KnuthMorrisPratt.h

/*
 * KnuthMorrisPratt.h
 *
 *  Created on: 5. 11. 2014
 *      Author: Jan Travnicek
 */

#ifndef _ARBOLOGY_KNUTH_MORRIS_PRATT_H_
#define _ARBOLOGY_KNUTH_MORRIS_PRATT_H_

#include <measure>

#include <alib/set>
#include <alib/vector>

#include <tree/properties/BorderArrayNaive.h>
#include <tree/properties/SubtreeJumpTable.h>
#include <tree/properties/ExactSubtreeRepeatsNaive.h>
#include <tree/exact/ForwardOccurrenceTest.h>

#include <tree/ranked/PrefixRankedBarTree.h>
#include <tree/ranked/PrefixRankedBarPattern.h>
#include <tree/ranked/PrefixRankedBarNonlinearPattern.h>
#include <tree/ranked/PrefixRankedTree.h>
#include <tree/ranked/PrefixRankedPattern.h>
#include <tree/ranked/PrefixRankedNonlinearPattern.h>

namespace arbology {

namespace exact {

/**
 * Implementation of BMH for MI(E+\eps)-EVY course 2014
 * To get rid of zeros in BCS table we ignore last haystack character
 */
class KnuthMorrisPratt {
public:
	/**
	 * Search for pattern in linear string.
	 * @return set set of occurences
	 */
	template < class SymbolType, class RankType >
	static ext::set < unsigned > match ( const tree::PrefixRankedBarTree < SymbolType, RankType > & subject, const tree::PrefixRankedBarTree < SymbolType, RankType > & pattern );
	template < class SymbolType, class RankType >
	static ext::set < unsigned > match ( const tree::PrefixRankedBarTree < SymbolType, RankType > & subject, const tree::PrefixRankedBarPattern < SymbolType, RankType > & pattern );
	template < class SymbolType, class RankType >
	static ext::set < unsigned > match ( const tree::PrefixRankedBarTree < SymbolType, RankType > & subject, const tree::PrefixRankedBarNonlinearPattern < SymbolType, RankType > & pattern );

	template < class SymbolType, class RankType >
	static ext::set < unsigned > match ( const tree::PrefixRankedTree < SymbolType, RankType > & subject, const tree::PrefixRankedTree < SymbolType, RankType > & pattern );
	template < class SymbolType, class RankType >
	static ext::set < unsigned > match ( const tree::PrefixRankedTree < SymbolType, RankType > & subject, const tree::PrefixRankedPattern < SymbolType, RankType > & pattern );
	template < class SymbolType, class RankType >
	static ext::set < unsigned > match ( const tree::PrefixRankedTree < SymbolType, RankType > & subject, const tree::PrefixRankedNonlinearPattern < SymbolType, RankType > & pattern );

};

template < class SymbolType, class RankType >
ext::set < unsigned > KnuthMorrisPratt::match ( const tree::PrefixRankedBarTree < SymbolType, RankType > & subject, const tree::PrefixRankedBarTree < SymbolType, RankType > & pattern ) {
	return match ( subject, tree::PrefixRankedBarPattern < SymbolType, RankType > ( pattern ) );
}

template < class SymbolType, class RankType >
ext::set < unsigned > KnuthMorrisPratt::match ( const tree::PrefixRankedBarTree < SymbolType, RankType > & subject, const tree::PrefixRankedBarPattern < SymbolType, RankType > & pattern ) {
	ext::set < unsigned > occ;
	ext::vector < size_t > ba = tree::properties::BorderArrayNaive::ba ( pattern );

	//measurements::start("Algorithm", measurements::Type::MAIN);

	ext::vector < int > subjectSubtreeJumpTable = tree::properties::SubtreeJumpTable::compute ( subject );

	 // index to the subject
	unsigned i = 0;

	 // main loop of the algorithm over all possible indexes where the pattern can start
	while ( i + pattern.getContent ( ).size ( ) <= subject.getContent ( ).size ( ) ) {
		 // index to the pattern
		unsigned j = tree::exact::ForwardOccurrenceTest::occurrence ( subject, subjectSubtreeJumpTable, pattern, i );

		 // match was found
		if ( j >= pattern.getContent ( ).size ( ) ) occ.insert ( i );

