Merge pull request #2 from OpenMS/develop

Update my fork

.gitpod.yml

@@ -1,12 +1,15 @@
 tasks:
-  - init:     cp -r .vscode-gitpod .vscode && echo "Welcome!" 
-    prebuild: git config -f .gitmodules submodule.THIRDPARTY.shallow true && 
-              git submodule update --init THIRDPARTY &&
-              export PATH=$PATH$( find ${PWD}/THIRDPARTY/All -type d -printf ":%p" ) &&
-              export PATH=$PATH$( find ${PWD}/THIRDPARTY/Linux/64bit -type d -printf ":%p" ) &&
-              mkdir -p build && pushd build && cmake -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -DCMAKE_PREFIX_PATH='/contrib-build/;/usr/;/usr/local' -DBOOST_USE_STATIC=OFF ../ && make -j16 && popd
-    command:  export PATH=$PATH$( find ${PWD}/THIRDPARTY/All -type d -printf ":%p" ) &&
-              export PATH=$PATH$( find ${PWD}/THIRDPARTY/Linux/64bit -type d -printf ":%p" )
+  - init: >
+      cp -r .vscode-gitpod .vscode && echo "Welcome!" 
+      git config -f .gitmodules submodule.THIRDPARTY.shallow true && 
+      git submodule update --init THIRDPARTY &&
+      export PATH=$PATH$( find ${PWD}/THIRDPARTY/All -type d -printf ":%p" ) &&
+      export PATH=$PATH$( find ${PWD}/THIRDPARTY/Linux/64bit -type d -printf ":%p" ) &&
+      mkdir -p build && pushd build && cmake -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -DCMAKE_PREFIX_PATH='/contrib-build/;/usr/;/usr/local' -DBOOST_USE_STATIC=OFF ../ &&
+      make -j16 && popd
+    command:  >
+      export PATH=$PATH$( find ${PWD}/THIRDPARTY/All -type d -printf ":%p" ) &&
+      export PATH=$PATH$( find ${PWD}/THIRDPARTY/Linux/64bit -type d -printf ":%p" )
 image:
   file: .gitpod.Dockerfile
 github:
@@ -37,4 +40,4 @@ vscode:
     - cschlosser.doxdocgen@0.7.2:g0DIKlW09t+j2Xi04fzrAA==
     - hbenl.vscode-test-explorer@2.19.2:8rKHUShFJJd0UivektEkng==
     - fredericbonnet.cmake-test-adapter@0.10.0:Fb9mp0fAtp8s6LKtpzJAyw==
-    - notskm.clang-tidy@0.5.1:+QMYmPGGWj0QCN6sba42Vw==
+    - notskm.clang-tidy@0.5.1:+QMYmPGGWj0QCN6sba42Vw==

AUTHORS

@@ -21,6 +21,7 @@ the authors tag in the respective file header.
  - Daniel Jameson
  - Darren Kessner
  - David Wojnar
+ - David Voigt
  - Dilek Dere
  - Dimitri Schachmann
  - Dominik Schmitz

CHANGELOG

@@ -19,6 +19,7 @@ Adapters/Third-party support:
 - Added basic Triqler export
 - ParamEditor with more convenient StringList editing  (#5135)
 - TOPPAS: add a `recent files` submenu
+- removed InspectAdapter
 
 Further fixes:
 - support for GLPK 5.x (#5127)

README.md

@@ -5,6 +5,7 @@ OpenMS
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/93e71bad214f46d2a534ec92dbc2efc9)](https://www.codacy.com/app/OpenMS/OpenMS?utm_source=github.com&utm_medium=referral&utm_content=OpenMS/OpenMS&utm_campaign=badger)
 [![Build Status](https://travis-ci.org/OpenMS/OpenMS.svg?branch=develop)](https://travis-ci.org/OpenMS/OpenMS)
 [![Project Stats](https://www.openhub.net/p/open-ms/widgets/project_thin_badge.gif)](https://www.openhub.net/p/open-ms)
+![Discord Shield](https://discordapp.com/api/guilds/832282841836159006/widget.png?style=shield)
 [![Gitter](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/OpenMS/OpenMS?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/openms-meta/README.html)
 [![documentation](https://codedocs.xyz/doxygen/doxygen.svg)](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/index.html)
@@ -38,7 +39,7 @@ Berlin, and the ETH Zürich.
 
