using SXSI::TextCollection;
+// Save file version info
+const uchar CSA::versionFlag = 2;
////////////////////////////////////////////////////////////////////////////
// Class CSA::THuffAlphabetRank
delete bitrank;
}
+/**
+ * Saving data fields:
+ BitRank *bitrank;
+ bool leaf;
+ uchar ch;
+ left child;
+ right child;
+*/
+void CSA::THuffAlphabetRank::Save(FILE *file)
+{
-////////////////////////////////////////////////////////////////////////////
+}
+
+CSA::THuffAlphabetRank::THuffAlphabetRank(FILE *file)
+{
+
+
+}
+
+/////////////////////////////////////////////f///////////////////////////////
// Class CSA
/**
* Samplerate defaults to TEXTCOLLECTION_DEFAULT_SAMPLERATE.
*/
CSA::CSA(unsigned samplerate)
- : n(0), alphabetrank(0), sampled(0), suffixes(0), positions(0),
- codetable(0), dynFMI(0)
+ : n(0), samplerate(0), alphabetrank(0), sampled(0), suffixes(0), suffixDocId(0), positions(0),
+ codetable(0), dynFMI(0), numberOfTexts(0), numberOfAllTexts(0), maxTextLength(0), endmarkerDocId(0),
+ textLength(0), textStartPos(0), emptyTextRank(0)
{
this->samplerate = samplerate;
temp[i] = i+1;
temp[255] = 0;
dynFMI = new DynFMI(temp, 1, 255, false);
+
+ /* Debug code: take char distribution from data.txt.
+ uchar *temp = Tools::GetFileContents("data.txt", 0);
+ dynFMI = new DynFMI(temp,1790000, strlen((char *)temp), false);
+ delete [] temp;*/
}
/**
void CSA::InsertText(uchar const * text)
{
// Sanity check:
- assert(dynFMI != 0);
+ assert(dynFMI != 0);
TextPosition m = std::strlen((char *)text) + 1;
- // Store text length and starting position
- textLength.push_back(make_pair(m, n));
- this->n += m;
- dynFMI->addText(text, m);
+ if (m > maxTextLength)
+ maxTextLength = m; // Store length of the longest text seen so far.
+
+ if (m > 1)
+ {
+ this->n += m;
+ this->numberOfTexts ++;
+ this->numberOfAllTexts ++;
+ dynFMI->addText(text, m);
+ }
+ else
+ {
+ emptyTextId.insert(numberOfAllTexts); // FIXME Using too much space here
+ this->numberOfAllTexts ++; // Replace with dynamic bitvector
+ }
}
void CSA::MakeStatic()
{
// Sanity check:
if (dynFMI == 0)
+ throw std::runtime_error("CSA::MakeStatic(): Data structure is already static (dynFMI == 0).");
+
+ // Bitvector of empty texts
{
- std::cerr << "Data structure is already static (dynFMI == 0)." << std::endl;
- std::exit(0);
+ //std::cout << std::endl << "texts: " << numberOfTexts << ", all texts " << numberOfAllTexts << ", size : " << emptyTextId.size() <<std::endl;
+ ulong *tempB = new ulong[numberOfAllTexts/W + 1];
+ for (ulong i = 0; i < numberOfAllTexts/W + 1; ++i)
+ tempB[i] = 0;
+ for (std::set<unsigned>::const_iterator it = emptyTextId.begin(); it != emptyTextId.end(); ++it)
+ Tools::SetField(tempB, 1, (*it), 1);
+ emptyTextId.clear();
+ emptyTextRank = new BSGAP(tempB, numberOfAllTexts, true);
}
-
+
uchar *bwt = dynFMI->getBWT();
- /*printf("1234567890123456789\n");
+ /*printf("123456789012345678901234567890123456789\n");
for (TextPosition i = 0; i < n; i ++)
if (bwt[i] < 50)
printf("%d", (int)bwt[i]);
else
printf("%c", bwt[i]);
- printf("\n");
- */
+ printf("\n");*/
+
/* for (TextPosition i = 1; i <= n; i ++)
{
}*/
// Sanity check
- assert(textLength.size() == dynFMI->getCollectionSize());
+ assert(numberOfTexts == dynFMI->getCollectionSize());
delete dynFMI;
dynFMI = 0;
- makewavelet(bwt);
+ makewavelet(bwt); // Deletes bwt!
+ bwt = 0;
// Calculate BWT end-marker position (of last inserted text)
+ // and the length of the first text (counter l):
ulong i = 0;
- while (bwt[i] != '\0')
+ ulong l = 1;
+
+ uchar c = alphabetrank->access(i);
+ while (c != '\0')
{
- uchar c = bwt[i];
i = C[c]+alphabetrank->rank(c, i)-1;
+ ++l;
+ c = alphabetrank->access(i);
}
bwtEndPos = i;
+ assert(bwtEndPos < n);
//printf("bwtEndPos = %lu\n", bwtEndPos);
- delete [] bwt;
-
+ // Build up arrays for text length and starting positions
+ // FIXME Remove, temp data
+ textLength = new BlockArray(numberOfTexts, Tools::CeilLog2(maxTextLength));
+ textStartPos = new BlockArray(numberOfTexts, Tools::CeilLog2(this->n));
+ (*textLength)[0] = l;
+ (*textStartPos)[0] = 0; // Rest of the values are updated in CSA::maketables().
