Changeset 1045

Timestamp:

Apr 24, 2009, 10:52:57 PM (14 years ago)

Author:

Jari Häkkinen

Message:

Missing values now works with the implemented fix to avoid a bug in yat, ​http://dev.thep.lu.se/yat/ticket/535

File:

• plugins/base2/net.sf.basedb.normalizers/trunk/src/c++/bin/qQN.cc (modified) (7 diffs)

plugins/base2/net.sf.basedb.normalizers/trunk/src/c++/bin/qQN.cc

@@ -43 +43 @@
 using namespace theplu::yat::utility;
 
-void create_target(std::vector<double>&, const MatrixWeighted&);
-void create_target(std::vector<double>&, const MatrixWeighted&,
-                   const std::string&);
+void create_target_and_fix_nans(std::vector<double>&, MatrixWeighted&);
+void create_target_and_fix_nans(std::vector<double>&, MatrixWeighted&,
+                                const std::string&);
 /**
    writes the data values in the matrix ignoring the weights, i.e.,
@@ -100 +100 @@
 
   std::vector<double> target(m.rows());
-  ( assay.present() ? create_target(target,m,assay.value()) :
-                      create_target(target,m) );
+  ( assay.present() ? create_target_and_fix_nans(target,m,assay.value()) :
+                      create_target_and_fix_nans(target,m) );
   qQuantileNormalizer qqn(target.begin(), target.end(), 100);
   ColumnNormalizer<qQuantileNormalizer> cn(qqn);
@@ -125 +125 @@
 
 
-void create_target(std::vector<double>& t, const MatrixWeighted& m,
-                   const std::string& assay)
+void create_target_and_fix_nans(std::vector<double>& t, MatrixWeighted& m,
+                                const std::string& assay)
 {
   std::ifstream is(assay.c_str());
@@ -142 +142 @@
           ++yes[row];
         }
+        else
+          m(row,column).data()=0;
     }
     ++column;
@@ -155 +157 @@
 
 
-void create_target(std::vector<double>& t, const MatrixWeighted& m)
+void create_target_and_fix_nans(std::vector<double>& t, MatrixWeighted& m)
 {
   for (size_t row=0; row<m.rows(); ++row) {
@@ -165 +167 @@
         ++column_contribs;
       }
+      else
+        m(row,column).data()=0;
     if (!column_contribs)
       throw std::runtime_error("At least one row with no valid reference");
@@ -178 +182 @@
   for(size_t i=0, j=0; i<m.rows(); i++)
     for (j=0; j<m.columns(); j++) {
-      s << m(i,j).data();
+      if (m(i,j).weight())
+        s << m(i,j).data();
+      else
+        s << "nan";
       if (j<m.columns()-1)
         s << s.fill();