rphast (version 1.6.9)

is.ordered.msa: MSA is Ordered?

Description

Determines if an MSA object represents an ordered alignment.

Usage

# S3 method for msa
is.ordered(x)

Arguments

x

an MSA object

Value

a boolean indicating whether the columns are in order

Examples

# NOT RUN {
m <- msa(seqs=c("A--ACGTAT", "AG-AGGTAA", "AGGAGGTAG"),
         names=c("human", "mouse", "rat"))
is.ordered.msa(m)
m <- msa(seqs=c("A--ACGTAT", "AG-AGGTAA", "AGGAGGTAG"),
         names=c("human", "mouse", "rat"), is.ordered=FALSE)
is.ordered.msa(m)
# }