XStringViews-constructors {Biostrings} | R Documentation |
A set of basic functions for creating or modifying XStringViews objects.
views(subject, start=NA, end=NA) adjacentViews(subject, width, gapwidth=0) XStringViews(x, subjectClass, collapse="") trim(x, use.names=TRUE) subviews(x, start=NA, end=NA, width=NA, use.names=TRUE)
subject |
An XString 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. |
x |
An XString object or a character vector for XStringViews .
An XStringViews object for trim and subviews .
|
subjectClass |
The class to be given to the subject of the XStringViews object
created and returned by the function.
Must be the name of one of the direct XString subtypes i.e.
"BString" , "DNAString" , "RNAString"
or "AAString" .
|
collapse |
An optional character string to be inserted between the views of the XStringViews object created and returned by the function. |
use.names |
[TODO] |
The views
function returns an XStringViews object
containing views on subject
with start and end positions
given in the start
and end
vectors.
The adjacentViews
function returns an XStringViews 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 XStringViews
constructor will try to create an XStringViews
object from the value passed to its x
argument.
If x
itself is an XStringViews object, the returned
object is obtained by coercing its subject to the class specified by
subjectClass
.
If x
is an XString object, the returned object is made of
a single view that starts at the first letter and ends at the last letter
of x
(in addition x
itself is coerced to the class
specified by subjectClass
when specified).
If x
is a character vector, the returned object has one view
per character string in x
(and its subject is an instance of
the class specified by subjectClass
).
All these functions return an XStringViews 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 XStringViews
constructor, length(y)
is 1
when x
is an XString object and length(x)
otherwise.
XStringViews-class,
XString-class,
gaps
## '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) XStringViews(v12, subjectClass="RNAString") XStringViews(AAString("MARKSLEMSIR*")) XStringViews("abcdefghij", subjectClass="BString") ## Applying gaps() to an XStringViews object v2 <- views("abCDefgHIJK", start=c(8, 3), end=c(14, 4)) gaps(v2)