Tmt vis

.github/workflows/openms_ci_matrix_full.yml

@@ -453,14 +453,17 @@ jobs:
     - name: Create tarball
       if: steps.set-vars.outputs.pkg_type != 'none' && startsWith(matrix.os, 'ubuntu') && runner.arch == 'arm64'
       run: |
+        # Write the archive to RUNNER_TEMP, i.e. OUTSIDE ${{ github.workspace }} (the directory
+        # being archived). Writing it in-tree makes the output file grow inside the directory tar
+        # is reading, so GNU tar reports "tar: .: file changed as we read it" and exits 1, which
+        # fails the step under `bash -e`.
         tar --exclude='bld/*' \
-            --exclude='OpenMS-${{ steps.create_changelog.outputs.version_number }}.tar.gz' \
             --exclude='THIRDPARTY/**' \
             --exclude='contrib/**' \
             --exclude='.git/**' \
             --exclude='.github/**' \
             --exclude='vcpkg*/**' \
-            -czf OpenMS-${{ steps.create_changelog.outputs.version_number }}.tar.gz -C ${{ github.workspace }} .
+            -czf ${{ runner.temp }}/OpenMS-${{ steps.create_changelog.outputs.version_number }}.tar.gz -C ${{ github.workspace }} .
 
    # Upload the source tar
     - name: Upload source tar as artifact
@@ -469,7 +472,7 @@ jobs:
       with:
         name: OpenMS-${{ steps.create_changelog.outputs.version_number }}.tar.gz
         path: |
-          ${{ github.workspace }}/OpenMS-${{ steps.create_changelog.outputs.version_number }}.tar.gz
+          ${{ runner.temp }}/OpenMS-${{ steps.create_changelog.outputs.version_number }}.tar.gz
 
 
     # Only upload docs when we are building the package, use the ubuntu build simply 'cause its fast

cmake/add_library_macros.cmake

@@ -55,22 +55,19 @@ endfunction(convert_to_unity_build)
 ## @note This macro will do nothing outside of Windows since the linker will find the libs.
 macro(copy_dll_to_extern_bin targetname)
   if (WIN32)
-    if (CMAKE_GENERATOR MATCHES "Visual Studio")
-      file(TO_NATIVE_PATH "${OPENMS_HOST_BINARY_DIRECTORY}/src/tests/class_tests/bin/$(ConfigurationName)/$(TargetFileName)" DLL_TEST_TARGET)
-      file(TO_NATIVE_PATH "${OPENMS_HOST_BINARY_DIRECTORY}/src/tests/class_tests/bin/$(ConfigurationName)" DLL_TEST_TARGET_PATH)
+    get_property(_copy_dll_is_multi_config GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
+    if(_copy_dll_is_multi_config)
+      file(TO_NATIVE_PATH "${OPENMS_HOST_BINARY_DIRECTORY}/src/tests/class_tests/bin/$<CONFIG>/$<TARGET_FILE_NAME:${targetname}>" DLL_TEST_TARGET)
+      file(TO_NATIVE_PATH "${OPENMS_HOST_BINARY_DIRECTORY}/src/tests/class_tests/bin/$<CONFIG>" DLL_TEST_TARGET_PATH)
 
-      file(TO_NATIVE_PATH "${OPENMS_HOST_BINARY_DIRECTORY}/doc/doxygen/parameters/$(ConfigurationName)/$(TargetFileName)" DLL_DOC_TARGET)
-      file(TO_NATIVE_PATH "${OPENMS_HOST_BINARY_DIRECTORY}/doc/doxygen/parameters/$(ConfigurationName)" DLL_DOC_TARGET_PATH)
-    elseif(NOT GENERATOR_IS_MULTI_CONFIG)
-      file(TO_NATIVE_PATH "${OPENMS_HOST_BINARY_DIRECTORY}/src/tests/class_tests/bin/" DLL_TEST_TARGET)
+      file(TO_NATIVE_PATH "${OPENMS_HOST_BINARY_DIRECTORY}/doc/doxygen/parameters/$<CONFIG>/$<TARGET_FILE_NAME:${targetname}>" DLL_DOC_TARGET)
+      file(TO_NATIVE_PATH "${OPENMS_HOST_BINARY_DIRECTORY}/doc/doxygen/parameters/$<CONFIG>" DLL_DOC_TARGET_PATH)
+    else()
+      file(TO_NATIVE_PATH "${OPENMS_HOST_BINARY_DIRECTORY}/src/tests/class_tests/bin/$<TARGET_FILE_NAME:${targetname}>" DLL_TEST_TARGET)
       file(TO_NATIVE_PATH "${OPENMS_HOST_BINARY_DIRECTORY}/src/tests/class_tests/bin/" DLL_TEST_TARGET_PATH)
 
