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author | upstream source tree <ports@midipix.org> | 2015-03-15 20:14:05 -0400 |
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committer | upstream source tree <ports@midipix.org> | 2015-03-15 20:14:05 -0400 |
commit | 554fd8c5195424bdbcabf5de30fdc183aba391bd (patch) | |
tree | 976dc5ab7fddf506dadce60ae936f43f58787092 /libgo/go/index/suffixarray | |
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Diffstat (limited to 'libgo/go/index/suffixarray')
-rw-r--r-- | libgo/go/index/suffixarray/qsufsort.go | 164 | ||||
-rw-r--r-- | libgo/go/index/suffixarray/suffixarray.go | 182 | ||||
-rw-r--r-- | libgo/go/index/suffixarray/suffixarray_test.go | 234 |
3 files changed, 580 insertions, 0 deletions
diff --git a/libgo/go/index/suffixarray/qsufsort.go b/libgo/go/index/suffixarray/qsufsort.go new file mode 100644 index 000000000..0e6894a8b --- /dev/null +++ b/libgo/go/index/suffixarray/qsufsort.go @@ -0,0 +1,164 @@ +// Copyright 2011 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. + +// This algorithm is based on "Faster Suffix Sorting" +// by N. Jesper Larsson and Kunihiko Sadakane +// paper: http://www.larsson.dogma.net/ssrev-tr.pdf +// code: http://www.larsson.dogma.net/qsufsort.c + +// This algorithm computes the suffix array sa by computing its inverse. +// Consecutive groups of suffixes in sa are labeled as sorted groups or +// unsorted groups. For a given pass of the sorter, all suffixes are ordered +// up to their first h characters, and sa is h-ordered. Suffixes in their +// final positions and unambiguouly sorted in h-order are in a sorted group. +// Consecutive groups of suffixes with identical first h characters are an +// unsorted group. In each pass of the algorithm, unsorted groups are sorted +// according to the group number of their following suffix. + +// In the implementation, if sa[i] is negative, it indicates that i is +// the first element of a sorted group of length -sa[i], and can be skipped. +// An unsorted group sa[i:k] is given the group number of the index of its +// last element, k-1. The group numbers are stored in the inverse slice (inv), +// and when all groups are sorted, this slice is the inverse suffix array. + +package suffixarray + +import "sort" + +func qsufsort(data []byte) []int { + // initial sorting by first byte of suffix + sa := sortedByFirstByte(data) + if len(sa) < 2 { + return sa + } + // initialize the group lookup table + // this becomes the inverse of the suffix array when all groups are sorted + inv := initGroups(sa, data) + + // the index starts 1-ordered + sufSortable := &suffixSortable{sa, inv, 1} + + for sa[0] > -len(sa) { // until all suffixes are one big sorted group + // The suffixes are h-ordered, make them 2*h-ordered + pi := 0 // pi is first position of first group + sl := 0 // sl is negated length of sorted groups + for pi < len(sa) { + if s := sa[pi]; s < 0 { // if pi starts sorted group + pi -= s // skip over sorted group + sl += s // add negated length to sl + } else { // if pi starts unsorted group + if sl != 0 { + sa[pi+sl] = sl // combine sorted groups before pi + sl = 0 + } + pk := inv[s] + 1 // pk-1 is last position of unsorted group + sufSortable.sa = sa[pi:pk] + sort.Sort(sufSortable) + sufSortable.updateGroups(pi) + pi = pk // next group + } + } + if sl != 0 { // if the array ends with a sorted group + sa[pi+sl] = sl // combine sorted groups at end of sa + } + + sufSortable.h *= 2 // double sorted depth + } + + for i := range sa { // reconstruct suffix array from inverse + sa[inv[i]] = i + } + return sa +} + + +func sortedByFirstByte(data []byte) []int { + // total byte counts + var count [256]int + for _, b := range data { + count[b]++ + } + // make count[b] equal index of first occurence of b in sorted array + sum := 0 + for b := range count { + count[b], sum = sum, count[b]+sum + } + // iterate through bytes, placing index into the correct spot in sa + sa := make([]int, len(data)) + for i, b := range data { + sa[count[b]] = i + count[b]++ + } + return sa +} + + +func initGroups(sa []int, data []byte) []int { + // label contiguous same-letter groups with the same group number + inv := make([]int, len(data)) + prevGroup := len(sa) - 1 + groupByte := data[sa[prevGroup]] + for