Structstrings-internals {Structstrings} | R Documentation |
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 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
seqtype, x, start, end, width, value, i, j, ... |
used internally |
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
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]