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/************************************************************************** |
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* This code is part of the supporting infrastructure for ATA Mapper. |
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* Copyright (C) 2002,2003,2004 Applera Corporation. All rights reserved. |
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* Author: Nathan Edwards |
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* |
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* This program is free software; you can redistribute it and/or modify |
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* it under the terms of the GNU General Public License as published by |
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* the Free Software Foundation; either version 2 of the License, or |
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* (at your option) any later version. |
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* |
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* This program is distributed in the hope that it will be useful, |
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* but WITHOUT ANY WARRANTY; without even the implied warranty of |
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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* GNU General Public License for more details. |
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* |
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* You should have received (LICENSE.txt) a copy of the GNU General Public |
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* License along with this program; if not, write to the Free Software |
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* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA |
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*************************************************************************/ |
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#ifndef _IBPEP_EXACT_HALVES_H |
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#define _IBPEP_EXACT_HALVES_H |
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|
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#include <iostream> |
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#include <utility> |
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#include <vector> |
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#include <map> |
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#include "char_io.h" |
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#include "keyword_tree.h" |
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#include "types.h" |
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|
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#if !defined(NO_STD_NAMESPACE) |
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using namespace std; |
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#endif |
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|
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class exact_halves : public PatternMatch { |
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private: |
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PatternMatch *pm_; |
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unsigned long int num_patterns_; |
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unsigned int k_; |
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unsigned char eos_; |
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bool _wc; |
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bool _textn; |
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bool _indels; |
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bool _dna_mut; |
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long unsigned int _mpl; |
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std::vector<FILE_POSITION_TYPE> lasthit_; |
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std::vector<tinylist<pattern_list_element>::const_iterator> plit_; |
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std::vector<std::string> pattern_halves_; |
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public: |
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exact_halves(PatternMatch *pm, |
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unsigned int k=0, unsigned char eos='\n', |
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bool wc=false, bool tn=false, bool indels=true, bool dna_mut=false); |
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exact_halves(PatternMatch *pm); |
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~exact_halves(); |
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long unsigned int add_pattern(std::string const & pat, unsigned long id=0, |
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int esb=0, int eeb=0); |
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bool find_patterns(CharacterProducer & cp, |
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pattern_hit_vector & kas, |
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long unsigned minka=1); |
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void init(CharacterProducer & cp); |
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void reset(); |
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unsigned int mismatches() const; |
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void mismatches(unsigned int k); |
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bool wildcards() const; |
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void wildcards(bool wc); |
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bool wildcard_text_N() const; |
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void wildcard_text_N(bool tn); |
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bool indels() const; |
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void indels(bool id); |
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bool dna_mut() const; |
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void dna_mut(bool dm); |
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unsigned char eos_char() const; |
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void eos_char(unsigned char c); |
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}; |
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|
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#endif |
