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author | Daniel Baumann <daniel.baumann@progress-linux.org> | 2024-04-16 19:23:18 +0000 |
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committer | Daniel Baumann <daniel.baumann@progress-linux.org> | 2024-04-16 19:23:18 +0000 |
commit | 43a123c1ae6613b3efeed291fa552ecd909d3acf (patch) | |
tree | fd92518b7024bc74031f78a1cf9e454b65e73665 /src/index/suffixarray/sais.go | |
parent | Initial commit. (diff) | |
download | golang-1.20-43a123c1ae6613b3efeed291fa552ecd909d3acf.tar.xz golang-1.20-43a123c1ae6613b3efeed291fa552ecd909d3acf.zip |
Adding upstream version 1.20.14.upstream/1.20.14upstream
Signed-off-by: Daniel Baumann <daniel.baumann@progress-linux.org>
Diffstat (limited to 'src/index/suffixarray/sais.go')
-rw-r--r-- | src/index/suffixarray/sais.go | 899 |
1 files changed, 899 insertions, 0 deletions
diff --git a/src/index/suffixarray/sais.go b/src/index/suffixarray/sais.go new file mode 100644 index 0000000..74c5235 --- /dev/null +++ b/src/index/suffixarray/sais.go @@ -0,0 +1,899 @@ +// Copyright 2019 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. + +// Suffix array construction by induced sorting (SAIS). +// See Ge Nong, Sen Zhang, and Wai Hong Chen, +// "Two Efficient Algorithms for Linear Time Suffix Array Construction", +// especially section 3 (https://ieeexplore.ieee.org/document/5582081). +// See also http://zork.net/~st/jottings/sais.html. +// +// With optimizations inspired by Yuta Mori's sais-lite +// (https://sites.google.com/site/yuta256/sais). +// +// And with other new optimizations. + +// Many of these functions are parameterized by the sizes of +// the types they operate on. The generator gen.go makes +// copies of these functions for use with other sizes. +// Specifically: +// +// - A function with a name ending in _8_32 takes []byte and []int32 arguments +// and is duplicated into _32_32, _8_64, and _64_64 forms. +// The _32_32 and _64_64_ suffixes are shortened to plain _32 and _64. +// Any lines in the function body that contain the text "byte-only" or "256" +// are stripped when creating _32_32 and _64_64 forms. +// (Those lines are typically 8-bit-specific optimizations.) +// +// - A function with a name ending only in _32 operates on []int32 +// and is duplicated into a _64 form. (Note that it may still take a []byte, +// but there is no need for a version of the function in which the []byte +// is widened to a full integer array.) + +// The overall runtime of this code is linear in the input size: +// it runs a sequence of linear passes to reduce the problem to +// a subproblem at most half as big, invokes itself recursively, +// and then runs a sequence of linear passes to turn the answer +// for the subproblem into the answer for the original problem. +// This gives T(N) = O(N) + T(N/2) = O(N) + O(N/2) + O(N/4) + ... = O(N). +// +// The outline of the code, with the forward and backward scans +// through O(N)-sized arrays called out, is: +// +// sais_I_N +// placeLMS_I_B +// bucketMax_I_B +// freq_I_B +// <scan +text> (1) +// <scan +freq> (2) +// <scan -text, random bucket> (3) +// induceSubL_I_B +// bucketMin_I_B +// freq_I_B +// <scan +text, often optimized away> (4) +// <scan +freq> (5) +// <scan +sa, random text, random bucket> (6) +// induceSubS_I_B +// bucketMax_I_B +// freq_I_B +// <scan +text, often optimized away> (7) +// <scan +freq> (8) +// <scan -sa, random text, random bucket> (9) +// assignID_I_B +// <scan +sa, random text substrings> (10) +// map_B +// <scan -sa> (11) +// recurse_B +// (recursive call to sais_B_B for a subproblem of size at most 1/2 input, often much smaller) +// unmap_I_B +// <scan -text> (12) +// <scan +sa> (13) +// expand_I_B +// bucketMax_I_B +// freq_I_B +// <scan +text, often optimized away> (14) +// <scan +freq> (15) +// <scan -sa, random text, random bucket> (16) +// induceL_I_B +// bucketMin_I_B +// freq_I_B +// <scan +text, often optimized away> (17) +// <scan +freq> (18) +// <scan +sa, random text, random bucket> (19) +// induceS_I_B +// bucketMax_I_B +// freq_I_B +// <scan +text, often optimized away> (20) +// <scan +freq> (21) +// <scan -sa, random text, random bucket> (22) +// +// Here, _B indicates the suffix array size (_32 or _64) and _I the input size (_8 or _B). +// +// The outline shows there are in general 