Merge branch 'develop' into toppas_outdir

AUTHORS

@@ -92,6 +92,7 @@ the authors tag in the respective file header.
  - Radu Suciu
  - Ralf Gabriels
  - Rene Hussong
+ - Rick Helmus
  - Ruben Grünberg
  - Samuel Wein
  - Sandro Andreotti

CHANGELOG

@@ -12,6 +12,7 @@ PR - Pull Request (on GitHub), i.e. integration of a new feature or bugfix
 ------------------------------------------------------------------------------------------
 ----                                OpenMS 3.3.0     (under development)              ----
 ------------------------------------------------------------------------------------------
+
 What's new:
 - Changes breaking backwards compatibility: 
   - the QualityControl TOPP tool has some renamed parameters and supports output directories (#7497)
@@ -22,14 +23,13 @@ Misc:
 - TOPPAS 
     - supports writing results to output directories  (for TOPP tools which have such parameters) (#7497)
     - TOPPAS tutorial enhanced (#7497)
-
+- FeatureFinderMetabo
+    - added report_smoothed_intensities parameter (#7594)
 
 ------------------------------------------------------------------------------------------
 ----                                OpenMS 3.2.0       (released 09/2024)             ----
 ------------------------------------------------------------------------------------------
 
-
-
 What's new:
 - Changes breaking backwards compatibility: 
    - Rename of parameters for TOPP tool FeatureFinderCentroided (debug -> advanced), and PeakPickerWavelet/TOFCalibration (optimization -> optimization:type) (#7154)

src/openms/include/OpenMS/FEATUREFINDER/FeatureFindingMetabo.h

@@ -306,7 +306,8 @@ namespace OpenMS
     bool enable_RT_filtering_;
     String isotope_filtering_model_;
     bool use_smoothed_intensities_;
-
+    bool report_smoothed_intensities_;
+
     bool use_mz_scoring_C13_;
     bool use_mz_scoring_by_element_range_;
     bool report_convex_hulls_;

src/openms/source/ANALYSIS/QUANTITATION/IsobaricIsotopeCorrector.cpp

@@ -43,14 +43,10 @@ namespace OpenMS
     {
       OPENMS_LOG_DEBUG << "Correction matrix is the identity matrix." << std::endl;
       OPENMS_LOG_DEBUG << correction_matrix << std::endl;
-
-      // workaround: TMT11plex has a special case where the correction matrix is the identity matrix
-      if (quant_method->getMethodName() != "tmt11plex")
-      {        
-        throw Exception::InvalidParameter(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
+
+      throw Exception::InvalidParameter(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
                                           "IsobaricIsotopeCorrector: The given isotope correction matrix is an identity matrix leading to no correction. "
-                                          "Please provide a valid isotope_correction matrix as it was provided with the sample kit!");
-      }
+                                          "Please provide a valid isotope_correction matrix as it was provided with the sample kit!");      
     }
 
     Eigen::FullPivLU<Eigen::MatrixXd> ludecomp(correction_matrix.getEigenMatrix());

src/openms/source/ANALYSIS/QUANTITATION/TMTElevenPlexQuantitationMethod.cpp

@@ -75,18 +75,21 @@ void TMTElevenPlexQuantitationMethod::setDefaultParams_()
     defaults_.setValue("reference_channel", "126", "The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C).");
     defaults_.setValidStrings("reference_channel", TMTElevenPlexQuantitationMethod::channel_names_);
 
-    defaults_.setValue("correction_matrix", std::vector<std::string>{"0.0/0.0/0.0/0.0",
-                                                                              "0.0/0.0/0.0/0.0",
-                                                                              "0.0/0.0/0.0/0.0",
-                                                                              "0.0/0.0/0.0/0.0",
-                                                                              "0.0/0.0/0.0/0.0",
-                                                                              "0.0/0.0/0.0/0.0",
-                                                                              "0.0/0.0/0.0/0.0",
-                                                                              "0.0/0.0/0.0/0.0",
-                                                                              "0.0/0.0/0.0/0.0",
-                                                                              "0.0/0.0/0.0/0.0",
-                                                                              "0.0/0.0/0.0/0.0"},
-                       "Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>; e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'");
+    // default: Product Number: A37725 Lot Number: ZF395505
+    defaults_.setValue("correction_matrix", std::vector<std::string>{
+        "0.0/0.0/8.6/0.3",
+        "0.0/0.1/7.8/0.1",
+        "0.0/0.8/6.9/0.1",
+        "0.0/7.4/7.4/0.0",
+        "0.0/1.5/6.2/0.2",
+        "0.0/1.5/5.7/0.1",
+        "0.0/2.6/4.8/0.0",
+        "0.0/2.2/4.6/0.0",
+        "0.0/2.8/4.5/0.1",
+        "0.1/2.9/3.8/0.0",
+        "0.0/3.9/2.8/0.0"
+        }, 
+        "Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>; e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'");
 
     defaultsToParam_();
 }

src/openms/source/ANALYSIS/QUANTITATION/TMTSixPlexQuantitationMethod.cpp

@@ -45,17 +45,16 @@ namespace OpenMS
     defaults_.setMinInt("reference_channel", 126);
     defaults_.setMaxInt("reference_channel", 131);
 
