Add mandatory context message to Exception::InvalidSize (OpenMS#8437)

Copilot · jpfeuffer · web-flow · commit 63474d02b2e3 · 2025-12-07T21:44:27.000+01:00
* Initial plan

* Add mandatory context message parameter to Exception::InvalidSize

Co-authored-by: jpfeuffer &lt;8102638+jpfeuffer@users.noreply.github.com&gt;

* Fix Tutorial_Precursor.cpp to use updated InvalidSize constructor

Co-authored-by: jpfeuffer &lt;8102638+jpfeuffer@users.noreply.github.com&gt;

---------

Co-authored-by: copilot-swe-agent[bot] &lt;198982749+Copilot@users.noreply.github.com&gt;
Co-authored-by: jpfeuffer &lt;8102638+jpfeuffer@users.noreply.github.com&gt;
diff --git a/doc/code_examples/Tutorial_Precursor.cpp b/doc/code_examples/Tutorial_Precursor.cpp
@@ -34,7 +34,7 @@ int main(int argc, const char** argv)
     const vector<Precursor>& precursors = spectrum.getPrecursors();
 
     // size check & throw exception if needed 
-    if (precursors.empty()) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, precursors.size());
+    if (precursors.empty()) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, precursors.size(), "precursors vector must not be empty");
 
     // get m/z and intensity of precursor
     double precursor_mz = precursors[0].getMZ();
diff --git a/src/openms/include/OpenMS/CONCEPT/Exception.h b/src/openms/include/OpenMS/CONCEPT/Exception.h
@@ -268,13 +268,14 @@ namespace OpenMS
       The constructor has an additional argument: the value of of the
       requested size.
       @param	size the size causing the problem
+      @param	message context message explaining why the size is invalid
 
       @ingroup Exceptions
     */
     class OPENMS_DLLAPI InvalidSize : public BaseException
     {
     public:
-      InvalidSize(const char* file, int line, const char* function, Size size = 0) noexcept;
+      InvalidSize(const char* file, int line, const char* function, Size size, const std::string& message) noexcept;
     };
 
 
diff --git a/src/openms/source/ANALYSIS/DECHARGING/ILPDCWrapper.cpp b/src/openms/source/ANALYSIS/DECHARGING/ILPDCWrapper.cpp
@@ -157,7 +157,7 @@ namespace OpenMS
 
     if (pairs_clique_ordered.size() != pairs.size())
     {
-      throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, pairs_clique_ordered.size() - pairs.size());
+      throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, pairs_clique_ordered.size() - pairs.size(), "pairs_clique_ordered size does not match pairs size");
     }
     /* swap pairs, such that edges are order by cliques (so we can make clean cuts) */
     pairs.swap(pairs_clique_ordered);
diff --git a/src/openms/source/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.cpp b/src/openms/source/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.cpp
@@ -497,7 +497,7 @@ namespace OpenMS
     scored_spectra.resize(annotated_spectra.size());
     if (compute_features && scored_spectra.size() != features.size())
     {
-      throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
+      throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, scored_spectra.size(), "scored_spectra size does not match features size");
     }
     for (Size i = 0; i < annotated_spectra.size(); ++i)
     {
@@ -587,7 +587,7 @@ namespace OpenMS
   {
     if (compute_features && scored_spectra.size() != features.size())
     {
-      throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
+      throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, scored_spectra.size(), "scored_spectra size does not match features size");
     }
     std::map<std::string,UInt> transition_best_spec;
     for (UInt i = 0; i < scored_spectra.size(); ++i)
@@ -774,7 +774,7 @@ namespace OpenMS
   {
     if (spectra.size() != features.size())
     {
-      throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
+      throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, spectra.size(), "spectra size does not match features size");
     }
 