-      file(TO_NATIVE_PATH "${OPENMS_HOST_BINARY_DIRECTORY}/doc/doxygen/parameters/" DLL_DOC_TARGET)
+      file(TO_NATIVE_PATH "${OPENMS_HOST_BINARY_DIRECTORY}/doc/doxygen/parameters/$<TARGET_FILE_NAME:${targetname}>" DLL_DOC_TARGET)
       file(TO_NATIVE_PATH "${OPENMS_HOST_BINARY_DIRECTORY}/doc/doxygen/parameters/" DLL_DOC_TARGET_PATH)
-    else()
-      message(WARNING "Sorry, multiconfig generators on windows other than Visual Studio not supported yet.
-              Please look for the line of this error and implement some CMake Generator expressions to copy
-              DLLs to the binaries, or modify your environment for the tests to find all library DLLs.")
     endif()
     add_custom_command(TARGET ${targetname}
             POST_BUILD
@@ -237,7 +234,8 @@ function(openms_add_library)
             $<TARGET_FILE_DIR:${openms_add_library_TARGET_NAME}>
             )
 
-    if(GENERATOR_IS_MULTI_CONFIG)
+    get_property(is_multi_config GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
+    if(is_multi_config)
       file(TO_NATIVE_PATH "${OPENMS_HOST_BINARY_DIRECTORY}/src/tests/class_tests/bin/$<CONFIG>/" DLL_TEST_TARGET_PATH)
       file(TO_NATIVE_PATH "${OPENMS_HOST_BINARY_DIRECTORY}/doc/doxygen/parameters/$<CONFIG>/" DLL_DOC_TARGET_PATH)
     else()

src/openms/include/OpenMS/ANALYSIS/ID/IDBoostGraph.h

@@ -133,7 +133,7 @@ namespace OpenMS
       template < typename Edge, typename Graph >
       void examine_edge(Edge e, const Graph & tg)
       {
-        if (m.find(e.m_target) == m.end())
+        if (!m.contains(e.m_target))
         {
           next_v = boost::add_vertex(tg[e.m_target], gs.back());
           m[e.m_target] = next_v;

src/openms/include/OpenMS/ANALYSIS/QUANTITATION/IsobaricQuantitationMethod.h

@@ -14,6 +14,8 @@
 
 #include <OpenMS/KERNEL/Peak2D.h>
 
+#include <array>
+#include <string_view>
 #include <utility>
 #include <vector>
 
@@ -32,6 +34,31 @@ namespace OpenMS
   {
 public:
 
+    /// Identifies a concrete isobaric quantitation method. UNKNOWN is used as a sentinel (disabled/none).
+    enum class MethodType
+    {
+      UNKNOWN = 0,
+      TMT_6PLEX,
+      TMT_10PLEX,
+      TMT_11PLEX,
+      TMT_16PLEX,
+      TMT_18PLEX,
+      TMT_32PLEX,
+      TMT_35PLEX,
+      ITRAQ_4PLEX,
+      ITRAQ_8PLEX,
+      SIZE_OF_METHODTYPE ///< keep last
+    };
+
+    /// String identifiers for each MethodType, indexed by static_cast<int>(MethodType).
+    static const std::array<std::string_view, static_cast<int>(MethodType::SIZE_OF_METHODTYPE)> METHOD_TYPE_NAMES;
+
+    /// Returns the string identifier for a given MethodType.
+    static std::string_view methodTypeName(MethodType mt);
+
+    /// Returns the MethodType corresponding to @p name, or MethodType::UNKNOWN if not found.
+    static MethodType methodTypeFromName(std::string_view name);
+
     /**
       @brief Summary of an isobaric quantitation channel.
     */
@@ -78,6 +105,9 @@ namespace OpenMS
     */
     virtual const String& getMethodName() const = 0;
 
+    /// Returns the MethodType enum value of this quantitation method.
+    virtual MethodType getMethodType() const = 0;
+
     /**
       @brief Returns information on the different channels used by the quantitation method.
 

src/openms/include/OpenMS/ANALYSIS/QUANTITATION/ItraqEightPlexQuantitationMethod.h

