msaReader.h

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#ifndef MSAREADER_H
#define MSAREADER_H
 
#include <vector>
#include <string>
#include <iostream>
#include "common.h"
 
class MSAReader
{
protected:
    std::string file;
    Alphabet alphabet;
    bool checkValidation;
    bool omitGaps;
    std::vector<Sequence> Sequences; // the sequences read from the file
 
    int isUnaligned();
 
    std::string containsInvalidLetters(Alphabet alphabet);
 
    void makeUppercase();
 
    void validateSequences(Alphabet alphabet);
 
    virtual void readFile(std::ifstream& file)=0;  //??
 
public:
    MSAReader(std::string _file, Alphabet _alphabet, bool _checkValidation, bool _omitGaps = false);
 
    std::vector<Sequence> read();
};
 
// Derived class for reading a2m format
class MSAReader_a2m : public MSAReader
{
public:
    using MSAReader::MSAReader;
private:
    void readFile(std::ifstream& file) override;
};
 
// Derived class for reading a3m format
class MSAReader_a3m : public MSAReader
{
public:
    using MSAReader::MSAReader;
private:
    void readFile(std::ifstream& file) override;
};
 
// Derived class for reading stockholm format
class MSAReader_sto : public MSAReader
{
public:
    using MSAReader::MSAReader;
private:
    void readFile(std::ifstream& file) override;
};
 
// Derived class for reading fasta format
class MSAReader_fasta : public MSAReader
{
public:
    using MSAReader::MSAReader;
private:
    void readFile(std::ifstream& file) override;
};
 
// Derived class for reading clustal format
class MSAReader_clustal : public MSAReader
{
public:
    using MSAReader::MSAReader;
private:
    void readFile(std::ifstream& file) override;
};
 
// Derived class for reading aln format
class MSAReader_aln : public MSAReader
{
public:
    using MSAReader::MSAReader;
private:
    void readFile(std::ifstream& file) override;
};
 
// Derived class for reading pfam format
class MSAReader_pfam : public MSAReader
{
public:
    using MSAReader::MSAReader;
private:
    void readFile(std::ifstream& file) override;
};
 
#endif