22 scans through +// O(N)-sized arrays for a given level of the recursion. +// In the top level, operating on 8-bit input text, +// the six freq scans are fixed size (256) instead of potentially +// input-sized. Also, the frequency is counted once and cached +// whenever there is room to do so (there is nearly always room in general, +// and always room at the top level), which eliminates all but +// the first freq_I_B text scans (that is, 5 of the 6). +// So the top level of the recursion only does 22 - 6 - 5 = 11 +// input-sized scans and a typical level does 16 scans. +// +// The linear scans do not cost anywhere near as much as +// the random accesses to the text made during a few of +// the scans (specifically #6, #9, #16, #19, #22 marked above). +// In real texts, there is not much but some locality to +// the accesses, due to the repetitive structure of the text +// (the same reason Burrows-Wheeler compression is so effective). +// For random inputs, there is no locality, which makes those +// accesses even more expensive, especially once the text +// no longer fits in cache. +// For example, running on 50 MB of Go source code, induceSubL_8_32 +// (which runs only once, at the top level of the recursion) +// takes 0.44s, while on 50 MB of random input, it takes 2.55s. +// Nearly all the relative slowdown is explained by the text access: +// +// c0, c1 := text[k-1], text[k] +// +// That line runs for 0.23s on the Go text and 2.02s on random text. + +//go:generate go run gen.go + +package suffixarray + +// text_32 returns the suffix array for the input text. +// It requires that len(text) fit in an int32 +// and that the caller zero sa. +func text_32(text []byte, sa []int32) { + if int(int32(len(text))) != len(text) || len(text) != len(sa) { + panic("suffixarray: misuse of text_32") + } + sais_8_32(text, 256, sa, make([]int32, 2*256)) +} + +// sais_8_32 computes the suffix array of text. +// The text must contain only values in [0, textMax). +// The suffix array is stored in sa, which the caller +// must ensure is already zeroed. +// The caller must also provide temporary space tmp +// with len(tmp) ≥ textMax. If len(tmp) ≥ 2*textMax +// then the algorithm runs a little faster. +// If sais_8_32 modifies tmp, it sets tmp[0] = -1 on return. +func sais_8_32(text []byte, textMax int, sa, tmp []int32) { + if len(sa) != len(text) || len(tmp) < int(textMax) { + panic("suffixarray: misuse of sais_8_32") + } + + // Trivial base cases. Sorting 0 or 1 things is easy. + if len(text) == 0 { + return + } + if len(text) == 1 { + sa[0] = 0 + return + } + + // Establish slices indexed by text character + // holding character frequency and bucket-sort offsets. + // If there's only enough tmp for one slice, + // we make it the bucket offsets and recompute + // the character frequency each time we need it. + var freq, bucket []int32 + if len(tmp) >= 2*textMax { + freq, bucket = tmp[:textMax], tmp[textMax:2*textMax] + freq[0] = -1 // mark as uninitialized + } else { + freq, bucket = nil, tmp[:textMax] + } + + // The SAIS algorithm. + // Each of these calls makes one scan through sa. + // See the individual functions for documentation + // about each's role in the algorithm. + numLMS := placeLMS_8_32(text, sa, freq, bucket) + if numLMS <= 1 { + // 0 or 1 items are already sorted. Do nothing. + } else { + induceSubL_8_32(text, sa, freq, bucket) + induceSubS_8_32(text, sa, freq, bucket) + length_8_32(text, sa, numLMS) + maxID := assignID_8_32(text, sa, numLMS) + if maxID < numLMS { + map_32(sa, numLMS) + recurse_32(sa, tmp, numLMS, maxID) + unmap_8_32(text, sa, numLMS) + } else { + // If maxID == numLMS, then each LMS-substring + // is unique, so the relative ordering of two LMS-suffixes + // is determined by just the leading LMS-substring. + // That is, the LMS-suffix sort order matches the + // (simpler) LMS-substring sort order. + // Copy the original LMS-substring order into the + // suffix array destination. + copy(sa, sa[len(sa)-numLMS:]) + } + expand_8_32(text, freq, bucket, sa, numLMS) + } + induceL_8_32(text, sa, freq, bucket) + induceS_8_32(text, sa, freq, bucket) + + // Mark for caller that we overwrote tmp. + tmp[0] = -1 +} + +// freq_8_32 returns the character frequencies +// for text, as a slice indexed by character value. +// If freq is nil, freq_8_32 