementation of a stopping condition that forces the optimizer to stop whenever a arbitrary fitness has been reached.

FASTADataSetBuilder
Builds the input data set that gets fed as sequences to be aligned.

GapPenaltiesMethod
Public common interface for gap penalties methods (GapFogel, GapFourFour and GapOpeningAndExtensionPenalty).

ScoringMethod
Public common interface to allow multiple scoring schemes, namely Similarity, MatchFogel, and BestMatch (DNA or any characters), BLOSUM and PAM (Proteins).