LongestCommonPrefix-class {Biostrings}R Documentation

Class of longest common prefix lengths for suffix array elemets

Description

This class represents a matrix of the length of the longest common prefixes between elements of a suffix array. The diagonal elements are all zero.

Objects from the Class

Objects can be created by calling the function LongestCommonPrefix with the (only) argument a suffix array.

Slots

abovediag:
Object of class "integer", represents the elements just above diagonal (ie. the elements of the matrix whose column numbers are one more than there row numbers).

Methods

lcp[i]
The only method for extracting elements from this class of objects. Here lcp is an object of class "LongestCommonPrefix" and i is a matrix of two columns, the columns representing the rwos and columns of the elements to be extracted. The result is an integer vector of the corresponding elements.

Author(s)

Saikat DebRoy

References

Dan Gusfield (1997) Algorithms on strings, trees, and sequences, Cambridge University Press, pp. 152

See Also

LongestCommonPrefix

Examples

data('yeastSEQCHR1')
yeast1 <- DNAString(yeastSEQCHR1)
x <- substring(yeast1, c(1, 30))
x
suf <- DNASuffixArray(x)
lcp <- LongestCommonPrefix(suf)
lcp[cbind(1, 1:30)]

[Package Biostrings version 1.4.0 Index]