Source file src/pkg/index/suffixarray/suffixarray.go

     1	// Copyright 2010 The Go Authors. All rights reserved.
     2	// Use of this source code is governed by a BSD-style
     3	// license that can be found in the LICENSE file.
     4	
     5	// Package suffixarray implements substring search in logarithmic time using
     6	// an in-memory suffix array.
     7	//
     8	// Example use:
     9	//
    10	//	// create index for some data
    11	//	index := suffixarray.New(data)
    12	//
    13	//	// lookup byte slice s
    14	//	offsets1 := index.Lookup(s, -1) // the list of all indices where s occurs in data
    15	//	offsets2 := index.Lookup(s, 3)  // the list of at most 3 indices where s occurs in data
    16	//
    17	package suffixarray
    18	
    19	import (
    20		"bytes"
    21		"encoding/binary"
    22		"errors"
    23		"io"
    24		"math"
    25		"regexp"
    26		"sort"
    27	)
    28	
    29	// Can change for testing
    30	var maxData32 int = realMaxData32
    31	
    32	const realMaxData32 = math.MaxInt32
    33	
    34	// Index implements a suffix array for fast substring search.
    35	type Index struct {
    36		data []byte
    37		sa   ints // suffix array for data; sa.len() == len(data)
    38	}
    39	
    40	// An ints is either an []int32 or an []int64.
    41	// That is, one of them is empty, and one is the real data.
    42	// The int64 form is used when len(data) > maxData32
    43	type ints struct {
    44		int32 []int32
    45		int64 []int64
    46	}
    47	
    48	func (a *ints) len() int {
    49		return len(a.int32) + len(a.int64)
    50	}
    51	
    52	func (a *ints) get(i int) int64 {
    53		if a.int32 != nil {
    54			return int64(a.int32[i])
    55		}
    56		return a.int64[i]
    57	}
    58	
    59	func (a *ints) set(i int, v int64) {
    60		if a.int32 != nil {
    61			a.int32[i] = int32(v)
    62		} else {
    63			a.int64[i] = v
    64		}
    65	}
    66	
    67	func (a *ints) slice(i, j int) ints {
    68		if a.int32 != nil {
    69			return ints{a.int32[i:j], nil}
    70		}
    71		return ints{nil, a.int64[i:j]}
    72	}
    73	
    74	// New creates a new Index for data.
    75	// Index creation time is O(N) for N = len(data).
    76	func New(data []byte) *Index {
    77		ix := &Index{data: data}
    78		if len(data) <= maxData32 {
    79			ix.sa.int32 = make([]int32, len(data))
    80			text_32(data, ix.sa.int32)
    81		} else {
    82			ix.sa.int64 = make([]int64, len(data))
    83			text_64(data, ix.sa.int64)
    84		}
    85		return ix
    86	}
    87	
    88	// writeInt writes an int x to w using buf to buffer the write.
    89	func writeInt(w io.Writer, buf []byte, x int) error {
    90		binary.PutVarint(buf, int64(x))
    91		_, err := w.Write(buf[0:binary.MaxVarintLen64])
    92		return err
    93	}
    94	
    95	// readInt reads an int x from r using buf to buffer the read and returns x.
    96	func readInt(r io.Reader, buf []byte) (int64, error) {
    97		_, err := io.ReadFull(r, buf[0:binary.MaxVarintLen64]) // ok to continue with error
    98		x, _ := binary.Varint(buf)
    99		return x, err
   100	}
   101	
   102	// writeSlice writes data[:n] to w and returns n.
   103	// It uses buf to buffer the write.
   104	func writeSlice(w io.Writer, buf []byte, data ints) (n int, err error) {
   105		// encode as many elements as fit into buf
   106		p := binary.MaxVarintLen64
   107		m := data.len()
   108		for ; n < m && p+binary.MaxVarintLen64 <= len(buf); n++ {
   109			p += binary.PutUvarint(buf[p:], uint64(data.get(n)))
   110		}
   111	
   112		// update buffer size
   113		binary.PutVarint(buf, int64(p))
   114	
   115		// write buffer
   116		_, err = w.Write(buf[0:p])
   117		return
   118	}
   119	
   120	var errTooBig = errors.New("suffixarray: data too large")
   121	
   122	// readSlice reads data[:n] from r and returns n.
   123	// It uses buf to buffer the read.