 Features
 --------
-- Core C++ library under three-clause BSD licence using modern C++11
+- Core C++ library under three-clause BSD licence using modern C++17
 - Python bindings to the C++ API through pyOpenMS
 - Major community file formats supported (mzML, mzXML, mzIdentXML, pepXML etc)
 - Over 150+ individual analysis tools (TOPP Tools), covering most MS and LC-MS data processing and mining tasks

doc/code_examples/Tutorial_Param.cpp

@@ -28,6 +28,7 @@
 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 
+#include <OpenMS/CONCEPT/Types.h>
 #include <OpenMS/DATASTRUCTURES/Param.h>
 #include <iostream>
 
@@ -43,7 +44,7 @@ Int main()
   param.setValue("file:data:min_int", 0);
   param.setValue("file:data:max_int", 16459);
 
-  cout << "Name   : " << (String)(param.getValue("file:name")) << endl;
+  cout << "Name   : " << (string)(param.getValue("file:name")) << endl;
   cout << "Size   : " << (float)(param.getValue("file:size(MB)")) << endl;
   cout << "Min int: " << (UInt)(param.getValue("file:data:min_int")) << endl;
   cout << "Max int: " << (UInt)(param.getValue("file:data:max_int")) << endl;

doc/doxygen/parameters/DefaultParamHandlerDocumenter.cpp

@@ -189,18 +189,22 @@ void writeParameters(const String& class_name, const Param& param, bool table_on
   ofstream f((String("output/OpenMS_") + class_name + ".parameters").c_str());
 
   if (!table_only)
+  {
     f << "<B>Parameters of this class are:</B><BR><BR>\n";
+  }
   f << "<table border=\"1\" style=\"border-style:solid; border-collapse:collapse; border-color:#c0c0c0;\" width=\"100%\" cellpadding=\"4\">" << endl;
   f << "<tr style=\"border-bottom:1px solid black; background:#fffff0\"><th>Name</th><th>Type</th><th>Default</th><th>Restrictions</th><th>Description</th></tr>" << endl;
   String type, description, restrictions;
   for (Param::ParamIterator it = param.begin(); it != param.end(); ++it)
   {
     restrictions = "";
-    if (it->value.valueType() == DataValue::INT_VALUE || it->value.valueType() == DataValue::INT_LIST)
+    if (it->value.valueType() == ParamValue::INT_VALUE || it->value.valueType() == ParamValue::INT_LIST)
     {
       type = "int";
-      if (it->value.valueType() == DataValue::INT_LIST)
+      if (it->value.valueType() == ParamValue::INT_LIST)
+      {
         type += " list";
+      }
 
       //restrictions
       bool first = true;
@@ -212,14 +216,16 @@ void writeParameters(const String& class_name, const Param& param, bool table_on
       if (it->max_int != (numeric_limits<Int>::max)())
       {
         if (!first)
+        {
           restrictions += ' ';
+        }          
         restrictions += String("max: ") + it->max_int;
       }
     }
-    else if (it->value.valueType() == DataValue::DOUBLE_VALUE || it->value.valueType() == DataValue::DOUBLE_LIST)
+    else if (it->value.valueType() == ParamValue::DOUBLE_VALUE || it->value.valueType() == ParamValue::DOUBLE_LIST)
     {
       type = "float";
-      if (it->value.valueType() == DataValue::DOUBLE_LIST)
+      if (it->value.valueType() == ParamValue::DOUBLE_LIST)
         type += " list";
 
       //restrictions
@@ -236,10 +242,10 @@ void writeParameters(const String& class_name, const Param& param, bool table_on
         restrictions += String("max: ") + it->max_float;
       }
     }
-    else if (it->value.valueType() == DataValue::STRING_VALUE || it->value.valueType() == DataValue::STRING_LIST)
+    else if (it->value.valueType() == ParamValue::STRING_VALUE || it->value.valueType() == ParamValue::STRING_LIST)
     {
       type = "string";
-      if (it->value.valueType() == DataValue::STRING_LIST)
+      if (it->value.valueType() == ParamValue::STRING_LIST)
         type += " list";
 
