using std::pair;
using std::make_pair;
using std::map;
-
+using std::string;
namespace SXSI
{
// Save file version info
-const uchar TCImplementation::versionFlag = 6;
+const uchar TCImplementation::versionFlag = 8;
/**
* Constructor inits an empty dynamic FM-index.
* Samplerate defaults to TEXTCOLLECTION_DEFAULT_SAMPLERATE.
*/
-TCImplementation::TCImplementation(uchar * bwt, ulong length, unsigned samplerate_, unsigned numberOfTexts_, ulong maxTextLength_)
+TCImplementation::TCImplementation(uchar * bwt, ulong length, unsigned samplerate_,
+ unsigned numberOfTexts_, ulong maxTextLength_, ulong numberOfSamples_,
+ CSA::DeltaVector & notIndexed, const string & niText, char tsType)
: n(length), samplerate(samplerate_), alphabetrank(0), sampled(0), suffixes(0),
suffixDocId(0), numberOfTexts(numberOfTexts_), maxTextLength(maxTextLength_), Doc(0)
{
makewavelet(bwt); // Deletes bwt!
bwt = 0;
-
+
// Make sampling tables
- maketables();
+ maketables(numberOfSamples_, tsType, notIndexed, niText);
}
bool TCImplementation::EmptyText(DocId k) const
res[i-j-1] = result[j];
return res;*/
}
+
/*
- * Not supported
+ * Substring queries are supported via the pointer returned by TextStorage::GetText
uchar* TCImplementation::GetText(DocId k, TextPosition i, TextPosition j) const
{
assert(k < (DocId)numberOfTexts);
return Substring(i + start, j-i+1);
}*/
+
+
/******************************************************************
* Existential queries
*/
return result;
}
+
+/**
+ ***
+* * FIXME Lessthan or equal
+ */
TextCollection::document_result TCImplementation::LessThan(uchar const * pattern) const
{
TextPosition m = strlen((char *)pattern);
}
-TextCollection::document_result TCImplementation::Kmismaches(uchar const * pattern, unsigned k) const
+TextCollection::document_result TCImplementation::KMismaches(uchar const * pattern, unsigned k) const
{
TextPosition m = strlen((char *)pattern);
if (m == 0)
return result;
}
-TextCollection::document_result TCImplementation::Kerrors(uchar const * pattern, unsigned k) const
+TextCollection::document_result TCImplementation::KErrors(uchar const * pattern, unsigned k) const
{
TextPosition m = strlen((char *)pattern);
if (m == 0)
return result;
}
-TextCollection::full_result TCImplementation::FullKmismatches(uchar const * pattern, unsigned k) const
+TextCollection::full_result TCImplementation::FullKMismatches(uchar const * pattern, unsigned k) const
{
TextPosition m = strlen((char *)pattern);
if (m == 0)
return result;
}
-TextCollection::full_result TCImplementation::FullKerrors(uchar const * pattern, unsigned k) const
+TextCollection::full_result TCImplementation::FullKErrors(uchar const * pattern, unsigned k) const
{
TextPosition m = strlen((char *)pattern);
if (m == 0)
*
* Throws a std::runtime_error exception on i/o error.
* For more info, see TCImplementation::Save().
+ *
+ * index_mode_t is defined in TextCollection.h and
+ * defaults to both the index and "naive" text.
+ *
+ * Note: Samplerate can not be changed during load.