     std::vector<Size> no_matches_idx; // to keep track of those features without a match
diff --git a/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp b/src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp
@@ -718,8 +718,8 @@ namespace OpenMS
     {
       case Residue::AIon: intensity = a_intensity_; break;
       case Residue::BIon: intensity = b_intensity_; break;
-      case Residue::CIon: if (peptide.size() < 2) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 1); intensity = c_intensity_; break;
-      case Residue::XIon: if (peptide.size() < 2) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 1); intensity = x_intensity_; break;
+      case Residue::CIon: if (peptide.size() < 2) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 1, "peptide must have at least 2 residues for c-ion generation"); intensity = c_intensity_; break;
+      case Residue::XIon: if (peptide.size() < 2) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 1, "peptide must have at least 2 residues for x-ion generation"); intensity = x_intensity_; break;
       case Residue::YIon: intensity = y_intensity_; break;
       case Residue::ZIon: intensity = z_intensity_; break;
       // TODO use different intensities?
diff --git a/src/openms/source/CHEMISTRY/TheoreticalSpectrumGeneratorXLMS.cpp b/src/openms/source/CHEMISTRY/TheoreticalSpectrumGeneratorXLMS.cpp
@@ -251,8 +251,8 @@ namespace OpenMS
     {
       case Residue::AIon: intensity = a_intensity_; break;
       case Residue::BIon: intensity = b_intensity_; break;
-      case Residue::CIon: if (peptide.size() < 2) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 1); intensity = c_intensity_; break;
-      case Residue::XIon: if (peptide.size() < 2) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 1); intensity = x_intensity_; break;
+      case Residue::CIon: if (peptide.size() < 2) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 1, "peptide must have at least 2 residues for c-ion generation"); intensity = c_intensity_; break;
+      case Residue::XIon: if (peptide.size() < 2) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 1, "peptide must have at least 2 residues for x-ion generation"); intensity = x_intensity_; break;
       case Residue::YIon: intensity = y_intensity_; break;
       case Residue::ZIon: intensity = z_intensity_; break;
       default: break;
@@ -456,8 +456,8 @@ namespace OpenMS
     {
       case Residue::AIon: intensity = a_intensity_; break;
       case Residue::BIon: intensity = b_intensity_; break;
-      case Residue::CIon: if (peptide.size() < 2) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 1); intensity = c_intensity_; break;
-      case Residue::XIon: if (peptide.size() < 2) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 1); intensity = x_intensity_; break;
+      case Residue::CIon: if (peptide.size() < 2) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 1, "peptide must have at least 2 residues for c-ion generation"); intensity = c_intensity_; break;
+      case Residue::XIon: if (peptide.size() < 2) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 1, "peptide must have at least 2 residues for x-ion generation"); intensity = x_intensity_; break;
       case Residue::YIon: intensity = y_intensity_; break;
       case Residue::ZIon: intensity = z_intensity_; break;
       default: break;
@@ -1005,8 +1005,8 @@ namespace OpenMS
     {
       case Residue::AIon: intensity = a_intensity_; break;
       case Residue::BIon: intensity = b_intensity_; break;
-      case Residue::CIon: if (peptide.size() < 2) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 1); intensity = c_intensity_; break;
-      case Residue::XIon: if (peptide.size() < 2) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 1); intensity = x_intensity_; break;
+      case Residue::CIon: if (peptide.size() < 2) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 1, "peptide must have at least 2 residues for c-ion generation"); intensity = c_intensity_; break;
+      case Residue::XIon: if (peptide.size() < 2) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 1, "peptide must have at least 2 residues for x-ion generation"); intensity = x_intensity_; break;
       case Residue::YIon: intensity = y_intensity_; break;
       case Residue::ZIon: intensity = z_intensity_; break;
       default: break;
diff --git a/src/openms/source/CONCEPT/Exception.cpp b/src/openms/source/CONCEPT/Exception.cpp
@@ -145,8 +145,8 @@ namespace OpenMS
       GlobalExceptionHandler::getInstance().setMessage(what());
     }
 
-    InvalidSize::InvalidSize(const char* file, int line, const char* function, Size size) noexcept :
-      BaseException(file, line, function, "InvalidSize", "the given size was not expected: " + String(size))
+    InvalidSize::InvalidSize(const char* file, int line, const char* function, Size size, const std::string& message) noexcept :
+      BaseException(file, line, function, "InvalidSize", "the given size was not expected: " + String(size) + " (" + message + ")")
     {
       GlobalExceptionHandler::getInstance().setMessage(what());
     }
diff --git a/src/openms/source/FEATUREFINDER/MassTraceDetection.cpp b/src/openms/source/FEATUREFINDER/MassTraceDetection.cpp
@@ -120,7 +120,7 @@ namespace OpenMS
           {
             if (fda[idx].size() != spec.size())
             {
-              throw OpenMS::Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, spec.size());
+              throw OpenMS::Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, spec.size(), "FloatDataArray size does not match spectrum size");
             }
             ++valid_count;
           }
diff --git a/src/openms/source/FEATUREFINDER/MultiplexDeltaMassesGenerator.cpp b/src/openms/source/FEATUREFINDER/MultiplexDeltaMassesGenerator.cpp
@@ -356,7 +356,7 @@ namespace OpenMS
     if (delta_masses_list_.empty())
     {
       // Even in the case of a singlet search, there should be one mass shift (zero mass shift) in the list.
-      throw OpenMS::Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 0);
+      throw OpenMS::Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 0, "delta_masses_list_ must not be empty");
     }
 
