Eric Coissac
f142d0e904
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@221 60f365c0-8329-0410-b2a4-ec073aeeaa1d
106 lines
4.0 KiB
C
106 lines
4.0 KiB
C
//=============================================================================
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// Module: thermalign.h
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// Project: Diploma Thesis - Probe Selection for DNA Microarrays
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// Type: header file - Thermodynamic Alignment.
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// Language: c++
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// Compiler: microsoft visual c++ 6.0, unix/linux gcc
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// System/OS: Windows 32, Sun solaris, Linux, other unix systems (untested)
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// Database: none
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// Description: class CThermAlign - Thermodynamic Alignment Algorithm
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// Author: kaderali
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// Date: 9/2000 - 12/2000
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// Copyright: (c) L. Kaderali, 9/2000 - 12/2000
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//
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// Revision History
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// $ 00sep04 LK : created
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// $ 00dec30 LK : changed to do local alignment of probe against
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// one entire sequence
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// $ 01feb07 LK : optimized
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// #$
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//=============================================================================
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#if !defined(AFX_THERMALIGN_H__1B9227F7_82AB_11D4_9FFF_000000000000__INCLUDED_)
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#define AFX_THERMALIGN_H__1B9227F7_82AB_11D4_9FFF_000000000000__INCLUDED_
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//#if _MSC_VER > 1000
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//#pragma once
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//#endif // _MSC_VER > 1000
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//#include <iostream>
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//#include <strstream>
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//#include <ostream>
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#include "nnparams.h" // Nearest Neighbor Parameters
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//#include "../gsfxtree/gsfxtree.h" // Suffix Tree Stuff
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//using namespace std;
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//#ifdef _pack
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//#pragma pack(1)
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//#endif
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//-----------------------------------------------------------------------------
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// class CThermAlign
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//#pragma GCC visibility push(hidden)
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//typedef class CThermAlign* PThermAlign;
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typedef struct CThermAlign_t
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{
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//public:
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#ifdef _output_alignment
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/* void printAlignment(ostream &outputStream);
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void OutputAlignment(ostream &outputStream);
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bool OutputAlignment(ostream &outputStream, int, int, int, bool local=false);
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void OutputLocalAlignment(ostream &outputStream);
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void PrintDPTable(ostream&);*/
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#endif
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// lk01feb07: removed maxlocstuff as not requiered by thermtreealign...
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float maxloctm; // maximum local temperature found
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int maxloci; // i position thereof
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int maxlocj; // j position thereof
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int maxloct; // and type of maximum alignment!
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int targetNumber; // id number of target sequence
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// PGSfxLeaf probeNode; // identifier for probe sequence
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char *seq1; // Sequence 1
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char *seq2; // Sequence 2
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int seq1len; // Length of Sequence 1
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int seq2len; // Length of Sequence 2
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int maxseq1len; // length of longest target...
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//private:
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float *dH; // Dynamic Programming Table for Entropy
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float *dS; // Dynamic Programming Table for Enthalpy
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PNNParams NNParams; // Nearest Neighbor parameters
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// float forbidden_entropy;
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#ifdef _output_alignment
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//ostrstream *s1aptr, *s2aptr, *atypptr;
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// Used to buffer aligned sequences (on output)
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//ostrstream s1align;
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//ostrstream s2align;
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//ostrstream aligntype; // insert, deletion, match, unmatch (for output)
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// same for local alignment:
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/* removed lk00jan08: use global instead!
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ostrstream ls1align;
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ostrstream ls2align;
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ostrstream laligntype; // insert, deletion, match, unmatch (for output)
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*/
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#endif
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}CThermAlign, * PThermAlign;
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//#pragma GCC visibility pop
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float therm_GetEntropy(PThermAlign thrma, int, int);
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float therm_GetEnthalpy(PThermAlign thrma, int, int);
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float therm_GetFreeEnergy(PThermAlign thrma, int, int);
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float therm_GetFreeEnergyK(PThermAlign thrma, int, int, float);
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float therm_GetFreeEnergyC(PThermAlign thrma, int, int, float);
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float therm_GetMeltingTempC(PThermAlign thrma, int, int);
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float therm_GetMeltingTempK(PThermAlign thrma, int, int);
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void therm_initCThermAlign(PThermAlign thrma, int, int, PNNParams);
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void therm_finiCThermAlign(PThermAlign thrma);
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//void therm_InitStrings(PThermAlign thrma, char*,char*,int,int,int=0);
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void therm_InitStrings(PThermAlign thrma, char*,char*,int,int,int);
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void therm_InitBorder(PThermAlign thrma);
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//void therm_CalculateTable(PThermAlign thrma, int=1);
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void therm_CalculateTable(PThermAlign thrma, int);
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#endif // !defined(AFX_THERMALIGN_H__1B9227F7_82AB_11D4_9FFF_000000000000__INCLUDED_)
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