Changeset 1224 for plugins/base2/net.sf.basedb.normalizers/trunk

Timestamp:

May 3, 2010, 10:18:46 AM (13 years ago)

Author:

Jari Häkkinen

Message:

Reverting changset:1164.

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

@@ -59 +59 @@
 
 
-void create_matrix_until_183_fixed(MatrixWeighted**, const MatrixWeighted&,
-                                   const std::string&);
 void create_target(std::vector<double>&, const MatrixWeighted&, bool use_median);
 void create_target(std::vector<double>&, const MatrixWeighted&,
@@ -123 +121 @@
   }
 
-  // The BASE core API deprecated exportPlainMatrix method of the
-  // deprecated BioAssaySetExporter does not behave well when
-  // exporting bioassaysets where assays have been filtered out in
-  // some filter step. Variables and functions with 183 in their name
-  // should be removed when http://baseplugins.thep.lu.se/ticket/183
-  // is fixed.
-
-  // m is a pointer below, should be changed to a normal variable when
-  // http://baseplugins.thep.lu.se/ticket/183 is fixed.
-
-  // Change to m when http://baseplugins.thep.lu.se/ticket/183 fixed.
-  MatrixWeighted m_tmp_until_183_fixed(std::cin,'\t');
+  MatrixWeighted m(std::cin,'\t');
   if (indata.present()) {
     std::cin.rdbuf(cin_buffer); // restore old input buffer
@@ -140 +127 @@
     delete infile;
   }
-  // Remove until HERE below when
-  // http://baseplugins.thep.lu.se/ticket/183 fixed.
-  MatrixWeighted* m=NULL;
-  if (assay.present())
-    create_matrix_until_183_fixed(&m, m_tmp_until_183_fixed, assay.value());
-  else
-    m = &m_tmp_until_183_fixed;
-  // HERE remove until here.
-
-  std::transform(m->begin(), m->end(), m->begin(), CleanUpMatrix());
+
+  std::transform(m.begin(), m.end(), m.begin(), CleanUpMatrix());
   std::vector<double> target;
   ( assay.present() ?
-    create_target(target, *m, assay.value(), target_median.value()) :
-    create_target(target, *m, target_median.value()) );
+    create_target(target, m, assay.value(), target_median.value()) :
+    create_target(target, m, target_median.value()) );
   std::transform(target.begin(), target.end(),
                  target.begin(), theplu::yat::utility::Log<double>());
-  std::transform(data_iterator(m->begin()), data_iterator(m->end()),
-                 data_iterator(m->begin()), theplu::yat::utility::Log<double>());
+  std::transform(data_iterator(m.begin()), data_iterator(m.end()),
+                 data_iterator(m.begin()), theplu::yat::utility::Log<double>());
   // q = min(100,target_size/10) but no smaller than 10
   unsigned int q=target.size()/10;
@@ -163 +142 @@
   qQuantileNormalizer qqn(target.begin(), target.end(), q);
   ColumnNormalizer<qQuantileNormalizer> cn(qqn);
-  MatrixWeighted result(m->rows(),m->columns());
-  cn(*m,result);
+  MatrixWeighted result(m.rows(),m.columns());
+  cn(m,result);
   std::transform(data_iterator(result.begin()), data_iterator(result.end()),
                  data_iterator(result.begin()), theplu::yat::utility::Exp<double>());
@@ -182 +161 @@
   }
 
-  // clean up until http://baseplugins.thep.lu.se/ticket/183 fixed.
-  if (assay.present())
-    delete m;
-
   return EXIT_SUCCESS;
-}
-
-
-void create_matrix_until_183_fixed(MatrixWeighted** m,
-                                   const MatrixWeighted& m_tmp_183,
-                                   const std::string& assay)
-{
-  std::ifstream is(assay.c_str());
-  std::vector<size_t> idx;
-  while (is.good()) {
-    size_t i;
-    is >> i;
-    if (is.good()) idx.push_back(i);
-    std::string line;
-    getline(is, line);
-    if (idx.size()>m_tmp_183.columns())
-      throw std::runtime_error(std::string("183_tmp: Too many annotation ") +
-                               "columns wrt data matrix");
-  }
-
-  if (*m) delete *m;
-  size_t rows=m_tmp_183.rows();
-  size_t cols=idx.size();
-  *m=new MatrixWeighted(rows,cols);
-  for (size_t i=0; i<rows; ++i)
-    for (size_t j=0; j<cols; ++j)
-      (**m)(i,j)=m_tmp_183(i,idx[j]-1);
 }