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// 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
}