Removed FORCE_FLOAT from a few more files.

1 files changed, 45 insertions, 36 deletions

diff --git a/src/mvlmm.h b/src/mvlmm.h
index 9ff567c..d495c26 100644
--- a/src/mvlmm.h
+++ b/src/mvlmm.h
@@ -1,6 +1,6 @@
 /*
  Genome-wide Efficient Mixed Model Association (GEMMA)
- Copyright (C) 2011  Xiang Zhou
+ Copyright (C) 2011-2017, Xiang Zhou
 
  This program is free software: you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
@@ -13,36 +13,25 @@
  GNU General Public License for more details.
 
  You should have received a copy of the GNU General Public License
- along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+*/
 
 #ifndef __MVLMM_H__
 #define __MVLMM_H__
 
 #include "gsl/gsl_vector.h"
 #include "gsl/gsl_matrix.h"
-
-
-#ifdef FORCE_FLOAT
-#include "param_float.h"
-#include "io_float.h"
-#else
 #include "param.h"
 #include "io.h"
-#endif
 
 using namespace std;
 
-
-
-
-
 class MVLMM {
 
 public:
-	// IO related parameters
-	int a_mode;				//analysis mode, 1/2/3/4 for Frequentist tests
-	size_t d_pace;		//display pace
+	// IO-related parameters.
+	int a_mode;	// Analysis mode: 1/2/3/4 for Frequentist tests.
+	size_t d_pace;	// Display pace.
 
 	string file_bfile;
 	string file_geno;
@@ -50,48 +39,68 @@ public:
 	string file_out;
 	string path_out;
 
-	// MVLMM related parameters
+	// MVLMM-related parameters.
 	double l_min;
 	double l_max;
 	size_t n_region;
 	double logl_remle_H0, logl_mle_H0;
 	vector<double> Vg_remle_null, Ve_remle_null, Vg_mle_null, Ve_mle_null;
-	vector<double> VVg_remle_null, VVe_remle_null, VVg_mle_null, VVe_mle_null;
-	vector<double> beta_remle_null, se_beta_remle_null, beta_mle_null, se_beta_mle_null;
+        vector<double> VVg_remle_null, VVe_remle_null, VVg_mle_null;
+        vector<double> VVe_mle_null;
+        vector<double> beta_remle_null, se_beta_remle_null, beta_mle_null;
+        vector<double> se_beta_mle_null;
 	double p_nr;
 	size_t em_iter, nr_iter;
 	double em_prec, nr_prec;
 	size_t crt;
 
-	// Summary statistics
-	size_t ni_total, ni_test;	//number of individuals
-	size_t ns_total, ns_test;	//number of snps
+	// Summary statistics.
+	size_t ni_total, ni_test; // Number of individuals.
+	size_t ns_total, ns_test; // Number of SNPs.
 	size_t n_cvt;
 	size_t n_ph;
-	double time_UtX;		//time spent on optimization iterations
-	double time_opt;		//time spent on optimization iterations
+	double time_UtX;	  // Time spent on optimization iterations.
+	double time_opt;	  // Time spent on optimization iterations.
+
+        // Indicator for individuals (phenotypes): 0 missing, 1
+        // available for analysis.
+	vector<int> indicator_idv;
 
-	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
+    	// Sequence indicator for SNPs: 0 ignored because of (a) maf,
+    	// (b) miss, (c) non-poly; 1 available for analysis.
+	vector<int> indicator_snp;
 
-	vector<SNPINFO> snpInfo;		//record SNP information
+	vector<SNPINFO> snpInfo;    // Record SNP information.
 
-	// Not included in PARAM
-	vector<MPHSUMSTAT> sumStat;		//Output SNPSummary Data
+	// Not included in PARAM.
+	vector<MPHSUMSTAT> sumStat; // Output SNPSummary Data.
 
 	// Main functions
 	void CopyFromParam (PARAM &cPar);
 	void CopyToParam (PARAM &cPar);
-	void AnalyzeBimbam (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY);
-	void AnalyzePlink (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY);
-	void Analyzebgen (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY);
-	void AnalyzeBimbamGXE (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY, const gsl_vector *env);
-	void AnalyzePlinkGXE (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY, const gsl_vector *env);
+	void AnalyzeBimbam (const gsl_matrix *U, const gsl_vector *eval,
+			    const gsl_matrix *UtW, const gsl_matrix *UtY);
+	void AnalyzePlink (const gsl_matrix *U, const gsl_vector *eval,
+			   const gsl_matrix *UtW, const gsl_matrix *UtY);
+	void Analyzebgen (const gsl_matrix *U, const gsl_vector *eval,
+			  const gsl_matrix *UtW, const gsl_matrix *UtY);
+	void AnalyzeBimbamGXE (const gsl_matrix *U, const gsl_vector *eval,
+			       const gsl_matrix *UtW, const gsl_matrix *UtY,
+			       const gsl_vector *env);
+        void AnalyzePlinkGXE (const gsl_matrix *U, const gsl_vector *eval,
+			      const gsl_matrix *UtW, const gsl_matrix *UtY,
+			      const gsl_vector *env);
 	void WriteFiles ();
 
 };
 
-void CalcMvLmmVgVeBeta (const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY, const size_t em_iter, const size_t nr_iter, const double em_prec, const double nr_prec, const double l_min, const double l_max, const size_t n_region, gsl_matrix *V_g, gsl_matrix *V_e, gsl_matrix *B, gsl_matrix *se_B);
+void CalcMvLmmVgVeBeta (const gsl_vector *eval, const gsl_matrix *UtW,
+			const gsl_matrix *UtY, const size_t em_iter,
+			const size_t nr_iter, const double em_prec,
+			const double nr_prec, const double l_min,
+			const double l_max, const size_t n_region,
+			gsl_matrix *V_g, gsl_matrix *V_e, gsl_matrix *B,
+			gsl_matrix *se_B);
 
 #endif