Removed FORCE_FLOAT from a few more files.

1 files changed, 101 insertions, 57 deletions

diff --git a/src/bslmm.h b/src/bslmm.h
index 07aac67..da185fa 100644
--- a/src/bslmm.h
+++ b/src/bslmm.h
@@ -40,96 +40,140 @@ public:
 	string file_out;
 	string path_out;
 	
-	// LMM related parameters
+	// LMM-related parameters.
 	double l_min;
 	double l_max;
 	size_t n_region;
 	double pve_null;
 	double pheno_mean;
 	
-	// BSLMM MCMC related parameters
-	double h_min, h_max, h_scale;			//priors for h
-	double rho_min, rho_max, rho_scale;		//priors for rho
-	double logp_min, logp_max, logp_scale;		//priors for log(pi)
-	size_t s_min, s_max;			//minimum and maximum number of gammas
-	size_t w_step;					//number of warm up/burn in iterations
-	size_t s_step;					//number of sampling iterations
-	size_t r_pace;					//record pace
-	size_t w_pace;					//write pace
-	size_t n_accept;				//number of acceptance
-	size_t n_mh;					//number of MH steps within each iteration
-	double geo_mean;				//mean of the geometric distribution
+	// BSLMM MCMC-related parameters
+	double h_min, h_max, h_scale;	       // Priors for h.
+	double rho_min, rho_max, rho_scale;    // Priors for rho.
+	double logp_min, logp_max, logp_scale; // Priors for log(pi).
+	size_t s_min, s_max;		       // Min. & max. number of gammas.
+	size_t w_step;			       // Number of warm up/burn in
+                                               // iterations.
+	size_t s_step;			       // Num. sampling iterations.
+	size_t r_pace;			       // Record pace.
+	size_t w_pace;			       // Write pace.
+	size_t n_accept;		       // Number of acceptances.
+	size_t n_mh;			       // Number of MH steps per iter.
+	double geo_mean;		       // Mean of geometric dist.
 	long int randseed;
 	double trace_G;	
 	
 	HYPBSLMM cHyp_initial;
 
-	// Summary statistics
-	size_t ni_total, ns_total;	//number of total individuals and snps
-	size_t ni_test, ns_test;	//number of individuals and snps used for analysis
-	size_t n_cvt;				//number of covariates
+	// Summary statistics.
+	size_t ni_total, ns_total; // Number of total individuals and SNPs
+	size_t ni_test, ns_test;   // Num. individuals & SNPs used in analysis.
+	size_t n_cvt;		   // Number of covariates.
 	double time_UtZ;
-	double time_Omega;		//time spent on optimization iterations
-	double time_Proposal;        //time spent on constructing the proposal distribution for gamma (i.e. lmm or lm analysis)
-	vector<int> indicator_idv;				//indicator for individuals (phenotypes), 0 missing, 1 available for analysis
-	vector<int> indicator_snp;				//sequence indicator for SNPs: 0 ignored because of (a) maf, (b) miss, (c) non-poly; 1 available for analysis
-	
-	vector<SNPINFO> snpInfo;		//record SNP information
+	double time_Omega;	   // Time spent on optimization iterations.
+
+        // Time spent on constructing the proposal distribution for
+        // gamma (i.e. lmm or lm analysis).
+	double time_Proposal;        
+
+        // Indicator for individuals (phenotypes): 0 missing, 1
+        // available for analysis.
+	vector<int> indicator_idv;				
+
+	// Sequence indicator for SNPs: 0 ignored because of (a) maf,
+	// (b) miss, (c) non-poly; 1 available for analysis.
+	vector<int> indicator_snp;	
+
+        // Record SNP information.
+	vector<SNPINFO> snpInfo;		
 	
-	// Not included in PARAM
+	// Not included in PARAM.
 	gsl_rng *gsl_r; 
 	gsl_ran_discrete_t *gsl_t;	
 	map<size_t, size_t> mapRank2pos;	
 	
-	// Main Functions
+	// Main functions.
 	void CopyFromParam (PARAM &cPar);
 	void CopyToParam (PARAM &cPar);
 	
-	void RidgeR(const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *Uty, const gsl_vector *eval, const double lambda);
+	void RidgeR(const gsl_matrix *U, const gsl_matrix *UtX,
+		    const gsl_vector *Uty, const gsl_vector *eval,
+		    const double lambda);
 	