		 // shift heuristics
		i += j - ba[j];
	}

	//measurements::end();

	return occ;
}

template < class SymbolType, class RankType >
ext::set < unsigned > KnuthMorrisPratt::match ( const tree::PrefixRankedBarTree < SymbolType, RankType > & subject, const tree::PrefixRankedBarNonlinearPattern < SymbolType, RankType > & pattern ) {
	ext::set < unsigned > occ;
	ext::vector < size_t > ba = tree::properties::BorderArrayNaive::ba ( pattern );

	//measurements::start("Algorithm", measurements::Type::MAIN);

	ext::vector < int > subjectSubtreeJumpTable = tree::properties::SubtreeJumpTable::compute ( subject );
	tree::PrefixRankedBarTree < unsigned, RankType > repeats = tree::properties::ExactSubtreeRepeatsNaive::repeats ( subject );

	 // index to the subject
	unsigned i = 0;

	 // main loop of the algorithm over all possible indexes where the pattern can start
	while ( i + pattern.getContent ( ).size ( ) <= subject.getContent ( ).size ( ) ) {
		 // index to the pattern
		unsigned j = tree::exact::ForwardOccurrenceTest::occurrence ( subject, subjectSubtreeJumpTable, repeats, pattern, i );

		 // match was found
		if ( j >= pattern.getContent ( ).size ( ) ) occ.insert ( i );

		 // shift heuristics
		i += j - ba[j];
	}

	//measurements::end();

	return occ;
}

template < class SymbolType, class RankType >
ext::set < unsigned > KnuthMorrisPratt::match ( const tree::PrefixRankedTree < SymbolType, RankType > & subject, const tree::PrefixRankedTree < SymbolType, RankType > & pattern ) {
	return match ( subject, tree::PrefixRankedPattern < SymbolType, RankType > ( pattern ) );
}

template < class SymbolType, class RankType >
ext::set < unsigned > KnuthMorrisPratt::match ( const tree::PrefixRankedTree < SymbolType, RankType > & subject, const tree::PrefixRankedPattern < SymbolType, RankType > & pattern ) {
	ext::set < unsigned > occ;
	ext::vector < size_t > ba = tree::properties::BorderArrayNaive::ba ( pattern );

	//measurements::start("Algorithm", measurements::Type::MAIN);

	ext::vector < int > subjectSubtreeJumpTable = tree::properties::SubtreeJumpTable::compute ( subject );

	 // index to the subject
	unsigned i = 0;

	 // main loop of the algorithm over all possible indexes where the pattern can start
	while ( i + pattern.getContent ( ).size ( ) <= subject.getContent ( ).size ( ) ) {
		 // index to the pattern
		unsigned j = tree::exact::ForwardOccurrenceTest::occurrence ( subject, subjectSubtreeJumpTable, pattern, i );

		 // match was found
		if ( j >= pattern.getContent ( ).size ( ) ) occ.insert ( i );

		 // shift heristics
		i += j - ba[j];
	}

	//measurements::end();

	return occ;
}

template < class SymbolType, class RankType >
ext::set < unsigned > KnuthMorrisPratt::match ( const tree::PrefixRankedTree < SymbolType, RankType > & subject, const tree::PrefixRankedNonlinearPattern < SymbolType, RankType > & pattern ) {
	ext::set < unsigned > occ;
	ext::vector < size_t > ba = tree::properties::BorderArrayNaive::ba ( pattern );

	//measurements::start("Algorithm", measurements::Type::MAIN);

	ext::vector < int > subjectSubtreeJumpTable = tree::properties::SubtreeJumpTable::compute ( subject );
	tree::PrefixRankedTree < unsigned, RankType > repeats = tree::properties::ExactSubtreeRepeatsNaive::repeats ( subject );

	 // index to the subject
	unsigned i = 0;

	 // main loop of the algorithm over all possible indexes where the pattern can start
	while ( i + pattern.getContent ( ).size ( ) <= subject.getContent ( ).size ( ) ) {
		 // index to the pattern
		unsigned j = tree::exact::ForwardOccurrenceTest::occurrence ( subject, subjectSubtreeJumpTable, repeats, pattern, i );

		 // match was found
		if ( j >= pattern.getContent ( ).size ( ) ) occ.insert ( i );

		 // shift heristics
		i += j - ba[j];
	}

	//measurements::end();

	return occ;
}

} /* namespace exact */

} /* namespace arbology */

#endif /* _ARBOLOGY_KNUTH_MORRIS_PRATT_H_ */