func (s *S) TestReadFasta(c *check.C) {
if r, err := fasta.NewReaderName(fa); err != nil {
c.Fatalf("Failed to open %q: %s", fa, err)
} else {
if a, err := NewReader(r).Read(); err != nil {
c.Fatalf("Failed to read %q: %s", fa, err)
} else {
c.Check(len(a), check.Equals, 11)
}
}
}
func BenchmarkAlign(b *testing.B) {
b.StopTimer()
if r, err := fasta.NewReaderName("../testdata/crsp.fa"); err != nil {
return
} else {
swsa, _ := r.Read()
swsb, _ := r.Read()
swm := [][]int{
{2, -1, -1, -1, -1},
{-1, 2, -1, -1, -1},
{-1, -1, 2, -1, -1},
{-1, -1, -1, 2, -1},
{-1, -1, -1, -1, 0},
}
smith := &Aligner{Matrix: swm, LookUp: LookUpN, GapChar: '-'}
b.StartTimer()
for i := 0; i < b.N; i++ {
smith.Align(swsa, swsb)
}
}
}
func BenchmarkAlign(b *testing.B) {
b.StopTimer()
if r, err := fasta.NewReaderName("../testdata/crsp.fa"); err != nil {
return
} else {
nwsa, _ := r.Read()
nwsb, _ := r.Read()
nwm := [][]int{
{10, -3, -1, -4, -5},
{-3, 9, -5, 0, -5},
{-1, -5, 7, -3, -5},
{-4, 0, -3, 8, -5},
{-4, -4, -4, -4, 0},
}
needle := &Aligner{Matrix: nwm, LookUp: LookUpN, GapChar: '-'}
b.StartTimer()
for i := 0; i < b.N; i++ {
needle.Align(nwsa, nwsb)
}
}
}