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

//

// STAMP version 1.3

//

// Written By: Shaun Mahony

//

// Motif.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

//

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

#ifndef Motif_MARK

#define Motif_MARK

#include "globals.h"

#include <stdio.h>

#include <stdlib.h>

const double CONS1 = 0.6;

const double CONS2 = 0.8;

const double CONS3 = 0.99;

class Motif {

public:

int len;

double **f;

double **n;

double **pwm;

double *gaps;

double members;

char name[STR_LEN];

double weighting; //Only used to provide weighting for motifs in an FBP.

char famName[STR_LEN]; //Only used in testing!

//Constructor

Motif(int l=0);

//Accessors

int GetLen(){return len;}

char* GetName(){return name;}

//Reverse-complement the motif

void RevCompMotif(Motif* out);

//Reverse complement a single column

void RevCompColumn(int i);

//Copy a motif

void CopyMotif(Motif* out);

//Consensus letter for a column (taken from f)

char ColConsensus(int i);

//Find the information content of a column in f

double Info(int i);

//Print the motif in TRANSFAC format

void PrintMotif(FILE* out=NULL, bool famNames=false);

//Print the motif's consensus

void PrintMotifConsensus();

//log base 2

double log_2(double x){ return(log(x) / LOG_2);}

//Reset method

void Reset();

//Destructor

~Motif();

};

#endif