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Commit 1d66e564 authored by Jan Trávníček's avatar Jan Trávníček
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remove BNDM from experimental

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alib2algo_experimental/src/stringology/exact/BackwardNondeterministicDAWGMatching.cpp deleted 100644 → 0
+ 0
− 130
View file @ 2af48bbe
/*
* Author: Radovan Cerveny
*/
#include "BackwardNondeterministicDAWGMatching.hpp"
#include <string/LinearString.h>
#include <alphabet/Symbol.h>
#include <map>
#include <bitset>
#include <measure>
namespace stringology {
namespace exact {
template < size_t BitmaskBitCount >
std::set < unsigned > BackwardNondeterministicDAWGMatching::matchTemplate ( const string::String & subject, const string::String & pattern ) {
return dispatch ( subject.getData ( ), pattern.getData ( ) );
}
template < size_t BitmaskBitCount >
std::set < unsigned > BackwardNondeterministicDAWGMatching::matchTemplate ( const string::LinearString < > & subject, const string::LinearString < > & pattern ) {
std::set < unsigned > occ;
// Setup helper variables
using BitmaskType = std::bitset < BitmaskBitCount >;
bool patternIsLong = BitmaskBitCount < pattern.getContent ( ).size ( );
size_t bitmaskLength = patternIsLong ? BitmaskBitCount : pattern.getContent ( ).size ( );
measurements::start ( "Preprocess", measurements::Type::PREPROCESS );
std::map < DefaultSymbolType, BitmaskType > symbolBitmaskLookupTable;
// Initialize the bitmasks with zeros for each symbol in the alphabet
for ( const auto & symbol : pattern.getAlphabet ( ) )
symbolBitmaskLookupTable[symbol] = BitmaskType ( 0 );
// Mark the position in the bitmask for each symbol in the pattern
for ( size_t i = 0; i < bitmaskLength; i++ )
symbolBitmaskLookupTable[pattern.getContent ( ).at ( i )].set ( bitmaskLength - i - 1 );
measurements::end ( );
measurements::start ( "Algorithm", measurements::Type::ALGORITHM );
size_t posInSubject = 0;
BitmaskType currentBitmask;
while ( posInSubject <= subject.getContent ( ).size ( ) - pattern.getContent ( ).size ( ) ) {
size_t posInPattern = bitmaskLength;
size_t lastPosOfFactor = bitmaskLength;
// Set the bitmask to all ones
currentBitmask.set ( );
while ( posInPattern > 0 && currentBitmask.any ( ) ) {
currentBitmask &= symbolBitmaskLookupTable[subject.getContent ( ).at ( posInSubject + posInPattern - 1 )];
posInPattern--;
// Test whether the most significant bit is set
if ( currentBitmask.test ( bitmaskLength - 1 ) ) {
if ( posInPattern > 0 ) {
lastPosOfFactor = posInPattern;
} else {
if ( !patternIsLong ) {
// Yay, there is match!!!
occ.insert ( posInSubject );
} else {
// if the pattern is longer then BitmaskBitCount characters switch to brute force check
size_t k = bitmaskLength;
while ( k < pattern.getContent ( ).size ( ) && pattern.getContent ( ).at ( k ) == subject.getContent ( ).at ( posInSubject + k ) ) k++;
if ( k == pattern.getContent ( ).size ( ) )
// Yay, there is match!!!
