#ifndef _CSA_H_
#define _CSA_H_
-
-#include <map>
-#include <vector>
-#include "BitRank.h"
#include "dynFMI.h"
+#include "BitRank.h"
#include "TextCollection.h"
#include "BlockArray.h"
+#include "RLWaveletTree.h"
+#include <set>
+#include <vector>
+
+// Include from XMLTree/libcds
+#include <basics.h> // Defines W == 32
+#include <static_bitsequence.h>
+#include <alphabet_mapper.h>
+#include <static_sequence.h>
+
+// Re-define word size to ulong:
+#undef W
+#if __WORDSIZE == 64
+# define W 64
+#else
+# define W 32
+#endif
+#undef bitset
+
+// Un-comment to compare BWT against a BWT generated from class dynFMI:
+//#define CSA_TEST_BWT
/**
* Implementation of the TextCollection interface
*
- * Implementation notes:
- *
- * Dynamic construction (via InsertText()) uses dynamic (balanced) wavelet tree
- * which requires O(n log \sigma) bits of memory. If we know the distribution
- * of characters beforehand, space can easily be made O(nH_0).
- *
- * The method MakeStatic() constructs a Succinct Suffix Array with a huffman
- * shaped wavelet tree. This structure achieves only zero'th order entropy. (FIXME)
- *
- * Query methods Prefix, Suffix, Equal, Contains and LessThan can be used
- * with any FM-index variant supporting LF-mapping.
*/
class CSA : public SXSI::TextCollection {
public:
void MakeStatic();
bool EmptyText(DocId) const;
uchar* GetText(DocId) const;
- uchar* GetText(DocId, TextPosition, TextPosition) const;
+ /**
+ * Next method is not supported:
+ * Supporting GetText for some substring [i,j]
+ * would require more space.
+ */
+// uchar* GetText(DocId, TextPosition, TextPosition) const;
bool IsPrefix(uchar const *) const;
bool IsSuffix(uchar const *) const;
bool IsContains(uchar const *) const;
bool IsLessThan(uchar const *) const;
+ ulong Count(uchar const *) const;
unsigned CountPrefix(uchar const *) const;
unsigned CountSuffix(uchar const *) const;
unsigned CountEqual(uchar const *) const;
void Load(FILE *, unsigned);
void Save(FILE *) const;
- // debug
- TextPosition Lookup(TextPosition) const;
+
+ // FIXME Remove
+ void deleteWT()
+ {
+ delete alphabetrank;
+ alphabetrank = 0;
+ delete [] codetable;
+ codetable = 0;
+ }
+ void deleteSamples()
+ {
+ delete sampled;
+ sampled =0;
+ delete suffixes;
+ suffixes = 0;
+ delete suffixDocId;
+ suffixDocId = 0;
+ }
+ void deleteEndmarker()
+ {
+ delete endmarkerDocId;
+ endmarkerDocId = 0;
+ }
private:
+ // FIXME Unused code
class TCodeEntry {
public:
unsigned count;
};
+ // FIXME Unused code
class THuffAlphabetRank {
// using fixed 0...255 alphabet
private:
bool leaf;
public:
THuffAlphabetRank(uchar *, TextPosition, TCodeEntry *, unsigned);
+ THuffAlphabetRank(FILE *);
~THuffAlphabetRank();
+
+ void Save(FILE *);
bool Test(uchar *, TextPosition);
inline TextPosition rank(int c, TextPosition i) const { // returns the number of characters c before and including position i
}
return true;
}
- inline int charAtPos(TextPosition i) const {
+ inline uchar access(TextPosition i) const {
THuffAlphabetRank const * temp=this;
while (!temp->leaf) {
if (temp->bitrank->IsBitSet(i)) {
temp = temp->left;
}
}
- return (int)temp->ch;
+ return temp->ch;
+ }
+
+ inline uchar charAtPos(ulong i, TextPosition *rank) const {
+ THuffAlphabetRank const * temp=this;
+ while (!temp->leaf) {
+ if (temp->bitrank->IsBitSet(i)) {
+ i = temp->bitrank->rank(i)-1;
+ temp = temp->right;
+ } else {
+ i = i-temp->bitrank->rank(i);
+ temp = temp->left;
+ }
+ }
+ (*rank)=i;
+ return temp->ch;
}
};
+ // FIXME Unused code
class node {
private:
unsigned weight;
static TCodeEntry *makecodetable(uchar *, TextPosition);
};
- static const unsigned char print = 1;
- static const unsigned char report = 1;
+ static const uchar versionFlag;
TextPosition n;
unsigned samplerate;
unsigned C[256];
TextPosition bwtEndPos;
- THuffAlphabetRank *alphabetrank;
- BitRank *sampled;
- BlockArray *suffixes;
- BlockArray *positions;
- TCodeEntry *codetable;
+// THuffAlphabetRank *alphabetrank;
+ // RLWaveletTree *alphabetrank;
+ static_sequence * alphabetrank;
+
+#ifdef CSA_TEST_BWT
DynFMI *dynFMI;
+#endif
+ TCodeEntry *codetable;
+
+ // Sample structures for texts longer than samplerate
+ BSGAP *sampled;
+ BlockArray *suffixes;
+ BlockArray *suffixDocId;
// Total number of texts in the collection
unsigned numberOfTexts;
+ // Total number of texts including empty texts
+ unsigned numberOfAllTexts;
// Length of the longest text
ulong maxTextLength;
-
-
+
// Array of document id's in the order of end-markers in BWT
// Access by endmarkerDocId[rank_$(L, p) - 1].
BlockArray *endmarkerDocId;
- // Array of text lengths (in the inserted order)
- BlockArray *textLength;
- // Array of text starting positions (in the inserted order)
- BlockArray *textStartPos;
-
- // Private methods
+
+ // FIXME Replace with a more succinct data structure
+ // Note: Empty texts are already handled inside XMLTree class.
+ std::set<unsigned> emptyTextId;
+ BSGAP *emptyTextRank;
+
+ // FIXME A better solution?
+ std::string texts;
+
+ // Following are not part of the public API
uchar * BWT(uchar *);
- uchar * LoadFromFile(const char *);
- void SaveToFile(const char *, uchar *);
void makewavelet(uchar *);
void maketables();
-
- // Following are not part of the public API
- DocId DocIdAtTextPos(TextPosition) const;
- unsigned CountEndmarkers(TextPosition, TextPosition) const;
+ DocId DocIdAtTextPos(BlockArray*, TextPosition) const;
ulong Search(uchar const *, TextPosition, TextPosition *, TextPosition *) const;
- TextPosition Inverse(TextPosition) const;
- TextPosition LF(uchar c, TextPosition &sp, TextPosition &ep) const;
- TextPosition Psi(TextPosition) const;
- uchar * Substring(TextPosition, TextPosition) const;
+// TextPosition Inverse(TextPosition) const;
+// TextPosition LF(uchar c, TextPosition &sp, TextPosition &ep) const;
+// TextPosition Psi(TextPosition) const;
+// uchar * Substring(TextPosition, TextPosition) const;
+// TextPosition Lookup(TextPosition) const;
+
+ /**
+ * Count end-markers in given interval
+ */
+ inline unsigned CountEndmarkers(TextPosition sp, TextPosition ep) const
+ {
+ if (sp > ep)
+ return 0;
+
+ ulong ranksp = 0;
+ if (sp != 0)
+ ranksp = alphabetrank->rank(0, sp - 1);
+
+ return alphabetrank->rank(0, ep) - ranksp;
+ }
};
#endif
projects / SXSI / TextCollection.git / blobdiff