// Copyright 2010 The Go 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 suffixarray implements substring search in logarithmic time using // an in-memory suffix array. // // Example use: // // // create index for some data // index := suffixarray.New(data) // // // lookup byte slice s // offsets1 := index.Lookup(s, -1) // the list of all indices where s occurs in data // offsets2 := index.Lookup(s, 3) // the list of at most 3 indices where s occurs in data package suffixarray import ( "bytes" "encoding/binary" "errors" "io" "math" "regexp" "sort" ) // Can change for testing var maxData32 int = realMaxData32 const realMaxData32 = math.MaxInt32 // Index implements a suffix array for fast substring search. type Index struct { data []byte sa ints // suffix array for data; sa.len() == len(data) } // An ints is either an []int32 or an []int64. // That is, one of them is empty, and one is the real data. // The int64 form is used when len(data) > maxData32 type ints struct { int32 []int32 int64 []int64 } func (a *ints) len() int { return len(a.int32) + len(a.int64) } func (a *ints) get(i int) int64 { if a.int32 != nil { return int64(a.int32[i]) } return a.int64[i] } func (a *ints) set(i int, v int64) { if a.int32 != nil { a.int32[i] = int32(v) } else { a.int64[i] = v } } func (a *ints) slice(i, j int) ints { if a.int32 != nil { return ints{a.int32[i:j], nil} } return ints{nil, a.int64[i:j]} } // New creates a new [Index] for data. // [Index] creation time is O(N) for N = len(data). func New(data []byte) *Index { ix := &Index{data: data} if len(data) <= maxData32 { ix.sa.int32 = make([]int32, len(data)) text_32(data, ix.sa.int32) } else { ix.sa.int64 = make([]int64, len(data)) text_64(data, ix.sa.int64) } return ix } // writeInt writes an int x to w using buf to buffer the write. func writeInt(w io.Writer, buf []byte, x int) error { binary.PutVarint(buf, int64(x)) _, err := w.Write(buf[0:binary.MaxVarintLen64]) return err } // readInt reads an int x from r using buf to buffer the read and returns x. func readInt(r io.Reader, buf []byte) (int64, error) { _, err := io.ReadFull(r, buf[0:binary.MaxVarintLen64]) // ok to continue with error x, _ := binary.Varint(buf) return x, err } // writeSlice writes data[:n] to w and returns n. // It uses buf to buffer the write. func writeSlice(w io.Writer, buf []byte, data ints) (n int, err error) { // encode as many elements as fit into buf p := binary.MaxVarintLen64 m := data.len() for ; n < m && p+binary.MaxVarintLen64 <= len(buf); n++ { p += binary.PutUvarint(buf[p:], uint64(data.get(n))) } // update buffer size binary.PutVarint(buf, int64(p)) // write buffer _, err = w.Write(buf[0:p]) return } var errTooBig = errors.New("suffixarray: data too large") // readSlice reads data[:n] from r and returns n. // It uses buf to buffer the read. func readSlice(r io.Reader, buf []byte, data ints) (n int, err error) { // read buffer size var size64 int64 size64, err = readInt(r, buf) if err != nil { return } if int64(int(size64)) != size64 || int(size64) < 0 { // We never write chunks this big anyway. return 0, errTooBig } size := int(size64) // read buffer w/o the size if _, err = io.ReadFull(r, buf[binary.MaxVarintLen64:size]); err != nil { return } // decode as many elements as present in buf for p := binary.MaxVarintLen64; p < size; n++ { x, w := binary.Uvarint(buf[p:]) data.set(n, int64(x)) p += w } return } const bufSize = 16 << 10 // reasonable for BenchmarkSaveRestore // Read reads the index from r into x; x must not be nil. func (x *Index) Read(r io.Reader) error { // buffer for all reads buf := make([]byte, bufSize) // read length n64, err := readInt(r, buf) if err != nil { return err } if int64(int(n64)) != n64 || int(n64) < 0 { return errTooBig } n := int(n64) // allocate space if 2*n < cap(x.data) || cap(x.data) < n || x.sa.int32 != nil && n > maxData32 || x.sa.int64 != nil && n <= maxData32 { // new data is significantly smaller or larger than // existing buffers - allocate new ones x.data = make([]byte, n) x.sa.int32 = nil x.sa.int64 = nil if n <= maxData32 { x.sa.int32 = make([]int32, n) } else { x.sa.int64 = make([]int64, n) } } else { // re-use existing buffers x.data = x.data[0:n] x.sa = x.sa.slice(0, n) } // read data if _, err := io.ReadFull(r, x.data); err != nil { return err } // read index sa := x.sa for sa.len() > 0 { n, err := readSlice(r, buf, sa) if err != nil { return err } sa = sa.slice(n, sa.len()) } return nil } // Write writes the index x to w. func (x *Index) Write(w io.Writer) error { // buffer for all writes buf := make([]byte, bufSize) // write length if err := writeInt(w, buf, len(x.data)); err != nil { return err } // write data if _, err := w.Write(x.data); err != nil { return err } // write index sa := x.sa for sa.len() > 0 { n, err := writeSlice(w, buf, sa) if err != nil { return err } sa = sa.slice(n, sa.len()) } return nil } // Bytes returns the data over which the index was created. // It must not be modified. func (x *Index) Bytes() []byte { return x.data } func (x *Index) at(i int) []byte { return x.data[x.sa.get(i):] } // lookupAll returns a slice into the matching region of the index. // The runtime is O(log(N)*len(s)). func (x *Index) lookupAll(s []byte) ints { // find matching suffix index range [i:j] // find the first index where s would be the prefix i := sort.Search(x.sa.len(), func(i int) bool { return bytes.Compare(x.at(i), s) >= 0 }) // starting at i, find the first index at which s is not a prefix j := i + sort.Search(x.sa.len()-i, func(j int) bool { return !bytes.HasPrefix(x.at(j+i), s) }) return x.sa.slice(i, j) } // Lookup returns an unsorted list of at most n indices where the byte string s // occurs in the indexed data. If n < 0, all occurrences are returned. // The result is nil if s is empty, s is not found, or n == 0. // Lookup time is O(log(N)*len(s) + len(result)) where N is the // size of the indexed data. func (x *Index) Lookup(s []byte, n int) (result []int) { if len(s) > 0 && n != 0 { matches := x.lookupAll(s) count := matches.len() if n < 0 || count < n { n = count } // 0 <= n <= count if n > 0 { result = make([]int, n) if matches.int32 != nil { for i := range result { result[i] = int(matches.int32[i]) } } else { for i := range result { result[i] = int(matches.int64[i]) } } } } return } // FindAllIndex returns a sorted list of non-overlapping matches of the // regular expression r, where a match is a pair of indices specifying // the matched slice of x.Bytes(). If n < 0, all matches are returned // in successive order. Otherwise, at most n matches are returned and // they may not be successive. The result is nil if there are no matches, // or if n == 0. func (x *Index) FindAllIndex(r *regexp.Regexp, n int) (result [][]int) { // a non-empty literal prefix is used to determine possible // match start indices with Lookup prefix, complete := r.LiteralPrefix() lit := []byte(prefix) // worst-case scenario: no literal prefix if prefix == "" { return r.FindAllIndex(x.data, n) } // if regexp is a literal just use Lookup and convert its // result into match pairs if complete { // Lookup returns indices that may belong to overlapping matches. // After eliminating them, we may end up with fewer than n matches. // If we don't have enough at the end, redo the search with an // increased value n1, but only if Lookup returned all the requested // indices in the first place (if it returned fewer than that then // there cannot be more). for n1 := n; ; n1 += 2 * (n - len(result)) /* overflow ok */ { indices := x.Lookup(lit, n1) if len(indices) == 0 { return } sort.Ints(indices) pairs := make([]int, 2*len(indices)) result = make([][]int, len(indices)) count := 0 prev := 0 for _, i := range indices { if count == n { break } // ignore indices leading to overlapping matches if prev <= i { j := 2 * count pairs[j+0] = i pairs[j+1] = i + len(lit) result[count] = pairs[j : j+2] count++ prev = i + len(lit) } } result = result[0:count] if len(result) >= n || len(indices) != n1 { // found all matches or there's no chance to find more // (n and n1 can be negative) break } } if len(result) == 0 { result = nil } return } // regexp has a non-empty literal prefix; Lookup(lit) computes // the indices of possible complete matches; use these as starting // points for anchored searches // (regexp "^" matches beginning of input, not beginning of line) r = regexp.MustCompile("^" + r.String()) // compiles because r compiled // same comment about Lookup applies here as in the loop above for n1 := n; ; n1 += 2 * (n - len(result)) /* overflow ok */ { indices := x.Lookup(lit, n1) if len(indices) == 0 { return } sort.Ints(indices) result = result[0:0] prev := 0 for _, i := range indices { if len(result) == n { break } m := r.FindIndex(x.data[i:]) // anchored search - will not run off // ignore indices leading to overlapping matches if m != nil && prev <= i { m[0] = i // correct m m[1] += i result = append(result, m) prev = m[1] } } if len(result) >= n || len(indices) != n1 { // found all matches or there's no chance to find more // (n and n1 can be negative) break } } if len(result) == 0 { result = nil } return }