i := len(sa) - 1; i >= 0; i-- { + if b := data[sa[i]]; b < groupByte { + if prevGroup == i+1 { + sa[i+1] = -1 + } + groupByte = b + prevGroup = i + } + inv[sa[i]] = prevGroup + if prevGroup == 0 { + sa[0] = -1 + } + } + // Separate out the final suffix to the start of its group. + // This is necessary to ensure the suffix "a" is before "aba" + // when using a potentially unstable sort. + lastByte := data[len(data)-1] + s := -1 + for i := range sa { + if sa[i] >= 0 { + if data[sa[i]] == lastByte && s == -1 { + s = i + } + if sa[i] == len(sa)-1 { + sa[i], sa[s] = sa[s], sa[i] + inv[sa[s]] = s + sa[s] = -1 // mark it as an isolated sorted group + break + } + } + } + return inv +} + + +type suffixSortable struct { + sa []int + inv []int + h int +} + +func (x *suffixSortable) Len() int { return len(x.sa) } +func (x *suffixSortable) Less(i, j int) bool { return x.inv[x.sa[i]+x.h] < x.inv[x.sa[j]+x.h] } +func (x *suffixSortable) Swap(i, j int) { x.sa[i], x.sa[j] = x.sa[j], x.sa[i] } + + +func (x *suffixSortable) updateGroups(offset int) { + prev := len(x.sa) - 1 + group := x.inv[x.sa[prev]+x.h] + for i := prev; i >= 0; i-- { + if g := x.inv[x.sa[i]+x.h]; g < group { + if prev == i+1 { // previous group had size 1 and is thus sorted + x.sa[i+1] = -1 + } + group = g + prev = i + } + x.inv[x.sa[i]] = prev + offset + if prev == 0 { // first group has size 1 and is thus sorted + x.sa[0] = -1 + } + } +} diff --git a/libgo/go/index/suffixarray/suffixarray.go b/libgo/go/index/suffixarray/suffixarray.go new file mode 100644 index 000000000..628e000e1 --- /dev/null +++ b/libgo/go/index/suffixarray/suffixarray.go @@ -0,0 +1,182 @@ +// 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. + +// The suffixarray package 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" + "regexp" + "sort" +) + + +// Index implements a suffix array for fast substring search. +type Index struct { + data []byte + sa []int // suffix array for data +} + + +// New creates a new Index for data. +// Index creation time is O(N*log(N)) for N = len(data). +func New(data []byte) *Index { + return &Index{data, qsufsort(data)} +} + + +// 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[i]:] +} + + +func (x *Index) search(s []byte) int { + return sort.Search(len(x.sa), func(i int) bool { return bytes.Compare(x.at(i), s) >= 0 }) +} + + +// 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(result))*len(s)) 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 { + // find matching suffix index i + i := x.search(s) + // x.at(i-1) < s <= x.at(i) + + // collect the following suffixes with matching prefixes + for (n < 0 || len(result) < n) && i < len(x.sa) && bytes.HasPrefix(x.at(i), s) { + result = append(result, x.sa[i]) + 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.SortInts(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.SortInts(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 +} diff --git a/libgo/go/index/suffixarray/suffixarray_test.go b/libgo/go/index/suffixarray/suffixarray_test.go new file mode 100644 index 000000000..b3486a96d --- /dev/null +++ b/libgo/go/index/suffixarray/suffixarray_test.go @@ -0,0 +1,234 @@ +// 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 + +import ( + "bytes" + "container/vector" + "regexp" + "sort" + "strings" + "testing" +) + + +type testCase struct { + name string // name of test case + source string // source to index + patterns []string // patterns to lookup +} + + +var testCases = []testCase{ + { + "empty string", + "", + []string{ + "", + "foo", + "(foo)", + ".*", + "a*", + }, + }, + + { + "all a's", + "aaaaaaaaaa", // 10 a's + []string{ + "", + "a", + "aa", + "aaa", + "aaaa", + "aaaaa", + "aaaaaa", + "aaaaaaa", + "aaaaaaaa", + "aaaaaaaaa", + "aaaaaaaaaa", + "aaaaaaaaaaa", // 11 a's + ".", + ".