Structstrings-internals: Structstrings internals

In FelixErnst/Structstrings: Implementation of the dot bracket annotations with Biostrings

Structstrings internals

Description

Analog to Biostrings there are a few objects, which should only be used internally, but may be of use to other package developers. Otherwise take care.

Usage

DOTBRACKET_CHAR_VALUES

DOTBRACKET_ALPHABET

STRUCTURE_NEUTRAL_CHR

STRUCTURE_OPEN_CHR

STRUCTURE_CLOSE_CHR

## S4 replacement method for signature 'DotBracketDataFrame'
x[i, j, ...] <- value

## S4 replacement method for signature 'CompressedSplitDotBracketDataFrameList'
colnames(x) <- value

## S4 method for signature 'DotBracketString'
seqtype(x)

## S4 method for signature 'DotBracketString'
subseq(x, start = NA, end = NA, width = NA)

## S4 replacement method for signature 'DotBracketString'
subseq(x, start = NA, end = NA, width = NA) <- value

## S4 replacement method for signature 'DotBracketStringSet'
subseq(x, start = NA, end = NA, width = NA) <- value

Arguments

seqtype, x, start, end, width, value, i, j, ...

used internally

Format

a integer vector of length 9 containing the integer values of the dotbracket alphabet

a character vector of length 9 containing the single characters of the dotbracket alphabet

a character vector of length 1 containing the character for unpaired positions

a character vector of length 4 containing the opening character of the dotbracket alphabet

a character vector of length 4 containing the closing character of the dotbracket alphabet

Examples

DOTBRACKET_CHAR_VALUES
DOTBRACKET_ALPHABET
STRUCTURE_NEUTRAL_CHR
STRUCTURE_OPEN_CHR
STRUCTURE_CLOSE_CHR

# the replace method for a DotBracketDataFrame had to be reimplemented
# because of the requirement of columns for a DotBracketDataFrameList and
# DotBracketDataFrame
data("dbs", package = "Structstrings")
dbdfl <- getBasePairing(dbs)
# Elements are returned as DotBracketDataFrames
dbdf <- dbdfl[[1]]
dbdfl[[1]] <- dbdf
dbdfl[1] <- dbdfl[1]

FelixErnst/Structstrings documentation built on Nov. 6, 2024, 12:11 a.m.