multimerHandler.h

Go to the documentation of this file.

 
#ifndef MULTIMER_HANDLER
#define MULTIMER_HANDLER
 
#include <iostream>
#include <vector>
#include <tuple>
 
class MultimerHandler {
public:
    MultimerHandler(std::string _stoichiom);
 
    std::string chainIndexToStoichiomLetter(int index);
 
    bool getHeteromerMSAs(const std::vector<std::vector<int>>& vectors);
 
    // The letters must appear in the correct alphabetical order (e.g., A before B, B before C, etc.).
    // If a letter appears, all preceding letters in the alphabet must also appear.
    // Each letter is followed by a number greater than 0.
    bool isHeteromerFormat();
 
 
    bool isHomomerFormat();
 
    std::vector<std::vector<int>> getHomomerIndividualMSA(const std::vector<std::vector<int>>& sequences2num) ;
 
    std::vector<std::vector<std::vector<int>>> getHetoromerMSAs(const std::vector<std::vector<int>>& sequences2num, const std::vector<int>& chainLengths);
 
private:
    //stoichiometry
    std::string stoichiom;
 
    // Number of repeatition of each chain in the multimer
    std::vector<int> numbers;
 
    // Number of distinct chains for a heteromer
    int chainsCount;
 
    // Indexes of start and end of each chain
    std::vector<int> chainIntervals;
 
    std::vector<int> getSequenceSegment(const std::vector<int>& row, int chainIndex, int repeat=1) const;
 
    std::vector<int> checkRepeatedChainAndReturnOneSegment(const std::vector<int>& row, int rowIndex, int chainIndex);
    
    bool includesInPairedMSA(const std::vector<int>& row);
 
    int checkRowCorrespondsOnlyToOneChainAndReturnChainIndex(const std::vector<int>& row, int row_index);
 
    std::vector<int> checkMSAFormatAndReturnRowIndexIntervalsCorrespondingToChains(const std::vector<int>& chainIndexOfRows);
};
 
#endif // MULTIMER_HANDLER