SimilarityScan: Reference class to store the results from sequence similarity...

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

Description

Reference class to store the results from sequence similarity analyses, and block detection runs for a given triplet.

Fields

TableFile

A length 1 character vector storing the temporary filepath of the datatable of sequence similarity table.

Table

Accessor function for the datatable of sequence similarity that is stored on temporary files.

WindowSizeUsed

Single integer value, stores the size of the sliding window used for the scan.

StepSizeUsed

Single integer value, stores the size of the sliding window used for the scan.

Methods

blankTable()

Method clears the SS analysis results table.

finalize()

Called when the object is destroyed, makes sure to delete the file saved in the system's temporary directory.

initialize(HCDir)

Method initializes the object, generates temporary filenames for the sequence similarity table.

tableIsBlank()

Returns TRUE, if the SS analysis table is blank and no results are contained in it.

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