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

//

// STAMP version 1.3

//

// Written By: Shaun Mahony

//

// main.cpp

//

// Started: 4th Feb 2006

//

// 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 PROTEIN_MARK

#define PROTEIN_MARK

//Includes

#include<stdio.h>

#include<stdlib.h>

#include<string.h>

#include<ctype.h>

#include "globals.h"

#include "Motif.h"

#include "Alignment.h"

class ProteinMotif

{

private:

int len;

public:

char name[STR_LEN];

double** f;

//Constructor

ProteinMotif(int l);

//Accessor

int GetLen(){return len;}

//Print the motif

void PrintMotif();

//the information content of a column

double Info(int col);

//log base 2

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

//Destructor

~ProteinMotif();

};

//Protein Domain Handler

class ProteinDomains

{

private:

int numDomains;

char inputFN[STR_LEN];

public:

//The overall and single motifs

ProteinMotif* domainMotif;

ProteinMotif** individualMotifs;

//Constructor

ProteinDomains(){numDomains=0; domainMotif=NULL; individualMotifs=NULL;}

//Read in the motifs

void ReadDomains(char* inFileName, Motif** inputMotifs, int numMotifs);

//Do the mutual information analysis

void MutualInformation(MultiAlignRec* pssmAlignment, Motif* alignmentMotif, Motif** inputMotifs, int numMotifs);

//Convert an amino acid to a number

int char2num(char x);

//log base 2

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

//Destructor

~ProteinDomains();

};

#endif