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