LoadMSP (#544)

* fix: prioritized the use of subordinate metadata when choosing between feature level and subordinate level

* fix: update to feature map after call to targetedMatching

* feat, test: added rawDataHandler member for Library

* fix, feat, tests: added LoadMSP and associated tests

* fix: matchSpectra requirements for msp

* fix: changed getRequirements to getFilenameRequirements

* fix: renamed library to spectra library

* tests: fixed broken tests

* fix: failing UIUtilities_test

* fix, tests: updated RawDataHandler pointer logic for spectra_library

Author: dmccloskey

src/examples/source/SmartPeakGUI.cpp

@@ -646,7 +646,7 @@ int main(int argc, char** argv)
           }
           else
           {
-            auto requirements = workflow_manager_.getRequirements(buildCommandsFromNames.commands_);
+            auto requirements = workflow_manager_.getFilenameRequirements(buildCommandsFromNames.commands_);
             bool missing_requirement = workflow_manager_.isMissingRequirements(application_handler_.filenames_, requirements);
             if (missing_requirement)
             {

src/smartpeak/include/SmartPeak/core/ApplicationProcessor.h

@@ -48,7 +48,7 @@ namespace SmartPeak
     /* IProcessorDescription */
     virtual std::string getDescription() const override { return ""; }
     virtual ParameterSet getParameterSchema() const override { return ParameterSet(); };
-    virtual std::vector<std::string> getRequirements() const override { return {}; };
+    virtual std::vector<std::string> getFilenameRequirements() const override { return {}; };
     virtual std::set<std::string> getInputs() const override { return {}; };
     virtual std::set<std::string> getOutputs() const override { return {}; };
 

src/smartpeak/include/SmartPeak/core/RawDataHandler.h

@@ -132,6 +132,12 @@ namespace SmartPeak
     const OpenMS::MRMFeatureQC& getFeatureBackgroundEstimations() const;
     std::shared_ptr<OpenMS::MRMFeatureQC>& getFeatureBackgroundEstimationsShared();
 
+    void setSpectraLibrary(const OpenMS::MSExperiment& library);
+    void setSpectraLibrary(std::shared_ptr<OpenMS::MSExperiment>& library);
+    OpenMS::MSExperiment& getSpectraLibrary();
+    const OpenMS::MSExperiment& getSpectraLibrary() const;
+    std::shared_ptr<OpenMS::MSExperiment>& getSpectraLibraryShared();
+
     void setFeatureMapHistory(const OpenMS::FeatureMap& feature_map_history);
     OpenMS::FeatureMap& getFeatureMapHistory();
     const OpenMS::FeatureMap& getFeatureMapHistory() const;
@@ -208,5 +214,6 @@ namespace SmartPeak
     std::shared_ptr<OpenMS::MRMFeatureQC> feature_background_qc_ = nullptr;  ///< Feature QCs; shared between all raw data handlers in the sequence segment
     std::shared_ptr<OpenMS::MRMFeatureQC> feature_rsd_estimations_ = nullptr;  ///< Percent RSD estimations; shared between all raw data handlers in the sequence segment
     std::shared_ptr<OpenMS::MRMFeatureQC> feature_background_estimations_ = nullptr;  ///< Background interference estimations; shared between all raw data handlers in the sequence segment
+    std::shared_ptr<OpenMS::MSExperiment> spectra_library_;  ///< MS data derived from a (spectral) database used for annotation; shared between all raw data handlers in the sequence
   };
 }

src/smartpeak/include/SmartPeak/core/RawDataProcessor.h

@@ -44,7 +44,7 @@ namespace SmartPeak
 
     /* IProcessorDescription */
     virtual ParameterSet getParameterSchema() const override { return ParameterSet(); };
-    virtual std::vector<std::string> getRequirements() const override { return {}; };
+    virtual std::vector<std::string> getFilenameRequirements() const override { return {}; };
     virtual std::set<std::string> getInputs() const override { return {}; };
     virtual std::set<std::string> getOutputs() const override { return {}; };
 

src/smartpeak/include/SmartPeak/core/RawDataProcessors/CalculateIsotopicPurities.h

