/*
 *  test_GenSequence.cc	program for generating random sequences of
 *			amino acids that have lengths and compositions
 *			similar to sequences in real protein databases.
 *  Copyright (C) 2000,2005	Kevin Karplus
 *
 *  This library is free software; you can redistribute it and/or
 *  modify it under the terms of the GNU Lesser General Public
 *  License as published by the Free Software Foundation; 
 *  version 2.1 of the License.
 *
 *  This library is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 *  Lesser General Public License for more details.
 *
 *  See http://www.gnu.org/copyleft/lesser.html for the license details,
 *  or write to the Free Software Foundation, Inc., 59 Temple Place, Suite
 *  330, Boston, MA 02111-1307 USA
 */
 
/* gen_sequence.c
 * Kevin Karplus	7 Nov 2000
 *
 * This program generates random amino acid sequences.
 * It takes one command-line argument, the number of sequences to 
 * generate, and puts them out in FASTA format to standard out.
 *
 * The length of each sequence is taken from a discretized log-normal
 * distribution that was fit to the sequences in RSDB-60 [rsdb].
 *
 * The amino acids of a sequence are generated by an independent,
 * identically distributed process.  The probabilities for that
 * distribution are selected from a mixture of Dirichlet densities.
 * The mixture of Dirichlet densities was also trained on RSDB-60.
 * The particular mixture chosen here is not the best fit, but a
 * compromise between the number of components and the fit.
 *
 * A slightly more sophisticated generator (that accepts parameters for
 * different lognormal distributions and different Dirichlet mixtures
 * for the composition) will be included in a future release of the SAM
 * software suite.
 *
 *
 *[rsdb] Park J, Holm L, Heger A, Chothia C 
 *	 RSDB: representative protein sequence databases have high
 *		information content 
 *	 Bioinformatics 2000 May;16(5):458-64 
 * ftp://ftp.ebi.ac.uk/pub/contrib/jong/RSDB/Ver_1999_8_30/
 */


#include <math.h>
#include <stdio.h>
#include <assert.h>
#include <unistd.h>	/* used for getpid to initialize random */
#include <iostream>
using namespace std;

#include "Filenames/Filenames.h"
#include "Alphabet/Alph.h"	// get ExtAA alphabet
#include "Regularizer/DirichletReg.h"
#include "Utilities/Random.h"

#include "GenSequence.h"

int main(int argc, const char **argv)
{
    if (argc!=3)
    {   cerr << "ERROR: test_gen_sequence requires exactly 2 arguments:\n"
    		<< "\tthe number of random sequences to generate and\n"
		<< "\ta file with the Dirichlet regularizer for the composition.\n";
        return 1;
    }
    int count=atoi(argv[1]);	// number of sequences to generate
    
    Alphabet::set_default(Alph::ExtAA());
    
    gzifstream *reg_in = Filenames::open_input(argv[2]);
    if (!reg_in) return 1;
    Regularizer *r= Regularizer::read_new(*reg_in);
    delete reg_in;

    if (!r || !r->is_a(DirichletReg::classID()))
    {    cerr << "ERROR: no DirichletReg found in " << argv[2] << "\n";
    	return 1;
    }
    
    GenSequence gen(static_cast<const DirichletReg*>(r), 237., 175.);
    
    set_random(getpid());
    
    vector<Base> seq;
    for (int s=0; s<count; s++)
    {   gen.generate(seq);
        int length=seq.size();		// length of seqence 
	cout << ">seq_"<< s<< "\n";	
	for (int p=0; p< length; p++)
	{   cout << seq[p];
	    if (p%50 == 49) cout << "\n";
	}
	cout << "\n";
    }
    
    return 0;
}

// CHANGE LOG:
// Thu Jul 21 10:35:59 PDT 2005 Kevin Karplus
//	New program (similer to old test_gen_sequence.cc)
//	to test GenSequence class