#include <fstream.h>
#include <iomanip.h>
#include <stdlib.h>
#include <math.h>
#include <ctype.h>
#include "arrays.h"
#include "maths.h"

#define PROGRAM_NAME "PASTE"
#define VERSION "1.0"
#define BUILD_DATE "7 October 96"

imatrix read_data(fstream& f,int& N,int& P,int& G);


main(int argc, char *argv[])   //argc is the number of command lines args (0 is progname)
{
	int NN,PP,GG,n,p,g;
	int COL=0,GROUP=0,k,l,i;
	NN=PP=GG=0;

	cerr << PROGRAM_NAME << " version " << VERSION << " built on " << BUILD_DATE << endl;
	if(argc < 3)
	{
		cerr << "\n----------------------------------------------------------\n";
		cerr << "Use this program by giving the command "<< endl;
		cerr << argv[0] << " <datafile_1> <datafile_2> ... <datafile_n>" << endl;
		cerr << "This program will paste these data files together into\n";
		cerr << "one large GELSTATS datafile\n";
		cerr << "See the documentation about how groups are numbered.\n";
		cerr << "\n----------------------------------------------------------\n";
		exit( 0);
	}



	fstream fin;
	//Read the files from the command line
	for(i=1;i<argc;i++)
	{
		//cout << "The argument number "<<i<<" is "<<argv[i] <<"\n";
		fin.open(argv[i],ios::in);

		if( fin.fail())
		{
			cout << "Sorry: can't seem to open file " << argv[i] << endl;;
			exit(11);
		}
		fin >> n >> p >>g;
		PP+=p;
		if(NN==0) NN=n;
		else
		{
			if (NN != n)
			{
				cerr << "Sorry: not all your data sets have the same number of bands\n";
				cerr << "File " << argv[i] << " has " << n << " bands while previous files\n";
				cerr << "had "<<NN<< " bands."<< endl;
				exit(12);
			}
		}
		GG+=g;
		fin.close();
		cerr << "File " << argv[i] << " has " << n <<" bands " << p << " lanes " << " and " << g << " groups\n";
	}

	//Get the dimensions of the data from them
	//Allocate a big enough data array
	imatrix bigdata(NN+1,PP),tempdata;
	//Loop to read each file, validate it, and then
	fstream gg;
	for(i=1;i<argc;i++)
	{

		fin.open(argv[i],ios::in);

		if( fin.fail())
		{
			cout << "Sorry: can't seem to open file " << argv[i] << endl;;
			exit(11);
		}
		tempdata=read_data(fin,n,p,g);
		//copy the columns starting in column COL , adding GROUP
		//to each group number
		for(int j=0;j<p;j++)
		{
			l=COL+j;
			bigdata[0][l] = GROUP+tempdata[0][j];
			for(k=1;k<=n;k++) bigdata[k][l]=tempdata[k][j];
		}
		GROUP += g;
		COL += p;
		fin.close();
	}
	//put its data in to the big array

	//write the big array to standard out
	cout << NN <<" " << PP << " " << GG << endl;
	l=NN+1;
	for(i=0;i<l;i++)
	{
		for(int j=0;j<PP;j++) cout << bigdata[i][j] << " ";
		cout << endl;
	}
	return 0;
}




imatrix read_data(fstream& f,int& N,int& P,int& G)
{
	int i,j;
	f >> N >> P >> G;
	imatrix data(N+1,P);
	for(i=0;i<N+1;i++)
	{
		for(j=0;j<P;j++)
		{
			f >> data[i][j];
			if(f.eof())
			{
				cerr << "Problem in read_data(): can't seem to read enough data" << endl;
				cerr << "EOF occurred before entire data array was read." << endl;
				exit(37);
			}
		}
	}
	/*
	cout << "Here's the data I've just read\n";
	cout << "\n\n-----------------------------------------------\n";
	for(i=0;i<N+1;i++)
	{
		for(j=0;j<P;j++)
		{
			cout << setw(2) << data[i][j] ;
		}
		cout << endl;
	}
	cout << "\n\n-----------------------------------------------\n";
	cout << "Number of bands = " << N << "\nNumber of lanes = " << P << "\nNumber of groups = " << G << endl;
	cout << "\n\n";
	 */
//Check to make sure the main array has only 0's and 1's
	for(i=1;i<N+1;i++)
	{
		for(j=0;j<P;j++)
		{
			if( data[i][j] <0 || data[i][j] > 1)
			{
				cerr << "Problem: your data file contains values other that 0 and 1\n";
				cerr << "For example, data["<< i << "][" << j << "] = " << data[i][j] << endl;
				cerr << "Check this.\n";
				exit(7);
			}
		}
	}
/// Check to make sure labels for groups in first row of data array are okay.
	for(j=0;j<(P);j++)
	{
		if(data[0][j] <0 || data[0][j] >(G)-1)
		{
			cerr << "Problem: your data file mentions more groups than expected\n";
			cerr << "With G = " << G << " only the values 0,...," << (G-1) << " should appear in\n";
			cerr << "the first row of data. But I found data[0][" << j << "]=" << data[0][j] << endl;
			cerr << "You'd better fix it before running the program on this data\n";
			exit(7);
		}
	}
	return data;
}