Triplets: Reference class storing all triplets in a HC analysis.

In Ward9250/HybridCheck: Detection and dating of Recombinant Regions in DNA sequence data

Description

The Triplets reference class stores and manages operations over many Triplet objects.

Methods

deleteAllTriplets()

Removes all current triplet data completely.

generateTriplets(dna, csettings, basefile)

Initializes all triplet objects based on the combination settings

getAllIndexes()

Returns the indexes of the sequences (according to their rows in the HC sequence object) in each triplet as a list.

getAllNames()

Returns the names of the sequences in each triplet as a list.

getTriplets(selections)

Returns a list of references to triplets according to user selection.

htmlSummary()

Prints a HTML summary of all the different triplet combinations.

initialize(dna)

Initializes the object.

tripletsGenerated()

Returns TRUE if the triplet generations have been prepared for.

Ward9250/HybridCheck documentation built on Jan. 30, 2022, 11:01 a.m.