?? rna_algebra.h
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#ifndef _RNA_ALGEBRA_H_#define _RNA_ALGEBRA_H_
#include <assert.h>#include <algorithm>#include "algebra.h"#include "debug.h"#include "misc.h"#include "rna_alphabet.h"#include "rnaforester_options.h"/* ****************************************** *//* Definitions and typedefs *//* ****************************************** */const double DBL_NEG = -100000000.0; // the values from limits.h caused problems..const double DBL_POS = 100000000.0;typedef Algebra<double,RNA_Alphabet_Profile> DoubleScoreProfileAlgebraType;
typedef Algebra<int,RNA_Alphabet> IntScore_AlgebraType;typedef RNA_Algebra<int,RNA_Alphabet> IntScoreRNA_AlgebraType;typedef SZAlgebra<int,RNA_Alphabet> IntScoreSZAlgebraType;/* ****************************************** *//* Class Score *//* ****************************************** *//** Class Score reads scoring parameters from RNAforester command line. */class Score{ private: bool m_isDistance; bool m_isLocal;
bool m_isRIBOSUM; public: int m_bp_rep_score; int m_bp_del_score; int m_b_match_score; int m_b_rep_score; int m_b_del_score; Score(RNAforesterOptions &options); Score(const Score &s); void print();};/* ****************************************** *//* RNA Algebra Classes *//* ****************************************** *//** Similarity algebra for RNA forests */class IntSimiRNA_Algebra : public IntScoreRNA_AlgebraType{ private: Score m_s; public: int empty() const {return 0;}; int replacepair(RNA_Alphabet la, RNA_Alphabet lb, int down, RNA_Alphabet ra, RNA_Alphabet rb, int over) const { return m_s.m_bp_rep_score+down+over; }; int replace(RNA_Alphabet a,int down, RNA_Alphabet b, int over) const { if(a==ALPHA_BASEPAIR && b == ALPHA_BASEPAIR) return m_s.m_bp_rep_score+down+over; else { if(a==ALPHA_BASEPAIR || b==ALPHA_BASEPAIR) return INT_MIN/4; else { if(a==b) return m_s.m_b_match_score+down+over; else return m_s.m_b_rep_score+down+over; } } }; int del(RNA_Alphabet a,int down, int over) const { if(a==ALPHA_BASEPAIR) return m_s.m_bp_del_score+down+over; else return m_s.m_b_del_score+down+over; }; int insert(int down,RNA_Alphabet b,int over) const { if(b==ALPHA_BASEPAIR) return m_s.m_bp_del_score+down+over; else return m_s.m_b_del_score+down+over; int choice(int a, int b) const {
return max(a,b);
}; int worst_score() const { return INT_MIN; }; IntSimiRNA_Algebra(const Score &s) : m_s(s) {};};/** Distance algebra for RNA forests */class IntDistRNA_Algebra : public IntScoreRNA_AlgebraType{ private: Score m_s; public: int empty() const {return 0;}; int replacepair(RNA_Alphabet la, RNA_Alphabet lb, int down, RNA_Alphabet ra, RNA_Alphabet rb, int over) const { return m_s.m_bp_rep_score+down+over; }; int replace(RNA_Alphabet a,int down, RNA_Alphabet b, int over) const { if(a==ALPHA_BASEPAIR && b == ALPHA_BASEPAIR) return m_s.m_bp_rep_score+down+over; else { if(a==ALPHA_BASEPAIR || b==ALPHA_BASEPAIR) return INT_MAX/4; else { if(a==b) return m_s.m_b_match_score+down+over; else return m_s.m_b_rep_score+down+over; } } }; int del(RNA_Alphabet a,int down,int over) const { if(a==ALPHA_BASEPAIR) return m_s.m_bp_del_score+down+over; else return m_s.m_b_del_score+down+over; }; int insert(int down,RNA_Alphabet b,int over) const { if(b==ALPHA_BASEPAIR) return m_s.m_bp_del_score+down+over; else return m_s.m_b_del_score+down+over; }; int choice(int a, int b) const {
return min(a,b);
}; int worst_score() const { return INT_MAX; }; IntDistRNA_Algebra(const Score &s) : m_s(s) {};};/** RIBOSUM85-60 matrix published in RSEARCH: Finding homologs of single structured RNA sequences * R. Klein and S. Eddy, BMC Bioinformatics 2003 Vol.4 */class RIBOSUM8560 : public IntScoreRNA_AlgebraType{ private: Score m_s; int m_baseSubstMtrx[4][4]; int m_basepairSubstMtrx[4][4][4][4]; public: int empty() const {return 0;}; int replacepair(RNA_Alphabet la, RNA_Alphabet lb, int down, RNA_Alphabet ra, RNA_Alphabet rb, int over) const { int i,j,k,l; i=alpha2RNA_Alpha(la); j=alpha2RNA_Alpha(ra); k=alpha2RNA_Alpha(lb); l=alpha2RNA_Alpha(rb); return m_basepairSubstMtrx[i][j][k][l]+down+over; }; int replace(RNA_Alphabet a,int down, RNA_Alphabet b, int over) const { assert(!