// WriteStockholm writes the given MSA to the writer in the Stockholm format.
// This does not write any features. It only creates a minimal valid Stockholm
// file with the header (and version) along with the sequences (names and
// residues).
func WriteStockholm(w io.Writer, msa seq.MSA) error {
var err error
pf := func(format string, v ...interface{}) {
if err != nil {
return
}
_, err = fmt.Fprintf(w, format, v...)
}
pf("# STOCKHOLM 1.0\n")
for row := 0; row < len(msa.Entries) && err == nil; row++ {
s := msa.GetA2M(row)
pf("%s %s\n", s.Name, s.Residues)
}
pf("//\n")
return err
}
// WriteA2M writes a multiple sequence alignment to the output in
// A2M format. A2M format uses upper case characters to indicate
// matches, lower case and '.' characters to indicate insertions, and '-'
// characters to indicate deletions.
func WriteA2M(w io.Writer, msa seq.MSA) error {
formatter := func(row int) seq.Sequence {
return msa.GetA2M(row)
}
return write(w, msa, formatter)
}