Changeset 759 for trunk/yat

Timestamp:

Feb 19, 2007, 8:41:25 PM (16 years ago)

Author:

Jari Häkkinen

Message:

Fixes #171 and addresses #2. A few more GSL_error exceptions. Removed Jari comments.

Location:

trunk/yat

Files:

• regression/Local.cc (modified) (1 diff)
• utility/WeNNI.cc (modified) (2 diffs)
• utility/kNNI.cc (modified) (2 diffs)
• utility/matrix.cc (modified) (2 diffs)
• utility/matrix.h (modified) (2 diffs)
• utility/vector.cc (modified) (1 diff)
• utility/vector.h (modified) (13 diffs)

trunk/yat/regression/Local.cc

@@ -52 +52 @@
   {
     if (step_size==0 || nof_points<3){
-      // Peter to Jari, throw exception?
-      std::cerr << "theplu::regression::Local "
+      std::cerr << "yat::regression::Local "
                 << "Parameters invalid. Fitting ignored." << std::endl;
       return;

trunk/yat/utility/WeNNI.cc

@@ -53 +53 @@
   {
     for (unsigned int i=0; i<data_.rows(); i++) {
-      // Jari, avoid copying in next line
       std::vector<std::pair<u_int,double> > distance=calculate_distances(i);
       std::sort(distance.begin(),distance.end(),
@@ -64 +63 @@
         for (std::vector<u_int>::const_iterator k=knn.begin(); k!=knn.end();
              ++k) {
-          // Jari, a small number needed here, use something standardized.
           // Avoid division with zero (perfect match vectors)
           double d=(distance[*k].second ? distance[*k].second : 1e-10);

trunk/yat/utility/kNNI.cc

@@ -58 +58 @@
   {
     for (unsigned int i=0; i<mv_rows_.size(); i++) {
-      // Jari, avoid copying in next line
       std::vector<std::pair<u_int,double> > distance=
         calculate_distances(mv_rows_[i]);
@@ -70 +69 @@
           for (std::vector<u_int>::const_iterator k=knn.begin(); k!=knn.end();
                ++k) {
-            // Jari, a small number needed here, use something standardized.
             // Avoid division with zero (perfect match vectors)
             double d=(distance[*k].second ? distance[*k].second : 1e-10);

trunk/yat/utility/matrix.cc

@@ -78 +78 @@
     : view_(NULL)
   {
-    // Markus to Jari, somewhere we should check that quiet_NaNs are supported
-    // std::numeric_limits<double>::has_quiet_NaN has to be true.
-    // Also in vector
-
     // read the data file and store in stl vectors (dynamically
     // expandable)
@@ -114 +110 @@
         }
         else {
-          // Jari, this should be communicated with as an exception.
-          std::cerr << "Warning: '" << element 
-                    << "' is not accepted as a matrix element." << std::endl;
+          std::stringstream ss("Warning: '");
+          ss << element << "' is not accepted as a matrix element.";
+          throw IO_error(ss.str());
         }
       }           

trunk/yat/utility/matrix.h

@@ -137 +137 @@
        file marker.
 
-       \throw GSL_error if memory allocation fails.
+       \throw GSL_error if memory allocation fails, IO_error if
+       unexpected input is found in the input stream.
     */
     explicit matrix(std::istream &, char sep='\0') 
@@ -189 +190 @@
     /// @return A const pointer to the internal GSL matrix.
     ///
-    const gsl_matrix* gsl_matrix_p(void) const;
+    const gsl_matrix* gsl_matrix_p(void) const;
 
     ///
     /// @return A pointer to the internal GSL matrix.
     ///
-    // Jari, is this needed?
-    gsl_matrix* gsl_matrix_p(void);
+    gsl_matrix* gsl_matrix_p(void);
 
     ///

trunk/yat/utility/vector.cc

@@ -145 +145 @@
         }
         else {
-          // Jari, this should be communicated with as an exception.
-          // std::cerr << "Warning: '" << element 
-          //           << "' is not an integer." << std::endl;
+          std::stringstream ss("Warning: '");
+          ss << element << "' is not an integer.";
+          throw IO_error(ss.str());
         }
       } 

trunk/yat/utility/vector.h

@@ -204 +204 @@
        to the vector is at end of file marker.
 
-       \throw GSL_error if memory allocation fails.
+       \throw GSL_error if memory allocation fails, IO_error if
+       unexpected input is found in the input stream.
     */
     explicit vector(std::istream &, char sep='\0')
@@ -263 +264 @@
     /// @return The maximum value of the vector.
     ///
-    // Jari, doxygen group as Finding maximum and minimum elements
     double max(void) const;
 
@@ -270 +270 @@
     /// vector. The lowest index has precedence.
     ///
-    // Jari, doxygen group as Finding maximum and minimum elements
     size_t max_index(void) const;
 
@@ -276 +275 @@
     /// @return The minimum value of the vector.
     ///
-    // Jari, doxygen group as Finding maximum and minimum elements
     double min(void) const;
 
@@ -283 +281 @@
     /// vector. The lowest index has precedence.
     ///
-    // Jari, doxygen group as Finding maximum and minimum elements
     size_t min_index(void) const;
 
@@ -291 +288 @@
     /// respectively.
     ///
-    // Jari, doxygen group as Finding maximum and minimum elements
     std::pair<double,double> minmax(void) const;
 
@@ -299 +295 @@
     /// \a pair, respectively. The lowest index has precedence.
     ///
-    // Jari, doxygen group as Finding maximum and minimum elements
     std::pair<size_t,size_t> minmax_index(void) const;
 
@@ -334 +329 @@
     /// Set all elements to \a value.
     ///
-    // Jari, doxygen group as Initializing vector elements
     void set_all(const double& value);
 
@@ -342 +336 @@
     /// one.
     ///
-    // Jari, doxygen group as Initializing vector elements
     void set_basis(const size_t i);
     
@@ -348 +341 @@
     /// Set all elements to zero.
     ///
-    // Jari, doxygen group as Initializing vector elements
     void set_zero(void);
 
@@ -361 +353 @@
     /// Bug in gsl: if vector contains NaN an infinite loop is entered.
     ///
-    // Markus to Jari, doxygen group as Exchanging elements ????
     void sort(void);
 
@@ -422 +413 @@
     /// @return Reference to element \a i.
     ///
-    // Jari, doxygen group as Accessing vector elements
     double& operator[](size_t i);
 
@@ -430 +420 @@
     /// @return The value of element \a i.
     ///
-    // Jari, doxygen group as Accessing vector elements
     const double& operator[](size_t i) const;