-	void MCMC (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *Uty, const gsl_vector *K_eval, const gsl_vector *y);
+	void MCMC (const gsl_matrix *U, const gsl_matrix *UtX,
+		   const gsl_vector *Uty, const gsl_vector *K_eval,
+		   const gsl_vector *y);
 	void WriteLog ();
 	void WriteLR ();
 	void WriteBV (const gsl_vector *bv);
-	void WriteParam (vector<pair<double, double> > &beta_g, const gsl_vector *alpha, const size_t w);
+	void WriteParam (vector<pair<double, double> > &beta_g,
+			 const gsl_vector *alpha, const size_t w);
 	void WriteParam (const gsl_vector *alpha);
-	void WriteResult (const int flag, const gsl_matrix *Result_hyp, const gsl_matrix *Result_gamma, const size_t w_col);
+	void WriteResult (const int flag, const gsl_matrix *Result_hyp,
+			  const gsl_matrix *Result_gamma, const size_t w_col);
 	
-	//Subfunctions inside MCMC
+	// Subfunctions inside MCMC.
 	void CalcPgamma (double *p_gammar);
 	
-	double CalcPveLM (const gsl_matrix *UtXgamma, const gsl_vector *Uty, const double sigma_a2);
-	void InitialMCMC (const gsl_matrix *UtX, const gsl_vector *Uty, vector<size_t> &rank_old, class HYPBSLMM &cHyp, vector<pair<size_t, double> > &pos_loglr);
-	double CalcPosterior (const gsl_vector *Uty, const gsl_vector *K_eval, gsl_vector *Utu, gsl_vector *alpha_prime, class HYPBSLMM &cHyp);
-	double CalcPosterior (const gsl_matrix *UtXgamma, const gsl_vector *Uty, const gsl_vector *K_eval, gsl_vector *UtXb, gsl_vector *Utu, gsl_vector *alpha_prime, gsl_vector *beta, class HYPBSLMM &cHyp);
-	void CalcCC_PVEnZ (const gsl_matrix *U, const gsl_vector *Utu, gsl_vector *z_hat, class HYPBSLMM &cHyp);
-	void CalcCC_PVEnZ (const gsl_matrix *U, const gsl_vector *UtXb, const gsl_vector *Utu, gsl_vector *z_hat, class HYPBSLMM &cHyp);
-	double CalcREMLE (const gsl_matrix *Utw, const gsl_vector *Uty, const gsl_vector *K_eval);
-	double CalcLR (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *Uty, const gsl_vector *K_eval, vector<pair<size_t, double> > &loglr_sort);		//calculate the maximum marginal likelihood ratio for each analyzed SNPs with gemma, use it to rank SNPs
-	void SampleZ (const gsl_vector *y, const gsl_vector *z_hat, gsl_vector *z);
-	double ProposeHnRho (const class HYPBSLMM &cHyp_old, class HYPBSLMM &cHyp_new, const size_t &repeat);
-	double ProposePi (const class HYPBSLMM &cHyp_old, class HYPBSLMM &cHyp_new, const size_t &repeat);
-	double ProposeGamma (const vector<size_t> &rank_old, vector<size_t> &rank_new, const double *p_gamma, const class HYPBSLMM &cHyp_old, class HYPBSLMM &cHyp_new, const size_t &repeat);
-	void SetXgamma (gsl_matrix *Xgamma, const gsl_matrix *X, vector<size_t> &rank);
-
-	void CalcXtX (const gsl_matrix *X_new, const gsl_vector *y, const size_t s_size, gsl_matrix *XtX_new, gsl_vector *Xty_new);
-	void SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old, const gsl_matrix *XtX_old, const gsl_vector *Xty_old, const gsl_vector *y, const vector<size_t> &rank_old, const vector<size_t> &rank_new, gsl_matrix *X_new, gsl_matrix *XtX_new, gsl_vector *Xty_new);
+	double CalcPveLM (const gsl_matrix *UtXgamma, const gsl_vector *Uty,
+			  const double sigma_a2);
+	void InitialMCMC (const gsl_matrix *UtX, const gsl_vector *Uty,
