Changeset 1047

Timestamp:

Apr 27, 2009, 3:24:16 PM (14 years ago)

Author:

Jari Häkkinen

Message:

Fixes #206. Missing values in reference now works. Each probe with no welldefined value in the reference are ignored.

File:

• plugins/base2/net.sf.basedb.normalizers/trunk/src/c++/bin/qQN.cc (modified) (5 diffs)

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

@@ -99 +99 @@
   }
 
-  std::vector<double> target(m.rows());
+  std::vector<double> target;
   ( assay.present() ? create_target_and_fix_nans(target,m,assay.value()) :
                       create_target_and_fix_nans(target,m) );
@@ -131 +131 @@
   std::string line;
   size_t column=0;
-  std::vector<size_t> yes(m.rows(),0);
-  for (size_t row=0; row<m.rows(); ++row)
-    t[row]=0;
+  std::vector<size_t> column_contribs(m.rows(),0);
+  std::vector<double> temp_target(m.rows(),0.0);
   while (getline(is, line)) {
     size_t found=line.find("yes");
@@ -139 +138 @@
       for (size_t row=0; row<m.rows(); ++row)
         if (m(row,column).weight()) { // weight either 0 or 1
-          t[row]+=m(row,column).data();
-          ++yes[row];
+          temp_target[row]+=m(row,column).data();
+          ++column_contribs[row];
         }
         else
@@ -149 +148 @@
       throw std::runtime_error("Too many annotation columns wrt data matrix");
   }
-  for (size_t row=0; row<m.rows(); ++row) {
-    if (!yes[row])
-      throw std::runtime_error("At least one row with no valid reference");
-    t[row]/=yes[row];
-  }
+  t.reserve(m.rows());
+  for (size_t row=0; row<m.rows(); ++row)
+    if (column_contribs[row])
+      t.push_back(temp_target[row]/=column_contribs[row]);
+  if (!t.size())
+    throw std::runtime_error("Not a well defined reference, aborting");
 }
 
@@ -159 +159 @@
 void create_target_and_fix_nans(std::vector<double>& t, MatrixWeighted& m)
 {
+  std::vector<double> temp_target(m.rows(),0.0);
+  t.reserve(m.rows());
   for (size_t row=0; row<m.rows(); ++row) {
-    t[row]=0;
     size_t column_contribs=0;
     for (size_t column=0; column<m.columns(); ++column)
       if (m(row,column).weight()) { // weight either 0 or 1
-        t[row]+=m(row,column).data();
+        temp_target[row]+=m(row,column).data();
         ++column_contribs;
       }
       else
         m(row,column).data()=0;
-    if (!column_contribs)
-      throw std::runtime_error("At least one row with no valid reference");
-    t[row]/=column_contribs;
+    if (column_contribs)
+      t.push_back(temp_target[row]/=column_contribs);
   }
+  if (!t.size())
+    throw std::runtime_error("Not a well defined reference, aborting");
 }