DotBracketString {Structstrings} | R Documentation |
The DotBracketString
extends the
BString
class. The
DotBracketStringSet
and DotBracketStringSetList
classes are
implemented accordingly.
The alphabet consists of the letters
(
, )
, .
, <
, >
, [
, ]
,
{
and }
, which describes base pairing between positions. The
.
letter describes an unpaired position. The number of opening and
closing letters need to be equal within a DotBracketString
to be a
valid dot bracket annotation. This is checked upon creation and modificiation
of the object.
The objects can also be created using the shorter function names DB
,
DBS
and DBSL
.
Currently, there is no distinction in base pairing strength between the different bracket types.
DotBracketString(x = "", start = 1, nchar = NA) DB(x = character(), start = 1, nchar = NA) DotBracketStringSet(x = character()) DBS(x = character()) DotBracketStringSetList(..., use.names = TRUE) DBSL(..., use.names = TRUE) ## S4 method for signature 'DotBracketString' alphabet(x) ## S4 method for signature 'DotBracketString' encoding(x)
x |
|
start |
|
nchar |
|
... |
|
use.names |
|
a DotBracketString*
object.
str <- "((.))..[[..]]...{{..}}..<<..>>" db <- DotBracketString(str) dbs <- DotBracketStringSet(c("structure1" = str, "structure2" = str)) dbsl <- DotBracketStringSetList(list(first = dbs, second = dbs))