     unsigned n = delta_masses_list_[0].getDeltaMasses().size();    // n=1 for singlets, n=2 for doublets, n=3 for triplets, n=4 for quadruplets
diff --git a/src/openms/source/FEATUREFINDER/MultiplexFiltering.cpp b/src/openms/source/FEATUREFINDER/MultiplexFiltering.cpp
@@ -483,7 +483,7 @@ namespace OpenMS
       // Calculate Pearson and Spearman rank correlations
       if ((intensities_model.size() < isotopes_per_peptide_min_) || (intensities_data.size() < isotopes_per_peptide_min_))
       {
-        throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 0);
+        throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 0, "intensity vectors too small for correlation calculation");
       }
       double correlation_Pearson = OpenMS::Math::pearsonCorrelationCoefficient(intensities_model.begin(), intensities_model.end(), intensities_data.begin(), intensities_data.end());
       double correlation_Spearman = OpenMS::Math::rankCorrelationCoefficient(intensities_model.begin(), intensities_model.end(), intensities_data.begin(), intensities_data.end());
diff --git a/src/openms/source/FEATUREFINDER/MultiplexFilteringProfile.cpp b/src/openms/source/FEATUREFINDER/MultiplexFilteringProfile.cpp
@@ -332,7 +332,7 @@ namespace OpenMS
       // Calculate Pearson and Spearman rank correlations
       if ((intensities_model.size() < isotopes_per_peptide_min_) || (intensities_data.size() < isotopes_per_peptide_min_))
       {
-        throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 0);
+        throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 0, "intensity vectors too small for correlation calculation");
       }
       double correlation_Pearson = OpenMS::Math::pearsonCorrelationCoefficient(intensities_model.begin(), intensities_model.end(), intensities_data.begin(), intensities_data.end());
       double correlation_Spearman = OpenMS::Math::rankCorrelationCoefficient(intensities_model.begin(), intensities_model.end(), intensities_data.begin(), intensities_data.end());
diff --git a/src/openms/source/PROCESSING/MISC/SplineInterpolatedPeaks.cpp b/src/openms/source/PROCESSING/MISC/SplineInterpolatedPeaks.cpp
@@ -171,7 +171,7 @@ namespace OpenMS
   {
     if (packages_.empty())
     {
-      throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 0);
+      throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 0, "packages_ must not be empty");
     }
     return Navigator(&packages_, pos_max_, scaling);
   }
diff --git a/src/openms_gui/source/VISUAL/MISC/GUIHelpers.cpp b/src/openms_gui/source/VISUAL/MISC/GUIHelpers.cpp
@@ -288,7 +288,7 @@ namespace OpenMS
   GUIHelpers::OverlapDetector::OverlapDetector(int levels)
   {
     if (levels <= 0)
-      throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, levels);
+      throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, levels, "levels must be positive");
     rows_.resize(levels, 0);
   }
 
diff --git a/src/topp/MultiplexResolver.cpp b/src/topp/MultiplexResolver.cpp
@@ -405,7 +405,7 @@ class TOPPMultiplexResolver :
     
     if (pattern.size() != delta_mass_matched.size())
     {
-       throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, delta_mass_matched.size());
+       throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, delta_mass_matched.size(), "pattern size does not match delta_mass_matched size");
     }
     
     // new complete consensus feature
diff --git a/src/topp/SpectraMerger.cpp b/src/topp/SpectraMerger.cpp
@@ -105,7 +105,7 @@ class TOPPSpectraMerger :
     exp.updateRanges();
 
     auto levels = exp.getMSLevels();
-    if (levels.empty()) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, levels.size());
+    if (levels.empty()) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, levels.size(), "experiment has no MS levels");
     int min_ms_level = levels.front();
     int max_ms_level = levels.back();
     //-------------------------------------------------------------

