79 lines
3.0 KiB
C++
79 lines
3.0 KiB
C++
#ifndef ANUBIS_SEARCHER_HDR
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#define ANUBIS_SEARCHER_HDR
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#include <boost/shared_ptr.hpp>
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#include "concordia/common/config.hpp"
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#include "concordia/common/utils.hpp"
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#include "concordia/substring_occurence.hpp"
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#include "concordia/concordia_exception.hpp"
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#include "concordia/concordia_config.hpp"
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#include "concordia/anubis_search_result.hpp"
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#include "concordia/tm_matches.hpp"
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#include<vector>
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#include <divsufsort.h>
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/*!
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Class for searching using Anubis algorithm.
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*/
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class AnubisSearcher {
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public:
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explicit AnubisSearcher();
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/*! Destructor.
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*/
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virtual ~AnubisSearcher();
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std::vector<AnubisSearchResult> anubisSearch(
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boost::shared_ptr<ConcordiaConfig> config,
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boost::shared_ptr<std::vector<sauchar_t> > T,
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boost::shared_ptr<std::vector<SUFFIX_MARKER_TYPE> > markers,
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boost::shared_ptr<std::vector<saidx_t> > SA,
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const std::vector<INDEX_CHARACTER_TYPE> & pattern)
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throw(ConcordiaException);
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boost::shared_ptr<TmMatchesMap> getTmMatches(
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boost::shared_ptr<std::vector<sauchar_t> > T,
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boost::shared_ptr<std::vector<SUFFIX_MARKER_TYPE> > markers,
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boost::shared_ptr<std::vector<saidx_t> > SA,
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const std::vector<INDEX_CHARACTER_TYPE> & pattern)
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throw(ConcordiaException);
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std::vector<SubstringOccurence> lcpSearch(
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boost::shared_ptr<std::vector<sauchar_t> > T,
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boost::shared_ptr<std::vector<SUFFIX_MARKER_TYPE> > markers,
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boost::shared_ptr<std::vector<saidx_t> > SA,
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const std::vector<sauchar_t> & pattern,
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SUFFIX_MARKER_TYPE & length) throw(ConcordiaException);
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private:
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void _collectResults(std::vector<SubstringOccurence> & result,
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boost::shared_ptr<std::vector<SUFFIX_MARKER_TYPE> > markers,
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boost::shared_ptr<std::vector<saidx_t> > SA,
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saidx_t left, saidx_t size);
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void _addToMap(boost::shared_ptr<std::vector<saidx_t> > SA,
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boost::shared_ptr<std::vector<SUFFIX_MARKER_TYPE> > markers,
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boost::shared_ptr<TmMatchesMap> tmMatchesMap,
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saidx_t sa_pos,
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SUFFIX_MARKER_TYPE totalPatternLength,
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SUFFIX_MARKER_TYPE matchedFragmentLength,
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SUFFIX_MARKER_TYPE patternOffset);
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bool _getOccurenceFromSA(boost::shared_ptr<std::vector<saidx_t> > SA,
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boost::shared_ptr<std::vector<SUFFIX_MARKER_TYPE> > markers,
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saidx_t sa_pos,
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SubstringOccurence & occurence);
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void _addOccurenceToMap(boost::shared_ptr<TmMatchesMap> tmMatchesMap,
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SubstringOccurence & occurence,
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SUFFIX_MARKER_TYPE totalPatternLength,
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SUFFIX_MARKER_TYPE matchedFragmentLength,
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SUFFIX_MARKER_TYPE patternOffset);
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};
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#endif
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