(a==ALPHA_BASEPAIR && b==ALPHA_BASEPAIR)); if(a==ALPHA_BASEPAIR || b==ALPHA_BASEPAIR) return INT_MIN/4; else { int i,j; i=alpha2RNA_Alpha(a); j=alpha2RNA_Alpha(b); return m_baseSubstMtrx[i][j]+down+over; } }; int del(RNA_Alphabet a,int down, int over) const { if(a==ALPHA_BASEPAIR) return m_s.m_bp_del_score+down+over; else return m_s.m_b_del_score+down+over; }; int insert(int down,RNA_Alphabet b,int over) const { if(b==ALPHA_BASEPAIR) return m_s.m_bp_del_score+down+over; else return m_s.m_b_del_score+down+over; }; int choice(int a, int b) const { return max(a,b); }; int worst_score() const { return INT_MIN; }; RIBOSUM8560(const Score &s) : m_s(s) { int i,j,k,l; // set substitution matrices // base replacement m_baseSubstMtrx[ALPHA_PRO_BASE_A][ALPHA_PRO_BASE_A]=222; m_baseSubstMtrx[ALPHA_PRO_BASE_A][ALPHA_PRO_BASE_C]=-186; m_baseSubstMtrx[ALPHA_PRO_BASE_A][ALPHA_PRO_BASE_G]=-146; m_baseSubstMtrx[ALPHA_PRO_BASE_A][ALPHA_PRO_BASE_U]=-139; m_baseSubstMtrx[ALPHA_PRO_BASE_C][ALPHA_PRO_BASE_C]=116; m_baseSubstMtrx[ALPHA_PRO_BASE_C][ALPHA_PRO_BASE_G]=-248; m_baseSubstMtrx[ALPHA_PRO_BASE_C][ALPHA_PRO_BASE_U]=-105; m_baseSubstMtrx[ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_G]=103; m_baseSubstMtrx[ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_U]=-174; m_baseSubstMtrx[ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_U]=165; // copy triangle for(i=0;i<=ALPHA_PRO_BASE_U;i++) for(j=0;j<i;j++) m_baseSubstMtrx[i][j]=m_baseSubstMtrx[j][i]; // basepair replacement // set default score. This score should never be used since the scores for canonical basepairs are defined later for(i=0;i<=ALPHA_PRO_BASE_U;i++) for(j=0;j<=ALPHA_PRO_BASE_U;j++) for(k=i;k<=ALPHA_PRO_BASE_U;k++) for(l=j;l<=ALPHA_PRO_BASE_U;l++) m_basepairSubstMtrx[i][j][k][l]=-1000; m_basepairSubstMtrx[ALPHA_PRO_BASE_A][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_A][ALPHA_PRO_BASE_U]=449; m_basepairSubstMtrx[ALPHA_PRO_BASE_A][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_C][ALPHA_PRO_BASE_G]=167; m_basepairSubstMtrx[ALPHA_PRO_BASE_A][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_C]=270; m_basepairSubstMtrx[ALPHA_PRO_BASE_A][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_U]=59; m_basepairSubstMtrx[ALPHA_PRO_BASE_A][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_A]=161; m_basepairSubstMtrx[ALPHA_PRO_BASE_A][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_G]=-51; m_basepairSubstMtrx[ALPHA_PRO_BASE_C][ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_C][ALPHA_PRO_BASE_G]=536; m_basepairSubstMtrx[ALPHA_PRO_BASE_C][ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_C]=211; m_basepairSubstMtrx[ALPHA_PRO_BASE_C][ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_U]=-27; m_basepairSubstMtrx[ALPHA_PRO_BASE_C][ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_A]=275; m_basepairSubstMtrx[ALPHA_PRO_BASE_C][ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_G]=132; m_basepairSubstMtrx[ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_C][ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_C]=562; m_basepairSubstMtrx[ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_C][ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_U]=121; m_basepairSubstMtrx[ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_C][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_A]=167; m_basepairSubstMtrx[ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_C][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_G]=-8; m_basepairSubstMtrx[ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_U]=347; m_basepairSubstMtrx[ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_A]=-57; m_basepairSubstMtrx[ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_G]=-209; m_basepairSubstMtrx[ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_A][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_A]=497; m_basepairSubstMtrx[ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_A][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_G]=114; m_basepairSubstMtrx[ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_G][ALPHA_PRO_BASE_U][ALPHA_PRO_BASE_G]=336; // copy triangle for(i=0;i<=ALPHA_PRO_BASE_U;i++) for(j=0;j<=ALPHA_PRO_BASE_U;j++) for(k=0;k<=ALPHA_PRO_BASE_U;k++) for(l=0;l<=ALPHA_PRO_BASE_U;l++) if(k<i || (k==i && l<j)) m_basepairSubstMtrx[i][j][k][l]=m_basepairSubstMtrx[k][l][i][j]; };};/* ****************************************** *//* RNA Profile Algebra Classes *//* ****************************************** *//** Similarity algebra for RNA profile forests */class DoubleSimiProfileAlgebra : public DoubleScoreProfileAlgebraType{?? 快捷鍵說明
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