BStringViews-constructors {Biostrings} | R Documentation |
A set of basic functions for creating BStringViews objects.
views(subject, start=NA, end=NA) adjacentViews(subject, width, gapwidth=0) BStringViews(src, subjectClass, collapse="")
subject |
A BString (or derived) object or a single string. |
start |
An integer vector containing the start positions of the views. |
end |
An integer vector containing the end positions of the views. |
width |
An integer vector containing the widths of the views. |
gapwidth |
An integer vector containing the widths of the gaps between the views. |
src |
A BString (or derived) object or a character vector. |
subjectClass |
The class to be given to the subject of the BStringViews object
created and returned by the function.
Must be "BString" or one of its subclasses: "DNAString" ,
"RNAString" or "AAString" .
|
collapse |
An optional character string to be inserted between the views of the BStringViews object created and returned by the function. |
The views
function returns a BStringViews object
containing views on subject
with start and end positions
given in the start
and end
vectors.
The adjacentViews
function returns a BStringViews object
containing views on subject
with widths given in the width
vector and separated by gaps of width gapwidth
.
The first view starts at position 1.
The BStringViews
constructor will try to create a BStringViews
object from the value passed to its src
argument.
If src
itself is a BStringViews object, the returned
object is obtained by coercing its subject to the class specified by
subjectClass
.
If src
is a BString object, the returned object is made of
a single view that starts at the first letter and ends at the last letter
of src
(in addition src
itself is coerced to the class
specified by subjectClass
when specified).
If src
is a character vector, the returned object has one view
per character string in src
(and its subject is an instance of
the class specified by subjectClass
).
All these functions return a BStringViews object y
with the following
number of views (length(y)
):
max(length(start), length(end)
for the views
function
and length(width)
for the adjacentViews
function.
For the BStringViews
constructor, length(y)
is 1
when src
is a BString object and length(src)
otherwise.
BStringViews-class, BString, DNAString, RNAString
## 'start' and 'end' are recycled views("abcdefghij", 2:1, 4) views("abcdefghij", 5:7, ) views("abcdefghij", , 5:7) ## Views can be "out of limits" views("abcdefghij", 2:0, 4) ## Views on a DNAString object v12 <- views(DNAString("TAATAATG"), -2:9, 0:11) ## Creating adjacent views v3 <- adjacentViews("abcdefghij", 4:2, gapwidth=1) BStringViews(v12, subjectClass="RNAString") BStringViews(AAString("MARKSLEMSIR*")) BStringViews("abcdefghij", subjectClass="BString")