       //restrictions
@@ -289,7 +295,7 @@ void writeParameters(const String& class_name, const Param& param, bool table_on
     }
 
     //replace # and @ in values
-    String value = it->value;
+    String value = it->value.toString(true);
     value.substitute("@", "XXnot_containedXX");
     value.substitute("XXnot_containedXX", "@@");
     value.substitute("#", "XXnot_containedXX");
@@ -480,7 +486,7 @@ int main(int argc, char** argv)
   // some classes require a QApplication
   QApplication app(argc, argv);
 
-  DOCME(TOPPViewBase);
+  DOCME2(TOPPViewBase, TOPPViewBase(TOPPViewBase::TOOL_SCAN::SKIP_SCAN));
   DOCME(TOPPASBase);
 
   DOCME2(Plot1DCanvas, Plot1DCanvas(Param(), nullptr));

doc/doxygen/parameters/TOPPDocumenter.cpp

@@ -100,7 +100,7 @@ void convertINI2HTML(const Param& p, ostream& os)
       s_attr += " item_advanced"; // optionally add advanced class
     if (it->tags.find("required") != it->tags.end())
       s_req += " item_required"; // optionally add required class
-    DataValue::DataType value_type = it->value.valueType();
+    ParamValue::ValueType value_type = it->value.valueType();
     //write opening tag
     os << indentation
        << "<div class=\"item"
@@ -123,7 +123,7 @@ void convertINI2HTML(const Param& p, ostream& os)
 
     //tags
     String list;
-    for (set<String>::const_iterator tag_it = it->tags.begin(); tag_it != it->tags.end(); ++tag_it)
+    for (auto tag_it = it->tags.begin(); tag_it != it->tags.end(); ++tag_it)
     {
       if (*tag_it == "advanced")
         continue; // do not list "advanced" or "required" (this is done by color coding)
@@ -139,8 +139,8 @@ void convertINI2HTML(const Param& p, ostream& os)
     String restrictions = "";
     switch (value_type)
     {
-    case DataValue::INT_VALUE:
-    case DataValue::INT_LIST:
+    case ParamValue::INT_VALUE:
+    case ParamValue::INT_LIST:
     {
       bool min_set = (it->min_int != -numeric_limits<Int>::max());
       bool max_set = (it->max_int != numeric_limits<Int>::max());
@@ -159,8 +159,8 @@ void convertINI2HTML(const Param& p, ostream& os)
     }
     break;
 
-    case DataValue::DOUBLE_VALUE:
-    case DataValue::DOUBLE_LIST:
+    case ParamValue::DOUBLE_VALUE:
+    case ParamValue::DOUBLE_LIST:
     {
       bool min_set = (it->min_float != -numeric_limits<double>::max());
       bool max_set = (it->max_float != numeric_limits<double>::max());
@@ -179,8 +179,8 @@ void convertINI2HTML(const Param& p, ostream& os)
     }
     break;
 
-    case DataValue::STRING_VALUE:
-    case DataValue::STRING_LIST:
+    case ParamValue::STRING_VALUE:
+    case ParamValue::STRING_LIST:
       if (it->valid_strings.size() != 0)
       {
         restrictions.concatenate(it->valid_strings.begin(), it->valid_strings.end(), ",");

doc/doxygen/public/TOPP.doxygen

@@ -118,7 +118,6 @@
   - @subpage TOPP_CompNovo - Performs a peptide/protein identification with the CompNovo engine.
   - @subpage TOPP_CompNovoCID - Performs a peptide/protein identification with the CompNovo engine in CID mode.
   - @subpage TOPP_CruxAdapter - Identifies peptides in MS/MS spectra via Crux and tide-search (external).
-  - @subpage TOPP_InspectAdapter - Identifies MS/MS spectra using Inspect (external).
   - @subpage TOPP_MascotAdapter - Identifies MS/MS spectra using Mascot (external).
   - @subpage TOPP_MascotAdapterOnline - Identifies MS/MS spectra using Mascot (external).
   - @subpage TOPP_MSGFPlusAdapter - Identifies MS/MS spectra using MSGFPlus (external).

doc/doxygen/public/UTILS.doxygen

@@ -53,7 +53,6 @@
   - @subpage UTILS_PeakPickerIterative - A tool for peak detection in profile data.
 