+
// Make sampling tables
maketables();
}
+bool CSA::EmptyText(DocId k) const
+{
+ assert(k < (DocId)numberOfTexts);
+ if (emptyTextRank->IsBitSet(k))
+ return true;
+ return false;
+}
uchar* CSA::GetText(DocId k) const
{
- assert(k < (DocId)textLength.size());
+ assert(k < (DocId)numberOfTexts);
- uchar* result = new uchar[textLength[k].first];
+ ulong textRank = 0;
+ if (emptyTextRank->IsBitSet(k, &textRank))
+ {
+ uchar* result = new uchar[1];
+ result[0] = 0;
+ return result;
+ }
+ // Map to non-empty text
+ k -= textRank; //emptyTextRank->rank(k);
+
TextPosition i = k;
- TextPosition j = textLength[k].first-1;
- result[j] = '\0';
- uchar c = alphabetrank->charAtPos(i);
+ string result;
+ // Reserve average string length to avoid reallocs
+ result.reserve(n/numberOfTexts);
+
+ uchar c = alphabetrank->access(i);
while (c != '\0')
{
- --j;
- result[j] = c;
+ result.push_back(c);
i = C[c]+alphabetrank->rank(c,i)-1;
- c = alphabetrank->charAtPos(i); // "next" char.
+ c = alphabetrank->access(i); // "next" char.
}
- assert(j == 0);
- return result;
+
+ // Convert to uchar (FIXME return string?)
+ i = result.size();
+ uchar* res = new uchar[i+1];
+ res[i] = '\0';
+ for (ulong j = 0; j < i; ++j)
+ res[i-j-1] = result[j];
+ return res;
}
-
+/*
+ * Not supported
uchar* CSA::GetText(DocId k, TextPosition i, TextPosition j) const
{
- assert(k < (DocId)textLength.size());
- assert(j < textLength[k].first);
+ assert(k < (DocId)numberOfTexts);
+ assert(j < (*textLength)[k]);
assert(i <= j);
+ ulong textRank = 0;
+ if (emptyTextRank->IsBitSet(k, &textRank))
+ {
+ uchar* result = new uchar[1];
+ result[0] = 0;
+ return result;
+ }
+
+ // Map to non-empty text
+ k -= textRank; // emptyTextRank->rank(k);
+
// Start position of k'th text
- ulong start = textLength[k].second;
+ ulong start = (*textStartPos)[k];
return Substring(i + start, j-i+1);
-}
+ }*/
-/**
+/******************************************************************
* Existential queries
*/
bool CSA::IsPrefix(uchar const * pattern) const
{
TextPosition m = strlen((char *)pattern);
if (m == 0)
- return textLength.size();
+ return true;
TextPosition sp = 0, ep = 0;
Search(pattern, m, &sp, &ep);
// Check for end-marker(s) in result interval
- map<TextPosition, pair<DocId, TextPosition> >::const_iterator it;
- it = endmarkers.lower_bound(sp);
- if (it != endmarkers.end() && it->first <= ep)
+ if (CountEndmarkers(sp, ep))
return true;
return false;
}
bool CSA::IsSuffix(uchar const *pattern) const
{
- // Here counting is as fast as isSuffix():
+ // Here counting is as fast as IsSuffix():
if (CountSuffix(pattern) > 0)
return true;
return false;
{
TextPosition m = std::strlen((char *)pattern);
if (m == 0)
- return textLength.size();
+ {
+ if (numberOfAllTexts - numberOfTexts > 0u)
+ return true; // Empty texts exists
+ return false; // No empty texts exists
+ }
TextPosition sp = 0, ep = 0;
// Match including end-marker
Search(pattern, m+1, &sp, &ep);
// Check for end-marker(s) in result interval
- map<TextPosition, pair<DocId, TextPosition> >::const_iterator it;
- it = endmarkers.lower_bound(sp);
- if (it != endmarkers.end() && it->first <= ep)
+ if (CountEndmarkers(sp, ep))
return true;
return false;
}
bool CSA::IsLessThan(uchar const*) const
{
// TODO
+ assert(0);
return false;
}
-/**
+/******************************************************************
* Counting queries
*/
unsigned CSA::CountPrefix(uchar const * pattern) const
{
TextPosition m = strlen((char *)pattern);
if (m == 0)
- return textLength.size();
+ return numberOfAllTexts;
TextPosition sp = 0, ep = 0;
Search(pattern, m, &sp, &ep);
// Count end-markers in result interval
- map<TextPosition, pair<DocId, TextPosition> >::const_iterator it;
- it = endmarkers.lower_bound(sp);
- unsigned count = 0;
- while (it != endmarkers.end() && it->first <= ep)
- {
- ++ count;
- ++ it;
- }
-
- return count;
+ return CountEndmarkers(sp, ep);
}
unsigned CSA::CountSuffix(uchar const * pattern) const
{
TextPosition m = strlen((char *)pattern);
if (m == 0)
- return textLength.size();
+ return numberOfAllTexts;
TextPosition sp = 0, ep = 0;
// Search with end-marker
{
TextPosition m = strlen((char const *)pattern);
if (m == 0)
- return textLength.size();
+ return numberOfAllTexts - numberOfTexts; // Empty texts.
TextPosition sp = 0, ep = 0;
// Match including end-marker
Search(pattern, m+1, &sp, &ep);
// Count end-markers in result interval
- map<TextPosition, pair<DocId, TextPosition> >::const_iterator it;
- it = endmarkers.lower_bound(sp);
- unsigned count = 0;
- while (it != endmarkers.end() && it->first <= ep)
- {
- ++ count;
- ++ it;
- }
-
- return count;
+ return CountEndmarkers(sp, ep);
}
unsigned CSA::CountContains(uchar const * pattern) const
{
+ TextPosition m = strlen((char const *)pattern);
+ if (m == 0)
+ return numberOfAllTexts; // Total number of texts.
