source: tags/cvs_2_svn/GENOM_IMPORT/GASourceFileSwitcher.cpp

#ifndef GASOURCEFILESWITCHER_H
#include "GASourceFileSwitcher.h"
#endif

gellisary::GASourceFileSwitcher::GASourceFileSwitcher(const char * nFile_name)
{
    file_name = nFile_name;
}

int gellisary::GASourceFileSwitcher::make_a_decision()
{
    int file_name_size = file_name.size();

    for(int i = (file_name_size-1); i >= 0; i--)
    {
        if(file_name[i] == '.')
        {
            for(int j = (i+1); j < file_name_size; j++)
            {
                extension += file_name[j];
            }
        }
    }
    if((extension != "embl") && (extension != "gbk") && (extension != "dat") && (extension != "ff") && (extension != "ddbj"))
    {
        flat_file.open(file_name.c_str());
        char tmp_line[128];
        flat_file.getline(tmp_line,128);
        std::string t_string(tmp_line);
        if(t_string.size() > 0)
        {
            if((t_string[0] == 'I') && (t_string[1] == 'D') && (t_string[2] == ' '))
            {
                extension = "embl";
            }
            else if((t_string[0] == 'L') && (t_string[1] == 'O') && (t_string[2] == 'C') && (t_string[3] == 'U') && (t_string[4] == 'S') && (t_string[5] == ' '))
            {
                extension = "gbk";
            }
        }
        flat_file.close();
    }
    if(extension == "embl" || extension == "dat")
    {
        return EMBL;
    }
    else if(extension == "gbk")
    {
        return GENBANK;
    }
    else if((extension == "ff") || (extension == "ddbj"))
    {
        if(containsHeader())
        {
            return DDBJ;
        }
        else
        {
            return DDBJ_WITHOUT_HEADER;
        }
    }
    else
    {
        return UNKNOWN;
    }
}

bool gellisary::GASourceFileSwitcher::containsHeader()
{

    flat_file.open(file_name.c_str());
    char buffer[100];
    while(!flat_file.eof())
    {
        flat_file.getline(buffer,100);
        std::string t_line(buffer);
        std::string::size_type pos_first = t_line.find_first_of(" ");
        if(pos_first != std::string::npos)
        {
            std::string key_string = t_line.substr(0,pos_first);
            if(key_string == "ACCESSION" || key_string == "accession")
            {
                pos_first += 3;
                std::string value_string = t_line.substr(pos_first);
                std::string::size_type pos_second = value_string.find_first_of(" ");
                if(pos_second != std::string::npos)
                {
                    flat_file.close();
                    return false;
                }
                else
                {
                    flat_file.close();
                    return true;
                }
                break;
            }
            else
            {
                continue;
            }
        }
    }
    if(flat_file.is_open())
    {
        flat_file.close();
    }
    return false;
}

gellisary::GASourceFileSwitcher::~GASourceFileSwitcher()
{

}