-    //    {0.0, 1.0, 5.9, 0.2},   //114
-    //    {0.0, 2.0, 5.6, 0.1},
-    //    {0.0, 3.0, 4.5, 0.1},
-    //    {0.1, 4.0, 3.5, 0.1}    //117
-    defaults_.setValue("correction_matrix", std::vector<std::string>{"0.0/0.0/0.0/0.0",
-                                                               "0.0/0.0/0.0/0.0",
-                                                               "0.0/0.0/0.0/0.0",
-                                                               "0.0/0.0/0.0/0.0",
-                                                               "0.0/0.0/0.0/0.0",
-                                                               "0.0/0.0/0.0/0.0"},
-                       "Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>; e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'");
+    // default: Product Number: 90061 Lot Number: ZE386964
+    defaults_.setValue("correction_matrix", std::vector<std::string>{
+      "0.0/0.0/8.6/0.3",
+      "0.0/0.1/7.8/0.1",
+      "0.0/1.5/6.2/0.2",
+      "0.0/1.5/5.7/0.1",
+      "0.0/3.1/3.6/0.0",
+      "0.1/2.9/3.8/0.0"
+      },
+      "Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>; e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'");
 
     defaultsToParam_();
   }

src/openms/source/FEATUREFINDER/FeatureFindingMetabo.cpp

@@ -265,6 +265,8 @@ namespace OpenMS
 
     defaults_.setValue("use_smoothed_intensities", "true", "Use LOWESS intensities instead of raw intensities.", {"advanced"});
     defaults_.setValidStrings("use_smoothed_intensities", {"false","true"});
+    defaults_.setValue("report_smoothed_intensities", "true", "Report smoothed intensities (only if use_smoothed_intensities is true).", {"advanced"});
+    defaults_.setValidStrings("report_smoothed_intensities", {"false","true"});
 
     defaults_.setValue("report_convex_hulls", "false", "Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably).");
     defaults_.setValidStrings("report_convex_hulls", {"false","true"});
@@ -307,6 +309,14 @@ namespace OpenMS
 
     isotope_filtering_model_ = param_.getValue("isotope_filtering_model").toString();
     use_smoothed_intensities_ = param_.getValue("use_smoothed_intensities").toBool();
+    bool use_smoothed = param_.getValue("use_smoothed_intensities").toBool();
+    bool report_smoothed = param_.getValue("report_smoothed_intensities").toBool();
+    if (report_smoothed && !use_smoothed) {
+      OPENMS_LOG_WARN << "Warning: 'report_smoothed_intensities' is set to true, but 'use_smoothed_intensities' is false. Ignoring 'report_smoothed_intensities'." << std::endl;
+      report_smoothed = false;
+    }
+    use_smoothed_intensities_ = use_smoothed;
+    report_smoothed_intensities_ = report_smoothed;
 
     use_mz_scoring_C13_ = param_.getValue("mz_scoring_13C").toBool();
     report_convex_hulls_ = param_.getValue("report_convex_hulls").toBool();
@@ -1002,20 +1012,20 @@ namespace OpenMS
 
       if (report_summed_ints_)
       {
-        f.setIntensity(feat_hypos[hypo_idx].getSummedFeatureIntensity(use_smoothed_intensities_));
+        f.setIntensity(feat_hypos[hypo_idx].getSummedFeatureIntensity(report_smoothed_intensities_));
       }
       else
       {
-        f.setIntensity(feat_hypos[hypo_idx].getMonoisotopicFeatureIntensity(use_smoothed_intensities_));
+        f.setIntensity(feat_hypos[hypo_idx].getMonoisotopicFeatureIntensity(report_smoothed_intensities_));
       }
 
       f.setWidth(feat_hypos[hypo_idx].getFWHM());
       f.setCharge(feat_hypos[hypo_idx].getCharge());
       f.setMetaValue(3, feat_hypos[hypo_idx].getLabel());
-      f.setMetaValue("max_height", feat_hypos[hypo_idx].getMaxIntensity(use_smoothed_intensities_));
+      f.setMetaValue("max_height", feat_hypos[hypo_idx].getMaxIntensity(report_smoothed_intensities_));
 
