Merge branch 'feature/oswSpeedUp' of github.com:jcharkow/OpenMS into …

…feature/oswSpeedUp
jcharkow · Dec 19, 2023 · f64476a · f64476a
2 parents 7423fa4 + 562e281
commit f64476a
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -8,3 +8,5 @@ updates:
     directory: "/"
     schedule:
       interval: "daily"
+    ignore:
+      - dependency-name: "vcpkg"
diff --git a/doc/OpenMS_tutorial/developer_Tutorial.doxygen b/doc/OpenMS_tutorial/developer_Tutorial.doxygen
@@ -159,7 +159,6 @@ The extensible %OpenMS library implements common mass spectrometric data process
     - Identification:
         - Database search:
             - Peptides (Tool %SimpleSearchEngine and its classes - started simple but is, by now, rather complete peptide identification engine)
-            - Protein-RNA cross-links (Tool %RNPxlSearch and its classes)
             - Protein-Protein cross-links (Tool OpenPepXL)
         - Spectral library search:
             - Tool SpecLibSearcher and its classes

diff --git a/doc/doxygen/images/TOPPAS_Ecoli_Identification.png b/doc/doxygen/images/TOPPAS_Ecoli_Identification.png
diff --git a/doc/doxygen/images/TOPPAS_edges.png b/doc/doxygen/images/TOPPAS_edges.png
diff --git a/doc/doxygen/images/TOPPAS_example_profile_data_processing.png b/doc/doxygen/images/TOPPAS_example_profile_data_processing.png
diff --git a/doc/doxygen/images/TOPPAS_parameters.png b/doc/doxygen/images/TOPPAS_parameters.png
diff --git a/doc/doxygen/images/TOPPAS_run_options.png b/doc/doxygen/images/TOPPAS_run_options.png
diff --git a/doc/doxygen/images/TOPPAS_simple_example.png b/doc/doxygen/images/TOPPAS_simple_example.png
diff --git a/doc/doxygen/public/TOPP.doxygen b/doc/doxygen/public/TOPP.doxygen
@@ -173,7 +173,6 @@
   <b>Cross-linking</b>
   - @subpage TOPP_OpenPepXL - Search for peptide pairs linked with a labeled cross-linker.
   - @subpage TOPP_OpenPepXLLF - Search for cross-linked peptide pairs in tandem MS spectra.
-  - @subpage TOPP_RNPxlSearch - Annotates RNA-to-peptide cross-links in MS/MS spectra.
   - @subpage TOPP_RNPxlXICFilter - Removes MS2 spectra from treatment based on the fold change between control and treatment for RNA-to-peptide cross-linking experiments.
   - @subpage TOPP_XFDR - Calculates false discovery rate estimates on cross-link identifications.
 

diff --git a/doc/doxygen/public/TOPPAS.doxygen b/doc/doxygen/public/TOPPAS.doxygen
diff --git a/share/OpenMS/examples/ID/Ecoli_MS2_small.mzML b/share/OpenMS/examples/ID/Ecoli_MS2_small.mzML
diff --git a/share/OpenMS/examples/TOPPAS/Ecoli_Identification.toppas b/share/OpenMS/examples/TOPPAS/Ecoli_Identification.toppas
diff --git a/share/OpenMS/examples/TOPPAS/QualityControl.toppas b/share/OpenMS/examples/TOPPAS/QualityControl.toppas
diff --git a/share/OpenMS/examples/TOPPAS/peakpicker_tutorial.toppas b/share/OpenMS/examples/TOPPAS/peakpicker_tutorial.toppas
diff --git a/src/openms/source/APPLICATIONS/ToolHandler.cpp b/src/openms/source/APPLICATIONS/ToolHandler.cpp
@@ -169,7 +169,6 @@ namespace OpenMS
     tools_map["Resampler"] = Internal::ToolDescription("Resampler", cat_signal_proc_misc);
     tools_map["RNADigestor"] = Internal::ToolDescription("RNADigestor", cat_rna);
     tools_map["RNAMassCalculator"] = Internal::ToolDescription("RNAMassCalculator", cat_rna);
-    tools_map["RNPxlSearch"] = Internal::ToolDescription("RNPxlSearch", cat_crosslinking);
     tools_map["RNPxlXICFilter"] = Internal::ToolDescription("RNPxlXICFilter", cat_crosslinking);
     tools_map["SageAdapter"] = Internal::ToolDescription("SageAdapter", cat_ID_search);
     tools_map["SeedListGenerator"] = Internal::ToolDescription("SeedListGenerator", cat_quant);

diff --git a/src/openms/source/FORMAT/HANDLERS/TraMLHandler.cpp b/src/openms/source/FORMAT/HANDLERS/TraMLHandler.cpp
@@ -6,6 +6,7 @@
 // $Authors: Andreas Bertsch, Hannes Roest $
 // --------------------------------------------------------------------------
 
+#include "OpenMS/CONCEPT/LogStream.h"
 #include <OpenMS/FORMAT/HANDLERS/TraMLHandler.h>
 
 #include <OpenMS/CHEMISTRY/ModificationsDB.h>
@@ -1046,6 +1047,8 @@ namespace OpenMS::Internal
               // means no annotation and no input cvParam - to write out a cvParam, use Residue::NonIdentified
               break;
             // invalid values
+            case Residue::Zp1Ion: OPENMS_LOG_ERROR << "Zp1 ions not supported. Ignoring." << std::endl; break;
+            case Residue::Zp2Ion: OPENMS_LOG_ERROR << "Zp2 ions not supported. Ignoring." << std::endl; break;
             case Residue::Full: break;
             case Residue::Internal: break;
             case Residue::NTerminal: break;

diff --git a/src/topp/OpenMSInfo.cpp b/src/topp/OpenMSInfo.cpp
@@ -76,6 +76,9 @@ Architecture: 64 bit
 // We do not want this class to show up in the docu:
 /// @cond TOPPCLASSES
 
+/// this needs to be done before TOPPBase is initialized, since it will set OMP's max_threads to 1
+const auto max_threads = Internal::OpenMSBuildInfo::getOpenMPMaxNumThreads();
+
 class TOPPOpenMSInfo : public TOPPBase
 {
 public:
@@ -123,7 +126,7 @@ class TOPPOpenMSInfo : public TOPPBase
     cout << "LP-Solver    : GLPK\n";
 #endif
     #ifdef _OPENMP
-    cout << "OpenMP       : " << "enabled (maxThreads = " << Internal::OpenMSBuildInfo::getOpenMPMaxNumThreads() << ")" << "\n";
+    cout << "OpenMP       : " << "enabled (maxThreads = " << max_threads << ")" << "\n";
     #else
     cout << "OpenMP       : " << "disabled" << "\n";
     #endif

diff --git a/workflow/cwl/RNPxlSearch.cwl b/workflow/cwl/RNPxlSearch.cwl