*/
-TCImplementation::TCImplementation(FILE *file, unsigned samplerate_)
+TCImplementation::TCImplementation(FILE *file, index_mode_t im, unsigned samplerate_)
: n(0), samplerate(samplerate_), alphabetrank(0), sampled(0), suffixes(0),
suffixDocId(0), numberOfTexts(0), maxTextLength(0), Doc(0)
{
throw std::runtime_error("TCImplementation::Load(): file read error (bwt end position).");
alphabetrank = static_sequence::load(file);
+ if (im == index_mode_text_only) { delete alphabetrank; alphabetrank = 0; }
+
sampled = static_bitsequence::load(file);
+ if (im == index_mode_text_only) { delete sampled; sampled = 0; }
suffixes = new BlockArray(file);
+ if (im == index_mode_text_only) { delete suffixes; suffixes = 0; }
suffixDocId = new BlockArray(file);
+ if (im == index_mode_text_only) { delete suffixDocId; suffixDocId = 0; }
if (std::fread(&(this->numberOfTexts), sizeof(unsigned), 1, file) != 1)
throw std::runtime_error("TCImplementation::Load(): file read error (numberOfTexts).");
if (std::fread(&(this->maxTextLength), sizeof(ulong), 1, file) != 1)
throw std::runtime_error("TCImplementation::Load(): file read error (maxTextLength).");
- Doc = static_sequence::load(file);
- textStorage = new TextStorage(file);
+ Doc = new ArrayDoc(file); //static_sequence::load(file);
+ if (im == index_mode_text_only) { delete Doc; Doc = 0; }
+
+ textStorage = TextStorage::Load(file);
// FIXME Construct data structures with new samplerate
//maketables();
//first call kerrors(pattern,1,n,m+k,k,d,m), where d[i]=i
ulong TCImplementation::kerrors(suffix_range_vector &result, uchar const *pattern, ulong sp, ulong ep, ulong j, unsigned k, ulong const *d, ulong m) const
{
- cout << "j = " << j << ", k = " << k << ", d:";
- for (unsigned i = 0; i < m+1; ++i)
- cout << " " << d[i];
- cout << endl;
-
+ ulong sum=0;
if (d[m]<=k) // range of suffixes with at most k-errors found
{
if (sp<=ep)
result.push_back(std::make_pair(sp, ep));
- return (sp<=ep)?ep-sp+1:0ul;
+ sum += (sp<=ep)?ep-sp+1:0ul;
}
if (sp>ep || j==0)
- return 0;
+ return sum;
ulong *dnew = new ulong[m+1];
int c;
ulong spnew;
ulong p,lowerbound;
ulong epnew;
- ulong sum=0;
vector<int> chars = alphabetrank->accessAll(sp, ep);
for (vector<int>::iterator it = chars.begin(); it != chars.end(); ++it)
{
#ifdef DEBUG_MEMUSAGE
std::cerr << "max heap usage before WT: " << HeapProfiler::GetMaxHeapConsumption()/(1024*1024) << " Mbytes" << std::endl;
- HeapProfiler::ResetMaxHeapConsumption(); // FIXME remove
+ HeapProfiler::ResetMaxHeapConsumption();
#endif
alphabet_mapper * am = new alphabet_mapper_none();
- static_bitsequence_builder * bmb = new static_bitsequence_builder_rrr02(8); // FIXME samplerate?
- wt_coder * wtc = new wt_coder_binary(bwt,n,am);
+ static_bitsequence_builder * bmb = new static_bitsequence_builder_brw32(8); //rrr02(8); // FIXME samplerate?
+ wt_coder * wtc = new wt_coder_huff(bwt,n,am);//binary(bwt,n,am); // FIXME Huffman shape
alphabetrank = new static_sequence_wvtree(bwt,n,wtc,bmb,am);
delete bmb;
bwt = 0; // already deleted
#endif
}
-void TCImplementation::maketables()
+void TCImplementation::maketables(ulong sampleLength, char tsType, CSA::DeltaVector & notIndexed, const string & niText)
{
// Calculate BWT end-marker position (of last inserted text)
{
this->bwtEndPos = i;
}
+#ifdef DEBUG_MEMUSAGE
+ std::cerr << "heap usage before BWT traverse: " << HeapProfiler::GetHeapConsumption()/(1024*1024) << " / " << HeapProfiler::GetMaxHeapConsumption()/(1024*1024) << " Mbytes, " << HeapProfiler::GetHeapConsumption() << " / " << HeapProfiler::GetMaxHeapConsumption() << std::endl;
+ HeapProfiler::ResetMaxHeapConsumption();
+#endif
+
// Build up array for text starting positions
- BlockArray* textStartPos = new BlockArray(numberOfTexts, Tools::CeilLog2(this->n));
- (*textStartPos)[0] = 0;
+// BlockArray* textStartPos = new BlockArray(numberOfTexts, Tools::CeilLog2(this->n));
+// (*textStartPos)[0] = 0;
// Mapping from end-markers to doc ID's:
- uint *endmarkerDocId = new uint[numberOfTexts]; // FIXME Use BlockArray with static_sequence_wvtree_noptrs.