uses and returns bucket. +// If freq is non-nil, freq_8_32 assumes that freq[0] >= 0 +// means the frequencies are already computed. +// If the frequency data is overwritten or uninitialized, +// the caller must set freq[0] = -1 to force recomputation +// the next time it is needed. +func freq_8_32(text []byte, freq, bucket []int32) []int32 { + if freq != nil && freq[0] >= 0 { + return freq // already computed + } + if freq == nil { + freq = bucket + } + + freq = freq[:256] // eliminate bounds check for freq[c] below + for i := range freq { + freq[i] = 0 + } + for _, c := range text { + freq[c]++ + } + return freq +} + +// bucketMin_8_32 stores into bucket[c] the minimum index +// in the bucket for character c in a bucket-sort of text. +func bucketMin_8_32(text []byte, freq, bucket []int32) { + freq = freq_8_32(text, freq, bucket) + freq = freq[:256] // establish len(freq) = 256, so 0 ≤ i < 256 below + bucket = bucket[:256] // eliminate bounds check for bucket[i] below + total := int32(0) + for i, n := range freq { + bucket[i] = total + total += n + } +} + +// bucketMax_8_32 stores into bucket[c] the maximum index +// in the bucket for character c in a bucket-sort of text. +// The bucket indexes for c are [min, max). +// That is, max is one past the final index in that bucket. +func bucketMax_8_32(text []byte, freq, bucket []int32) { + freq = freq_8_32(text, freq, bucket) + freq = freq[:256] // establish len(freq) = 256, so 0 ≤ i < 256 below + bucket = bucket[:256] // eliminate bounds check for bucket[i] below + total := int32(0) + for i, n := range freq { + total += n + bucket[i] = total + } +} + +// The SAIS algorithm proceeds in a sequence of scans through sa. +// Each of the following functions implements one scan, +// and the functions appear here in the order they execute in the algorithm. + +// placeLMS_8_32 places into sa the indexes of the +// final characters of the LMS substrings of text, +// sorted into the rightmost ends of their correct buckets +// in the suffix array. +// +// The imaginary sentinel character at the end of the text +// is the final character of the final LMS substring, but there +// is no bucket for the imaginary sentinel character, +// which has a smaller value than any real character. +// The caller must therefore pretend that sa[-1] == len(text). +// +// The text indexes of LMS-substring characters are always ≥ 1 +// (the first LMS-substring must be preceded by one or more L-type +// characters that are not part of any LMS-substring), +// so using 0 as a “not present” suffix array entry is safe, +// both in this function and in most later functions +// (until induceL_8_32 below). +func placeLMS_8_32(text []byte, sa, freq, bucket []int32) int { + bucketMax_8_32(text, freq, bucket) + + numLMS := 0 + lastB := int32(-1) + bucket = bucket[:256] // eliminate bounds check for bucket[c1] below + + // The next stanza of code (until the blank line) loop backward + // over text, stopping to execute a code body at each position i + // such that text[i] is an L-character and text[i+1] is an S-character. + // That is, i+1 is the position of the start of an LMS-substring. + // These could be hoisted out into a function with a callback, + // but at a significant speed cost. Instead, we just write these + // seven lines a few times in this source file. The copies below + // refer back to the pattern established by this original as the + // "LMS-substring iterator". + // + // In every scan through the text, c0, c1 are successive characters of text. + // In this backward scan, c0 == text[i] and c1 == text[i+1]. + // By scanning backward, we can keep track of whether the current + // position is type-S or type-L according to the usual definition: + // + // - position len(text) is type S with text[len(text)] == -1 (the sentinel) + // - position i is type S if text[i] < text[i+1], or if text[i] == text[i+1] && i+1 is type S. + // - position i is type L if text[i] > text[i+1], or if text[i] == text[i+1] && i+1 is type L. + // + // The backward scan lets us maintain the current type, + // update it when we see c0 != c1, and otherwise leave it alone. + // We want to identify all S positions with a preceding L. + // Position len(text) is one such position by definition, but we have + // nowhere to write it down, so we eliminate it by untruthfully + // setting isTypeS = false at the start of the loop. + c0, c1, isTypeS := byte(0), byte(0), false + for i := len(text) - 1; i >= 0; i-- { + c0, c1 = text[i], c0 + if c0 < c1 { + isTypeS = true + } else if c0 > c1 && isTypeS { + isTypeS = false + + // Bucket the index i+1 for the start of an LMS-substring. + b := bucket[c1] - 1 + bucket[c1] = b + sa[b] = int32(i + 1) + lastB = b + numLMS++ + } + } + + // We recorded the LMS-substring starts but really want the ends. + // Luckily, with two differences, the start indexes and the end indexes are the same. + // The first difference is that the rightmost LMS-substring's end index is len(text), + // so the caller must pretend that sa[-1] == len(text), as noted above. + // The second difference is that the first leftmost LMS-substring start index + // does not end an earlier LMS-substring, so as an optimization we can omit + // that leftmost LMS-substring start index (the last one we wrote). + // + // Exception: if numLMS <= 1, the caller is not going to bother with + // the recursion at all and will treat the result as containing LMS-substring starts. + // In that case, we don't remove the final entry. + if numLMS > 1 { + sa[lastB] = 0 + } + return numLMS +} + +// induceSubL_8_32 inserts the L-type text indexes of LMS-substrings +// into sa, assuming that the final characters of the LMS-substrings +// are already inserted into sa, sorted by final character, and at the +// right (not left) end of the corresponding character bucket. +// Each LMS-substring has the form (as a regexp) /S+L+S/: +// one or more S-type, one or more L-type, final S-type. +// induceSubL_8_32 leaves behind only the leftmost L-type text +// index for each LMS-substring. That is, it removes the final S-type +// indexes that are present on entry, and it inserts but then removes +// the interior L-type indexes too. +// (Only the leftmost L-type index is needed by induceSubS_8_32.) +func induceSubL_8_32(text []byte, sa, freq, bucket []int32) { + // Initialize positions for left side of character buckets. + bucketMin_8_32(text, freq, bucket) + bucket = bucket[:256] // eliminate bounds check for bucket[cB] below + + // As we scan the array left-to-right, each sa[i] = j > 0 is a correctly + // sorted suffix array entry (for text[j:]) for which we know that j-1 is type L. + // Because j-1 is type L, inserting it into sa now will sort it correctly. + // But we want to distinguish a j-1 with j-2 of type L from type S. + // We can process the former but want to leave the latter for the caller. + // We record the difference by negating j-1 if it is preceded by type S. + // Either way, the insertion (into the text[j-1] bucket) is guaranteed to + // happen at sa[i´] for some i´ > i, that is, in the portion of sa we have + // yet to scan. A single pass therefore sees indexes j, j-1, j-2, j-3, + // and so on, in sorted but not necessarily adjacent order, until it finds + // one preceded by an index of type S, at which point it must stop. + // + // As we scan through the array, we clear the worked entries (sa[i] > 0) to zero, + // and we flip sa[i] < 0 to -sa[i], so that the loop finishes with sa containing + // only the indexes of the leftmost L-type indexes for each LMS-substring. + // + // The suffix array sa therefore serves simultaneously as input, output, + // and a miraculously well-tailored work queue. + + // placeLMS_8_32 left out the implicit entry sa[-1] == len(text), + // corresponding to the identified type-L index len(text)-1. + // Process it before the left-to-right scan of sa proper. + // See body in loop for commentary. + k := len(text) - 1 + c0, c1 := text[k-1], text[k] + if c0 < c1 { + k = -k + } + + // Cache recently used bucket index: + // we're processing suffixes in sorted order + // and accessing buckets indexed by the + // byte before the sorted order, which still + // has very good locality. + // Invariant: b is cached, possibly dirty copy of bucket[cB]. + cB := c1 + b := bucket[cB] + sa[b] = int32(k) + b++ + + for i := 0; i < len(sa); i++ { + j := int(sa[i]) + if j == 0 { + // Skip empty entry. + continue + } + if j < 0 { + // Leave discovered type-S index for caller. + sa[i] = int32(-j) + continue + } + sa[i] = 0 + + // Index j was on work queue, meaning k := j-1 is L-type, + // so we can now place k correctly into