//////////////////////////////////////////////////////////////////////////////////

//

// STAMP version 1.3

//

// Written By: Shaun Mahony

//

// main.cpp

//

// Started: 5th Dec 2005

//

// Copyright 2007-2015 Shaun Mahony

//

// This file is part of STAMP.

//

// STAMP is free software; you can redistribute it and/or modify

// it under the terms of the GNU General Public License as published by

// the Free Software Foundation; either version 2 of the License, or

// (at your option) any later version.

//

// STAMP 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 General Public License for more details.

//

// You should have received a copy of the GNU General Public License

// along with STAMP; if not, write to the Free Software

// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

//

////////////////////////////////////////////////////////////////////////////////////

#ifndef RANDPSSM_MARK

#define RANDPSSM_MARK

#include <stdio.h>

#include <stdlib.h>

#include <string.h>

#include <math.h>

#include "Motif.h"

#include "globals.h"

#include <gsl/gsl_histogram.h>

class RandPSSMGen{

private:

int numRandomMats;

int numMatrices;

char outFN[STR_LEN];

Motif** matrices;

public:

RandPSSMGen(Motif** baseMats, int n_mat, int n_rand, char* outFilename){matrices = baseMats; numMatrices = n_mat, numRandomMats=n_rand; strcpy(outFN, outFilename);}

//Run generator

void RunGenerator();

//Associate methods

bool Invariant(double* col, int& zeros);

int WhatColumn(int i, int len);

double SumColumn(double* col);

};

#endif