print.fasta: Printing Sequence Alignments

Description

Print method for fasta and pdbs sequence alignment objects.

Usage

## S3 method for class 'fasta':
print(x, alignment=TRUE, ...)
.print.fasta.ali(x, width = NULL, col.inds = NULL, numbers = TRUE, ...)

Arguments

a sequence alignment object as obtained from the functions read.fasta, read.fasta.pdb, pdbaln

alignment

logical, if TRUE the sequence alignment will be printed to screen.

width

a single numeric value giving the number of residues per printed sequence block. By default this is determined from considering alignment identifier widths given a standard 85 column terminal window.

col.inds

an optional numeric vector that can be used to select subsets of alignment positions/columns for printing.

numbers

logical, if TRUE position numbers and a tick-mark every 10 positions are printed above and below sequence blocks.

...

additional arguments to .print.fasta.ali.

Value

Called mostly for its effect but also silently returns block divided concatenated sequence strings as a matrix.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

Examples

Run this code

file <- system.file("examples/kif1a.fa",package="bio3d")
     aln  <- read.fasta(file)
     print(aln)

     # print(aln, col.inds=30:100, numbers=FALSE)

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