Changeset 1432 for trunk/yat/normalization/QuantileNormalizer.cc

Timestamp:

Aug 25, 2008, 3:54:18 PM (15 years ago)

Author:

Peter

Message:

refs #416 moving quantile normalizer to new dir. Also moved the algorithm to a class (rather than free function).

File:

• trunk/yat/normalization/QuantileNormalizer.cc (copied) (copied from trunk/yat/utility/utility.cc) (3 diffs)

trunk/yat/normalization/QuantileNormalizer.cc

@@ -4 +4 @@
   Copyright (C) 2005, 2006 Jari Häkkinen, Markus Ringnér
   Copyright (C) 2007 Jari Häkkinen, Peter Johansson
+  Copyright (C) 2008 Peter Johansson
 
-  This file is part of the yat library, http://trac.thep.lu.se/yat
+  This file is part of the yat library, http://dev.thep.lu.se/yat
 
   The yat library is free software; you can redistribute it and/or
@@ -23 +24 @@
 */
 
-#include "utility.h"
+#include "QuantileNormalizer.h"
 
-#include "Matrix.h"
-#include "stl_utility.h"
-#include "VectorConstView.h"
 #include "yat/statistics/Averager.h"
 
-#include <sstream>
-#include <string>
+#include "yat/utility/Matrix.h"
+#include "yat/utility/VectorConstView.h"
 
 namespace theplu {
 namespace yat {
-namespace utility {
+namespace normalization {
 
-  bool is_double(const std::string& s)
+  void QuantileNormalizer::operator()(utility::Matrix& data) const
   {
-    return is<double>(s);
-  }
-  
-
-  bool is_equal(std::string s, std::string other)
-  {
-    std::stringstream ss(s);
-    std::string s2;
-    ss >> s2; // to trim surrounding whitespaces
-    to_lower(s2);
-    // Check that nothing is left on stream
-    std::string s3;
-    ss >> s3;
-    if(s3.size())
-      return false;
-    return (other==s2);
-  }
-
-
-  bool is_float(const std::string& s)
-  {
-    return is<float>(s);
-  }
-
-
-  bool is_int(const std::string& s)
-  {
-    return is<int>(s);
-  }
-
-  bool is_nan(const std::string& s)
-  {
-    return is_equal(s, "nan");
-  }
-
-
-  void quantile_normalize(Matrix& data)
-  {
-    Matrix data_copy(data);
+    utility::Matrix data_copy(data);
     
     // sort columns in copy
@@ -92 +52 @@
     for (size_t column=0; column<data.columns(); ++column){
       std::vector<size_t> index;
-      yat::utility::sort_index(index, data.column_const_view(column));
+      utility::sort_index(index, data.column_const_view(column));
                                
       for (size_t row=0; row<data.rows(); ++row)