       // store isotope intensities
-      std::vector<double> all_ints(feat_hypos[hypo_idx].getAllIntensities(use_smoothed_intensities_));
+      std::vector<double> all_ints(feat_hypos[hypo_idx].getAllIntensities(report_smoothed_intensities_));
       f.setMetaValue(Constants::UserParam::NUM_OF_MASSTRACES, all_ints.size());
       if (report_convex_hulls_) f.setConvexHulls(feat_hypos[hypo_idx].getConvexHulls());
       f.setOverallQuality(feat_hypos[hypo_idx].getScore());

src/openms/source/METADATA/SpectrumLookup.cpp

@@ -318,11 +318,18 @@ namespace OpenMS
       boost::sregex_token_iterator current_begin(native_id.begin(), native_id.end(), regexp, subgroups);
       boost::sregex_token_iterator current_end(native_id.end(), native_id.end(), regexp, subgroups);
       matches.insert(matches.end(), current_begin, current_end);
-      if (matches.size() == 1) // default case: one native identifier
+
+      if (matches.size() < subgroups.size()) {
+          OPENMS_LOG_WARN << "native_id '" << native_id <<"' is invalid. Could not extract scan number." << std::endl;
+          return -1;
+      }
+
+      if (subgroups.size() == 1) // default case: one native identifier
       {
         try
         {
-          String value = String(matches[0]);
+          // In case of merged spectra the last native id matches the scan number of the merged scan.
+          String value = String(matches[matches.size() - 1]);
           if (native_id_type_accession == "MS:1000774")
           {
             return value.toInt() + 1; // if the native ID is index=.., the scan number is usually considered index+1 (especially for pepXML)
@@ -334,27 +341,31 @@ namespace OpenMS
         }
         catch (Exception::ConversionError&)
         {
-          OPENMS_LOG_WARN << "Value: '" << String(matches[0]) << "' could not be converted to int in string. Native ID='" << native_id << "'" << std::endl;
+          OPENMS_LOG_WARN << "Value: '" << String(matches[matches.size() - 1]) << "' could not be converted to int in string. Native ID='" << native_id << "'" << std::endl;
           return -1;
         }
       }
-      else if (matches.size() == 2) // special case: wiff file with two native identifiers
+      else if (subgroups.size() == 2) // special case: wiff file with two native identifiers
       {
         try
         {
-          if (String(matches[1]).toInt() < 1000) // checks if value of experiment is smaller than 1000 (cycle * 1000 + experiment)
+          // In case of merged spectra the last native id matches the scan number of the merged scan.
+          String cycle_str = matches[matches.size() - 2];
+          String experiment_str = matches[matches.size() - 1];
+
+          if (experiment_str.toInt() < 1000) // checks if value of experiment is smaller than 1000 (cycle * 1000 + experiment)
           {
-            int value = String(matches[0]).toInt() * 1000 + String(matches[1]).toInt();
+            int value = cycle_str.toInt() * 1000 + experiment_str.toInt();
             return value; 
           }
           else
           {
-            throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "The value of experiment is too large and can not be handled properly.", String(matches[1]));
+            throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "The value of experiment is too large and can not be handled properly.", experiment_str);
           }
         }
         catch (Exception::ConversionError&)
         {
-          OPENMS_LOG_WARN << "Value: '" << String(matches[0]) << "' could not be converted to int in string. Native ID='" 
+          OPENMS_LOG_WARN << "Values: '" << matches[matches.size() - 2] << "', '" << matches[matches.size() - 1] << "' could not be converted to int in string. Native ID='" 
             << native_id << "' accession='" << native_id_type_accession << "'" << std::endl;
           return -1;
         }

src/tests/class_tests/openms/source/TMTElevenPlexQuantitationMethod_test.cpp

@@ -181,8 +181,8 @@ START_SECTION((virtual Matrix<double> getIsotopeCorrectionMatrix() const ))
   {
     for (size_t j = 0; j < m.cols(); ++j)
     {
-      if (i == j) { TEST_REAL_SIMILAR(m(i,j), 1.0) }
-      else { TEST_REAL_SIMILAR(m(i,j), 0.0) }
+      if (i == j) { TEST_TRUE(m(i,j) > 0.5 ) } // diagonal entries should be largest
+      else { TEST_TRUE(m(i,j) < 0.5) }
     }
   }
 }

src/tests/class_tests/openms/source/TMTSixPlexQuantitationMethod_test.cpp

@@ -113,10 +113,8 @@ START_SECTION((virtual Matrix<double> getIsotopeCorrectionMatrix() const ))
   {
     for(size_t j = 0; j < m.cols(); ++j)
     {
-      if (i == j)
-        TEST_REAL_SIMILAR(m(i,j), 1.0)
-      else
-        TEST_REAL_SIMILAR(m(i,j), 0.0)
+      if (i == j) { TEST_TRUE(m(i,j) > 0.5) } // diagonal entries should be largest
+      else { TEST_TRUE(m(i,j) < 0.5) }
     }
   }
 }