[Genabel-commits] r1709 - pkg/ProbABEL/src

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2014-04-28 16:42:18 +0200 (Mon, 28 Apr 2014)
New Revision: 1709

Modified:
   pkg/ProbABEL/src/coxph_data.cpp
   pkg/ProbABEL/src/coxph_data.h
Log:
Replace the masked_data pointer to array in the coxph_data class to a std::vector() like we did in the regadata class.

Also added a few more consts.


Modified: pkg/ProbABEL/src/coxph_data.cpp
===================================================================
--- pkg/ProbABEL/src/coxph_data.cpp	2014-04-28 14:14:25 UTC (rev 1708)
+++ pkg/ProbABEL/src/coxph_data.cpp	2014-04-28 14:42:18 UTC (rev 1709)
@@ -80,21 +80,17 @@
     stime       = obj.stime;
     gcount      = 0;
     freq        = 0;
-    masked_data = new unsigned short int[nids];
-
-    std::copy(obj.masked_data, obj.masked_data + nids, masked_data);
+    masked_data = obj.masked_data;
 }
 
-coxph_data::coxph_data(phedata &phed, gendata &gend, const int snpnum)
+coxph_data::coxph_data(const phedata &phed, const gendata &gend,
+                       const int snpnum)
 {
     freq        = 0;
     gcount      = 0;
     nids        = gend.nids;
-    masked_data = new unsigned short int[nids];
+    masked_data = std::vector<bool>(nids, false);
 
-
-    std::fill(masked_data,masked_data + nids, 0);
-
     ngpreds = gend.ngpreds;
     if (snpnum >= 0)
     {
@@ -237,14 +233,14 @@
 
     for (int j = 0; j < ngpreds; j++) {
         double *snpdata = new double[nids];
-        std::fill (masked_data, masked_data + nids, 0);
+        masked_data = std::vector<bool>(nids, false);
 
         gend->get_var(snpnum * ngpreds + j, snpdata);
 
         for (int i = 0; i < nids; i++) {
             X.put(snpdata[i], (ncov - j - 1), order[i]);
             if (std::isnan(snpdata[i])) {
-                masked_data[order[i]] = 1;
+                masked_data[order[i]] = true;
                 // snp not masked
             } else {
                 // check for first predictor
@@ -256,14 +252,14 @@
                         freq += snpdata[i];
                     }
                 } else if (j == 1) {
-                    // add second genotype in two predicor data form
+                    // Add second genotype in two predicor data form
                     freq += snpdata[i] * 0.5;
                 }
             }    // end std::isnan(snpdata[i]) snp
-        }    // end i for loop
+        }    // end for loop: i=0 to nids
 
         delete[] snpdata;
-    }    // end ngpreds loop
+    }    // End for loop: j=0 to ngpreds
 
     freq /= static_cast<double>(gcount);  // Allele frequency
 }
@@ -296,25 +292,14 @@
 
 coxph_data::~coxph_data()
 {
-    delete[] coxph_data::masked_data;
-    //      delete X;
-    //      delete sstat;
-    //      delete stime;
-    //      delete weights;
-    //      delete offset;
-    //      delete strata;
-    //      delete order;
 }
 
 
-coxph_data coxph_data::get_unmasked_data()
+coxph_data coxph_data::get_unmasked_data() const
 {
-    coxph_data to;  // = coxph_data(*this);
+    coxph_data to;
 
-    // filter missing data
-
-    int nmeasured = std::count(masked_data, masked_data + nids, 0);
-
+    int nmeasured = std::count(masked_data.begin(), masked_data.end(), 0);
     to.nids = nmeasured;
     to.ncov = ncov;
     to.ngpreds = ngpreds;
@@ -346,9 +331,7 @@
         }
     }
 
-    //delete [] to.masked_data;
-    to.masked_data = new unsigned short int[to.nids];
-    std::fill(to.masked_data, to.masked_data + to.nids, 0);
+    to.masked_data = masked_data;
     return (to);
 }
 
@@ -365,7 +348,7 @@
 }
 
 
-void coxph_reg::estimate(coxph_data &cdatain,
+void coxph_reg::estimate(const coxph_data &cdatain,
                         int maxiter, double eps,
                         double tol_chol, const int model,
                         const int interaction, const int ngpreds,

Modified: pkg/ProbABEL/src/coxph_data.h
===================================================================
--- pkg/ProbABEL/src/coxph_data.h	2014-04-28 14:14:25 UTC (rev 1708)
+++ pkg/ProbABEL/src/coxph_data.h	2014-04-28 14:42:18 UTC (rev 1709)
@@ -51,7 +51,7 @@
     mematrix<int>    strata;
     mematrix<double> X;
     mematrix<int>    order;
-    unsigned short int * masked_data;
+    std::vector<bool> masked_data;
 
 
     coxph_data()
@@ -59,17 +59,16 @@
         nids        = 0;
         ncov        = 0;
         ngpreds     = 0;
-        masked_data = NULL;
         gcount      = 0;
         freq        = 0;
     }
 
     coxph_data(const coxph_data &obj);
-    coxph_data(phedata &phed, gendata &gend, const int snpnum);
+    coxph_data(const phedata &phed, const gendata &gend, const int snpnum);
     ~coxph_data();
 
 
-    coxph_data get_unmasked_data();
+    coxph_data get_unmasked_data() const;
     void update_snp(const gendata *gend, const int snpnum);
     void remove_snp_from_X();
 };
@@ -89,7 +88,7 @@
     coxph_reg(coxph_data &cdatain);
 
 
-    void estimate(coxph_data &cdatain, int maxiter,
+    void estimate(const coxph_data &cdatain, int maxiter,
                   double eps, double tol_chol, const int model,
                   const int interaction, const int ngpreds, const bool iscox,
                   const int nullmodel, const mlinfo &snpinfo, const int cursnp);