XStringSetList-class       package:Biostrings       R Documentation

XStringSetList objects

Description:

     The XStringSetList class is a virtual container for storing a list
     of XStringSet objects.

Details:

     Concrete flavors of the XStringSetList container are the
     BStringSetList, DNAStringSetList, RNAStringSetList and
     AAStringSetList containers for storing a list of BStringSet,
     DNAStringSet, RNAStringSet and AAStringSet objects, respectively.
     These four containers are direct subclasses of XStringSetList with
     no additional slots.

Methods:

     [TODO]

Author(s):

     H. Pages

See Also:

     XStringSet-class, Grouping-class, Sequence-class

Examples:

       unlisted <- DNAStringSet(c("AAA", "AC", "GGATA"))
       partitioning <- PartitioningByEnd(c(0, 2, 2, 3))
       x <- new("DNAStringSetList",
                unlisted=unlisted,
                partitioning=partitioning)
       x
       length(x)
       unlist(x)
       x[[1]]
       x[[2]]
       as.list(x)

       names(x) <- LETTERS[1:4]
       x[["A"]]
       x[["B"]]
       as.list(x)  # named list

       ## Using the Grouping core API on 'partitioning(x)':
       partitioning(x)
       length(partitioning(x))
       nobj(partitioning(x))
       grouplength(partitioning(x))  # same as 'unname(sapply(x, length))'

       ## Using the Ranges core API on 'partitioning(x)':
       start(partitioning(x))
       end(partitioning(x))
       width(partitioning(x))  # same as 'grouplength(partitioning(x))'