+
// Here counting is as slow as fetching the result set
// because we would have to filter out occ's that fall within same document.
TextCollection::document_result result = Contains(pattern);
unsigned CSA::CountLessThan(uchar const * pattern) const
{
// TODO
+ assert(0);
return 0;
}
{
TextPosition m = strlen((char *)pattern);
if (m == 0)
- return TextCollection::document_result();
+ return TextCollection::document_result(); // FIXME Should return all 1...k
TextPosition sp = 0, ep = 0;
Search(pattern, m, &sp, &ep);
TextCollection::document_result result;
// Report end-markers in result interval
- map<TextPosition, pair<DocId, TextPosition> >::const_iterator it;
- it = endmarkers.lower_bound(sp);
- unsigned count = 0;
- while (it != endmarkers.end() && it->first <= ep)
+ unsigned resultSize = CountEndmarkers(sp, ep);
+ if (resultSize == 0)
+ return result;
+
+ result.reserve(resultSize); // Try to avoid reallocation.
+
+ // Iterate through end-markers in [sp,ep]:
+ unsigned i = 0;
+ if (sp > 0)
+ i = alphabetrank->rank(0, sp - 1);
+ while (resultSize)
{
- // End-marker we found belongs to the "previous" doc in the collection
- DocId docId = ((it->second).first + 1) % textLength.size();
+ // End-marker we found belongs to the "preceeding" doc in the collection
+ DocId docId = ((*endmarkerDocId)[i] + 1) % numberOfTexts;
+ // Map to doc ID:
+ docId = emptyTextRank->select0(docId+1);
result.push_back(docId);
- ++ count;
- ++ it;
+
+ -- resultSize;
+ ++ i;
}
-
+
return result;
}
{
TextPosition m = strlen((char *)pattern);
if (m == 0)
- return TextCollection::document_result();
+ return TextCollection::document_result(); // FIXME Should return all 1...k
TextPosition sp = 0, ep = 0;
// Search with end-marker
Search(pattern, m+1, &sp, &ep);
TextCollection::document_result result;
+ result.reserve(ep-sp+1); // Try to avoid reallocation.
+ ulong sampled_rank_i = 0;
// Check each occurrence
for (; sp <= ep; ++sp)
{
TextPosition i = sp;
- uchar c = alphabetrank->charAtPos(i);
- while (c != '\0' && !sampled->IsBitSet(i))
+
+ uchar c = alphabetrank->access(i);
+ while (c != '\0' && !sampled->IsBitSet(i, &sampled_rank_i))
{
- i = C[c]+alphabetrank->rank(c,i)-1; // LF-mapping
- c = alphabetrank->charAtPos(i);
+ i = C[c]+alphabetrank->rank(c,i)-1;
+ c = alphabetrank->access(i);
}
+ // Assert: c == '\0' OR sampled->IsBitSet(i)
+
if (c == '\0')
{
- // map::operator[] is not const, using find() instead:
- pair<DocId, TextPosition> endm = (endmarkers.find(i))->second;
- // End-marker that we found belongs to the "previous" doc in collection:
- DocId docId = (endm.first + 1) % textLength.size();
+ // Rank among the end-markers in BWT
+ unsigned endmarkerRank = alphabetrank->rank(0, i) - 1;
+
+ // End-marker that we found belongs to the "preceeding" doc in collection:
+ DocId docId = ((*endmarkerDocId)[endmarkerRank] + 1) % numberOfTexts;
+ // Map to doc ID:
+ docId = emptyTextRank->select0(docId+1);
result.push_back(docId);
}
- else
+ else // Sampled position
{
- TextPosition textPos = suffixes[sampled->rank(i)-1];
- result.push_back(DocIdAtTextPos(textPos));
+ DocId docId = (*suffixDocId)[sampled_rank_i-1]; //sampled->rank(i)-1];
+ // Map to doc ID:
+ docId = emptyTextRank->select0(docId+1);
+ result.push_back(docId);
}
}
{
TextPosition m = strlen((char const *)pattern);
if (m == 0)
- return TextCollection::document_result();
+ return TextCollection::document_result(); // FIXME Should return all empty texts
TextPosition sp = 0, ep = 0;
// Match including end-marker
TextCollection::document_result result;
// Report end-markers in result interval
- map<TextPosition, pair<DocId, TextPosition> >::const_iterator it;
- it = endmarkers.lower_bound(sp);
- unsigned count = 0;
- while (it != endmarkers.end() && it->first <= ep)
+ unsigned resultSize = CountEndmarkers(sp, ep);
+ if (resultSize == 0)
+ return result;
+
+ result.reserve(resultSize); // Try to avoid reallocation.
