122 lines
2.6 KiB
Go
122 lines
2.6 KiB
Go
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package astrobwt
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import "math/rand"
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import "testing"
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// see https://www.geeksforgeeks.org/burrows-wheeler-data-transform-algorithm/
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func TestBWTAndInverseTransform(t *testing.T) {
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tests := []struct {
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input string
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bwt string
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}{
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{"BANANA", "ANNB$AA"}, // from https://www.geeksforgeeks.org/burrows-wheeler-data-transform-algorithm/
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{"abracadabra", "ard$rcaaaabb"},
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{"appellee", "e$elplepa"},
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{"GATGCGAGAGATG", "GGGGGGTCAA$TAA"},
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{"abcdefg", "g$abcdef"},
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}
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for _, test := range tests {
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trans2, eos := BWT([]byte(test.input))
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trans2[eos] = '$'
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if string(trans2) != test.bwt {
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t.Errorf("Test failed: Transform %s", test.input)
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}
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if string(InverseTransform([]byte(trans2), '$')) != test.input {
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t.Errorf("Test failed: InverseTransform expected '%s' actual '%s`", test.input, string(InverseTransform([]byte(trans2), '$')))
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}
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p := POW([]byte(test.input))
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p0 := POW_0alloc([]byte(test.input))
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if string(p[:]) != string(p0[:]) {
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t.Error("Test failed: difference between pow and pow_0alloc")
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}
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}
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}
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func TestFromSuffixArray(t *testing.T) {
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s := "GATGCGAGAGATG"
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trans := "GGGGGGTCAA$TAA"
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sa := SuffixArray([]byte(s))
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B, err := FromSuffixArray([]byte(s), sa, '$')
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if err != nil {
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t.Error("Test failed: FromSuffixArray error")
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}
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if string(B) != trans {
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t.Error("Test failed: FromSuffixArray returns wrong result")
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}
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}
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func TestPow_Powalloc(t *testing.T) {
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p := POW([]byte{0, 0, 0, 0})
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p0 := POW_0alloc([]byte{0, 0, 0, 0})
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if string(p[:]) != string(p0[:]) {
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t.Error("Test failed: POW and POW_0alloc returns different ")
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}
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}
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var cases [][]byte
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func init() {
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rand.Seed(1)
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alphabet := "abcdefghjijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ01234567890"
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n := len(alphabet)
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_ = n
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scales := []int{100000}
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cases = make([][]byte, len(scales))
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for i, scale := range scales {
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l := scale
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buf := make([]byte, int(l))
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for j := 0; j < int(l); j++ {
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buf[j] = byte(rand.Uint32() & 0xff) //alphabet[rand.Intn(n)]
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}
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cases[i] = buf
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}
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POW([]byte{0x99})
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}
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var result []byte
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func BenchmarkTransform(t *testing.B) {
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var r []byte
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var err error
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for i := 0; i < t.N; i++ {
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r, err = Transform(cases[0], '$')
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if err != nil {
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t.Error(err)
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return
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}
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}
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result = r
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}
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func BenchmarkTransform_quick(t *testing.B) {
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var r []byte
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for i := 0; i < t.N; i++ {
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//r, err = Transform(cases[0], '$')
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r, _ = BWT(cases[0])
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}
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result = r
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}
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func BenchmarkPOW(t *testing.B) {
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for i := 0; i < t.N; i++ {
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rand.Read(cases[0][:])
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_ = POW(cases[0][:])
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}
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}
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func BenchmarkPOW_0alloc(t *testing.B) {
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for i := 0; i < t.N; i++ {
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rand.Read(cases[0][:])
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_ = POW_0alloc(cases[0][:])
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}
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}
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