#include <iostream>
#include <fstream>
#include <vector>
#include <string>

#include "seqin.h"


int seqgroup::input()
{
	std::ifstream filein("seq",std::ios::in);
	char inputbuf[200];
	singleseq tmpseq;
	long endofline=0;
	bool start=true;
	int zda=0;
	int count=0;
	if(filein.fail())
		exit(-1);
	while(!filein.eof())
	{
		filein.clear();
		filein.getline(inputbuf,80);
	
		if(inputbuf[0]==' '||inputbuf[0]==0)
		{
			continue;
		}
		if(inputbuf[0]=='>')
		{
			
			if(start==false)
			{
				tmpseq.sseq[endofline]='\0';
				endofline++;
				tmpseq.length=endofline;
				seqgrp.push_back(tmpseq);
				count++;
				endofline=0;
			
			}
		//	tmpseq.init();
			start=false;
			continue;
  		   for(int i=0;i<80;i++)			
		   {
			   if(inputbuf[i]!='\0')
			   {
				   tmpseq.info[i]=inputbuf[i];
			   }
		   }
		   tmpseq.info[i]='\0';
		}	
		int i=0;
		while(inputbuf[i]!='\0'&&(inputbuf[i]=='A'||inputbuf[i]=='G'||inputbuf[i]=='T'||inputbuf[i]=='C'||inputbuf[i]=='a'||inputbuf[i]=='g'||inputbuf[i]=='t'||inputbuf[i]=='c'||inputbuf[i]=='U'||inputbuf[i]=='u'))
		{
			if(inputbuf[i]!=' ')
			{
				switch(inputbuf[i])
				{	
					case 'A':	tmpseq.sseq[endofline]='0';i++;endofline++;break;
					case 'a':	tmpseq.sseq[endofline]='0';i++;endofline++;break;
					case 'C':	tmpseq.sseq[endofline]='1';i++;endofline++;break;
					case 'c':	tmpseq.sseq[endofline]='1';i++;endofline++;break;
					case 'U':	tmpseq.sseq[endofline]='1';i++;endofline++;break;
					case 'u':	tmpseq.sseq[endofline]='1';i++;endofline++;break;
					case 'G':	tmpseq.sseq[endofline]='2';i++;endofline++;break;
					case 'g':	tmpseq.sseq[endofline]='2';i++;endofline++;break;
					case 'T':	tmpseq.sseq[endofline]='3';i++;endofline++;break;
					case 't':	tmpseq.sseq[endofline]='3';i++;endofline++;break;

				}

			}
			else 
			{
				std::cout<<tmpseq.info<<" "<<i<<std::endl;
			}
		}
	
	}

	return count;
}