+
+ unsigned i = 0;
+ if (sp > 0)
+ i = alphabetrank->rank(0, sp - 1);
+ while (resultSize)
{
- // End-marker that we found belongs to the "previous" doc in collection:
- DocId docId = ((it->second).first + 1) % textLength.size();
+ // End-marker we found belongs to the "previous" doc in the collection
+ DocId docId = ((*endmarkerDocId)[i] + 1) % numberOfTexts;
+ // Map to doc ID:
+ docId = emptyTextRank->select0(docId+1);
result.push_back(docId);
- ++ count;
- ++ it;
+
+ -- resultSize;
+ ++ i;
}
-
+
return result;
}
TextPosition sp = 0, ep = 0;
// Search all occurrences
Search(pattern, m, &sp, &ep);
-
+
// We want unique document indentifiers, using std::set to collect them
std::set<DocId> resultSet;
+ ulong sampled_rank_i = 0;
// Check each occurrence
for (; sp <= ep; ++sp)
{
TextPosition i = sp;
- uchar c = alphabetrank->charAtPos(i);
- while (c != '\0' && !sampled->IsBitSet(i))
+ uchar c = alphabetrank->access(i);
+ while (c != '\0' && !sampled->IsBitSet(i, &sampled_rank_i))
{
i = C[c]+alphabetrank->rank(c,i)-1; // LF-mapping
- c = alphabetrank->charAtPos(i);
+ c = alphabetrank->access(i);
}
if (c == '\0')
{
- // map::operator[] is not const, using find() instead:
- pair<DocId, TextPosition> endm = (endmarkers.find(i))->second;
- // End-marker we found belongs to the "previous" doc in collection
- DocId docId = (endm.first + 1) % textLength.size();
+ // Rank among the end-markers in BWT
+ unsigned endmarkerRank = alphabetrank->rank(0, i) - 1;
+
+ // End-marker that we found belongs to the "preceeding" doc in collection:
+ DocId docId = ((*endmarkerDocId)[endmarkerRank] + 1) % numberOfTexts;
resultSet.insert(docId);
}
else
{
- TextPosition textPos = suffixes[sampled->rank(i)-1];
- resultSet.insert(DocIdAtTextPos(textPos));
+ DocId di = (*suffixDocId)[sampled_rank_i-1]; //sampled->rank(i)-1];
+ assert((unsigned)di < numberOfTexts);
+ resultSet.insert(di);
}
}
- // Convert std::set to std::vector (TODO better way to construct result vector?)
- TextCollection::document_result result;
- for (std::set<DocId>::iterator it = resultSet.begin(); it != resultSet.end(); ++it)
- result.push_back(*it);
+ // Convert std::set to std::vector
+ TextCollection::document_result result(resultSet.begin(), resultSet.end());
+ // Map to doc ID's
+ for (document_result::iterator it = result.begin(); it != result.end(); ++it)
+ *it = emptyTextRank->select0(*it+1);
return result;
}
TextCollection::document_result CSA::LessThan(uchar const * pattern) const
{
// TODO
+ assert(0);
return document_result();
}
{
TextPosition m = strlen((char *)pattern);
if (m == 0)
- return full_result();
+ return full_result(); // FIXME Throw exception?
TextPosition sp = 0, ep = 0;
// Search all occurrences
Search(pattern, m, &sp, &ep);
full_result result;
+ result.reserve(ep-sp+1); // Try to avoid reallocation.
+ ulong sampled_rank_i = 0;
// Report each occurrence
for (; sp <= ep; ++sp)
{
TextPosition i = sp;
TextPosition dist = 0;
- uchar c = alphabetrank->charAtPos(i);
- while (c != '\0' && !sampled->IsBitSet(i))
+ uchar c = alphabetrank->access(i);
+ while (c != '\0' && !sampled->IsBitSet(i, &sampled_rank_i))
{
- i = C[c]+alphabetrank->rank(c,i)-1; // LF-mapping
- c = alphabetrank->charAtPos(i);
+ i = C[c]+alphabetrank->rank(c,i)-1;
+ c = alphabetrank->access(i);
++ dist;
}
if (c == '\0')
{
- // map::operator[] is not const, using find() instead:
- pair<DocId, TextPosition> endm = (endmarkers.find(i))->second;
- // End-marker we found belongs to the "previous" doc in the collection:
- DocId docId = (endm.first+1)%textLength.size();
+ // Rank among the end-markers in BWT
+ unsigned endmarkerRank = alphabetrank->rank(0, i) - 1;
+
+ // End-marker that we found belongs to the "preceeding" doc in collection:
+ DocId docId = ((*endmarkerDocId)[endmarkerRank] + 1) % numberOfTexts;
+ // Map to doc ID:
+ docId = emptyTextRank->select0(docId+1);
result.push_back(make_pair(docId, dist));
}
else
{
- TextPosition textPos = suffixes[sampled->rank(i)-1] + dist;
- // Read document identifier and its starting position in text order
- DocId docId = DocIdAtTextPos(textPos);
- result.push_back(make_pair(docId, textPos - textLength[docId].second));
+ TextPosition textPos = (*suffixes)[sampled_rank_i-1]+dist; //sampled->rank(i)-1] + dist;
+ DocId docId = (*suffixDocId)[sampled_rank_i-1]; //sampled->rank(i)-1];
+// textPos = textPos - (*textStartPos)[docId]; // Offset inside the text
+
+ // Map to doc ID:
+ docId = emptyTextRank->select0(docId+1);
+ result.push_back(make_pair(docId, textPos));
}
}
}
-/**
- * Finds document identifier for given text position
- *
- * Starting text position of the document is stored into second parameter.
- * Binary searching on text starting positions.
- */
-TextCollection::DocId CSA::DocIdAtTextPos(TextPosition i) const
-{
- assert(i < n);
-
- DocId a = 0;
- DocId b = textLength.size() - 1;
- while (a < b)
- {
- DocId c = a + (b - a)/2;
- if (textLength[c].second > i)
- b = c - 1;
- else if (textLength[c+1].second > i)
- return c;
- else
- a = c + 1;
- }
-
- assert(a < (DocId)textLength.size());
- assert(i > textLength[a].second);
- assert(i < (a == (DocId)textLength.size() - 1 ? n : textLength[a+1].second));
- return a;
-}
-
/**
* Save index to a file handle
*
* Throws a std::runtime_error exception on i/o error.
