1 files changed, 381 insertions, 0 deletions
diff --git a/src/index/suffixarray/suffixarray.go b/src/index/suffixarray/suffixarray.go
new file mode 100644
index 0000000..5c222a1
--- /dev/null
+++ b/src/index/suffixarray/suffixarray.go
@@ -0,0 +1,381 @@
+// 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
+}