@@ -39,7 +39,7 @@ namespace SmartPeak
     virtual std::string getName() const override { return "CALCULATE_MDV_ISOTOPIC_PURITIES"; }
     virtual std::string getDescription() const override { return "Calculate MDV Isotopic Purities."; }
     virtual ParameterSet getParameterSchema() const override;
-    virtual std::vector<std::string> getRequirements() const override;
+    virtual std::vector<std::string> getFilenameRequirements() const override;
     virtual std::set<std::string> getOutputs() const override;
     virtual std::set<std::string> getInputs() const override;
 

src/smartpeak/include/SmartPeak/core/RawDataProcessors/CalculateMDVAccuracies.h

@@ -39,7 +39,7 @@ namespace SmartPeak
     virtual std::string getName() const override { return "CALCULATE_MDV_ACCURACIES"; }
     virtual std::string getDescription() const override { return "Compare MDVs to Theoretical"; }
     virtual ParameterSet getParameterSchema() const override;
-    virtual std::vector<std::string> getRequirements() const override;
+    virtual std::vector<std::string> getFilenameRequirements() const override;
     virtual std::set<std::string> getOutputs() const override;
     virtual std::set<std::string> getInputs() const override;
 

src/smartpeak/include/SmartPeak/core/RawDataProcessors/CalculateMDVs.h

@@ -39,7 +39,7 @@ namespace SmartPeak
     virtual std::string getName() const override { return "CALCULATE_MDVS"; }
     virtual std::string getDescription() const override { return "Calculate MDVs."; }
     virtual ParameterSet getParameterSchema() const override;
-    virtual std::vector<std::string> getRequirements() const override;
+    virtual std::vector<std::string> getFilenameRequirements() const override;
     virtual std::set<std::string> getOutputs() const override;
     virtual std::set<std::string> getInputs() const override;
 

src/smartpeak/include/SmartPeak/core/RawDataProcessors/CheckFeatures.h

@@ -39,7 +39,7 @@ namespace SmartPeak
     virtual std::string getName() const override { return "CHECK_FEATURES"; }
     virtual std::string getDescription() const override { return "Flag and score transitions and transition groups based on a user defined criteria."; }
     virtual ParameterSet getParameterSchema() const override;
-    virtual std::vector<std::string> getRequirements() const override;
+    virtual std::vector<std::string> getFilenameRequirements() const override;
     virtual std::set<std::string> getOutputs() const override;
     virtual std::set<std::string> getInputs() const override;
 

src/smartpeak/include/SmartPeak/core/RawDataProcessors/CheckFeaturesBackgroundInterferences.h

@@ -39,7 +39,7 @@ namespace SmartPeak
     virtual std::string getName() const override { return "CHECK_FEATURES_BACKGROUND_INTERFERENCES"; }
     virtual std::string getDescription() const override { return "Flag and score transitions and transition groups based on a user defined criteria."; }
     virtual ParameterSet getParameterSchema() const override;
-    virtual std::vector<std::string> getRequirements() const override;
+    virtual std::vector<std::string> getFilenameRequirements() const override;
     virtual std::set<std::string> getOutputs() const override;
     virtual std::set<std::string> getInputs() const override;
 

src/smartpeak/include/SmartPeak/core/RawDataProcessors/CheckFeaturesRSDs.h

@@ -39,7 +39,7 @@ namespace SmartPeak
     virtual std::string getName() const override { return "CHECK_FEATURES_RSDS"; }
     virtual std::string getDescription() const override { return "Flag and score transitions and transition groups based on a user defined criteria."; }
     virtual ParameterSet getParameterSchema() const override;
-    virtual std::vector<std::string> getRequirements() const override;
+    virtual std::vector<std::string> getFilenameRequirements() const override;
     virtual std::set<std::string> getOutputs() const override;
     virtual std::set<std::string> getInputs() const override;