* First byte that is saved represents the version number of the save file.
- * In version 1 files, the data fields are:
- * <uchar version> version info;
- * <unsigned s> samplerate;
- * <ulong n> length of the BWT;
- * <ulong bwt> end marker position in BWT;
- * <uchar *> BWT string of length n;
- * <unsigned r> number of texts;
- * <vector textLength>
- * array of <ulong, ulong> pairs.
- *
- * TODO: Save the data structures instead of BWT sequence?
+ * In version 2 files, the data fields are:
+ * uchar versionFlag;
+ TextPosition n;
+ unsigned samplerate;
+ unsigned C[256];
+ TextPosition bwtEndPos;
+ static_sequence * alphabetrank;
+ BSGAP *sampled;
+ BlockArray *suffixes;
+ BlockArray *suffixDocId;
+ unsigned numberOfTexts;
+ unsigned numberOfAllTexts;
+ ulong maxTextLength;
+ BlockArray *endmarkerDocId;
+ BSGAP *emptyTextRank;
*/
void CSA::Save(FILE *file) const
{
- // Saving version 1 data:
- uchar versionFlag = 1;
+ // Saving version info:
if (std::fwrite(&versionFlag, 1, 1, file) != 1)
throw std::runtime_error("CSA::Save(): file write error (version flag).");
+ if (std::fwrite(&(this->n), sizeof(TextPosition), 1, file) != 1)
+ throw std::runtime_error("CSA::Save(): file write error (n).");
if (std::fwrite(&(this->samplerate), sizeof(unsigned), 1, file) != 1)
throw std::runtime_error("CSA::Save(): file write error (samplerate).");
- if (std::fwrite(&(this->n), sizeof(TextPosition), 1, file) != 1)
- throw std::runtime_error("CSA::Save(): file write error (n).");
+ for(ulong i = 0; i < 256; ++i)
+ if (std::fwrite(this->C + i, sizeof(unsigned), 1, file) != 1)
+ throw std::runtime_error("CSA::Save(): file write error (C table).");
if (std::fwrite(&(this->bwtEndPos), sizeof(TextPosition), 1, file) != 1)
throw std::runtime_error("CSA::Save(): file write error (bwt end position).");
-
- for (ulong offset = 0; offset < n; offset ++)
- {
- uchar c = alphabetrank->charAtPos(offset);
- if (std::fwrite(&c, sizeof(uchar), 1, file) != 1)
- throw std::runtime_error("CSA::Save(): file write error (bwt sequence).");
- }
- unsigned r = textLength.size();
- if (std::fwrite(&r, sizeof(unsigned), 1, file) != 1)
- throw std::runtime_error("CSA::Save(): file write error (r).");
-
- for (r = 0; r < textLength.size(); ++ r)
- {
- if (std::fwrite(&(textLength[r].first), sizeof(TextPosition), 1, file) != 1)
- throw std::runtime_error("CSA::Save(): file write error (text length).");
- if (std::fwrite(&(textLength[r].second), sizeof(TextPosition), 1, file) != 1)
- throw std::runtime_error("CSA::Save(): file write error (text start).");
- }
+ alphabetrank->save(file);
+ sampled->Save(file);
+ suffixes->Save(file);
+ suffixDocId->Save(file);
+
+ if (std::fwrite(&(this->numberOfTexts), sizeof(unsigned), 1, file) != 1)
+ throw std::runtime_error("CSA::Save(): file write error (numberOfTexts).");
+ if (std::fwrite(&(this->numberOfAllTexts), sizeof(unsigned), 1, file) != 1)
+ throw std::runtime_error("CSA::Save(): file write error (numberOfAllTexts).");
+ if (std::fwrite(&(this->maxTextLength), sizeof(ulong), 1, file) != 1)
+ throw std::runtime_error("CSA::Save(): file write error (maxTextLength).");
+
+ endmarkerDocId->Save(file);
+ emptyTextRank->Save(file);
}
delete dynFMI; dynFMI = 0;
delete alphabetrank; alphabetrank = 0;
delete sampled; sampled = 0;
- delete [] suffixes; suffixes = 0;
- delete [] positions; positions = 0;
+ delete suffixes; suffixes = 0;
+ delete suffixDocId; suffixDocId = 0;
+ delete positions; positions = 0;
delete [] codetable; codetable = 0;
- endmarkers.clear();
- textLength.clear();
+ delete endmarkerDocId; endmarkerDocId = 0;
+ delete emptyTextRank; emptyTextRank = 0;
+ // FIXME Remove following:
+ delete textLength; textLength = 0;
+ delete textStartPos; textStartPos = 0;
+ this->maxTextLength = 0;
+ this->numberOfTexts = 0;
+ this->numberOfAllTexts = 0;
this->samplerate = samplerate;
this->n = 0;
- uchar versionFlag = 0;
- if (std::fread(&versionFlag, 1, 1, file) != 1)
+ uchar verFlag = 0;
+ if (std::fread(&verFlag, 1, 1, file) != 1)
throw std::runtime_error("CSA::Load(): file read error (version flag).");
- if (versionFlag != 1)
- throw std::runtime_error("CSA::Load(): invalid start byte.");
+ if (verFlag != CSA::versionFlag)
+ throw std::runtime_error("CSA::Load(): invalid save file version.");
+ if (std::fread(&(this->n), sizeof(TextPosition), 1, file) != 1)
+ throw std::runtime_error("CSA::Load(): file read error (n).");
if (std::fread(&samplerate, sizeof(unsigned), 1, file) != 1)
throw std::runtime_error("CSA::Load(): file read error (samplerate).");
- if (this->samplerate == 0)
- this->samplerate = samplerate;
+// FIXME samplerate can not be changed during load.
