106 lines
4.0 KiB
C
106 lines
4.0 KiB
C
|
//=============================================================================
|
||
|
|
// Module: thermalign.h
|
||
|
|
// Project: Diploma Thesis - Probe Selection for DNA Microarrays
|
||
|
|
// Type: header file - Thermodynamic Alignment.
|
||
|
|
// 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 CThermAlign - Thermodynamic Alignment Algorithm
|
||
|
|
// Author: kaderali
|
||
|
|
// Date: 9/2000 - 12/2000
|
||
|
|
// Copyright: (c) L. Kaderali, 9/2000 - 12/2000
|
||
|
|
//
|
||
|
|
// Revision History
|
||
|
|
// $ 00sep04 LK : created
|
||
|
|
// $ 00dec30 LK : changed to do local alignment of probe against
|
||
|
|
// one entire sequence
|
||
|
|
// $ 01feb07 LK : optimized
|
||
|
|
// #$
|
||
|
|
//=============================================================================
|
||
|
|
|
||
|
|
#if !defined(AFX_THERMALIGN_H__1B9227F7_82AB_11D4_9FFF_000000000000__INCLUDED_)
|
||
|
|
#define AFX_THERMALIGN_H__1B9227F7_82AB_11D4_9FFF_000000000000__INCLUDED_
|
||
|
|
|
||
|
|
//#if _MSC_VER > 1000
|
||
|
|
//#pragma once
|
||
|
|
//#endif // _MSC_VER > 1000
|
||
|
|
|
||
|
|
//#include <iostream>
|
||
|
|
//#include <strstream>
|
||
|
|
//#include <ostream>
|
||
|
|
#include "nnparams.h" // Nearest Neighbor Parameters
|
||
|
|
//#include "../gsfxtree/gsfxtree.h" // Suffix Tree Stuff
|
||
|
|
|
||
|
|
//using namespace std;
|
||
|
|
|
||
|
|
//#ifdef _pack
|
||
|
|
//#pragma pack(1)
|
||
|
|
//#endif
|
||
|
|
|
||
|
|
//-----------------------------------------------------------------------------
|
||
|
|
// class CThermAlign
|
||
|
|
//#pragma GCC visibility push(hidden)
|
||
|
|
//typedef class CThermAlign* PThermAlign;
|
||
|
|
|
||
|
|
typedef struct CThermAlign_t
|
||
|
|
{
|
||
|
|
//public:
|
||
|
|
#ifdef _output_alignment
|
||
|
|
/* void printAlignment(ostream &outputStream);
|
||
|
|
void OutputAlignment(ostream &outputStream);
|
||
|
|
bool OutputAlignment(ostream &outputStream, int, int, int, bool local=false);
|
||
|
|
void OutputLocalAlignment(ostream &outputStream);
|
||
|
|
void PrintDPTable(ostream&);*/
|
||
|
|
#endif
|
||
|
|
// lk01feb07: removed maxlocstuff as not requiered by thermtreealign...
|
||
|
|
float maxloctm; // maximum local temperature found
|
||
|
|
int maxloci; // i position thereof
|
||
|
|
int maxlocj; // j position thereof
|
||
|
|
int maxloct; // and type of maximum alignment!
|
||
|
|
int targetNumber; // id number of target sequence
|
||
|
|
// PGSfxLeaf probeNode; // identifier for probe sequence
|
||
|
|
char *seq1; // Sequence 1
|
||
|
|
char *seq2; // Sequence 2
|
||
|
|
int seq1len; // Length of Sequence 1
|
||
|
|
int seq2len; // Length of Sequence 2
|
||
|
|
int maxseq1len; // length of longest target...
|
||
|
|
//private:
|
||
|
|
float *dH; // Dynamic Programming Table for Entropy
|
||
|
|
float *dS; // Dynamic Programming Table for Enthalpy
|
||
|
|
PNNParams NNParams; // Nearest Neighbor parameters
|
||
|
|
// float forbidden_entropy;
|
||
|
|
#ifdef _output_alignment
|
||
|
|
//ostrstream *s1aptr, *s2aptr, *atypptr;
|
||
|
|
// Used to buffer aligned sequences (on output)
|
||
|
|
//ostrstream s1align;
|
||
|
|
//ostrstream s2align;
|
||
|
|
//ostrstream aligntype; // insert, deletion, match, unmatch (for output)
|
||
|
|
// same for local alignment:
|
||
|
|
/* removed lk00jan08: use global instead!
|
||
|
|
ostrstream ls1align;
|
||
|
|
ostrstream ls2align;
|
||
|
|
ostrstream laligntype; // insert, deletion, match, unmatch (for output)
|
||
|
|
*/
|
||
|
|
#endif
|
||
|
|
}CThermAlign, * PThermAlign;
|
||
|
|
//#pragma GCC visibility pop
|
||
|
|
|
||
|
|
float therm_GetEntropy(PThermAlign thrma, int, int);
|
||
|
|
float therm_GetEnthalpy(PThermAlign thrma, int, int);
|
||
|
|
float therm_GetFreeEnergy(PThermAlign thrma, int, int);
|
||
|
|
float therm_GetFreeEnergyK(PThermAlign thrma, int, int, float);
|
||
|
|
float therm_GetFreeEnergyC(PThermAlign thrma, int, int, float);
|
||
|
|
float therm_GetMeltingTempC(PThermAlign thrma, int, int);
|
||
|
|
float therm_GetMeltingTempK(PThermAlign thrma, int, int);
|
||
|
|
void therm_initCThermAlign(PThermAlign thrma, int, int, PNNParams);
|
||
|
|
void therm_finiCThermAlign(PThermAlign thrma);
|
||
|
|
//void therm_InitStrings(PThermAlign thrma, char*,char*,int,int,int=0);
|
||
|
|
void therm_InitStrings(PThermAlign thrma, char*,char*,int,int,int);
|
||
|
|
void therm_InitBorder(PThermAlign thrma);
|
||
|
|
//void therm_CalculateTable(PThermAlign thrma, int=1);
|
||
|
|
void therm_CalculateTable(PThermAlign thrma, int);
|
||
|
|
|
||
|
|
|
||
|
|
#endif // !defined(AFX_THERMALIGN_H__1B9227F7_82AB_11D4_9FFF_000000000000__INCLUDED_)
|