   124	func readSlice(r io.Reader, buf []byte, data ints) (n int, err error) {
   125		// read buffer size
   126		var size64 int64
   127		size64, err = readInt(r, buf)
   128		if err != nil {
   129			return
   130		}
   131		if int64(int(size64)) != size64 || int(size64) < 0 {
   132			// We never write chunks this big anyway.
   133			return 0, errTooBig
   134		}
   135		size := int(size64)
   136	
   137		// read buffer w/o the size
   138		if _, err = io.ReadFull(r, buf[binary.MaxVarintLen64:size]); err != nil {
   139			return
   140		}
   141	
   142		// decode as many elements as present in buf
   143		for p := binary.MaxVarintLen64; p < size; n++ {
   144			x, w := binary.Uvarint(buf[p:])
   145			data.set(n, int64(x))
   146			p += w
   147		}
   148	
   149		return
   150	}
   151	
   152	const bufSize = 16 << 10 // reasonable for BenchmarkSaveRestore
   153	
   154	// Read reads the index from r into x; x must not be nil.
   155	func (x *Index) Read(r io.Reader) error {
   156		// buffer for all reads
   157		buf := make([]byte, bufSize)
   158	
   159		// read length
   160		n64, err := readInt(r, buf)
   161		if err != nil {
   162			return err
   163		}
   164		if int64(int(n64)) != n64 || int(n64) < 0 {
   165			return errTooBig
   166		}
   167		n := int(n64)
   168	
   169		// allocate space
   170		if 2*n < cap(x.data) || cap(x.data) < n || x.sa.int32 != nil && n > maxData32 || x.sa.int64 != nil && n <= maxData32 {
   171			// new data is significantly smaller or larger than
   172			// existing buffers - allocate new ones
   173			x.data = make([]byte, n)
   174			x.sa.int32 = nil
   175			x.sa.int64 = nil
   176			if n <= maxData32 {
   177				x.sa.int32 = make([]int32, n)
   178			} else {
   179				x.sa.int64 = make([]int64, n)
   180			}
   181		} else {
   182			// re-use existing buffers
   183			x.data = x.data[0:n]
   184			x.sa = x.sa.slice(0, n)
   185		}
   186	
   187		// read data
   188		if _, err := io.ReadFull(r, x.data); err != nil {
   189			return err
   190		}
   191	
   192		// read index
   193		sa := x.sa
   194		for sa.len() > 0 {
   195			n, err := readSlice(r, buf, sa)
   196			if err != nil {
   197				return err
   198			}
   199			sa = sa.slice(n, sa.len())
   200		}
   201		return nil
   202	}
   203	
   204	// Write writes the index x to w.
   205	func (x *Index) Write(w io.Writer) error {
   206		// buffer for all writes
   207		buf := make([]byte, bufSize)
   208	
   209		// write length
   210		if err := writeInt(w, buf, len(x.data)); err != nil {
   211			return err
   212		}
   213	
   214		// write data
   215		if _, err := w.Write(x.data); err != nil {
   216			return err
   217		}
   218	
   219		// write index
   220		sa := x.sa
   221		for sa.len() > 0 {
   222			n, err := writeSlice(w, buf, sa)
   223			if err != nil {
   224				return err
   225			}
   226			sa = sa.slice(n, sa.len())
   227		}
   228		return nil
   229	}
   230	
   231	// Bytes returns the data over which the index was created.
   232	// It must not be modified.
   233	//
   234	func (x *Index) Bytes() []byte {
   235		return x.data
   236	}
   237	
   238	func (x *Index) at(i int) []byte {
   239		return x.data[x.sa.get(i):]
   240	}
   241	
   242	// lookupAll returns a slice into the matching region of the index.
   243	// The runtime is O(log(N)*len(s)).
   244	func (x *Index) lookupAll(s []byte) ints {
   245		// find matching suffix index range [i:j]
   246		// find the first index where s would be the prefix
   247		i := sort.Search(x.sa.len(), func(i int) bool { return bytes.Compare(x.at(i), s) >= 0 })
   248		// starting at i, find the first index at which s is not a prefix
   249		j := i + sort.Search(x.sa.len()-i, func(j int) bool { return !bytes.HasPrefix(x.at(j+i), s) })
   250		return x.sa.slice(i, j)
   251	}
   252	
   253	// Lookup returns an unsorted list of at most n indices where the byte string s
   254	// occurs in the indexed data. If n < 0, all occurrences are returned.
   255	// The result is nil if s is empty, s is not found, or n == 0.