sa. + // If k-1 is L-type, queue k for processing later in this loop. + // If k-1 is S-type (text[k-1] < text[k]), queue -k to save for the caller. + k := j - 1 + c0, c1 := text[k-1], text[k] + if c0 < c1 { + k = -k + } + + if cB != c1 { + bucket[cB] = b + cB = c1 + b = bucket[cB] + } + sa[b] = int32(k) + b++ + } +} + +// induceSubS_8_32 inserts the S-type text indexes of LMS-substrings +// into sa, assuming that the leftmost L-type text indexes are already +// inserted into sa, sorted by LMS-substring suffix, and at the +// left end of the corresponding character bucket. +// Each LMS-substring has the form (as a regexp) /S+L+S/: +// one or more S-type, one or more L-type, final S-type. +// induceSubS_8_32 leaves behind only the leftmost S-type text +// index for each LMS-substring, in sorted order, at the right end of sa. +// That is, it removes the L-type indexes that are present on entry, +// and it inserts but then removes the interior S-type indexes too, +// leaving the LMS-substring start indexes packed into sa[len(sa)-numLMS:]. +// (Only the LMS-substring start indexes are processed by the recursion.) +func induceSubS_8_32(text []byte, sa, freq, bucket []int32) { + // Initialize positions for right side of character buckets. + bucketMax_8_32(text, freq, bucket) + bucket = bucket[:256] // eliminate bounds check for bucket[cB] below + + // Analogous to induceSubL_8_32 above, + // as we scan the array right-to-left, each sa[i] = j > 0 is a correctly + // sorted suffix array entry (for text[j:]) for which we know that j-1 is type S. + // Because j-1 is type S, inserting it into sa now will sort it correctly. + // But we want to distinguish a j-1 with j-2 of type S from type L. + // We can process the former but want to leave the latter for the caller. + // We record the difference by negating j-1 if it is preceded by type L. + // Either way, the insertion (into the text[j-1] bucket) is guaranteed to + // happen at sa[i´] for some i´ < i, that is, in the portion of sa we have + // yet to scan. A single pass therefore sees indexes j, j-1, j-2, j-3, + // and so on, in sorted but not necessarily adjacent order, until it finds + // one preceded by an index of type L, at which point it must stop. + // That index (preceded by one of type L) is an LMS-substring start. + // + // As we scan through the array, we clear the worked entries (sa[i] > 0) to zero, + // and we flip sa[i] < 0 to -sa[i] and compact into the top of sa, + // so that the loop finishes with the top of sa containing exactly + // the LMS-substring start indexes, sorted by LMS-substring. + + // Cache recently used bucket index: + cB := byte(0) + b := bucket[cB] + + top := len(sa) + for i := len(sa) - 1; i >= 0; i-- { + j := int(sa[i]) + if j == 0 { + // Skip empty entry. + continue + } + sa[i] = 0 + if j < 0 { + // Leave discovered LMS-substring start index for caller. + top-- + sa[top] = int32(-j) + continue + } + + // Index j was on work queue, meaning k := j-1 is S-type, + // so we can now place k correctly into sa. + // If k-1 is S-type, queue k for processing later in this loop. + // If k-1 is L-type (text[k-1] > text[k]), queue -k to save for the caller. + k := j - 1 + c1 := text[k] + c0 := text[k-1] + if c0 > c1 { + k = -k + } + + if cB != c1 { + bucket[cB] = b + cB = c1 + b = bucket[cB] + } + b-- + sa[b] = int32(k) + } +} + +// length_8_32 computes and records the length of each LMS-substring in text. +// The length of the LMS-substring at index j is stored at sa[j/2], +// avoiding the LMS-substring indexes already stored in the top half of sa. +// (If index j is an LMS-substring start, then index j-1 is type L and cannot be.) +// There are two exceptions, made for optimizations in name_8_32 below. +// +// First, the final LMS-substring is recorded as having length 0, which is otherwise +// impossible, instead of giving it a length that includes the implicit sentinel. +// This ensures the final LMS-substring has length unequal to all others +// and therefore can be detected as different without text comparison +// (it is unequal because it is the only one that ends in the implicit sentinel, +// and the text comparison would be problematic since the implicit sentinel +// is not actually present at text[len(text)]). +// +// Second, to avoid text comparison entirely, if an LMS-substring