-
+ unsigned logNumberOfTexts = Tools::CeilLog2(numberOfTexts);
+// uint *endmarkerDocId = new uint[(numberOfTexts * logNumberOfTexts)/(8*sizeof(uint)) + 1];
+ BlockArray *endmarkerDocId = new BlockArray(numberOfTexts, logNumberOfTexts);
+
+ BlockArray* positions = new BlockArray(sampleLength, Tools::CeilLog2(this->n));
uint *sampledpositions = new uint[n/(sizeof(uint)*8)+1];
for (ulong i = 0; i < n / (sizeof(uint)*8) + 1; i++)
sampledpositions[i] = 0;
ulong x,p=bwtEndPos;
ulong sampleCount = 0;
// Keeping track of text position of prev. end-marker seen
- ulong posOfSuccEndmarker = n;
+ ulong posOfSuccEndmarker = n-1;
DocId textId = numberOfTexts;
ulong ulongmax = 0;
ulongmax--;
uint alphabetrank_i_tmp =0;
- /**
- * First pass: populate tables textStartPos and sampledpositions.
- */
+ // Text length = n + number of bytes not indexed.
+ TextStorageBuilder tsbuilder(n + niText.length());
+ ulong tsb_i = n + niText.length(); // Iterator from text length to 0.
+ string::const_reverse_iterator nit_i = niText.rbegin(); // Iterator through non-indexed texts
+
for (ulong i=n-1;i<ulongmax;i--) {
// i substitutes SA->GetPos(i)
x=(i==n-1)?0:i+1;
- if (x % samplerate == 0 && posOfSuccEndmarker - x > samplerate) {
+ uchar c = alphabetrank->access(p, alphabetrank_i_tmp);
+
+ tsbuilder[--tsb_i] = c; // Build TextStorage
+
+ if ((posOfSuccEndmarker - i) % samplerate == 0 && c != '\0')
+ {
set_field(sampledpositions,1,p,1);
+ (*positions)[sampleCount] = p;
sampleCount ++;
}
- uchar c = alphabetrank->access(p, alphabetrank_i_tmp);
if (c == '\0')
{
- --textId;
+ unsigned prevTextId = textId; // Cache textId value.
+ --textId;
+ /**
+ * At first c == '\0' it holds that (prevTextId == numberOfTexts), thus,
+ * we have to search for the first text that is actually *indexed*
+ * to get correct prevTextId.
+ */
+ if (prevTextId == numberOfTexts)
+ {
+ prevTextId = 0;
+ while (notIndexed.isSet(prevTextId))
+ ++ prevTextId;
+ // Now prevTextId points to the first indexed Doc ID.
+ }
+
+ /**
+ * Insert non-indexed texts
+ */
+ while (notIndexed.isSet(textId))
+ {
+ do {
+ tsbuilder[tsb_i] = *nit_i;
+ -- tsb_i;
+ ++ nit_i;
+ } while (nit_i != niText.rend() && *nit_i != '\0');
+
+ tsbuilder[tsb_i] = '\0';
+
+ if (textId == 0)
+ break;
+ --textId;
+ }
// Record the order of end-markers in BWT:
ulong endmarkerRank = alphabetrank_i_tmp - 1;
- endmarkerDocId[endmarkerRank] = (textId + 1) % numberOfTexts;
+ //set_field(endmarkerDocId, logNumberOfTexts, endmarkerRank, (textId + 1) % numberOfTexts);
+ (*endmarkerDocId)[endmarkerRank] = prevTextId % numberOfTexts;
// Store text length and text start position:
if (textId < (DocId)numberOfTexts - 1)
{
- (*textStartPos)[textId + 1] = x; // x is the position of end-marker.
