Uses of Interface
pal.datatype.TransitionPenaltyTable
Packages that use TransitionPenaltyTable
Package
Description
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)
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Uses of TransitionPenaltyTable in pal.alignment
Methods in pal.alignment with parameters of type TransitionPenaltyTableModifier and TypeMethodDescriptionstatic double
AlignmentUtils.getAlignmentPenalty
(Alignment a, DataType dataType, TransitionPenaltyTable penalties, double gapCreation, double gapExtension, boolean local) Returns total sum of pairs alignment distance using gap creation and extension penalties and transition penalties as defined in the TransitionPenaltyTable provided.static double
AlignmentUtils.getAlignmentPenalty
(Alignment a, TransitionPenaltyTable penalties, double gapCreation, double gapExtension) Returns total sum of pairs alignment penalty using gap creation and extension penalties and transition penalties in the TransitionPenaltyTable provided. -
Uses of TransitionPenaltyTable in pal.datatype
Classes in pal.datatype that implement TransitionPenaltyTableModifier and TypeClassDescriptionclass
Implements a table of transition penalties for a DNA states and IUPAC ambiguous states.