Eric Coissac
e79738e170
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@223 60f365c0-8329-0410-b2a4-ec073aeeaa1d
71 lines
2.0 KiB
C
71 lines
2.0 KiB
C
/*
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* nnparams.h
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* PHunterLib
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*
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* Nearest Neighbor Model Parameters
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*
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* Created by Tiayyba Riaz on 02/07/09.
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*
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*/
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#ifndef NNPARAMS_H_
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#define NNPARAMS_H_
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#include <math.h>
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#include <string.h>
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//#include "../libecoprimer/ecoprimer.h"
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// following defines to simplify coding...
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#define ndH(a,b,c,d) nparm->dH[a][b][c][d]
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#define ndS(a,b,c,d) nparm->dS[a][b][c][d]
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#define forbidden_enthalpy 1000000000000000000.0f
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#define R 1.987f
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#define SALT_METHOD_SANTALUCIA 1
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#define SALT_METHOD_OWCZARZY 2
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#define DEF_CONC_PRIMERS 0.0000008
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#define DEF_CONC_SEQUENCES 0
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#define DEF_SALT 0.05
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#define GETNUMCODE(a) bpencoder[a - 'A']
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#define GETREVCODE(a) 5-bpencoder[a - 'A']
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extern float forbidden_entropy;
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static char bpencoder[] = { 1, // A
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0, // b
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2, // C
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0,0,0, // d, e, f
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3, // G
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0,0,0,0,0,0,0,0,0,0,0,0, // h,i,j,k,l,m,n,o,p,q,r,s
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4,0, // T,U
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0,0,0,0,0}; // v,w,x,y,z
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typedef struct CNNParams_st
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{
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float Ct1;
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float Ct2;
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float rlogc;
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float kplus;
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float kfac;
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int saltMethod;
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float gcContent;
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float new_TM;
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float dH[6][6][6][6]; // A-C-G-T + gap + initiation (dangling end, $ sign)
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float dS[6][6][6][6];
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}CNNParams, * PNNParams;
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void nparam_InitParams(PNNParams nparm, float c1, float c2, float kp, int sm);
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int nparam_CountGCContent(char * seq );
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float nparam_GetEntropy(PNNParams nparm, char x0, char x1, char y0, char y1);
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float nparam_GetEnthalpy(PNNParams nparm, char x0, char x1, char y0, char y1);
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float nparam_CalcTM(float entropy,float enthalpy);
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float nparam_CalcSelfTM(PNNParams nparm, char* seq, int len);
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float nparam_GetInitialEntropy(PNNParams nparm) ;
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float calculateMeltingTemperatureBasic (char * seq);
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//void getThermoProperties (ppair_t* pairs, size_t count, poptions_t options);
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#endif
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