Uses of Interface pal.datatype.TransitionPenaltyTable

Packages that use TransitionPenaltyTable
Package	Description
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.)

Methods in pal.alignment with parameters of type TransitionPenaltyTable
Modifier and Type	Method	Description
`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.

Classes in pal.datatype that implement TransitionPenaltyTable
Modifier and Type	Class	Description
`class`	`IUPACPenaltyTable`	Implements a table of transition penalties for a DNA states and IUPAC ambiguous states.

Uses of Interfacepal.datatype.TransitionPenaltyTable