[Genabel-commits] r1704 - pkg/ProbABEL/src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Apr 28 00:17:30 CEST 2014
Author: lckarssen
Date: 2014-04-28 00:17:28 +0200 (Mon, 28 Apr 2014)
New Revision: 1704
Modified:
pkg/ProbABEL/src/gendata.cpp
pkg/ProbABEL/src/gendata.h
pkg/ProbABEL/src/regdata.cpp
pkg/ProbABEL/src/regdata.h
Log:
Now that several of member functions of the eigen_mematrix class have been declared const (r1703), several other (member) functions of classed can be declared const as well. For example:
- gendata::getvar(const var, *data) is now a const member function (as it doesn't change the gendata object but it does change the (non-member) variable *data).
- the regdata(phedata&, gendata&, ...) constructor now has const references to the phedata and gendata objects (because, e.g., the eigen_mematrix::put function has been declared a const member function in r1703)
This change only added const keywords to the gendata and regdata classes. Others are still to be done.
Modified: pkg/ProbABEL/src/gendata.cpp
===================================================================
--- pkg/ProbABEL/src/gendata.cpp 2014-04-27 21:47:25 UTC (rev 1703)
+++ pkg/ProbABEL/src/gendata.cpp 2014-04-27 22:17:28 UTC (rev 1704)
@@ -36,8 +36,9 @@
#include "utilities.h"
-void gendata::mldose_line_to_matrix(int k, const char *all_numbers,
- int amount_of_numbers){
+void gendata::mldose_line_to_matrix(const int k,
+ const char *all_numbers,
+ const int amount_of_numbers){
int j = 0;
// Check if not a null pointer
if (!*all_numbers){
@@ -102,7 +103,7 @@
}
-void gendata::get_var(int var, double * data)
+void gendata::get_var(const int var, double * data) const
{
// Read the genetic data for SNP 'var' and store in the array 'data'
@@ -168,11 +169,13 @@
}
-void gendata::re_gendata(string filename, unsigned int insnps,
- unsigned int ingpreds, unsigned int npeople,
- unsigned int nmeasured,
- unsigned short int * allmeasured,
- std::string * idnames)
+void gendata::re_gendata(const string filename,
+ const unsigned int insnps,
+ const unsigned int ingpreds,
+ const unsigned int npeople,
+ const unsigned int nmeasured,
+ const unsigned short int * allmeasured,
+ const std::string * idnames)
{
nsnps = insnps;
ngpreds = ingpreds;
@@ -224,11 +227,14 @@
}
-void gendata::re_gendata(char * fname, unsigned int insnps,
- unsigned int ingpreds, unsigned int npeople,
- unsigned int nmeasured,
- unsigned short int * allmeasured, int skipd,
- std::string * idnames)
+void gendata::re_gendata(const char * fname,
+ const unsigned int insnps,
+ const unsigned int ingpreds,
+ const unsigned int npeople,
+ const unsigned int nmeasured,
+ const unsigned short int * allmeasured,
+ const int skipd,
+ const std::string * idnames)
{
nids = nmeasured;
nsnps = insnps;
Modified: pkg/ProbABEL/src/gendata.h
===================================================================
--- pkg/ProbABEL/src/gendata.h 2014-04-27 21:47:25 UTC (rev 1703)
+++ pkg/ProbABEL/src/gendata.h 2014-04-27 22:17:28 UTC (rev 1704)
@@ -41,18 +41,27 @@
unsigned int nids;
unsigned int ngpreds;
gendata();
- void mldose_line_to_matrix(int k, const char *all_numbers,
- int amount_of_numbers);
+ void mldose_line_to_matrix(const int k,
+ const char *all_numbers,
+ const int amount_of_numbers);
- void re_gendata(char * fname, unsigned int insnps, unsigned int ingpreds,
- unsigned int npeople, unsigned int nmeasured,
- unsigned short int * allmeasured, int skipd, std::string * idnames);
+ void re_gendata(const char * fname,
+ const unsigned int insnps,
+ const unsigned int ingpreds,
+ const unsigned int npeople,
+ const unsigned int nmeasured,
+ const unsigned short int * allmeasured,
+ const int skipd,
+ const std::string * idnames);
- void re_gendata(string filename, unsigned int insnps, unsigned int ingpreds,
- unsigned int npeople, unsigned int nmeasured,
- unsigned short int * allmeasured, std::string * idnames);
+ void re_gendata(const string filename, const unsigned int insnps,
+ const unsigned int ingpreds,
+ const unsigned int npeople,
+ const unsigned int nmeasured,
+ const unsigned short int * allmeasured,
+ const std::string * idnames);
- void get_var(int var, double * data);
+ void get_var(const int var, double * data) const;
~gendata();
Modified: pkg/ProbABEL/src/regdata.cpp
===================================================================
--- pkg/ProbABEL/src/regdata.cpp 2014-04-27 21:47:25 UTC (rev 1703)
+++ pkg/ProbABEL/src/regdata.cpp 2014-04-27 22:17:28 UTC (rev 1704)
@@ -96,7 +96,7 @@
* \param ext_is_interaction_excluded Boolean that shows whether
* interactions are excluded.
*/
-regdata::regdata(phedata &phed, gendata &gend, const int snpnum,
+regdata::regdata(const phedata &phed, const gendata &gend, const int snpnum,
const bool ext_is_interaction_excluded)
{
freq = 0;
@@ -163,7 +163,7 @@
* @param snpnum Number of the SNP for which the dosage/probability
* data will be extracted from the gend object.
*/
-void regdata::update_snp(gendata *gend, const int snpnum)
+void regdata::update_snp(const gendata *gend, const int snpnum)
{
// Reset counter for frequency since it is a new SNP
gcount = 0;
Modified: pkg/ProbABEL/src/regdata.h
===================================================================
--- pkg/ProbABEL/src/regdata.h 2014-04-27 21:47:25 UTC (rev 1703)
+++ pkg/ProbABEL/src/regdata.h 2014-04-27 22:17:28 UTC (rev 1704)
@@ -124,13 +124,13 @@
// Constructors and destructors
regdata();
regdata(const regdata &obj);
- regdata(phedata &phed, gendata &gend, const int snpnum,
+ regdata(const phedata &phed, const gendata &gend, const int snpnum,
const bool ext_is_interaction_excluded);
//~regdata();
// Member functions.
- void update_snp(gendata *gend, const int snpnum);
+ void update_snp(const gendata *gend, const int snpnum);
void remove_snp_from_X();
regdata get_unmasked_data();
mematrix<double> extract_genotypes();
More information about the Genabel-commits
mailing list