- posOfSuccEndmarker = x;
+// (*textStartPos)[textId + 1] = x; // x-1 is text position of end-marker.
+
+ posOfSuccEndmarker = i;
}
- // 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.
+ // LF-mapping from '\0' does not work with this (pseudo) BWT.
+ // Correct LF-mapping to the last char of the previous text:
+ p = textId - notIndexed.rank(textId);
}
else // Now c != '\0', do LF-mapping:
p = C[c]+alphabetrank_i_tmp-1;
}
+ while (textId > 0 && notIndexed.isSet(textId-1))
+ {
+ do {
+ -- tsb_i;
+ tsbuilder[tsb_i] = *nit_i;
+ ++ nit_i;
+ } while (nit_i != niText.rend() && *nit_i != '\0');
+ --textId;
+ }
assert(textId == 0);
-
+ assert(tsb_i == 0);
+ assert(nit_i == niText.rend());
+
+#ifdef DEBUG_MEMUSAGE
+ std::cerr << "heap usage before tsbuilder init: " << HeapProfiler::GetHeapConsumption()/(1024*1024) << " / " << HeapProfiler::GetMaxHeapConsumption()/(1024*1024) << " Mbytes, " << HeapProfiler::GetHeapConsumption() << " / " << HeapProfiler::GetMaxHeapConsumption() << std::endl;
+ HeapProfiler::ResetMaxHeapConsumption();
+#endif
+
+ textStorage = tsbuilder.InitTextStorage(tsType);
+
+#ifdef DEBUG_MEMUSAGE
+ std::cerr << "heap usage after tsbuilder init: " << HeapProfiler::GetHeapConsumption()/(1024*1024) << " / " << HeapProfiler::GetMaxHeapConsumption()/(1024*1024) << " Mbytes, " << HeapProfiler::GetHeapConsumption() << " / " << HeapProfiler::GetMaxHeapConsumption() << std::endl;
+ HeapProfiler::ResetMaxHeapConsumption();
+#endif
+
sampled = new static_bitsequence_rrr02(sampledpositions, n, 16);
delete [] sampledpositions;
- ulong sampleLength = sampled->rank1(n-1);
assert(sampleCount == sampleLength);
+ assert(sampled->rank1(n-1) == sampleLength);
+
+#ifdef DEBUG_MEMUSAGE
+ std::cerr << "heap usage after sampled bit vector: " << HeapProfiler::GetHeapConsumption()/(1024*1024) << " / " << HeapProfiler::GetMaxHeapConsumption()/(1024*1024) << " Mbytes, " << HeapProfiler::GetHeapConsumption() << " / " << HeapProfiler::GetMaxHeapConsumption() << std::endl;
+ HeapProfiler::ResetMaxHeapConsumption();
+#endif
// Suffixes store an offset from the text start position
suffixes = new BlockArray(sampleLength, Tools::CeilLog2(maxTextLength));
suffixDocId = new BlockArray(sampleLength, Tools::CeilLog2(numberOfTexts));
- p=bwtEndPos;
- textId = numberOfTexts;
-
- TextStorageBuilder tsbuilder(n);
-
- /**
- * Second pass: populate tables suffixes and suffixDocId.
