-package main
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
import (
"bufio"
- "bytes"
"fmt"
"io"
)
-const tagmapKeySize = 24
+const tagmapKeySize = 32
-type tagmapKey [tagmapKeySize]byte
+type tagmapKey uint64
type tagID int32
}
type tagLibrary struct {
- tagmap map[tagmapKey]tagInfo
- keylen int
+ tagmap map[tagmapKey]tagInfo
+ keylen int
+ keymask tagmapKey
}
func (taglib *tagLibrary) Load(rdr io.Reader) error {
return taglib.setTags(seqs)
}
-type tagMatch struct {
- id tagID
- pos int
-}
-
-func (taglib *tagLibrary) FindAll(buf []byte, fn func(id tagID, pos int)) {
+func (taglib *tagLibrary) FindAll(in *bufio.Reader, passthrough io.Writer, fn func(id tagID, pos, taglen int)) error {
+ var window = make([]byte, 0, taglib.keylen*1000)
var key tagmapKey
- for i := 0; i <= len(buf)-taglib.keylen; i++ {
- copy(key[:taglib.keylen], buf[i:])
- if taginfo, ok := taglib.tagmap[key]; !ok {
+ for offset := 0; ; {
+ base, err := in.ReadByte()
+ if err == io.EOF {
+ return nil
+ } else if err != nil {
+ return err
+ } else if base == '\r' || base == '\n' {
+ if buf, err := in.Peek(1); err == nil && len(buf) > 0 && buf[0] == '>' {
+ return nil
+ } else if err == io.EOF {
+ return nil
+ }
+ continue
+ } else if base == '>' || base == ' ' {
+ return fmt.Errorf("unexpected char %q at offset %d in fasta data", base, offset)
+ }
+
+ if passthrough != nil {
+ if base >= 'A' && base <= 'Z' {
+ // lowercase for passthrough
+ base += 'a' - 'A'
+ }
+ _, err = passthrough.Write([]byte{base})
+ if err != nil {
+ return err
+ }
+ }
+ offset++
+ if !isbase[int(base)] {
+ // 'N' or various other chars meaning exact
+ // base not known
+ window = window[:0]
+ continue
+ }
+ window = append(window, base)
+ if len(window) == cap(window) {
+ copy(window, window[len(window)-taglib.keylen:])
+ window = window[:taglib.keylen]
+ }
+ key = ((key << 2) | twobit[int(base)]) & taglib.keymask
+
+ if len(window) < taglib.keylen {
continue
- } else if len(taginfo.tagseq) > taglib.keylen && (len(buf) < i+len(taginfo.tagseq) || !bytes.Equal(taginfo.tagseq, buf[i:i+len(taginfo.tagseq)])) {
- // key portion matches, but not the entire tag
+ } else if taginfo, ok := taglib.tagmap[key]; !ok {
continue
+ } else if len(taginfo.tagseq) != taglib.keylen {
+ return fmt.Errorf("assertion failed: len(%q) != keylen %d", taginfo.tagseq, taglib.keylen)
} else {
- fn(taginfo.id, i)
- i += len(taginfo.tagseq) - 1 // don't try to match overlapping tags
+ fn(taginfo.id, offset-taglib.keylen, len(taginfo.tagseq))
+ window = window[:0] // don't try to match overlapping tags
}
}
+ return nil
}
func (taglib *tagLibrary) Len() int {
return len(taglib.tagmap)
}
+func (taglib *tagLibrary) TagLen() int {
+ return taglib.keylen
+}
+
+var (
+ twobit = func() []tagmapKey {
+ r := make([]tagmapKey, 256)
+ r[int('a')] = 0
+ r[int('A')] = 0
+ r[int('c')] = 1
+ r[int('C')] = 1
+ r[int('g')] = 2
+ r[int('G')] = 2
+ r[int('t')] = 3
+ r[int('T')] = 3
+ return r
+ }()
+ isbase = func() []bool {
+ r := make([]bool, 256)
+ r[int('a')] = true
+ r[int('A')] = true
+ r[int('c')] = true
+ r[int('C')] = true
+ r[int('g')] = true
+ r[int('G')] = true
+ r[int('t')] = true
+ r[int('T')] = true
+ return r
+ }()
+)
+
func (taglib *tagLibrary) setTags(tags [][]byte) error {
taglib.keylen = tagmapKeySize
for _, t := range tags {
taglib.keylen = l
}
}
+ taglib.keymask = tagmapKey((1 << (taglib.keylen * 2)) - 1)
taglib.tagmap = map[tagmapKey]tagInfo{}
- for i, t := range tags {
- t = bytes.ToLower(t)
+ for i, tag := range tags {
var key tagmapKey
- copy(key[:], t[:taglib.keylen])
+ for _, b := range tag[:taglib.keylen] {
+ key = (key << 2) | twobit[int(b)]
+ }
if _, ok := taglib.tagmap[key]; ok {
- return fmt.Errorf("first %d bytes of tag %d (%s) are not unique", taglib.keylen, i, key)
+ return fmt.Errorf("first %d bytes of tag %d (%x) are not unique", taglib.keylen, i, key)
}
- taglib.tagmap[key] = tagInfo{tagID(i), t}
+ taglib.tagmap[key] = tagInfo{tagID(i), tag}
}
return nil
}
+
+func (taglib *tagLibrary) Tags() [][]byte {
+ out := make([][]byte, len(taglib.tagmap))
+ untwobit := []byte{'a', 'c', 'g', 't'}
+ for key, info := range taglib.tagmap {
+ seq := make([]byte, taglib.keylen)
+ for i := len(seq) - 1; i >= 0; i-- {
+ seq[i] = untwobit[int(key)&3]
+ key = key >> 2
+ }
+ out[int(info.id)] = seq
+ }
+ return out
+}
projects / lightning.git / blobdiff