+// if (this->samplerate == 0)
+// this->samplerate = samplerate;
- if (std::fread(&(this->n), sizeof(TextPosition), 1, file) != 1)
- throw std::runtime_error("CSA::Load(): file read error (n).");
+ for(ulong i = 0; i < 256; ++i)
+ if (std::fread(this->C + i, sizeof(unsigned), 1, file) != 1)
+ throw std::runtime_error("CSA::Load(): file read error (C table).");
if (std::fread(&(this->bwtEndPos), sizeof(TextPosition), 1, file) != 1)
throw std::runtime_error("CSA::Load(): file read error (bwt end position).");
- uchar *bwt = new uchar[n];
- for (ulong offset = 0; offset < n; offset ++)
- if (std::fread((bwt + offset), sizeof(uchar), 1, file) != 1)
- throw std::runtime_error("CSA::Load(): file read error (bwt sequence).");
+ alphabetrank = static_sequence::load(file);
+ sampled = new BSGAP(file);
+ suffixes = new BlockArray(file);
+ suffixDocId = new BlockArray(file);
- unsigned r = 0;
- if (std::fread(&r, sizeof(unsigned), 1, file) != 1)
- throw std::runtime_error("CSA::Load(): file read error (r).");
-
- while (r > 0)
- {
- TextPosition length = 0, start = 0;
- if (std::fread(&length, sizeof(TextPosition), 1, file) != 1)
- throw std::runtime_error("CSA::Load(): file read error (text length).");
- if (std::fread(&start, sizeof(TextPosition), 1, file) != 1)
- throw std::runtime_error("CSA::Load(): file read error (text start).");
-
- textLength.push_back(make_pair(length, start));
- --r;
- }
+ if (std::fread(&(this->numberOfTexts), sizeof(unsigned), 1, file) != 1)
+ throw std::runtime_error("CSA::Load(): file read error (numberOfTexts).");
+ if (std::fread(&(this->numberOfAllTexts), sizeof(unsigned), 1, file) != 1)
+ throw std::runtime_error("CSA::Load(): file read error (numberOfAllTexts).");
+ if (std::fread(&(this->maxTextLength), sizeof(ulong), 1, file) != 1)
+ throw std::runtime_error("CSA::Load(): file read error (maxTextLength).");
- // Construct data structures
- makewavelet(bwt);
- delete [] bwt;
- maketables();
+ endmarkerDocId = new BlockArray(file);
+ emptyTextRank = new BSGAP(file);
+
+ // FIXME Construct data structures with new samplerate
+ //maketables(); // FIXME: this will redo text length tables
}
* Rest of the functions follow...
*/
+/*
+ * Not supported
uchar * CSA::Substring(TextPosition i, TextPosition l) const
{
uchar *result = new uchar[l + 1];
}
else
{
- j = positions[k/samplerate+1];
+ j = (*positions)[k/samplerate+1];
//cout << samplerate << ' ' << j << '\n';
}
for (dist = 0; dist < skip + l; dist++)
{
- int c = alphabetrank->charAtPos(j);
+ int c = alphabetrank->access(j); //charAtPos(j, &alphabetrank_tmp);
if (c == '\0')
{
- // map::operator[] is not const, using find() instead:
- pair<DocId, TextPosition> endm = (endmarkers.find(j))->second;
- j = endm.first; // LF-mapping for end-marker
+ // Rank among the end-markers in BWT
+ unsigned endmarkerRank = alphabetrank->rank(0, j) - 1;
+ j = (*endmarkerDocId)[endmarkerRank]; // LF-mapping for end-marker
}
else
j = C[c]+alphabetrank->rank(c,j)-1; // LF-mapping
result[l] = 0u;
return result;
}
-
+*/
/*TextPosition CSA::inverse(TextPosition i)
{
TextPosition skip = samplerate - i % samplerate;
}
else
{
- j = positions[i/samplerate+1];
+ j = (*positions)[i/samplerate+1];
//cout << samplerate << ' ' << j << '\n';
}
return j;
}*/
-ulong CSA::Search(uchar const * pattern, TextPosition m, TextPosition *spResult, TextPosition *epResult) const {
+ulong CSA::Search(uchar const * pattern, TextPosition m, TextPosition *spResult, TextPosition *epResult) const
+{
// use the FM-search replacing function Occ(c,1,i) with alphabetrank->rank(c,i)
int c = (int)pattern[m-1];
TextPosition i=m-1;
return ep - sp + 1;
else
return 0;
- }
+}
/*TextPosition CSA::LF(uchar c, TextPosition &sp, TextPosition &ep)
{
return 0;
}*/
-CSA::TextPosition CSA::Lookup(TextPosition i) const // Time complexity: O(samplerate log \sigma)
+CSA::TextPosition CSA::Lookup(TextPosition i) const
{
TextPosition dist=0;
while (!sampled->IsBitSet(i))
{
- int c = alphabetrank->charAtPos(i);
+
+ int c = alphabetrank->access(i);
if (c == '\0')
{
- // map::operator[] is not const, using find() instead:
- pair<DocId, TextPosition> endm = (endmarkers.find(i))->second;
- return endm.second + dist; // returns text position.
