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// Copyright ©2011-2012 The bíogo Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.
package alphabet
import (
"strings"
"testing"
"unicode"
"gopkg.in/check.v1"
)
// Tests
func Test(t *testing.T) { check.TestingT(t) }
type S struct{}
var _ = check.Suite(&S{})
func (s *S) TestInterfaces(c *check.C) {
var (
alpha Alphabet
comp Complementor
)
for _, a := range []interface{}{DNA, RNA, Protein} {
c.Check(a, check.Implements, &alpha)
}
for _, a := range []interface{}{DNA, DNAredundant, RNA, RNAredundant} {
c.Check(a, check.Implements, &comp)
}
c.Check(Protein, check.Not(check.Implements), &comp)
}
type testAlphabets struct {
alphabet Alphabet
letters string
}
func (s *S) TestIsValid(c *check.C) {
for _, t := range []testAlphabets{
{DNA, "acgt"},
{DNAgapped, "-acgt"},
{RNA, "acgu"},
{RNAgapped, "-acgu"},
{Protein, "-abcdefghijklmnpqrstvwxyz*"},
} {
for i := 0; i < 256; i++ {
c.Check(t.alphabet.IsValid(Letter(i)), check.Equals, strings.ContainsRune(t.letters, unicode.ToUpper(rune(i))) || strings.ContainsRune(t.letters, unicode.ToLower(rune(i))))
}
}
}
func uc(l Letter) Letter {
return Letter(unicode.ToUpper(rune(l)))
}
func (s *S) TestLetter(c *check.C) {
for _, t := range []Alphabet{
DNA,
RNA,
Protein,
} {
for i := 0; i < t.Len(); i++ {
c.Check(t.IndexOf(t.Letter(i)), check.Equals, i,
check.Commentf("Index %d: %c == %d", i, t.Letter(i), t.IndexOf(t.Letter(i))))
c.Check(t.IndexOf(uc(t.Letter(i))), check.Equals, i,
check.Commentf("Index %d: %c == %d", i, uc(t.Letter(i)), t.IndexOf(uc(t.Letter(i)))))
}
}
}
func (s *S) TestComplement(c *check.C) {
for _, t := range []Complementor{
DNA,
RNA,
} {
for i := 0; i < 256; i++ {
if sc, ok := t.Complement(Letter(i)); ok {
dc, ok := t.Complement(sc)
c.Check(ok, check.Equals, true)
c.Check(dc, check.Equals, Letter(i))
}
}
}
}
func (s *S) TestComplementDirect(c *check.C) {
for _, t := range []Complementor{
DNA,
RNA,
} {
complement := t.ComplementTable()
for i := 0; i < 256; i++ {
if sc := complement[i]; sc <= unicode.MaxASCII {
dc := complement[sc]
c.Check(dc <= unicode.MaxASCII, check.Equals, true)
c.Check(dc, check.Equals, Letter(i))
} else {
c.Check(sc&unicode.MaxASCII, check.Equals, Letter(i&unicode.MaxASCII))
}
}
}
}
func (s *S) TestLetters(c *check.C) {
for _, t := range []testAlphabets{
{DNA, "acgtACGT"},
{DNA, "acgtACGT"},
{RNAgapped, "-acgu-ACGU"},
{RNAgapped, "-acgu-ACGU"},
{Protein, "-abcdefghijklmnpqrstvwxyz*-ABCDEFGHIJKLMNPQRSTVWXYZ*"},
} {
c.Check(t.alphabet.Letters(), check.Equals, t.letters)
}
}
func (s *S) TestRangeCheck(c *check.C) {
var err error
_, err = newAlphabet(string([]rune{256}), 0, 0, 0, !CaseSensitive)
c.Check(err, check.Not(check.IsNil))
_, err = newAlphabet(string([]rune{0}), 0, 0, 0, !CaseSensitive)
c.Check(err, check.IsNil)
_, err = newAlphabet(string([]rune{127}), 0, 0, 0, !CaseSensitive)
c.Check(err, check.IsNil)
_, err = newAlphabet(string([]rune{-1}), 0, 0, 0, !CaseSensitive)
c.Check(err, check.Not(check.IsNil))
}
func BenchmarkIsValid(b *testing.B) {
g, _ := newAlphabet("-abcdefghijklmnpqrstvwxyz*", 0, 0, 0, !CaseSensitive)
b.ResetTimer()
for i := 0; i < b.N; i++ {
g.IsValid(Letter(i))
}
}
func BenchmarkIsValidProtein(b *testing.B) {
for i := 0; i < b.N; i++ {
Protein.IsValid(Letter(i))
}
}
func BenchmarkIsValidDNA(b *testing.B) {
for i := 0; i < b.N; i++ {
DNA.IsValid(Letter(i))
}
}
func BenchmarkIsValidDNADirect(b *testing.B) {
valid := DNA.ValidLetters()
for i := 0; i < b.N; i++ {
_ = valid[byte(i)]
}
}
func BenchmarkIndexDNA(b *testing.B) {
for i := 0; i < b.N; i++ {
DNA.IndexOf(Letter(i))
}
}
func BenchmarkIndexDNADirect(b *testing.B) {
index := DNA.LetterIndex()
for i := 0; i < b.N; i++ {
_ = index[byte(i)]
}
}
func BenchmarkComplementDNA(b *testing.B) {
for i := 0; i < b.N; i++ {
DNA.Complement(Letter(i))
}
}
func BenchmarkComplementDNADirect(b *testing.B) {
comp := DNA.ComplementTable()
var c Letter
for i := 0; i < b.N; i++ {
if c = comp[Letter(i)]; c != 0x80 {
}
}
}
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