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// Copyright © 2018-2021 Wei Shen <shenwei356@gmail.com>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
// THE SOFTWARE.
package sketches
import (
"testing"
"github.com/shenwei356/bio/seq"
)
func TestProteinIterator(t *testing.T) {
_s := "AAGTTTGAATCATTCAACTATCTAGTTTTCAGAGAACAATGTTCTCTAAAGAATAGAAAAGAGTCATTGTGCGGTGATGATGGCGGGAAGGATCCACCTG"
sequence, err := seq.NewSeq(seq.DNA, []byte(_s))
if err != nil {
t.Errorf("fail to create sequence: %s", _s)
}
k := 10
iter, err := NewProteinIterator(sequence, k, 1, 1)
if err != nil {
t.Errorf("fail to create aa iter rator")
}
var code uint64
var ok bool
// var idx int
codes := make([]uint64, 0, 1024)
for {
code, ok = iter.Next()
if !ok {
break
}
// idx = iter.Index()
// fmt.Printf("aa: %d-%s, %d\n", idx, iter.s.Seq[idx:idx+k], code)
codes = append(codes, code)
}
if len(codes) != len(_s)/3-k+1 {
t.Errorf("k-mer hashes number error")
}
}
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