ecoprimers/src/libthermo/nnparams.h

/*
 *  nnparams.h
 *  PHunterLib
 *
 *  Created by Tiayyba Riaz on 7/2/09.
 *  Copyright 2009 __MyCompanyName__. All rights reserved.
 *
 */

//=============================================================================
// Module:        nnparams.h
// Project:       Diploma Thesis - Probe Selection for DNA Microarrays
// Type:          header file - Nearest Neighbor Parameters / Model.
// Language:      c++
// Compiler:      microsoft visual c++ 6.0, unix/linux gcc
// System/OS:     Windows 32, Sun solaris, Linux, other unix systems (untested)
// Database:      none
// Description:   class CNNParams - Nearest Neighbor Model Parameters
// Author:        kaderali
// Date:          9-12/2000
// Copyright:     (c) L. Kaderali, 9/2000 - 12/2000
//
// Revision History
// $              00sep07 LK : created
//                00dec29 LK : changed to include dangling end data 
//                01jan09 LK : included CalcSelfTM function 
//                01feb07 LK : optimized
// #$
//=============================================================================

#if !defined(AFX_NNPARAMS_H__05604705_84E8_11D4_A001_000000000000__INCLUDED_)
#define AFX_NNPARAMS_H__05604705_84E8_11D4_A001_000000000000__INCLUDED_

#if _MSC_VER > 1000
#pragma once
#endif // _MSC_VER > 1000

#include <math.h>
#include <string.h>

#ifdef _pack
#pragma pack(1)
#endif


// following defines to simplify coding...
#define ndH(a,b,c,d) nparm->dH[a][b][c][d]
#define ndS(a,b,c,d) nparm->dS[a][b][c][d]
#define forbidden_enthalpy 1000000000000000000.0f
//#define forbidden_enthalpy_div1000 1000000000000000.0f
// forbidden entropy=-rlogc
// #define forbidden_entropy 30.205986374220235304486574573422f
// Boltzmann factor (cal/degrees C*mol)
#define	R 1.987f
#define	SALT_METHOD_SANTALUCIA 1
#define	SALT_METHOD_OWCZARZY 2
// Strand concentration (assumption!) (M)
// #define Ct  0.000001f
// r*ln(ct/4) as required by many formulas
//#define rlogc -30.205986374220235304486574573422f
extern float forbidden_entropy;

//-----------------------------------------------------------------------------
// class CNNParams
//typedef class CNNParams* PNNParams;

//#pragma GCC visibility push(hidden)
typedef struct CNNParams_st  
{
//public:
	float Ct1;
	float Ct2;
	float rlogc;
	float kplus;
	float kfac;
	int saltMethod;
	float gcContent;
	float new_TM; // ge‰ndert von ML!!!
	//CNNParams();
	//virtual ~CNNParams();
//private:
	float dH[6][6][6][6];  // A-C-G-T + gap + initiation (dangling end, $ sign)
	float dS[6][6][6][6];
}CNNParams, * PNNParams;

	//void nparam_InitParams(PNNParams nparm, float c1=0.000001f, float c2=0.000001f, float kp=1, int sm = SALT_METHOD_SANTALUCIA );
	void nparam_InitParams(PNNParams nparm, float c1, float c2, float kp, int sm);
	void nparam_UpdateParams(PNNParams nparm, char * s1, char * s2);
	float nparam_CountGCContent(char * seq );
	char nparam_convertNum(char c);
	float nparam_GetEntropy(PNNParams nparm, char x0, char x1, char y0, char y1);
	float nparam_GetEnthalpy(PNNParams nparm, char x0, char x1, char y0, char y1);
	float nparam_CalcTM(float entropy,float enthalpy);
    void nparam_AlterTM(PNNParams nparm, float tm_new);
	float nparam_CalcG(PNNParams nparm, float entropy, float enthalpy);
	float nparam_CalcSelfTM(PNNParams nparm, char* seq);
	float nparam_GetInitialEntropy(PNNParams nparm) ;
	char nparam_getComplement(char mychar, int asnum);
	int nparam_isMismatch(char,char);



//#pragma GCC visibility pop
#endif // !defined(AFX_NNPARAMS_H__05604705_84E8_11D4_A001_000000000000__INCLUDED_)