+ // End-markers are sampled
+ unsigned endmarkerRank = alphabetrank->rank(0, i) - 1;
+ DocId docId = (*endmarkerDocId)[endmarkerRank];
+ return (*textStartPos)[docId] + dist;
}
- i = C[c]+alphabetrank->rank(c,i)-1; // LF-mapping
+ i = C[c]+alphabetrank->rank(c,i)-1;
++dist;
}
- return suffixes[sampled->rank(i)-1]+dist;
+ return (*suffixes)[sampled->rank(i)-1]+dist;
}
CSA::~CSA() {
delete dynFMI;
delete alphabetrank;
delete sampled;
- delete [] suffixes;
- delete [] positions;
+ delete suffixes;
+ delete suffixDocId;
+ delete positions;
delete [] codetable;
+
+ delete endmarkerDocId;
+ delete textLength;
+ delete textStartPos;
+ delete emptyTextRank;
}
void CSA::makewavelet(uchar *bwt)
if (C[i]>0) {max = i; break;}
// Print frequencies
-/* for(i = 0; i < 256; i++)
+ /*for(i = 0; i < 256; i++)
if (C[i]>0) printf("C[%lu] = %lu\n", i, C[i]);
fflush(stdout);*/
C[i]=C[i-1]+prev;
prev = temp;
}
- this->codetable = node::makecodetable(bwt,n);
- alphabetrank = new THuffAlphabetRank(bwt,n, this->codetable,0);
- //if (alphabetrank->Test(bwt,n)) printf("alphabetrank ok\n");
+// this->codetable = node::makecodetable(bwt,n);
+// alphabetrank = new THuffAlphabetRank(bwt,n, this->codetable,0);
+// delete [] bwt;
+ //alphabetrank = new RLWaveletTree(bwt, n); // Deletes bwt!
+
+ uint *text = new uint[n];
+ for (i = 0; i < n; ++i) // Silly
+ text[i] = bwt[i];
+ delete [] bwt;
+ bwt = 0;
+
+ alphabet_mapper * am = new alphabet_mapper_none();
+ static_bitsequence_builder * bmb = new static_bitsequence_builder_brw32(16); // FIXME samplerate?
+
+ //cout << "Building Huffman table..."; cout.flush();
+
+ wt_coder * wtc = new wt_coder_huff(text,n,am);
+
+ //cout << "done" << endl; cout.flush();
+ //cout << "Building static_sequence..."; cout.flush();
+
+ alphabetrank = new static_sequence_wvtree(text,n,wtc,bmb,am);
+ delete [] text;
+ text = 0;
/* for (i = 0; i < n; ++i)
{
ulong sampleLength = (n%samplerate==0) ? n/samplerate : n/samplerate+1;
ulong *sampledpositions = new ulong[n/W+1];
- suffixes = new ulong[sampleLength];
- positions = new ulong[sampleLength];
-
+ unsigned ceilLog2n = Tools::CeilLog2(n);
+ positions = new BlockArray(sampleLength, ceilLog2n);
+ BlockArray* tmpSuffix = new BlockArray(sampleLength, ceilLog2n);
+
+ // Mapping from end-markers to doc ID's:
+ endmarkerDocId = new BlockArray(numberOfTexts, Tools::CeilLog2(numberOfTexts));
+
ulong i,j=0;
for (i=0;i<n/W+1;i++)
sampledpositions[i]=0lu;
ulong x,p=bwtEndPos;
- DocId textId = textLength.size();
+ ulong sampleCount = 0;
+ // Keeping track of text position of end-markers seen
+ ulong posOfSuccEndmarker = n;
+ DocId textId = numberOfTexts;
ulong ulongmax = 0;
ulongmax--;
- //positions:
+ //positions:
for (i=n-1;i<ulongmax;i--) { // TODO bad solution with ulongmax?
// i substitutes SA->GetPos(i)
x=(i==n-1)?0:i+1;
- if (x % samplerate == 0) {
+ if (x % samplerate == 0 && posOfSuccEndmarker - x > samplerate) {
Tools::SetField(sampledpositions,1,p,1);
- positions[x/samplerate] = p;
+ (*positions)[sampleCount] = p;
+ (*tmpSuffix)[sampleCount] = x; // FIXME remove
+ sampleCount ++;
}
- uchar c = alphabetrank->charAtPos(p);
+ uchar c = alphabetrank->access(p);
if (c == '\0')
{
- // Record the order of end-markers in BWT:
--textId;
- endmarkers[p] = make_pair(textId, (TextPosition)x);
+
+ // Record the order of end-markers in BWT:
+ ulong endmarkerRank = alphabetrank->rank(0, p) - 1;
+ (*endmarkerDocId)[endmarkerRank] = textId;
+
+ // Store text length and text start position:
+ if (textId < (DocId)numberOfTexts - 1)
+ {
+ (*textLength)[textId + 1] = posOfSuccEndmarker - x;
+ (*textStartPos)[textId + 1] = x; // x is the position of end-marker.
+ posOfSuccEndmarker = x;
+ }
+
// LF-mapping from '\0' does not work with this (pseudo) BWT (see details from Wolfgang's thesis).
p = textId; // Correct LF-mapping to the last char of the previous text.
