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

//

// STAMP version 1.3

//

// Written By: Shaun Mahony

//

// globals.h

//

// Started: 31st Oct 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

//

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

//Global definitions

#ifndef GLOB_MARK

#define GLOB_MARK

#include <math.h>

const int B=4;

const int AA=20;

const int STR_LEN = 500;

const int LONG_STR=1000;

const double DFLT_NUM_INSTANCES=30.0;

const int MAX_MOTIFS = 100001;

const int MAX_MOTIF_LEN = 200;

const int MAX_MARKOV = 6;

const int maxLen = 25;

const int minLen = 5;

const double SCALE_FACTOR = 0.001;

const int MIN_OVERLAP =3;

const double DFLT_GAP_OPEN = 1.0;

const double DFLT_GAP_EXTEND = 0.5;

const bool DFLT_OVLP_ALIGN= true;

const double LOG_2 = log(2.0);

const double DFLT_MIN_SCORE = -1;

const int minFBPLen=6;

const int NUM_INTEG = 1000; //number of iterations for integration in p_value calculation

const int RAND_MUTI_N=100000;

const int IR_MA_ITER=50;

const int IC_win_len=4;

const double MIN_INFO=0.4;

const double SQRT_2_PI = sqrt(2*M_PI);

const double Euler_Mascheroni = 0.577215664901532860606512090082402431042159335;

const int TOP_MATCH = 5;

#endif