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/*
* File: ExtractFeatures.h
*
* Author: Carlos Olivares
*
* This source code is distributed as part of the IGoR software.
* IGoR (Inference and Generation of Repertoires) is a versatile software to analyze and model immune receptors
* generation, selection, mutation and all other processes.
* Copyright (C) 2017- Quentin Marcou, 2019 - Carlos Olivares
*
* This program 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.
*
* This program 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 this program. If not, see <https://www.gnu.org/licenses/>.
*
*/
#ifndef EXTRACTFEATURES_H
#define EXTRACTFEATURES_H
#include <unordered_map>
#include <vector>
#include "CDR3SeqData.h"
#include "Aligner.h"
#include <sstream>
#include "Utils.h"
using namespace std;
/**
* \class ExtractFeatures ExtractFeatures.h
* \brief Class to extract sequences features (e.g. CDR3) of sequences using alignment and V, J anchors information.
* \author C. Olivares
*/
class ExtractFeatures {
public:
ExtractFeatures();
ExtractFeatures(const ExtractFeatures& orig);
virtual ~ExtractFeatures();
unordered_map<string, string> UMap_v_genomic;
unordered_map<string, string> UMap_j_genomic;
unordered_map<string, size_t> UMap_v_CDR3_anchors;
unordered_map<string, size_t> UMap_j_CDR3_anchors;
// vector<pair<const int, const string>> *p_indexed_seqlist;
unordered_map<int,pair<string,unordered_map<Gene_class,vector<Alignment_data>>>> *p_sorted_alignments;
void load_VJgenomicTemplates(vector<pair<string,string>> v_genomic, vector<pair<string,string>> j_genomic);
void load_VJanchors(string flnV_CDR3_anchors, string flnJ_CDR3_anchors);
void load_VJanchors(unordered_map<string, size_t> flnV_CDR3_anchors, unordered_map<string, size_t> flnJ_CDR3_anchors);
void print_VgenomicTemplates();
void print_JgenomicTemplates();
// void set_indexed_seqlist(vector<pair<const int, const string>>* pointer);
void set_sorted_alignments(unordered_map<int,pair<string,unordered_map<Gene_class,vector<Alignment_data>>>>* pointer);
CDR3SeqData extractCDR3(int seq_index);
int getVAnchor4Seq(string seq_str, Alignment_data v_alig);
int getJAnchor4Seq(string seq_str, Alignment_data j_alig);
string generateCDR3_csv_line(CDR3SeqData cdr3InputSeq);
private:
};
#endif /* EXTRACTFEATURES_H */
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