is very short, +// sa[j/2] records its actual text instead of its length, so that if two such +// substrings have matching “length,” the text need not be read at all. +// The definition of “very short” is that the text bytes must pack into an uint32, +// and the unsigned encoding e must be ≥ len(text), so that it can be +// distinguished from a valid length. +func length_8_32(text []byte, sa []int32, numLMS int) { + end := 0 // index of current LMS-substring end (0 indicates final LMS-substring) + + // The encoding of N text bytes into a “length” word + // adds 1 to each byte, packs them into the bottom + // N*8 bits of a word, and then bitwise inverts the result. + // That is, the text sequence A B C (hex 41 42 43) + // encodes as ^uint32(0x42_43_44). + // LMS-substrings can never start or end with 0xFF. + // Adding 1 ensures the encoded byte sequence never + // starts or ends with 0x00, so that present bytes can be + // distinguished from zero-padding in the top bits, + // so the length need not be separately encoded. + // Inverting the bytes increases the chance that a + // 4-byte encoding will still be ≥ len(text). + // In particular, if the first byte is ASCII (<= 0x7E, so +1 <= 0x7F) + // then the high bit of the inversion will be set, + // making it clearly not a valid length (it would be a negative one). + // + // cx holds the pre-inverted encoding (the packed incremented bytes). + cx := uint32(0) // byte-only + + // This stanza (until the blank line) is the "LMS-substring iterator", + // described in placeLMS_8_32 above, with one line added to maintain cx. + c0, c1, isTypeS := byte(0), byte(0), false + for i := len(text) - 1; i >= 0; i-- { + c0, c1 = text[i], c0 + cx = cx<<8 | uint32(c1+1) // byte-only + if c0 < c1 { + isTypeS = true + } else if c0 > c1 && isTypeS { + isTypeS = false + + // Index j = i+1 is the start of an LMS-substring. + // Compute length or encoded text to store in sa[j/2]. + j := i + 1 + var code int32 + if end == 0 { + code = 0 + } else { + code = int32(end - j) + if code <= 32/8 && ^cx >= uint32(len(text)) { // byte-only + code = int32(^cx) // byte-only + } // byte-only + } + sa[j>>1] = code + end = j + 1 + cx = uint32(c1 + 1) // byte-only + } + } +} + +// assignID_8_32 assigns a dense ID numbering to the +// set of LMS-substrings respecting string ordering and equality, +// returning the maximum assigned ID. +// For example given the input "ababab", the LMS-substrings +// are "aba", "aba", and "ab", renumbered as 2 2 1. +// sa[len(sa)-numLMS:] holds the LMS-substring indexes +// sorted in string order, so to assign numbers we can +// consider each in turn, removing adjacent duplicates. +// The new ID for the LMS-substring at index j is written to sa[j/2], +// overwriting the length previously stored there (by length_8_32 above). +func assignID_8_32(text []byte, sa []int32, numLMS int) int { + id := 0 + lastLen := int32(-1) // impossible + lastPos := int32(0) + for _, j := range sa[len(sa)-numLMS:] { + // Is the LMS-substring at index j new, or is it the same as the last one we saw? + n := sa[j/2] + if n != lastLen { + goto New + } + if uint32(n) >= uint32(len(text)) { + // “Length” is really encoded full text, and they match. + goto Same + } + { + // Compare actual texts. + n := int(n) + this := text[j:][:n] + last := text[lastPos:][:n] + for i := 0; i < n; i++ { + if this[i] != last[i] { + goto New + } + } + goto Same + } + New: + id++ + lastPos = j + lastLen = n + Same: + sa[j/2] = int32(id) + } + return id +} + +// map_32 maps the LMS-substrings in text to their new IDs, +// producing the subproblem for the recursion. +// The mapping itself was mostly applied by assignID_8_32: +// sa[i] is either 0, the ID for the LMS-substring at index 2*i, +// or the ID for the LMS-substring at index 2*i+1. +// To produce the subproblem we need only remove the zeros +// and change ID into ID-1 (our IDs start at 1, but text chars start at 0). +// +// map_32 packs the result, which is the input to the recursion, +// into the top of sa, so that the recursion result can be stored +// in the bottom of sa, which sets up for expand_8_32 well. +func map_32(sa []int32, numLMS int) { + w := len(sa) + for i := len(sa) / 2; i >= 0; i-- { + j := sa[i] + if j > 0 { + w-- + sa[w] = j - 1 + } + } +} + +// recurse_32 calls sais_32 recursively to