Original file line number	Diff line number	Diff line change
`@@ -157,7 +157,7 @@ namespace OpenMS`
`157`	`157`
`158`	`158`	`if (pairs_clique_ordered.size() != pairs.size())`
`159`	`159`	`{`
`160`		`- throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, pairs_clique_ordered.size() - pairs.size());`
	`160`	`+ throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, pairs_clique_ordered.size() - pairs.size(), "pairs_clique_ordered size does not match pairs size");`
`161`	`161`	`}`
`162`	`162`	`/* swap pairs, such that edges are order by cliques (so we can make clean cuts) */`
`163`	`163`	`pairs.swap(pairs_clique_ordered);`
Original file line number	Diff line number	Diff line change
`@@ -497,7 +497,7 @@ namespace OpenMS`
`497`	`497`	`scored_spectra.resize(annotated_spectra.size());`
`498`	`498`	`if (compute_features && scored_spectra.size() != features.size())`
`499`	`499`	`{`
`500`		`- throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);`
	`500`	`+ throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, scored_spectra.size(), "scored_spectra size does not match features size");`
`501`	`501`	`}`
`502`	`502`	`for (Size i = 0; i < annotated_spectra.size(); ++i)`
`503`	`503`	`{`
`@@ -587,7 +587,7 @@ namespace OpenMS`
`587`	`587`	`{`
`588`	`588`	`if (compute_features && scored_spectra.size() != features.size())`
`589`	`589`	`{`
`590`		`- throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);`
	`590`	`+ throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, scored_spectra.size(), "scored_spectra size does not match features size");`
`591`	`591`	`}`
`592`	`592`	`std::map<std::string,UInt> transition_best_spec;`
`593`	`593`	`for (UInt i = 0; i < scored_spectra.size(); ++i)`
`@@ -774,7 +774,7 @@ namespace OpenMS`
`774`	`774`	`{`
`775`	`775`	`if (spectra.size() != features.size())`
`776`	`776`	`{`
`777`		`- throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);`
	`777`	`+ throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, spectra.size(), "spectra size does not match features size");`
`778`	`778`	`}`
`779`	`779`
`780`	`780`	`std::vector<Size> no_matches_idx; // to keep track of those features without a match`
Original file line number	Diff line number	Diff line change
`@@ -145,8 +145,8 @@ namespace OpenMS`
`145`	`145`	`GlobalExceptionHandler::getInstance().setMessage(what());`
`146`	`146`	`}`
`147`	`147`
`148`		`- InvalidSize::InvalidSize(const char* file, int line, const char* function, Size size) noexcept :`
`149`		`- BaseException(file, line, function, "InvalidSize", "the given size was not expected: " + String(size))`
	`148`	`+ InvalidSize::InvalidSize(const char* file, int line, const char* function, Size size, const std::string& message) noexcept :`
	`149`	`+ BaseException(file, line, function, "InvalidSize", "the given size was not expected: " + String(size) + " (" + message + ")")`
`150`	`150`	`{`
`151`	`151`	`GlobalExceptionHandler::getInstance().setMessage(what());`
`152`	`152`	`}`
Original file line number	Diff line number	Diff line change
`@@ -120,7 +120,7 @@ namespace OpenMS`
`120`	`120`	`{`
`121`	`121`	`if (fda[idx].size() != spec.size())`
`122`	`122`	`{`
`123`		`- throw OpenMS::Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, spec.size());`
	`123`	`+ throw OpenMS::Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, spec.size(), "FloatDataArray size does not match spectrum size");`
`124`	`124`	`}`
`125`	`125`	`++valid_count;`
`126`	`126`	`}`
Original file line number	Diff line number	Diff line change
`@@ -356,7 +356,7 @@ namespace OpenMS`
`356`	`356`	`if (delta_masses_list_.empty())`
`357`	`357`	`{`
`358`	`358`	`// Even in the case of a singlet search, there should be one mass shift (zero mass shift) in the list.`
`359`		`- throw OpenMS::Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 0);`
	`359`	`+ throw OpenMS::Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 0, "delta_masses_list_ must not be empty");`
`360`	`360`	`}`
`361`	`361`
`362`	`362`	`unsigned n = delta_masses_list_[0].getDeltaMasses().size(); // n=1 for singlets, n=2 for doublets, n=3 for triplets, n=4 for quadruplets`
Original file line number	Diff line number	Diff line change
`@@ -483,7 +483,7 @@ namespace OpenMS`
`483`	`483`	`// Calculate Pearson and Spearman rank correlations`
`484`	`484`	`if ((intensities_model.size() < isotopes_per_peptide_min_) \|\| (intensities_data.size() < isotopes_per_peptide_min_))`
`485`	`485`	`{`
`486`		`- throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 0);`
	`486`	`+ throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 0, "intensity vectors too small for correlation calculation");`
`487`	`487`	`}`
`488`	`488`	`double correlation_Pearson = OpenMS::Math::pearsonCorrelationCoefficient(intensities_model.begin(), intensities_model.end(), intensities_data.begin(), intensities_data.end());`
`489`	`489`	`double correlation_Spearman = OpenMS::Math::rankCorrelationCoefficient(intensities_model.begin(), intensities_model.end(), intensities_data.begin(), intensities_data.end());`