The MIndex class is the basic container for storing the matches of
a set of patterns in a subject sequence.
Details
An MIndex object contains the matches (start/end locations) of
a set of patterns found in an XString object
called "the subject string" or "the subject sequence" or
simply "the subject".
matchPDict function returns an MIndex object.
Accessor methods
In the code snippets below, x is an MIndex object.
length(x):
The number of patterns that matches are stored for.
names(x):
The names of the patterns that matches are stored for.
startIndex(x):
A list containing the starting positions of the matches
for each pattern.
endIndex(x):
A list containing the ending positions of the matches
for each pattern.
elementNROWS(x):
An integer vector containing the number of matches
for each pattern.
Subsetting methods
In the code snippets below, x is an MIndex object.
x[[i]]:
Extract the matches for the i-th pattern as an
IRanges object.
Coercion
In the code snippets below, x is an MIndex object.
as(x, "CompressedIRangesList"):
Turns x into an
CompressedIRangesList object.
This coercion changes x from one
RangesList
subtype to another with the underlying
Ranges values remaining unchanged.
Other utility methods and functions
In the code snippets below,
x and mindex are MIndex objects
and subject is the XString object
containing the sequence in which the matches were found.
unlist(x, recursive=TRUE, use.names=TRUE):
Return all the matches in a single
IRanges object.
recursive and use.names are ignored.
extractAllMatches(subject, mindex):
Return all the matches in a single XStringViews object.