diff options
| author | Ondřej Surý <ondrej@sury.org> | 2011-09-13 13:11:55 +0200 |
|---|---|---|
| committer | Ondřej Surý <ondrej@sury.org> | 2011-09-13 13:11:55 +0200 |
| commit | 80f18fc933cf3f3e829c5455a1023d69f7b86e52 (patch) | |
| tree | 4b825dc642cb6eb9a060e54bf8d69288fbee4904 /src/pkg/index/suffixarray | |
| parent | 28592ee1ea1f5cdffcf85472f9de0285d928cf12 (diff) | |
| download | golang-80f18fc933cf3f3e829c5455a1023d69f7b86e52.tar.gz | |
Imported Upstream version 60
Diffstat (limited to 'src/pkg/index/suffixarray')
| -rw-r--r-- | src/pkg/index/suffixarray/Makefile | 12 | ||||
| -rw-r--r-- | src/pkg/index/suffixarray/qsufsort.go | 170 | ||||
| -rw-r--r-- | src/pkg/index/suffixarray/suffixarray.go | 188 | ||||
| -rw-r--r-- | src/pkg/index/suffixarray/suffixarray_test.go | 240 |
4 files changed, 0 insertions, 610 deletions
diff --git a/src/pkg/index/suffixarray/Makefile b/src/pkg/index/suffixarray/Makefile deleted file mode 100644 index 297c4279f..000000000 --- a/src/pkg/index/suffixarray/Makefile +++ /dev/null @@ -1,12 +0,0 @@ -# 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. - -include ../../../Make.inc - -TARG=index/suffixarray -GOFILES=\ - qsufsort.go\ - suffixarray.go\ - -include ../../../Make.pkg diff --git a/src/pkg/index/suffixarray/qsufsort.go b/src/pkg/index/suffixarray/qsufsort.go deleted file mode 100644 index 9751b5c76..000000000 --- a/src/pkg/index/suffixarray/qsufsort.go +++ /dev/null @@ -1,170 +0,0 @@ -// 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) { - bounds := make([]int, 0, 4) - group := x.inv[x.sa[0]+x.h] - for i := 1; i < len(x.sa); i++ { - if g := x.inv[x.sa[i]+x.h]; g > group { - bounds = append(bounds, i) - group = g - } - } - bounds = append(bounds, len(x.sa)) - - // update the group numberings after all new groups are determined - prev := 0 - for _, b := range bounds { - for i := prev; i < b; i++ { - x.inv[x.sa[i]] = offset + b - 1 - } - if b-prev == 1 { - x.sa[prev] = -1 - } - prev = b - } -} diff --git a/src/pkg/index/suffixarray/suffixarray.go b/src/pkg/index/suffixarray/suffixarray.go deleted file mode 100644 index 9d4e93217..000000000 --- a/src/pkg/index/suffixarray/suffixarray.go +++ /dev/null @@ -1,188 +0,0 @@ -// 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" - "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]:] -} - - -// 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) []int { - // find matching suffix index range [i:j] - // find the first index where s would be the prefix - i := sort.Search(len(x.sa), 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(len(x.sa)-i, func(j int) bool { return !bytes.HasPrefix(x.at(j+i), s) }) - return x.sa[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) - if len(matches) < n || n < 0 { - n = len(matches) - } - if n > 0 { - result = make([]int, n) - copy(result, matches) - } - } - 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 -} diff --git a/src/pkg/index/suffixarray/suffixarray_test.go b/src/pkg/index/suffixarray/suffixarray_test.go deleted file mode 100644 index 385ff0e56..000000000 --- a/src/pkg/index/suffixarray/suffixarray_test.go +++ /dev/null @@ -1,240 +0,0 @@ -// 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)?", - }, - }, - - { - "godoc simulation", - "package main\n\nimport(\n \"rand\"\n ", - []string{}, - }, -} - - -// find all occurrences of s in source; report at most n occurrences -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.Ints(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) - } -} |