occ.insert ( posInSubject );
}
}
}
currentBitmask <<= 1;
}
posInSubject += lastPosOfFactor;
}
measurements::end ( );
return occ;
}
std::set < unsigned > BackwardNondeterministicDAWGMatching::match ( const string::String & subject, const string::String & pattern ) {
return BackwardNondeterministicDAWGMatching::match32 ( subject, pattern );
}
std::set < unsigned > BackwardNondeterministicDAWGMatching::match ( const string::LinearString < > & subject, const string::LinearString < > & pattern ) {
return BackwardNondeterministicDAWGMatching::match32 ( subject, pattern );
}
std::set < unsigned > BackwardNondeterministicDAWGMatching::match32 ( const string::String & subject, const string::String & pattern ) {
return BackwardNondeterministicDAWGMatching::matchTemplate < 32 > ( subject, pattern );
}
std::set < unsigned > BackwardNondeterministicDAWGMatching::match32 ( const string::LinearString < > & subject, const string::LinearString < > & pattern ) {
return BackwardNondeterministicDAWGMatching::matchTemplate < 32 > ( subject, pattern );
}
std::set < unsigned > BackwardNondeterministicDAWGMatching::match64 ( const string::String & subject, const string::String & pattern ) {
return BackwardNondeterministicDAWGMatching::matchTemplate < 64 > ( subject, pattern );
}
std::set < unsigned > BackwardNondeterministicDAWGMatching::match64 ( const string::LinearString < > & subject, const string::LinearString < > & pattern ) {
return BackwardNondeterministicDAWGMatching::matchTemplate < 64 > ( subject, pattern );
}
std::set < unsigned > BackwardNondeterministicDAWGMatching::match128 ( const string::String & subject, const string::String & pattern ) {
return BackwardNondeterministicDAWGMatching::matchTemplate < 128 > ( subject, pattern );
}
std::set < unsigned > BackwardNondeterministicDAWGMatching::match128 ( const string::LinearString < > & subject, const string::LinearString < > & pattern ) {
return BackwardNondeterministicDAWGMatching::matchTemplate < 128 > ( subject, pattern );
}
auto BackwardNondeterministicDAWGMatchingLinearStringLinearString = BackwardNondeterministicDAWGMatching::RegistratorWrapper < std::set < unsigned >, string::LinearString < >, string::LinearString < > > ( BackwardNondeterministicDAWGMatching::match );
} /* namespace exact */
} /* namespace stringology */
alib2algo_experimental/src/stringology/exact/BackwardNondeterministicDAWGMatching.hpp deleted 100644 → 0
+ 0
− 53
View file @ 2af48bbe
/*
* Author: Radovan Cerveny
*/
#ifndef STRINGOLOGY_BACKWARD_NONDETERMINISTIC_DAWG_MATCHING_HPP__
#define STRINGOLOGY_BACKWARD_NONDETERMINISTIC_DAWG_MATCHING_HPP__
#include <string/String.h>
#include <string/StringFeatures.h>
#include <core/multipleDispatch.hpp>
#include <set>
namespace stringology {
namespace exact {
/**
* Implementation of Backward Nondeterministic DAWG Matching using bit parallelism with 32/64/128bit bitmask and brute force switch for longer patterns.
*/
class BackwardNondeterministicDAWGMatching : public std::DoubleDispatch < BackwardNondeterministicDAWGMatching, std::set < unsigned >, const string::StringBase &, const string::StringBase & > {
private:
/**
* Search for pattern in linear string.
* @return set set of occurences
*/
template <size_t BitmaskBitCount>
static std::set < unsigned > matchTemplate ( const string::String & subject, const string::String & pattern );
template <size_t BitmaskBitCount >
static std::set < unsigned > matchTemplate ( const string::LinearString < > & subject, const string::LinearString < > & pattern );
public:
// Defaults to 32 bits
static std::set < unsigned > match ( const string::String & subject, const string::String & pattern );
static std::set < unsigned > match ( const string::LinearString < > & subject, const string::LinearString < > & pattern );
static std::set < unsigned > match32 ( const string::String & subject, const string::String & pattern );
static std::set < unsigned > match32 ( const string::LinearString < > & subject, const string::LinearString < > & pattern );
static std::set < unsigned > match64 ( const string::String & subject, const string::String & pattern );
static std::set < unsigned > match64 ( const string::LinearString < > & subject, const string::LinearString < > & pattern );
static std::set < unsigned > match128 ( const string::String & subject, const string::String & pattern );
