BStringViews-class {Biostrings} | R Documentation |
A container for a set of views on the same BString (or derived) object.
A BStringViews object contains a set of views on the same BString (or derived) object called "the subject string" or "the subject sequence" or simply "the subject". Each view is defined by its start and end locations: both are integers such that start <= end. Note that two views can overlap and that a view can be "out of limits" i.e. it starts before the first letter of the subject or/and ends after its last letter.
In the code snippets below,
x
is a BStringViews object.
subject(x)
:
The subject of x
. This is always a BString
(or derived) object.
length(x)
:
The number of views in x
.
start(x)
:
The starting positions of the views.
An integer vector of the same length as x
.
first(x)
:
deprecated. Use 'start' instead.
end(x)
:
The ending positions of the views.
An integer vector of the same length as x
.
last(x)
:
deprecated. Use 'end' instead.
width(x)
:
The width of the views.
Equivalent to end(x) - start(x) + 1L
.
A vector of positive integers of the same length as x
.
nchar(x)
:
A vector of non-negative integers containing the number
of letters in each view.
Values in nchar(x)
coincide with values in width(x)
except for "out of limits" views where they are lower.
desc(x)
:
NULL
or a character vector of the same length as x
containing a short user provided description or comment for each view.
These are the only data in a BStringViews object that can safely
be changed by the user. All the other data are immutable!
As a general recommendation, the user should never try to modify
an object by accessing its slots directly.
In the code snippets below,
x
, object
, e1
and e2
are BStringViews objects,
and i
can be a numeric or logical vector.
x[i]
:
Return a new BStringViews object made of the selected views.
i
can be a numeric vector, a logical vector, NULL
or missing.
The returned object has the same subject as x
.
x[[i]]
:
Extract a view as a BString (or derived) object.
i
must be a single numeric value (a numeric vector of length 1).
Can't be used for extracting a view that is "out of limits" (raise an error).
The returned object belongs to the same class as subject(x)
.
e1 == e2
:
A vector of logicals indicating the result of the view by
view comparison. The views in the shorter of the two BStringViews
object being compared are recycled as necessary.
Like for comparison between BString objects, comparison between two BStringViews objects with subjects of different classes is not supported with one exception: when the subjects are DNAString and RNAString instances.
Also, like with BString objects, comparison between a BStringViews object with a subject of class "BString" and a character vector is supported (see examples below).
e1 != e2
:
Equivalent to !(e1 == e2)
.
as.character(x, use.names, check.limits)
:
Convert x
to a character vector of the same length as x
.
use.names
controls whether or not desc(x)
should be
used to set the names of the returned vector (default is TRUE
).
check.limits
controls whether or not an error should be raised
if x
contains "out of limit" views (default is TRUE
).
With check.limits=FALSE
then "out of limit" views are padded
with spaces.
as.matrix(x, mode, use.names, check.limits)
:
Depending on what mode
is choosen ("integer"
or
"character"
), return either a 2-column integer matrix containing
start(x)
and end(x)
or a character matrix containing the
"exploded" representation of the views.
mode="character"
can only be used on a BStringViews
object with equal-width views.
Arguments use.names
and check.limits
are ignored with
mode="integer"
.
With mode="character"
, use.names
controls
whether or not desc(x)
should be used to set the row names
of the returned matrix (default is TRUE
),
and check.limits
controls whether or not an error should be raised
if x
contains "out of limit" views (default is TRUE
).
With check.limits=FALSE
then "out of limit" views are padded
with spaces.
as.list(x)
:
Convert x
to a list of BString objects.
Can't be used if x
has "out of limits" views (raise an error).
toString(x)
:
Equivalent to toString(as.character(x))
.
H. Pages
BStringViews-constructors,
BString-class,
DNAString-class,
RNAString-class,
AAString-class,
letter
s <- DNAString("-CTC-N") ## One standard way to create a BStringViews object is to use ## the "views" constructor: v4 <- views(s, 3:0, 5:8) v4 subject(v4) length(v4) start(v4) end(v4) width(v4) ## Attach a comment to views #3 and #4: desc(v4)[3:4] <- "out of limits" desc(v4) ## A more programatical way to "tag" the "out of limits" views: desc(v4)[start(v4) < 1 | nchar(subject(v4)) < end(v4)] <- "out of limits" ## or just: desc(v4)[nchar(v4) < width(v4)] <- "out of limits" ## Make a new BStringViews object by selecting some views only: v4[4:2] # 3 views v4[-1] # 3 views v4[c(2,4)] # 2 views v4[width(v4) >= 5] # 3 views v4[is.na(desc(v4))] # 2 views v4[!is.na(desc(v4))] # 2 views v4[3] # 1 view v4[FALSE] # 0 view ## Two equivalent ways to extract a view as a BString (or derived) object: s2a <- v4[[2]] s2b <- subBString(subject(v4), start(v4)[2], end(v4)[2]) identical(s2a, s2b) # TRUE ## It is an error to try to extract an "out of limits" view: #v4[[3]] # Error! v12 <- views(DNAString("TAATAATG"), -2:9, 0:11) v12 == DNAString("TAA") v12[v12 == v12[4]] v12[v12 == v12[1]] v12[3] == views(RNAString("AU"), 0, 2)