taglib_test.go

   1 // Copyright (C) The Lightning Authors. All rights reserved.
   2 //
   3 // SPDX-License-Identifier: AGPL-3.0
   4
   5 package lightning
   6
   7 import (
   8         "bufio"
   9         "bytes"
  10         "fmt"
  11         "io"
  12         "math/rand"
  13         "os"
  14         "strings"
  15         "testing"
  16         "time"
  17
  18         "gopkg.in/check.v1"
  19 )
  20
  21 func Test(t *testing.T) { check.TestingT(t) }
  22
  23 type taglibSuite struct{}
  24
  25 var _ = check.Suite(&taglibSuite{})
  26
  27 type tagMatch struct {
  28         id     tagID
  29         pos    int
  30         taglen int
  31 }
  32
  33 func (s *taglibSuite) TestFindAllTinyData(c *check.C) {
  34         pr, pw, err := os.Pipe()
  35         c.Assert(err, check.IsNil)
  36         go func() {
  37                 defer pw.Close()
  38                 fmt.Fprintf(pw, `>0000.00
  39 ggagaactgtgctccgccttcaga
  40 acacatgctagcgcgtcggggtgg
  41 gactctagcagagtggccagccac
  42 `)
  43         }()
  44         var taglib tagLibrary
  45         err = taglib.Load(pr)
  46         c.Assert(err, check.IsNil)
  47         haystack := []byte(`ggagaactgtgctccgccttcagaccccccccccccccccccccacacatgctagcgcgtcggggtgggggggggggggggggggggggggggactctagcagagtggccagccac`)
  48         var matches []tagMatch
  49         taglib.FindAll(bufio.NewReader(bytes.NewBuffer(haystack)), nil, func(id tagID, pos, taglen int) {
  50                 matches = append(matches, tagMatch{id, pos, taglen})
  51         })
  52         c.Check(matches, check.DeepEquals, []tagMatch{{0, 0, 24}, {1, 44, 24}, {2, 92, 24}})
  53 }
  54
  55 func (s *taglibSuite) TestFindAllRealisticSize(c *check.C) {
  56         start := time.Now()
  57         acgt := []byte{'a', 'c', 'g', 't'}
  58         haystack := make([]byte, 25000000) // ~1/2 smallest human chromosome
  59         c.Logf("@%v haystack", time.Since(start))
  60         rand.Read(haystack)
  61         for i := range haystack {
  62                 haystack[i] = acgt[int(haystack[i]&3)]
  63         }
  64
  65         tagcount := 12500
  66         tagsize := 24
  67         var tags []string
  68         pr, pw := io.Pipe()
  69         go func() {
  70                 defer pw.Close()
  71                 w := bufio.NewWriter(pw)
  72                 defer w.Flush()
  73                 used := map[string]bool{}
  74                 fmt.Fprint(w, ">000\n")
  75                 for i := 0; len(tags) < tagcount; i += (len(haystack) - tagsize) / tagcount {
  76                         i := i
  77                         tag := haystack[i : i+tagsize]
  78                         for used[string(tag)] {
  79                                 i++
  80                                 tag = haystack[i : i+tagsize]
  81                         }
  82                         used[string(tag)] = true
  83                         tags = append(tags, strings.ToLower(string(tag)))
  84                         w.Write(tag)
  85                         w.Write([]byte{'\n'})
  86                 }
  87         }()
  88         c.Logf("@%v build library", time.Since(start))
  89         var taglib tagLibrary
  90         err := taglib.Load(pr)
  91         c.Assert(err, check.IsNil)
  92         c.Logf("@%v find tags in input", time.Since(start))
  93         var matches []tagMatch
  94         taglib.FindAll(bufio.NewReader(bytes.NewBuffer(haystack)), nil, func(id tagID, pos, taglen int) {
  95                 matches = append(matches, tagMatch{id, pos, taglen})
  96         })
  97         c.Logf("@%v done", time.Since(start))
  98         c.Check(matches[0], check.Equals, tagMatch{0, 0, tagsize})
  99         c.Check(matches[1].id, check.Equals, tagID(1))
 100 }