Changeset 1052

Timestamp:

May 7, 2009, 12:28:07 AM (14 years ago)

Author:

Jari Häkkinen

Message:

Fixes #208. Reverted changeset:1045 and added requirement on yat 0.5.3.

Location:

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

Files:

• README (modified) (1 diff)
• bin/qQN.cc (modified) (8 diffs)
• configure.ac (modified) (1 diff)

plugins/base2/net.sf.basedb.normalizers/trunk/src/c++/README

@@ -25 +25 @@
 Requirements
 
-You need to have a successful install of yat 0.5 or later.
+You need to have a successful install of yat 0.5.3 or later. The
+program can be made to compile with any 0.5 version of yat but the
+qQuantileNormalizer implementation in yat previous to 0.5.3 contains a
+serious bug. The configure script will check that your yat version is
+equal to or greater than 0.5.3.
 
 

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

@@ -44 +44 @@
 
 
-void create_target_and_fix_nans(std::vector<double>&, MatrixWeighted&);
-void create_target_and_fix_nans(std::vector<double>&, MatrixWeighted&,
-                                const std::string&);
+void create_target_and(std::vector<double>&, const MatrixWeighted&);
+void create_target_and(std::vector<double>&, const MatrixWeighted&,
+                       const std::string&);
 
 void exp_numbers(MatrixWeighted&);
@@ -106 +106 @@
 
   std::vector<double> target;
-  ( assay.present() ? create_target_and_fix_nans(target,m,assay.value()) :
-                      create_target_and_fix_nans(target,m) );
+  ( assay.present() ? create_target_and(target,m,assay.value()) :
+                      create_target_and(target,m) );
   log_numbers(target.begin(),target.end());
   log_numbers(m);
@@ -134 +134 @@
 
 
-void create_target_and_fix_nans(std::vector<double>& t, MatrixWeighted& m,
-                                const std::string& assay)
+void create_target_and(std::vector<double>& t, const MatrixWeighted& m,
+                       const std::string& assay)
 {
   std::ifstream is(assay.c_str());
@@ -144 +144 @@
   while (getline(is, line)) {
     size_t found=line.find("yes");
-
     if (found!=std::string::npos) {
       // use this assay as a part of reference
@@ -152 +151 @@
           ++column_contribs[row];
         }
-        else
-          m(row,column).data()=0;
     }
-    else
-      // this assay as not a part of the reference but fix nan
-      for (size_t row=0; row<m.rows(); ++row)
-        if (!m(row,column).weight()) // weight either 0 or 1
-          m(row,column).data()=0;
-
     ++column;
     if (column>m.columns())
@@ -174 +165 @@
 
 
-void create_target_and_fix_nans(std::vector<double>& t, MatrixWeighted& m)
+void create_target_and(std::vector<double>& t, const MatrixWeighted& m)
 {
   std::vector<double> temp_target(m.rows(),0.0);
@@ -185 +176 @@
         ++column_contribs;
       }
-      else
-        m(row,column).data()=0;
     if (column_contribs)
       t.push_back(temp_target[row]/=column_contribs);
@@ -230 +219 @@
   for(size_t i=0, j=0; i<m.rows(); i++)
     for (j=0; j<m.columns(); j++) {
-      if (m(i,j).weight())
-        s << m(i,j).data();
-      else
-        s << "nan";
+      s << m(i,j).data();
       if (j<m.columns()-1)
         s << s.fill();

plugins/base2/net.sf.basedb.normalizers/trunk/src/c++/configure.ac

@@ -69 +69 @@
 else
   yat_found="no"
-  yat_version="0.5"
+  yat_version="0.5.3"
   YAT_CHECK_YAT([${yat_version}],[yat_found="yes"])
   if (test "${yat_found}" = "yes") ; then