rphast (version 1.0)

summary.msa: MSA Summary

Description

Prints a short description of an MSA (multiple sequence alignment) object.

Usage

summary.msa(object, ..., print.seq=ifelse(ncol.msa(object) *
    nrow.msa(object) < 500, TRUE, FALSE), format="FASTA",
    pretty.print=FALSE)

Arguments

object

an MSA object

...

additional arguments sent to print

print.seq

whether to supress printing of the alignment

format

to print sequence in if printing alignment

pretty.print

whether to pretty.print pretty-print sequence if printing alignment

See Also

print.msa

Examples

# read in an MSA stored in R
m <- msa(seqs=c("ACGTAT", "AGGTAA", "AGGTAG"),
         names=c("human", "mouse", "rat"))
summary(m)

# read in an MSA stored by reference in C
m <- msa(seqs=c("ACGTAT", "AGGTAA", "AGGTAG"),
         names=c("human", "mouse", "rat"),
         pointer.only=TRUE)
summary(m)