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TargetMappings.h
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TargetMappings.h
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/*
* MinMaxMirnaGene - A program for computing optimal miRNA-gene covers.
* Copyright (C) 2016 Daniel Stöckel <dstoeckel@bioinf.uni-sb.de>
*
* MinMaxMirnaGene is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* MinMaxMirnaGene is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with MinMaxMirnaGene. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef MINMAX_TARGET_MAPPINGS_H
#define MINMAX_TARGET_MAPPINGS_H
#include <string>
#include <unordered_map>
#include <vector>
class TargetMapping
{
public:
TargetMapping(size_t m, size_t g) : mirna_(m), gene_(g) {}
size_t mirna() const { return mirna_; }
size_t gene() const { return gene_; }
bool operator==(const TargetMapping& t)
{
return mirna_ == t.mirna_ && gene_ == t.gene_;
}
private:
size_t mirna_;
size_t gene_;
};
class TargetMappings
{
public:
using iterator = std::vector<TargetMapping>::iterator;
using const_iterator = std::vector<TargetMapping>::const_iterator;
void add(const std::string& mirna, const std::string& gene);
iterator begin() { return mappings_.begin(); }
iterator end() { return mappings_.end(); }
const_iterator begin() const { return mappings_.begin(); }
const_iterator end() const { return mappings_.end(); }
const_iterator cbegin() const { return mappings_.begin(); }
const_iterator cend() { return mappings_.end(); }
size_t numGenes() const;
size_t numMirnas() const;
size_t numMappings() const;
const std::string& mirna(size_t i) { return mirna_names_[i]; }
const std::string& gene(size_t i) { return gene_names_[i]; }
void finalize();
private:
std::vector<std::string> gene_names_;
std::vector<std::string> mirna_names_;
std::unordered_map<std::string, int> gene_to_id_;
std::unordered_map<std::string, int> mirna_to_id_;
std::vector<TargetMapping> mappings_;
size_t findOrCreate_(const std::string& s,
std::unordered_map<std::string, int>& m,
std::vector<std::string>& v) const;
};
#endif // MINMAX_TARGET_MAPPINGS_H