   <b>File Handling</b>
-  - @subpage UTILS_CVInspector - A tool for visualization and validation of PSI mapping and CV files.
   - @subpage UTILS_FuzzyDiff - Compares two files, tolerating numeric differences.
   - @subpage UTILS_IDSplitter - Splits protein/peptide identifications off of annotated data files.
   - @subpage UTILS_MzMLSplitter - Splits an mzML file into multiple parts.

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

@@ -749,7 +749,7 @@ namespace OpenMS
 
       if ((stats_count_m_d + stats_count_m_td) == 0)
       {
-        String msg("No peptides were matched to the decoy portion of the database! Did you provide the correct concatenated database? Are your 'decoy_string' (=" + String(decoy_string_) + ") and 'decoy_string_position' (=" + String(param_.getValue("decoy_string_position")) + ") settings correct?");
+        String msg("No peptides were matched to the decoy portion of the database! Did you provide the correct concatenated database? Are your 'decoy_string' (=" + decoy_string_ + ") and 'decoy_string_position' (=" + std::string(param_.getValue("decoy_string_position")) + ") settings correct?");
         if (missing_decoy_action_ == MissingDecoy::IS_ERROR)
         {
           OPENMS_LOG_ERROR << "Error: " << msg << "\nSet 'missing_decoy_action' to 'warn' if you are sure this is ok!\nAborting ..." << std::endl;

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

@@ -193,7 +193,7 @@ namespace OpenMS
       explicit ParameterModifier(const String &param_name, SiriusAdapterAlgorithm *enclose) :
               openms_param_name(param_name), enclose(enclose) {}
 
-      void withValidStrings(initializer_list<String> choices)
+      void withValidStrings(initializer_list<std::string> choices)
       {
         enclose->defaults_.setValidStrings(openms_param_name, choices);
       }
@@ -219,7 +219,7 @@ namespace OpenMS
     protected:
       ParameterModifier parameter(
               const String &parameter_name,
-              const DataValue &default_value,
+              const ParamValue &default_value,
               const String &parameter_description);
       void flag(
               const String &parameter_name,

src/openms/include/OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h

@@ -35,6 +35,7 @@
 #pragma once
 
 #include <OpenMS/DATASTRUCTURES/Param.h>
+#include <OpenMS/DATASTRUCTURES/ListUtils.h>
 #include <OpenMS/ANALYSIS/MAPMATCHING/TransformationModel.h>
 #include <iostream>
 #include <map>

src/openms/include/OpenMS/ANALYSIS/MAPMATCHING/TransformationModel.h

@@ -35,6 +35,7 @@
 #pragma once
 
 #include <OpenMS/DATASTRUCTURES/Param.h>
+#include <OpenMS/DATASTRUCTURES/String.h>
 #include <OpenMS/KERNEL/StandardTypes.h>
 
 #include <tuple>

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

@@ -36,6 +36,7 @@
 
 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
 #include <OpenMS/DATASTRUCTURES/String.h>
+#include <OpenMS/DATASTRUCTURES/ListUtils.h>
 
 #include <OpenMS/KERNEL/Peak2D.h>
 
@@ -146,7 +147,7 @@ namespace OpenMS
       @param stringlist The StringList to convert.
       @return An isotope correction matrix as Matrix<double>.
     */
-    Matrix<double> stringListToIsotopCorrectionMatrix_(const StringList& stringlist) const;
+    Matrix<double> stringListToIsotopCorrectionMatrix_(const std::vector<String>& stringlist) const;
   };
 } // namespace
 

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

@@ -87,7 +87,7 @@ namespace OpenMS
     Size reference_channel_;
 
