// 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
}
func addToMSA(sequences chan seq.Sequence, msa *seq.MSA) {
wgSeqFragments.Add(1)
go func() {
for s := range sequences {
// We don't use Add or AddFasta since both are
// O(#sequences * #frag-length), which gets to be quite slow
// in the presence of a lot of sequences.
//
// The key here is that we know that every sequence has the same
// length and is in the same format, so we can add entries in a
// straight forward manner.
msa.Entries = append(msa.Entries, s)
}
wgSeqFragments.Done()
}()
}
func testEqualAlign(t *testing.T, computed, answer seq.MSA) {
if computed.Len() != answer.Len() {
t.Fatalf("Lengths of MSAs differ: %d != %d",
computed.Len(), answer.Len())
}
scomputed := makeStrings(computed.Entries)
sanswer := makeStrings(answer.Entries)
if len(scomputed) != len(sanswer) {
t.Fatalf("\nLengths of entries in MSAs differ: %d != %d",
len(scomputed), len(sanswer))
}
for i := 0; i < len(scomputed); i++ {
c, a := scomputed[i], sanswer[i]
if c != a {
t.Fatalf("\nComputed sequence in MSA is\n\n%s\n\n"+
"but answer is\n\n%s", c, a)
}
}
}
// WriteA3M writes a multiple sequence alignment to the output in
// A3M format. A3M format uses upper case characters to indicate
// matches, lower case characters to indicate insertions, and '-'
// characters to indicate deletions.
//
// A3M format is a more compact way to write an MSA than FASTA or A2M.
func WriteA3M(w io.Writer, msa seq.MSA) error {
formatter := func(row int) seq.Sequence {
return msa.GetA3M(row)
}
return write(w, msa, formatter)
}