+			  vector<size_t> &rank_old, class HYPBSLMM &cHyp,
+			  vector<pair<size_t, double> > &pos_loglr);
+	double CalcPosterior (const gsl_vector *Uty, const gsl_vector *K_eval,
+			      gsl_vector *Utu, gsl_vector *alpha_prime,
+			      class HYPBSLMM &cHyp);
+	double CalcPosterior (const gsl_matrix *UtXgamma,
+			      const gsl_vector *Uty, const gsl_vector *K_eval,
+			      gsl_vector *UtXb, gsl_vector *Utu,
+			      gsl_vector *alpha_prime, gsl_vector *beta,
+			      class HYPBSLMM &cHyp);
+	void CalcCC_PVEnZ (const gsl_matrix *U, const gsl_vector *Utu,
+			   gsl_vector *z_hat, class HYPBSLMM &cHyp);
+	void CalcCC_PVEnZ (const gsl_matrix *U, const gsl_vector *UtXb,
+			   const gsl_vector *Utu, gsl_vector *z_hat,
+			   class HYPBSLMM &cHyp);
+	double CalcREMLE (const gsl_matrix *Utw, const gsl_vector *Uty,
+			  const gsl_vector *K_eval);
+
+        // Calculate the maximum marginal likelihood ratio for each
+        // analyzed SNPs with gemma, use it to rank SNPs.
+	double CalcLR (const gsl_matrix *U, const gsl_matrix *UtX,
+		       const gsl_vector *Uty, const gsl_vector *K_eval,
+		       vector<pair<size_t, double> > &loglr_sort);
+	void SampleZ (const gsl_vector *y, const gsl_vector *z_hat,
+		      gsl_vector *z);
+	double ProposeHnRho (const class HYPBSLMM &cHyp_old,
+			     class HYPBSLMM &cHyp_new, const size_t &repeat);
+	double ProposePi (const class HYPBSLMM &cHyp_old,
+			  class HYPBSLMM &cHyp_new,
+			  const size_t &repeat);
+	double ProposeGamma (const vector<size_t> &rank_old,
+			     vector<size_t> &rank_new, const double *p_gamma,
+			     const class HYPBSLMM &cHyp_old,
+			     class HYPBSLMM &cHyp_new, const size_t &repeat);
+	void SetXgamma (gsl_matrix *Xgamma, const gsl_matrix *X,
+			vector<size_t> &rank);
+
+	void CalcXtX (const gsl_matrix *X_new, const gsl_vector *y,
+		      const size_t s_size, gsl_matrix *XtX_new,
+		      gsl_vector *Xty_new);
+	void SetXgamma (const gsl_matrix *X, const gsl_matrix *X_old,
+			const gsl_matrix *XtX_old, const gsl_vector *Xty_old,
+			const gsl_vector *y, const vector<size_t> &rank_old,
+			const vector<size_t> &rank_new, gsl_matrix *X_new,
+			gsl_matrix *XtX_new, gsl_vector *Xty_new);
 	double CalcPosterior (const double yty, class HYPBSLMM &cHyp);
-	double CalcPosterior (const gsl_matrix *Xgamma, const gsl_matrix *XtX, const gsl_vector *Xty, const double yty, const size_t s_size, gsl_vector *Xb, gsl_vector *beta, class HYPBSLMM &cHyp);
+	double CalcPosterior (const gsl_matrix *Xgamma, const gsl_matrix *XtX,
+			      const gsl_vector *Xty, const double yty,
+			      const size_t s_size, gsl_vector *Xb,
+			      gsl_vector *beta, class HYPBSLMM &cHyp);
 	void CalcCC_PVEnZ (gsl_vector *z_hat, class HYPBSLMM &cHyp);
-	void CalcCC_PVEnZ (const gsl_vector *Xb, gsl_vector *z_hat, class HYPBSLMM &cHyp);
+	void CalcCC_PVEnZ (const gsl_vector *Xb, gsl_vector *z_hat,
+			   class HYPBSLMM &cHyp);
 	void MCMC (const gsl_matrix *X, const gsl_vector *y);
-	
-	//utility functions
-//	double vec_sum (gsl_vector *v);
-//	void vec_center (gsl_vector *v);
-//	double calc_var (gsl_vector *v);
-//	void calc_sigma (MCMC &cMcmc);
-//	bool comp_lr (pair<size_t, double> a, pair<size_t, double> b);
 };
 
-
-
 #endif