static std::set < unsigned > match128 ( const string::LinearString < > & subject, const string::LinearString < > & pattern );
};
} /* namespace exact */
} /* namespace stringology */
#endif /* STRINGOLOGY_BACKWARD_NONDETERMINISTIC_DAWG_MATCHING_HPP__ */
alib2algo_experimental/test-src/stringology/exact/BackwardNondeterministicDAWGMatchingTest.cpp deleted 100644 → 0
+ 0
− 55
View file @ 2af48bbe
#include "BackwardNondeterministicDAWGMatchingTest.h"
#include "string/String.h"
#include "stringology/exact/BackwardNondeterministicDAWGMatching.hpp"
#include "stringology/exact/ExactFactorMatch.h"
#include "string/generate/RandomStringFactory.h"
#include "string/generate/RandomSubstringFactory.h"
CPPUNIT_TEST_SUITE_NAMED_REGISTRATION ( BackwardNondeterministicDAWGMatchingTest, "stringology" );
CPPUNIT_TEST_SUITE_REGISTRATION ( BackwardNondeterministicDAWGMatchingTest );
void BackwardNondeterministicDAWGMatchingTest::setUp ( ) {
}
void BackwardNondeterministicDAWGMatchingTest::tearDown ( ) {
}
void BackwardNondeterministicDAWGMatchingTest::testBNDM ( ) {
std::vector<std::string> subjects;
std::vector<std::string> patterns;
std::vector<std::set<unsigned>> expectedOccs;
subjects.push_back("a"); patterns.push_back("a"); expectedOccs.push_back({0});
subjects.push_back("a"); patterns.push_back("b"); expectedOccs.push_back({});
subjects.push_back("alfalfalfa"); patterns.push_back("alfalfalfa"); expectedOccs.push_back({0});
subjects.push_back("alfalfalfa"); patterns.push_back("blfalfalfa"); expectedOccs.push_back({});
subjects.push_back("alfalfalfa"); patterns.push_back("alfalfalfb"); expectedOccs.push_back({});
subjects.push_back("alfalfalfaalfalfalfaalfalfalfaalfalfalfaalfalfalfaalfalfalfaalfa"); patterns.push_back("alfalfalfaalfalfalfaalfalfalfaalfalfalfaalfalfalfaalfalfalfaalfa"); expectedOccs.push_back({0});
subjects.push_back("alfalfalfaalfalfalfaabfalfalfaalfalfalfaalfalfalfaalfalfalfaalfa"); patterns.push_back("alfalfalfaalfalfalfaalfalfalfaalfalfalfaalfalfalfaalfalfalfaalfa"); expectedOccs.push_back({});
subjects.push_back("alfalfalfaalfalfalfaalfalfalfaalfalfalfaalfalfalfaalfalfalfaalfaa"); patterns.push_back("alfalfalfaalfalfalfaalfalfalfaalfalfalfaalfalfalfaalfalfalfaalfaa"); expectedOccs.push_back({0});
subjects.push_back("atggccttgcc"); patterns.push_back("gcc"); expectedOccs.push_back({3,8});
subjects.push_back("aaaaaaaaaa"); patterns.push_back("a"); expectedOccs.push_back({0,1,2,3,4,5,6,7,8,9});
for(size_t i = 0; i < subjects.size(); ++i) {
string::String subject = string::stringFrom ( subjects[i] );
string::String pattern = string::stringFrom ( patterns[i] );
std::set < unsigned > res = stringology::exact::BackwardNondeterministicDAWGMatching::match ( subject, pattern );
CPPUNIT_ASSERT ( res == expectedOccs[i] );
res = stringology::exact::BackwardNondeterministicDAWGMatching::match64 ( subject, pattern );
CPPUNIT_ASSERT ( res == expectedOccs[i] );
res = stringology::exact::BackwardNondeterministicDAWGMatching::match128 ( subject, pattern );
CPPUNIT_ASSERT ( res == expectedOccs[i] );
std::cout << subjects[i] << ' ' << patterns[i] << ' ' << res << std::endl;
}
auto longSubject = string::generate::RandomStringFactory::generateLinearString (64 * 64 * 64, 512, false, true);
auto longPattern = string::generate::RandomSubstringFactory::generateSubstring(64 * 32 * 32, longSubject );
std::set < unsigned > res = stringology::exact::BackwardNondeterministicDAWGMatching::match ( longSubject, longPattern );
std::set < unsigned > resRef = stringology::exact::ExactFactorMatch::match ( longSubject, longPattern );
std::cout << "long: " << res << std::endl;
CPPUNIT_ASSERT ( res == resRef);
}
alib2algo_experimental/test-src/stringology/exact/BackwardNondeterministicDAWGMatchingTest.h deleted 100644 → 0
+ 0
− 18
View file @ 2af48bbe
#ifndef BACKWARD_NONDETERMINISTIC_DAWG_MATCHING_TEST_H_
#define BACKWARD_NONDETERMINISTIC_DAWG_MATCHING_TEST_H_
#include <cppunit/extensions/HelperMacros.h>
class BackwardNondeterministicDAWGMatchingTest : public CppUnit::TestFixture {
CPPUNIT_TEST_SUITE ( BackwardNondeterministicDAWGMatchingTest );
CPPUNIT_TEST ( testBNDM );
CPPUNIT_TEST_SUITE_END ( );
public:
void setUp ( );
void tearDown ( );
void testBNDM ( );
};
#endif // BACKWARD_NONDETERMINISTIC_DAWG_MATCHING_TEST_H_
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