98 lines
3.4 KiB
C
98 lines
3.4 KiB
C
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/*
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* galign.h
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* PHunterLib
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*
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* Created by Tiayyba Riaz on 7/2/09.
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* Copyright 2009 __MyCompanyName__. All rights reserved.
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*
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*/
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//=============================================================================
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// Module: galign.h
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// Project: Cubic Project - Calculation of melting temperature and free
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// energy of two DNA strands
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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 GAlign - Thermodynamic Alignment Algorithm
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// Author: leber
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// Date: 01/2002 - 02/2002
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// Copyright: (c) L. Kaderali & M. Leber, 01/2002 - 02/2002
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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_GAlign_H__1B9227F7_82AB_11D4_9FFF_000000000000__INCLUDED_)
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#define AFX_GAlign_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 GAlign
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//#pragma GCC visibility push(hidden)
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//typedef class GAlign* GGAlign;
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typedef struct GAlign_st
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{
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//public:
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// lk01feb07: removed maxlocstuff as not requiered by thermtreealign...
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float maxlocg; // maximum local dG value 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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//private:
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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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float *dH; // Dynamic Programming Table for Entropy
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float *dS; // Dynamic Programming Table for Enthalpy
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PNNParams GNNParams; // Nearest Neighbor parameters
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// float forbidden_entropy;
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}GAlign, * GGAlign;
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void galn_initGAlign(GGAlign galn, int, int, PNNParams);
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void galn_finiGAlign(GGAlign galn);
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//void galn_InitStrings(GGAlign galn, char*,char*,int,int,int=0);
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void galn_InitStrings(GGAlign galn, char*,char*,int,int,int);
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void galn_InitBorder(GGAlign galn);
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//void galn_CalculateTable(GGAlign galn, int=1);
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void galn_CalculateTable(GGAlign galn, int);
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float galn_GetEntropy(GGAlign galn, int, int);
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float galn_GetEnthalpy(GGAlign galn, int, int);
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float galn_GetFreeEnergyK(GGAlign galn, int, int, float);
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float galn_GetFreeEnergyC(GGAlign galn, int, int, float);
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float galn_GetMeltingTempC(GGAlign galn, int, int);
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float galn_GetMeltingTempK(GGAlign galn, int, int);
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void galn_printEnthalpyTable(GGAlign galn, int level);
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void galn_printEntropyTable(GGAlign galn, int level);
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//#pragma GCC visibility pop
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#endif //!defined(AFX_GAlign_H__1B9227F7_82AB_11D4_9FFF_000000000000__INCLUDED_)
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