     /// List of available channel names as they are presented to the user
-    static const std::vector<String> channel_names_;
+    static const std::vector<std::string> channel_names_;
 
   protected:
     /// implemented for DefaultParamHandler

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

@@ -87,7 +87,7 @@ namespace OpenMS
     Size reference_channel_;
 
     /// List of available channel names as they are presented to the user
-    static const std::vector<String> channel_names_;
+    static const std::vector<std::string> channel_names_;
 
   protected:
     /// implemented for DefaultParamHandler

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

@@ -87,7 +87,7 @@ namespace OpenMS
     Size reference_channel_;
 
     /// List of available channel names as they are presented to the user
-    static const std::vector<String> channel_names_;
+    static const std::vector<std::string> channel_names_;
 
   protected:
     /// implemented for DefaultParamHandler

src/openms/include/OpenMS/APPLICATIONS/MapAlignerBase.h

@@ -84,7 +84,7 @@ class TOPPMapAlignerBase :
     Param params;
     params.setValue("type", default_model, "Type of model");
     // TODO: avoid referring to each TransformationModel subclass explicitly
-    StringList model_types = ListUtils::create<String>("linear,b_spline,lowess,interpolated");
+    std::vector<std::string> model_types = {"linear","b_spline","lowess","interpolated"};
     if (!ListUtils::contains(model_types, default_model))
     {
       model_types.insert(model_types.begin(), default_model);

src/openms/include/OpenMS/APPLICATIONS/OpenSwathBase.h

@@ -403,7 +403,7 @@ class TOPPOpenSwathBase :
       model_params.setValue("symmetric_regression", "false");
       model_params.setValue("span", irt_detection_param.getValue("lowess:span"));
       model_params.setValue("num_nodes", irt_detection_param.getValue("b_spline:num_nodes"));
-      String model_type = irt_detection_param.getValue("alignmentMethod");
+      String model_type = irt_detection_param.getValue("alignmentMethod").toString();
       trafo_rtnorm.fitModel(model_type, model_params);
     }
     else if (!irt_tr_file.empty())

src/openms/include/OpenMS/APPLICATIONS/ParameterInformation.h

@@ -36,7 +36,7 @@
 
 #include <OpenMS/DATASTRUCTURES/String.h>
 #include <OpenMS/DATASTRUCTURES/StringListUtils.h>
-#include <OpenMS/DATASTRUCTURES/DataValue.h>
+#include <OpenMS/DATASTRUCTURES/ParamValue.h>
 
 namespace OpenMS
 {
@@ -70,7 +70,7 @@ namespace OpenMS
     /// type of the parameter
     ParameterTypes type;
     /// default value of the parameter stored as string
-    DataValue default_value;
+    ParamValue default_value;
     /// description of the parameter
     String description;
     /// argument in the description
@@ -84,15 +84,15 @@ namespace OpenMS
 
     ///@name Restrictions for different parameter types
     //@{
-    std::vector<String> valid_strings;
+    StringList valid_strings;
     Int min_int;
     Int max_int;
     double min_float;
     double max_float;
     //@}
 
     /// Constructor that takes all members in declaration order
-    ParameterInformation(const String& n, ParameterTypes t, const String& arg, const DataValue& def, const String& desc, bool req, bool adv, const StringList& tag_values = StringList());
+    ParameterInformation(const String& n, ParameterTypes t, const String& arg, const ParamValue& def, const String& desc, bool req, bool adv, const StringList& tag_values = StringList());
 
     ParameterInformation();
 

src/openms/include/OpenMS/APPLICATIONS/TOPPBase.h

@@ -354,7 +354,7 @@ namespace OpenMS
     bool getParamAsBool_(const String& key) const;
 
     /**
-      @brief Return the value @p key of parameters as DataValue. DataValue::EMPTY indicates that a parameter was not found.
+      @brief Return the value @p key of parameters as DataValue. ParamValue::EMPTY indicates that a parameter was not found.
 
       Parameters are searched in this order:
       -# command line
@@ -364,7 +364,7 @@ namespace OpenMS
 
       where "some_key" == key in the examples.
     */
-    const DataValue& getParam_(const String& key) const;
+    const ParamValue& getParam_(const String& key) const;
 
     /**
       @brief Get the part of a parameter name that makes up the subsection