solve the subproblem we've built. +// The subproblem is at the right end of sa, the suffix array result will be +// written at the left end of sa, and the middle of sa is available for use as +// temporary frequency and bucket storage. +func recurse_32(sa, oldTmp []int32, numLMS, maxID int) { + dst, saTmp, text := sa[:numLMS], sa[numLMS:len(sa)-numLMS], sa[len(sa)-numLMS:] + + // Set up temporary space for recursive call. + // We must pass sais_32 a tmp buffer with at least maxID entries. + // + // The subproblem is guaranteed to have length at most len(sa)/2, + // so that sa can hold both the subproblem and its suffix array. + // Nearly all the time, however, the subproblem has length < len(sa)/3, + // in which case there is a subproblem-sized middle of sa that + // we can reuse for temporary space (saTmp). + // When recurse_32 is called from sais_8_32, oldTmp is length 512 + // (from text_32), and saTmp will typically be much larger, so we'll use saTmp. + // When deeper recursions come back to recurse_32, now oldTmp is + // the saTmp from the top-most recursion, it is typically larger than + // the current saTmp (because the current sa gets smaller and smaller + // as the recursion gets deeper), and we keep reusing that top-most + // large saTmp instead of the offered smaller ones. + // + // Why is the subproblem length so often just under len(sa)/3? + // See Nong, Zhang, and Chen, section 3.6 for a plausible explanation. + // In brief, the len(sa)/2 case would correspond to an SLSLSLSLSLSL pattern + // in the input, perfect alternation of larger and smaller input bytes. + // Real text doesn't do that. If each L-type index is randomly followed + // by either an L-type or S-type index, then half the substrings will + // be of the form SLS, but the other half will be longer. Of that half, + // half (a quarter overall) will be SLLS; an eighth will be SLLLS, and so on. + // Not counting the final S in each (which overlaps the first S in the next), + // This works out to an average length 2×½ + 3×¼ + 4×⅛ + ... = 3. + // The space we need is further reduced by the fact that many of the + // short patterns like SLS will often be the same character sequences + // repeated throughout the text, reducing maxID relative to numLMS. + // + // For short inputs, the averages may not run in our favor, but then we + // can often fall back to using the length-512 tmp available in the + // top-most call. (Also a short allocation would not be a big deal.) + // + // For pathological inputs, we fall back to allocating a new tmp of length + // max(maxID, numLMS/2). This level of the recursion needs maxID, + // and all deeper levels of the recursion will need no more than numLMS/2, + // so this one allocation is guaranteed to suffice for the entire stack + // of recursive calls. + tmp := oldTmp + if len(tmp) < len(saTmp) { + tmp = saTmp + } + if len(tmp) < numLMS { + // TestSAIS/forcealloc reaches this code. + n := maxID + if n < numLMS/2 { + n = numLMS / 2 + } + tmp = make([]int32, n) + } + + // sais_32 requires that the caller arrange to clear dst, + // because in general the caller may know dst is + // freshly-allocated and already cleared. But this one is not. + for i := range dst { + dst[i] = 0 + } + sais_32(text, maxID, dst, tmp) +} + +// unmap_8_32 unmaps the subproblem back to the original. +// sa[:numLMS] is the LMS-substring numbers, which don't matter much anymore. +// sa[len(sa)-numLMS:] is the sorted list of those LMS-substring numbers. +// The key part is that if the list says K that means the K'th substring. +// We can replace sa[:numLMS] with the indexes of the LMS-substrings. +// Then if the list says K it really means sa[K]. +// Having mapped the list back to LMS-substring indexes, +// we can place those into the right buckets. +func unmap_8_32(text []byte, sa []int32, numLMS int) { + unmap := sa[len(sa)-numLMS:] + j := len(unmap) + + // "LMS-substring iterator" (see placeLMS_8_32 above). + c0, c1, isTypeS := byte(0), byte(0), false + for i := len(text) - 1; i >= 0; i-- { + c0, c1 = text[i], c0 + if c0 < c1 { + isTypeS = true + } else if c0 > c1 && isTypeS { + isTypeS = false + + // Populate inverse map. + j-- + unmap[j] = int32(i + 1) + } + } + + // Apply inverse map to subproblem suffix array. + sa = sa[:numLMS] + for i := 0; i < len(sa); i++ { + sa[i] = unmap[sa[i]] + } +} + +// expand_8_32 distributes the compacted, sorted LMS-suffix indexes +// from sa[:numLMS] into the tops of the appropriate buckets in sa, +// preserving the sorted order and making room for the L-type indexes +// to be slotted into the sorted sequence by induceL_8_32. +func expand_8_32(text []byte, freq, bucket, sa []int32, numLMS int) { + bucketMax_8_32(text, freq, bucket) + bucket = bucket[:256] // eliminate bound check for bucket[c] below + + // Loop backward through sa, always tracking + // the next index to populate from sa[:numLMS]. + // When we get to one, populate it. + // Zero the rest of the slots; they have dead values in them. + x := numLMS - 1 + saX := sa[x] + c := text[saX] + b := bucket[c] - 1 + bucket[c] = b + + for i := len(sa) - 1; i >= 0; i-- { + if i != int(b) { + sa[i] = 0 + continue + } + sa[i] = saX + + // Load next entry to put down (if any). + if x > 0 { + x-- + saX = sa[x] // TODO bounds check + c = text[saX] + b = bucket[c] - 1 + bucket[c] = b + } + } +} + +// induceL_8_32 inserts L-type text indexes into sa, +// assuming that the leftmost S-type indexes are inserted +// into sa, in sorted order, in the right bucket halves. +// It leaves all the L-type indexes in sa, but the +// leftmost L-type indexes are negated, to mark them +// for processing by induceS_8_32. +func induceL_8_32(text []byte, sa, freq, bucket []int32) { + // Initialize positions for left side of character buckets. + bucketMin_8_32(text, freq, bucket) + bucket = bucket[:256] // eliminate bounds check for bucket[cB] below + + // This scan is similar to the one in induceSubL_8_32 above. + // That one arranges to clear all but the leftmost L-type indexes. + // This scan leaves all the L-type indexes and the original S-type + // indexes, but it negates the positive leftmost L-type indexes + // (the ones that induceS_8_32 needs to process). + + // expand_8_32 left out the implicit entry sa[-1] == len(text), + // corresponding to the identified type-L index len(text)-1. + // Process it before the left-to-right scan of sa proper. + // See body in loop for commentary. + k := len(text) - 1 + c0, c1 := text[k-1], text[k] + if c0 < c1 { + k = -k + } + + // Cache recently used bucket index. + cB := c1 + b := bucket[cB] + sa[b] = int32(k) + b++ + + for i := 0; i < len(sa); i++ { + j := int(sa[i]) + if j <= 0 { + // Skip empty or negated entry (including negated zero). + continue + } + + // Index j was on work queue, meaning k := j-1 is L-type, + // so we can now place k correctly into sa. + // If k-1 is L-type, queue k for processing later in this loop. + // If k-1 is S-type (text[k-1] < text[k]), queue -k to save for the caller. + // If k is zero, k-1 doesn't exist, so we only need to leave it + // for the caller. The caller can't tell the difference between + // an empty slot and a non-empty zero, but there's no need + // to distinguish them anyway: the final suffix array will end up + // with one zero somewhere, and that will be a real zero. + k := j - 1 + c1 := text[k] + if k > 0 { + if c0 := text[k-1]; c0 < c1 { + k = -k + } + } + + if cB != c1 { + bucket[cB] = b + cB = c1 + b = bucket[cB] + } + sa[b] = int32(k) + b++ + } +} + +func induceS_8_32(text []byte, sa, freq, bucket []int32) { + // Initialize positions for right side of character buckets. + bucketMax_8_32(text, freq, bucket) + bucket = bucket[:256] // eliminate bounds check for bucket[cB] below + + cB := byte(0) + b := bucket[cB] + + for i := len(sa) - 1; i >= 0; i-- { + j := int(sa[i]) + if j >= 0 { + // Skip non-flagged entry. + // (This loop can't see an empty entry; 0 means the real zero index.) + continue + } + + // Negative j is a work queue entry; rewrite to positive j for final suffix array. + j = -j + sa[i] = int32(j) + + // Index j was on work queue (encoded as -j but now decoded), + // meaning k := j-1 is L-type, + // so we can now place k correctly into sa. + // If k-1 is S-type, queue -k for processing later in this loop. + // If k-1 is L-type (text[k-1] > text[k]), queue k to save for the caller. + // If k is zero, k-1 doesn't exist, so we only need to leave it + // for the caller. + k := j - 1 + c1 := text[k] + if k > 0 { + if c0 := text[k-1]; c0 <= c1 { + k = -k + } + } + + if cB != c1 { + bucket[cB] = b + cB = c1 + b = bucket[cB] + } + b-- + sa[b] = int32(k) + } +} |