MIndex-class           package:Biostrings           R Documentation

MIndex objects

Description:

     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.

      'countIndex(x)': An integer vector containing the number of
          matches for each pattern. Equivalent to 'elementLengths(x)'.


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.


Author(s):

     H. Pages

See Also:

     'matchPDict', PDict-class, IRanges-class, XStringViews-class

Examples:

       ## See ?matchPDict and ?`matchPDict-inexact` for some examples.