}
p = C[c]+alphabetrank->rank(c, p)-1;
}
assert(textId == 0);
- /*for (map<ulong, pair<DocId, ulong> >::iterator it = endmarkers.begin(); it != endmarkers.end(); ++it)
+
+ /*i = 0;
+ for (map<ulong, pair<DocId, ulong> >::iterator it = endmarkers.begin(); it != endmarkers.end(); ++it, ++i)
{
- printf("endm[%u] = %lu (text pos: %lu)\n", (it->second).first, it->first, (it->second).second);
+ int docc = (*endmarkerDocId)[i];
+ ulong poss = (*endmarkerPos)[i];
+ printf("endm[%u] = %lu (text pos: %lu) (recorded: %d, %lu)\n", (it->second).first, it->first, (it->second).second, docc, poss);
}*/
+/*
+ for (i = 0; i < numberOfTexts; ++ i)
+ {
+ //std::cout << "textlength = " << dynTextLength[i].first << " vs " << (*textLength)[i] << ", textStartPos = " << dynTextLength[i].second << " vs " << (*textStartPos)[i] << std::endl;
+ assert(dynTextLength[i].first == (*textLength)[i]);
+ assert(dynTextLength[i].second == (*textStartPos)[i]);
+ }
+*/
+ sampled = new BSGAP(sampledpositions,n,true);
+ sampleLength = sampled->rank(n-1);
+ assert(sampleCount == sampleLength);
+// std::cout << ";sampleLength;" << sampleLength << std::endl;
+ // Suffixes == offset from text start position
+ suffixes = new BlockArray(sampleLength, Tools::CeilLog2(maxTextLength));
+ suffixDocId = new BlockArray(sampleLength, Tools::CeilLog2(numberOfTexts));
- sampled = new BitRank(sampledpositions,n,true);
-
//suffixes:
for(i=0; i<sampleLength; i++) {
- j = sampled->rank(positions[i]);
+ assert((*positions)[i] < n);
+ j = sampled->rank((*positions)[i]);
if (j==0) j=sampleLength;
- suffixes[ j-1] = (i*samplerate==n)?0:i*samplerate;
- }
-}
+ TextPosition textPos = (*tmpSuffix)[i]; //(i*samplerate==n)?0:i*samplerate;
+ (*suffixDocId)[j-1] = DocIdAtTextPos(textPos); // (*suffixes)[j-1]);
-uchar * CSA::LoadFromFile(const char *filename)
-{
- uchar *s;
- std::ifstream file (filename, std::ios::in|std::ios::binary);
- if (file.is_open())
- {
- std::cerr << "Loading CSA from file: " << filename << std::endl;
- file.read((char *)&bwtEndPos, sizeof(TextPosition));
- s = new uchar[n];
- for (ulong offset = 0; offset < n; offset ++)
- file.read((char *)(s + offset), sizeof(char));
- file.close();
- }
- else
- {
- std::cerr << "Unable to open file " << filename << std::endl;
- exit(1);
+ assert((unsigned)DocIdAtTextPos(textPos) < numberOfTexts);
+ assert((*suffixDocId)[j-1] < numberOfTexts);
+ // calculate offset from text start:
+ (*suffixes)[j-1] = textPos - (*textStartPos)[(*suffixDocId)[j-1]];
}
- return s;
+ // FIXME Temp, remove
+ delete tmpSuffix;
+ tmpSuffix=0;
+ delete positions;
+ positions =0;
+ delete textLength;
+ textLength = 0;
+ delete textStartPos;
+ textStartPos = 0;
}
-void CSA::SaveToFile(const char *filename, uchar *bwt)
+
+/**
+ * Finds document identifier for given text position
+ *
+ * Starting text position of the document is stored into second parameter.
+ * Binary searching on text starting positions.
+ */
+TextCollection::DocId CSA::DocIdAtTextPos(TextPosition i) const
{
- std::ofstream file (filename, std::ios::out|std::ios::binary|std::ios::trunc);
- if (file.is_open())
- {
- std::cerr << "Writing CSA to file: " << filename << std::endl;
- file.write((char *)&bwtEndPos, sizeof(TextPosition));
- std::cerr << "Writing BWT of " << n << " bytes." << std::endl;
- for (ulong offset = 0; offset < n; offset ++)
- file.write((char *)(bwt + offset), sizeof(char));
- file.close();
- }
- else
+ assert(i < n);
+
+ DocId a = 0;
+ DocId b = numberOfTexts - 1;
+ while (a < b)
{
- std::cerr << "Unable to open file " << filename << std::endl;
- exit(1);
+ DocId c = a + (b - a)/2;
+ if ((*textStartPos)[c] > i)
+ b = c - 1;
+ else if ((*textStartPos)[c+1] > i)
+ return c;
+ else
+ a = c + 1;
}
-}
-/*uchar * CSA::BWT(uchar *text)
-{
- uchar *s;
-
- DynFMI *wt = new DynFMI((uchar *) text, n);
- s = wt->getBWT();
- for (ulong i=0;i<n;i++)
- if (s[i]==0u) {
- bwtEndPos = i; // TODO: better solution ?
- i=n;
- }
-
- delete wt;
- return s;
- }*/
+ assert(a < (DocId)numberOfTexts);
+ assert(i >= (*textStartPos)[a]);
+ assert(i < (a == (DocId)numberOfTexts - 1 ? n : (*textStartPos)[a+1]));
+ return a;
+}
CSA::TCodeEntry * CSA::node::makecodetable(uchar *text, TextPosition n)
{
projects / SXSI / TextCollection.git / blobdiff