Uses of Interface
pal.datatype.TransitionPenaltyTable
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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.) -
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Uses of TransitionPenaltyTable in pal.alignment
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. -
Uses of TransitionPenaltyTable in pal.datatype
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.
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