- */
- for (ulong i=n-1;i<ulongmax;i--) {
- x=(i==n-1)?0:i+1;
-
- if (sampled->access(p)) {
- ulong j = sampled->rank1(p)-1;
-
- (*suffixDocId)[j] = DocIdAtTextPos(textStartPos, x);
-
- // calculate offset from text start:
- (*suffixes)[j] = x - (*textStartPos)[(*suffixDocId)[j]];
+ x = n + niText.length() - 2;
+ textId = numberOfTexts - 1;
+ posOfSuccEndmarker = x + 1;
+ for(ulong i = 0; i < sampleLength; i ++) {
+ // Find next sampled text position
+ while ((posOfSuccEndmarker - x) % samplerate != 0
+ || notIndexed.isSet(textId)) // Loop over non-indexed
+ {
+ --x;
+ assert(x != ~0lu);
+ if (textStorage->IsEndmarker(x))
+ {
+ posOfSuccEndmarker = x--;
+ -- textId;
+ }
}
+ assert((*positions)[i] < n);
+ ulong j = sampled->rank1((*positions)[i]);
- uchar c = alphabetrank->access(p, alphabetrank_i_tmp);
- tsbuilder[i] = c;
-
- if (c == '\0')
+ assert(j != 0); // if (j==0) j=sampleLength;
+
+ TextPosition textPos = (x==n-1)?0:x+1;
+ (*suffixDocId)[j-1] = textId; // textStorage->DocIdAtTextPos(textPos);
+ assert(textStorage->DocIdAtTextPos(textPos) == textId);
+
+ assert((*suffixDocId)[j-1] < numberOfTexts);
+ // calculate offset from text start:
+ (*suffixes)[j-1] = textPos - textStorage->TextStartPos((*suffixDocId)[j-1]);
+ --x;
+ if (x != ~0lu && textStorage->IsEndmarker(x))
{
- --textId;
- // 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.
+ posOfSuccEndmarker = x--;
+ -- textId;
}
- else // Now c != '\0', do LF-mapping:
- p = C[c]+alphabetrank_i_tmp-1;
}
- assert(textId == 0);
- delete textStartPos;
- textStorage = tsbuilder.InitTextStorage();
+ delete positions;
+
+#ifdef DEBUG_MEMUSAGE
+ std::cerr << "heap usage after sampled arrays: " << HeapProfiler::GetHeapConsumption()/(1024*1024) << " / " << HeapProfiler::GetMaxHeapConsumption()/(1024*1024) << " Mbytes, " << HeapProfiler::GetHeapConsumption() << " / " << HeapProfiler::GetMaxHeapConsumption() << std::endl;
+ HeapProfiler::ResetMaxHeapConsumption();
+#endif
#ifdef DEBUG_MEMUSAGE
std::cerr << "max heap usage before Doc: " << HeapProfiler::GetMaxHeapConsumption()/(1024*1024) << " Mbytes" << std::endl;
HeapProfiler::ResetMaxHeapConsumption();
#endif
- alphabet_mapper * am = new alphabet_mapper_none();
- static_bitsequence_builder * bmb = new static_bitsequence_builder_brw32(16); // FIXME samplerate?
- Doc = new static_sequence_wvtree_noptrs(endmarkerDocId, numberOfTexts, bmb, am, true);
- delete bmb;
+ /*alphabet_mapper * am = new alphabet_mapper_none();
+ static_bitsequence_builder * bmb = new static_bitsequence_builder_rrr02(32); // FIXME samplerate?
+ Doc = new static_sequence_wvtree_noptrs(endmarkerDocId, numberOfTexts, logNumberOfTexts, bmb, am, true);
+ delete bmb;*/
// delete [] endmarkerDocId; // already deleted in static_sequence_wvtree_noptrs!
+ Doc = new ArrayDoc(endmarkerDocId);
+
#ifdef DEBUG_MEMUSAGE
std::cerr << "max heap usage after Doc: " << HeapProfiler::GetMaxHeapConsumption()/(1024*1024) << " Mbytes" << std::endl;
#endif
projects / SXSI / TextCollection.git / blobdiff