BString objects
The BString class is a general container for storing a big string (a long sequence of characters) and for making its manipulation easy and efficient.
All those containers derive directly (and with no additional slots) from the XString virtual class.
The 2 main differences between an XString object and a standard character vector are: (1) the data stored in an XString object are not copied on object duplication and (2) an XString object can only store a single string (see the XStringSet container for an efficient way to store a big collection of strings in a single object).
In the code snippet below,
x can be a single string (character vector of length 1)
or an XString object.
BString(x="", start=1, nchar=NA):
Tries to convert x into a BString object by reading
nchar letters starting at position start in x.
In the code snippets below, x is an XString object.
In the code snippets below, x is an XString object.
as.character(x):
Converts x to a character string.
toString(x):
Equivalent to as.character(x).
In the code snippets below, x is an XString object.
x[i]:
Return a new XString object made of the selected letters (subscript
i must be an NA-free numeric vector specifying the positions of
the letters to select).
The returned object belongs to the same class as x.
Note that, unlike subseq, x[i] does copy the sequence
data and therefore will be very inefficient for extracting a big number
of letters (e.g. when i contains millions of positions).
In the code snippets below, e1 and e2 are XString objects.
e1 == e2:
TRUE if e1 is equal to e2.
FALSE otherwise.
Comparison between two XString objects of different base types (e.g. a BString object and a DNAString object) is not supported with one exception: a DNAString object and an RNAString object can be compared (see RNAString-class for more details about this).
Comparison between a BString object and a character string is also supported (see examples below).
e1 != e2:
Equivalent to !(e1 == e2).
H. Pagès
b <- BString("I am a BString object")
b
length(b)
## Extracting a linear subsequence:
subseq(b)
subseq(b, start=3)
subseq(b, start=-3)
subseq(b, end=-3)
subseq(b, end=-3, width=5)
## Subsetting:
b2 <- b[length(b):1] # better done with reverse(b)
as.character(b2)
b2 == b # FALSE
b2 == as.character(b2) # TRUE
## b[1:length(b)] is equal but not identical to b!
b == b[1:length(b)] # TRUE
identical(b, 1:length(b)) # FALSE
## This is because subsetting an XString object with [ makes a copy
## of part or all its sequence data. Hence, for the resulting object,
## the internal slot containing the memory address of the sequence
## data differs from the original. This is enough for identical() to
## see the 2 objects as different.
## Compacting. As a particular type of XVector objects, XString
## objects can optionally be compacted. Compacting is done typically
## before serialization. See ?compact for more information.Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.