msaWriter.h

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#ifndef MSAWRITER_H
#define MSAWRITER_H
 
#include <vector>
#include <string>
#include <iostream>
#include <set>
#include "common.h"
 
class MSAWriter
{
    protected:
        std::string file;
        std::string fileName;
        std::string format;
        std::vector<Sequence> Sequences;
        int IDspace; // the max space needed to write ID, in order to all sequences be aligned in output file
 
        virtual void writeFile(std::ofstream& file) = 0;
 
        void generateIdForSequences();
 
    public:
       
        MSAWriter(std::vector<Sequence> sequences, std::string file);
 
        void write(); 
};
 
// Derived class for writing in a2m format
class MSAWriter_a2m : public MSAWriter
{
    public:
        using MSAWriter::MSAWriter;
    private:   
        void writeFile(std::ofstream& file) override;
};
 
// Derived class for writing in a3m format
class MSAWriter_a3m : public MSAWriter
{
    public:
        using MSAWriter::MSAWriter;
    private:
        void writeFile(std::ofstream& file) override;
};
 
// Derived class for writing in stockholm format
class MSAWriter_sto : public MSAWriter
{
    public:
        using MSAWriter::MSAWriter;
    private:     
        void writeFile(std::ofstream& file) override;
};
 
// Derived class for writing in fasta format
class MSAWriter_fasta : public MSAWriter
{
    public:
        using MSAWriter::MSAWriter;
    private:
        void writeFile(std::ofstream& file) override;
};
 
// Derived class for writing in clustal format
class MSAWriter_clustal : public MSAWriter
{
    public:
        using MSAWriter::MSAWriter;
    private:
        void writeFile(std::ofstream& file) override;
};
 
// Derived class for writing in aln format
class MSAWriter_aln : public MSAWriter
{
    public:
        using MSAWriter::MSAWriter;
    private:      
        void writeFile(std::ofstream& file) override;
};
 
// Derived class for writing in pfam format
class MSAWriter_pfam : public MSAWriter
{
    public:
        using MSAWriter::MSAWriter;
    private:      
        void writeFile(std::ofstream& file) override;
};
 
#endif