*", + "a+", + "aa+", + "aaaa[b]?", + "aaa*", + }, + }, + + { + "abc", + "abc", + []string{ + "a", + "b", + "c", + "ab", + "bc", + "abc", + "a.c", + "a(b|c)", + "abc?", + }, + }, + + { + "barbara*3", + "barbarabarbarabarbara", + []string{ + "a", + "bar", + "rab", + "arab", + "barbar", + "bara?bar", + }, + }, + + { + "typing drill", + "Now is the time for all good men to come to the aid of their country.", + []string{ + "Now", + "the time", + "to come the aid", + "is the time for all good men to come to the aid of their", + "to (come|the)?", + }, + }, +} + + +// find all occurrences of s in source; report at most n occurences +func find(src, s string, n int) []int { + var res vector.IntVector + if s != "" && n != 0 { + // find at most n occurrences of s in src + for i := -1; n < 0 || len(res) < n; { + j := strings.Index(src[i+1:], s) + if j < 0 { + break + } + i += j + 1 + res.Push(i) + } + } + return res +} + + +func testLookup(t *testing.T, tc *testCase, x *Index, s string, n int) { + res := x.Lookup([]byte(s), n) + exp := find(tc.source, s, n) + + // check that the lengths match + if len(res) != len(exp) { + t.Errorf("test %q, lookup %q (n = %d): expected %d results; got %d", tc.name, s, n, len(exp), len(res)) + } + + // if n >= 0 the number of results is limited --- unless n >= all results, + // we may obtain different positions from the Index and from find (because + // Index may not find the results in the same order as find) => in general + // we cannot simply check that the res and exp lists are equal + + // check that each result is in fact a correct match and there are no duplicates + sort.SortInts(res) + for i, r := range res { + if r < 0 || len(tc.source) <= r { + t.Errorf("test %q, lookup %q, result %d (n = %d): index %d out of range [0, %d[", tc.name, s, i, n, r, len(tc.source)) + } else if !strings.HasPrefix(tc.source[r:], s) { + t.Errorf("test %q, lookup %q, result %d (n = %d): index %d not a match", tc.name, s, i, n, r) + } + if i > 0 && res[i-1] == r { + t.Errorf("test %q, lookup %q, result %d (n = %d): found duplicate index %d", tc.name, s, i, n, r) + } + } + + if n < 0 { + // all results computed - sorted res and exp must be equal + for i, r := range res { + e := exp[i] + if r != e { + t.Errorf("test %q, lookup %q, result %d: expected index %d; got %d", tc.name, s, i, e, r) + } + } + } +} + + +func testFindAllIndex(t *testing.T, tc *testCase, x *Index, rx *regexp.Regexp, n int) { + res := x.FindAllIndex(rx, n) + exp := rx.FindAllStringIndex(tc.source, n) + + // check that the lengths match + if len(res) != len(exp) { + t.Errorf("test %q, FindAllIndex %q (n = %d): expected %d results; got %d", tc.name, rx, n, len(exp), len(res)) + } + + // if n >= 0 the number of results is limited --- unless n >= all results, + // we may obtain different positions from the Index and from regexp (because + // Index may not find the results in the same order as regexp) => in general + // we cannot simply check that the res and exp lists are equal + + // check that each result is in fact a correct match and the result is sorted + for i, r := range res { + if r[0] < 0 || r[0] > r[1] || len(tc.source) < r[1] { + t.Errorf("test %q, FindAllIndex %q, result %d (n == %d): illegal match [%d, %d]", tc.name, rx, i, n, r[0], r[1]) + } else if !rx.MatchString(tc.source[r[0]:r[1]]) { + t.Errorf("test %q, FindAllIndex %q, result %d (n = %d): [%d, %d] not a match", tc.name, rx, i, n, r[0], r[1]) + } + } + + if n < 0 { + // all results computed - sorted res and exp must be equal + for i, r := range res { + e := exp[i] + if r[0] != e[0] || r[1] != e[1] { + t.Errorf("test %q, FindAllIndex %q, result %d: expected match [%d, %d]; got [%d, %d]", + tc.name, rx, i, e[0], e[1], r[0], r[1]) + } + } + } +} + + +func testLookups(t *testing.T, tc *testCase, x *Index, n int) { + for _, pat := range tc.patterns { + testLookup(t, tc, x, pat, n) + if rx, err := regexp.Compile(pat); err == nil { + testFindAllIndex(t, tc, x, rx, n) + } + } +} + + +// index is used to hide the sort.Interface +type index Index + +func (x *index) Len() int { return len(x.sa) } +func (x *index) Less(i, j int) bool { return bytes.Compare(x.at(i), x.at(j)) < 0 } +func (x *index) Swap(i, j int) { x.sa[i], x.sa[j] = x.sa[j], x.sa[i] } +func (a *index) at(i int) []byte { return a.data[a.sa[i]:] } + + +func testConstruction(t *testing.T, tc *testCase, x *Index) { + if !sort.IsSorted((*index)(x)) { + t.Errorf("testConstruction failed %s", tc.name) + } +} + + +func TestIndex(t *testing.T) { + for _, tc := range testCases { + x := New([]byte(tc.source)) + testConstruction(t, &tc, x) + testLookups(t, &tc, x, 0) + testLookups(t, &tc, x, 1) + testLookups(t, &tc, x, 10) + testLookups(t, &tc, x, 2e9) + testLookups(t, &tc, x, -1) + } +} |