   256	// Lookup time is O(log(N)*len(s) + len(result)) where N is the
   257	// size of the indexed data.
   258	//
   259	func (x *Index) Lookup(s []byte, n int) (result []int) {
   260		if len(s) > 0 && n != 0 {
   261			matches := x.lookupAll(s)
   262			count := matches.len()
   263			if n < 0 || count < n {
   264				n = count
   265			}
   266			// 0 <= n <= count
   267			if n > 0 {
   268				result = make([]int, n)
   269				if matches.int32 != nil {
   270					for i := range result {
   271						result[i] = int(matches.int32[i])
   272					}
   273				} else {
   274					for i := range result {
   275						result[i] = int(matches.int64[i])
   276					}
   277				}
   278			}
   279		}
   280		return
   281	}
   282	
   283	// FindAllIndex returns a sorted list of non-overlapping matches of the
   284	// regular expression r, where a match is a pair of indices specifying
   285	// the matched slice of x.Bytes(). If n < 0, all matches are returned
   286	// in successive order. Otherwise, at most n matches are returned and
   287	// they may not be successive. The result is nil if there are no matches,
   288	// or if n == 0.
   289	//
   290	func (x *Index) FindAllIndex(r *regexp.Regexp, n int) (result [][]int) {
   291		// a non-empty literal prefix is used to determine possible
   292		// match start indices with Lookup
   293		prefix, complete := r.LiteralPrefix()
   294		lit := []byte(prefix)
   295	
   296		// worst-case scenario: no literal prefix
   297		if prefix == "" {
   298			return r.FindAllIndex(x.data, n)
   299		}
   300	
   301		// if regexp is a literal just use Lookup and convert its
   302		// result into match pairs
   303		if complete {
   304			// Lookup returns indices that may belong to overlapping matches.
   305			// After eliminating them, we may end up with fewer than n matches.
   306			// If we don't have enough at the end, redo the search with an
   307			// increased value n1, but only if Lookup returned all the requested
   308			// indices in the first place (if it returned fewer than that then
   309			// there cannot be more).
   310			for n1 := n; ; n1 += 2 * (n - len(result)) /* overflow ok */ {
   311				indices := x.Lookup(lit, n1)
   312				if len(indices) == 0 {
   313					return
   314				}
   315				sort.Ints(indices)
   316				pairs := make([]int, 2*len(indices))
   317				result = make([][]int, len(indices))
   318				count := 0
   319				prev := 0
   320				for _, i := range indices {
   321					if count == n {
   322						break
   323					}
   324					// ignore indices leading to overlapping matches
   325					if prev <= i {
   326						j := 2 * count
   327						pairs[j+0] = i
   328						pairs[j+1] = i + len(lit)
   329						result[count] = pairs[j : j+2]
   330						count++
   331						prev = i + len(lit)
   332					}
   333				}
   334				result = result[0:count]
   335				if len(result) >= n || len(indices) != n1 {
   336					// found all matches or there's no chance to find more
   337					// (n and n1 can be negative)
   338					break
   339				}
   340			}
   341			if len(result) == 0 {
   342				result = nil
   343			}
   344			return
   345		}
   346	
   347		// regexp has a non-empty literal prefix; Lookup(lit) computes
   348		// the indices of possible complete matches; use these as starting
   349		// points for anchored searches
   350		// (regexp "^" matches beginning of input, not beginning of line)
   351		r = regexp.MustCompile("^" + r.String()) // compiles because r compiled
   352	
   353		// same comment about Lookup applies here as in the loop above
   354		for n1 := n; ; n1 += 2 * (n - len(result)) /* overflow ok */ {
   355			indices := x.Lookup(lit, n1)
   356			if len(indices) == 0 {
   357				return
   358			}
   359			sort.Ints(indices)
   360			result = result[0:0]
   361			prev := 0
   362			for _, i := range indices {
   363				if len(result) == n {
   364					break
   365				}
   366				m := r.FindIndex(x.data[i:]) // anchored search - will not run off
   367				// ignore indices leading to overlapping matches
   368				if m != nil && prev <= i {
   369					m[0] = i // correct m
   370					m[1] += i
   371					result = append(result, m)
   372					prev = m[1]
   373				}
   374			}
   375			if len(result) >= n || len(indices) != n1 {
   376				// found all matches or there's no chance to find more
   377				// (n and n1 can be negative)
   378				break
   379			}
   380		}
   381		if len(result) == 0 {
   382			result = nil
   383		}
   384		return
   385	}
   386	

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