Structstrings internals

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.

DOTBRACKET_CHAR_VALUES

DOTBRACKET_ALPHABET

STRUCTURE_NEUTRAL_CHR

STRUCTURE_OPEN_CHR

STRUCTURE_CLOSE_CHR

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

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

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

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

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

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

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

Arguments

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

used internally

Examples

DOTBRACKET_CHAR_VALUES
#> [1]  40  41  46  60  62  91  93 123 125
DOTBRACKET_ALPHABET
#> [1] "(" ")" "." "<" ">" "[" "]" "{" "}"
STRUCTURE_NEUTRAL_CHR
#> [1] "."
STRUCTURE_OPEN_CHR
#> [1] "\\(" "<"   "\\[" "\\{"
STRUCTURE_CLOSE_CHR
#> [1] "\\)" ">"   "\\]" "\\}"

# 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]