@@ -40,6 +40,8 @@ namespace OpenMS
 
     const String& getMethodName() const override;
 
+    MethodType getMethodType() const override { return METHOD_TYPE; }
+
     const IsobaricChannelList& getChannelInformation() const override;
 
     Size getNumberOfChannels() const override;
@@ -50,13 +52,12 @@ namespace OpenMS
 
     /// @}
 
+    static constexpr MethodType METHOD_TYPE = MethodType::ITRAQ_8PLEX;
+
   private:
     /// the actual information on the different itraq8plex channels.
     IsobaricChannelList channels_;
 
-    /// The name of the quantitation method.
-    static const String name_;
-
     /// The reference channel for this experiment.
     Size reference_channel_;
 

src/openms/include/OpenMS/ANALYSIS/QUANTITATION/ItraqFourPlexQuantitationMethod.h

@@ -38,23 +38,24 @@ namespace OpenMS
 
     const String& getMethodName() const override;
 
+    MethodType getMethodType() const override { return METHOD_TYPE; }
+
     const IsobaricChannelList& getChannelInformation() const override;
 
     Size getNumberOfChannels() const override;
 
     Matrix<double> getIsotopeCorrectionMatrix() const override;
 
     Size getReferenceChannel() const override;
-    
+
     /// @}
 
+    static constexpr MethodType METHOD_TYPE = MethodType::ITRAQ_4PLEX;
+
 private:
     /// the actual information on the different itraq4plex channels.
     IsobaricChannelList channels_;
 
-    /// The name of the quantitation method.
-    static const String name_;
-
     /// The reference channel for this experiment.
     Size reference_channel_;
 

src/openms/include/OpenMS/ANALYSIS/QUANTITATION/TMTEighteenPlexQuantitationMethod.h

@@ -40,6 +40,8 @@ namespace OpenMS
 
     const String& getMethodName() const override;
 
+    MethodType getMethodType() const override { return METHOD_TYPE; }
+
     const IsobaricChannelList& getChannelInformation() const override;
 
     Size getNumberOfChannels() const override;
@@ -50,13 +52,12 @@ namespace OpenMS
 
     /// @}
 
+    static constexpr MethodType METHOD_TYPE = MethodType::TMT_18PLEX;
+
   private:
     /// the actual information on the different tmt18plex channels.
     IsobaricChannelList channels_;
 
-    /// The name of the quantitation method.
-    static const String name_;
-
     /// The reference channel for this experiment.
     Size reference_channel_;
 

src/openms/include/OpenMS/ANALYSIS/QUANTITATION/TMTElevenPlexQuantitationMethod.h

@@ -40,6 +40,8 @@ namespace OpenMS
 
     const String& getMethodName() const override;
 
+    MethodType getMethodType() const override { return METHOD_TYPE; }
+
     const IsobaricChannelList& getChannelInformation() const override;
 
     Size getNumberOfChannels() const override;
@@ -50,13 +52,12 @@ namespace OpenMS
 
     /// @}
 
+    static constexpr MethodType METHOD_TYPE = MethodType::TMT_11PLEX;
+
   private:
     /// the actual information on the different tmt11plex channels.
     IsobaricChannelList channels_;
 
-    /// The name of the quantitation method.
-    static const String name_;
-
     /// The reference channel for this experiment.
     Size reference_channel_;
 

src/openms/include/OpenMS/ANALYSIS/QUANTITATION/TMTSixPlexQuantitationMethod.h

@@ -40,6 +40,8 @@ namespace OpenMS
 
     const String& getMethodName() const override;
 
+    MethodType getMethodType() const override { return METHOD_TYPE; }
+
     const IsobaricChannelList& getChannelInformation() const override;
 
     Size getNumberOfChannels() const override;
@@ -50,13 +52,12 @@ namespace OpenMS
 
     /// @}
 
+    static constexpr MethodType METHOD_TYPE = MethodType::TMT_6PLEX;
+
   private:
     /// the actual information on the different tmt 6plex channels.
     IsobaricChannelList channels_;
 
-    /// The name of the quantitation method.
-    static const String name_;
-
     /// The reference channel for this experiment.
     Size reference_channel_;
 

src/openms/include/OpenMS/ANALYSIS/QUANTITATION/TMTSixteenPlexQuantitationMethod.h

@@ -40,6 +40,8 @@ namespace OpenMS
 
     const String& getMethodName() const override;
 
+    MethodType getMethodType() const override { return METHOD_TYPE; }
+
     const IsobaricChannelList& getChannelInformation() const override;
 
