Uses of Interface
pal.datatype.TransitionPenaltyTable

Packages that use TransitionPenaltyTable
pal.alignment Classes dealing with sequence alignments, including methods for reading and printing in several possible formats, as well as rearranging and concatenating. 
pal.datatype Classes describing data types (nucleotides, amino acids, codons, codon tables etc.) 
 

Uses of TransitionPenaltyTable in pal.alignment
 

Methods in pal.alignment with parameters of type TransitionPenaltyTable
static 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 TransitionPenaltyTable
 class IUPACPenaltyTable
          Implements a table of transition penalties for a DNA states and IUPAC ambiguous states.