     Size getNumberOfChannels() const override;
@@ -50,13 +52,12 @@ namespace OpenMS
 
     /// @}
 
+    static constexpr MethodType METHOD_TYPE = MethodType::TMT_16PLEX;
+
   private:
     /// the actual information on the different tmt16plex channels.
     IsobaricChannelList channels_;
 
-    /// The name of the quantitation method.
-    static const String name_;
-
     /// The reference channel for this experiment.
     Size reference_channel_;
 

src/openms/include/OpenMS/ANALYSIS/QUANTITATION/TMTTenPlexQuantitationMethod.h

@@ -40,6 +40,8 @@ namespace OpenMS
 
     const String& getMethodName() const override;
 
+    MethodType getMethodType() const override { return METHOD_TYPE; }
+
     const IsobaricChannelList& getChannelInformation() const override;
 
     Size getNumberOfChannels() const override;
@@ -50,13 +52,12 @@ namespace OpenMS
 
     /// @}
 
+    static constexpr MethodType METHOD_TYPE = MethodType::TMT_10PLEX;
+
   private:
     /// the actual information on the different tmt10plex channels.
     IsobaricChannelList channels_;
 
-    /// The name of the quantitation method.
-    static const String name_;
-
     /// The reference channel for this experiment.
     Size reference_channel_;
 

src/openms/include/OpenMS/ANALYSIS/QUANTITATION/TMTThirtyFivePlexQuantitationMethod.h

@@ -32,21 +32,22 @@ namespace OpenMS{
             /// @brief Methods to implement from IsobaricQuantitationMethod
             /// @{
             const String& getMethodName() const override;
+            MethodType getMethodType() const override { return METHOD_TYPE; }
             const IsobaricChannelList& getChannelInformation() const override;
             Size getNumberOfChannels() const override;
             Matrix<double> getIsotopeCorrectionMatrix() const override;
             Size getReferenceChannel() const override;
             /// @}
+
+            static constexpr MethodType METHOD_TYPE = MethodType::TMT_35PLEX;
+
         private:
             /// The actual information on the different TMT 35plex channels.
             IsobaricChannelList channels_;
 
-            /// The name of the quantitation method.
-            static const String name_;
-
             /// The reference channel for this experiment.
             Size reference_channel_;
-            
+
             /// List of available channel names as they are presented to the user
             static const std::vector<std::string> channel_names_;
 

src/openms/include/OpenMS/ANALYSIS/QUANTITATION/TMTThirtyTwoPlexQuantitationMethod.h

@@ -32,21 +32,22 @@ namespace OpenMS{
             /// @brief Methods to implement from IsobaricQuantitationMethod
             /// @{
             const String& getMethodName() const override;
+            MethodType getMethodType() const override { return METHOD_TYPE; }
             const IsobaricChannelList& getChannelInformation() const override;
             Size getNumberOfChannels() const override;
             Matrix<double> getIsotopeCorrectionMatrix() const override;
             Size getReferenceChannel() const override;
             /// @}
+
+            static constexpr MethodType METHOD_TYPE = MethodType::TMT_32PLEX;
+
         private:
             /// The actual information on the different TMT 32plex channels.
             IsobaricChannelList channels_;
 
-            /// The name of the quantitation method.
-            static const String name_;
-
             /// The reference channel for this experiment.
             Size reference_channel_;
-            
+
             /// List of available channel names as they are presented to the user
             static const std::vector<std::string> channel_names_;
 

src/openms/include/OpenMS/CHEMISTRY/DigestionEnzymeDB.h

@@ -110,19 +110,19 @@ namespace OpenMS
     /// returns true if the db contains a enzyme with the given name (supports synonym names)
     bool hasEnzyme(const String& name) const
     {
-      return (enzyme_names_.find(name) != enzyme_names_.end());
+      return (enzyme_names_.contains(name));
     }
 
     /// returns true if the db contains a enzyme with the given regex
     bool hasRegEx(const String& cleavage_regex) const
     {
-      return (enzyme_regex_.find(cleavage_regex) != enzyme_regex_.end());
+      return (enzyme_regex_.contains(cleavage_regex));
     }
 
     /// returns true if the db contains the enzyme of the given pointer
     bool hasEnzyme(const DigestionEnzymeType* enzyme) const
     {
-      return (const_enzymes_.find(enzyme) != const_enzymes_.end() );
+      return (const_enzymes_.contains(enzyme) );
     }
     //@}