. Feature/fgid

.gitignore

@@ -3,7 +3,6 @@ DartConfiguration.tcl
 /*.cmake
 Testing
 CMakeCache.txt
-contrib
 CMakeFiles
 Makefile
 lib
@@ -21,3 +20,6 @@ OpenMS.includes
 .DS_Store
 src/.DS_Store
 src/openms/.DS_Store
+.vscode
+contrib-build
+openms-build

.gitmodules

@@ -0,0 +1,6 @@
+[submodule "contrib"]
+	path = contrib
+	url = https://github.com/OpenMS/contrib
+[submodule "THIRDPARTY"]
+	path = THIRDPARTY
+	url = https://github.com/OpenMS/THIRDPARTY

.travis.yml

@@ -73,25 +73,29 @@ matrix:
 
 ## see for example https://github.com/taocpp/PEGTL/blob/master/.travis.yml
 ## gcc tests class and TOPP tests
-    - env: ENABLE_STYLE_TESTING=OFF ENABLE_TOPP_TESTING=ON ENABLE_CLASS_TESTING=ON WITH_GUI=ON ADDRESS_SANITIZER=Off BUILD_TYPE=Release
+    - env: ENABLE_STYLE_TESTING=OFF ENABLE_TOPP_TESTING=ON ENABLE_CLASS_TESTING=ON WITH_GUI=ON ADDRESS_SANITIZER=Off BUILD_TYPE=Release OPENMP=On
       os: linux
       compiler: gcc
 
 ## pyopenms test
-    - env: ENABLE_STYLE_TESTING=OFF WITH_GUI=OFF ENABLE_TOPP_TESTING=OFF ENABLE_CLASS_TESTING=OFF ADDRESS_SANITIZER=Off BUILD_TYPE=Release PYOPENMS=ON PY_NO_OPTIMIZATION=ON
-      os: linux
-      compiler: clang
-
-## clang tests class and TOPP tests: without gui and without address sanitizer (debug build)
-    - env: ENABLE_STYLE_TESTING=OFF WITH_GUI=OFF ENABLE_TOPP_TESTING=ON ENABLE_CLASS_TESTING=ON ADDRESS_SANITIZER=Off BUILD_TYPE=Debug CXX_FLAGS="-Qunused-arguments" CFLAGS="-Qunused-arguments" CCACHE_CPP2=1
-      os: linux
-      compiler: clang
-
-## clang tests class and TOPP tests: without gui and without address sanitizer (release build)
-    - env: ENABLE_STYLE_TESTING=OFF WITH_GUI=ON ENABLE_TOPP_TESTING=ON ENABLE_CLASS_TESTING=ON ADDRESS_SANITIZER=Off BUILD_TYPE=Release CXX_FLAGS="-Qunused-arguments" CFLAGS="-Qunused-arguments" CCACHE_CPP2=1
+    - env: ENABLE_STYLE_TESTING=OFF WITH_GUI=OFF ENABLE_TOPP_TESTING=OFF ENABLE_CLASS_TESTING=OFF ADDRESS_SANITIZER=Off BUILD_TYPE=Release PYOPENMS=ON PY_NO_OPTIMIZATION=ON OPENMP=Off
       os: linux
       compiler: clang
 
+# ## clang tests class and TOPP tests: without gui and without address sanitizer (debug build)
+#     - env: ENABLE_STYLE_TESTING=OFF WITH_GUI=OFF ENABLE_TOPP_TESTING=ON ENABLE_CLASS_TESTING=OFF ADDRESS_SANITIZER=Off BUILD_TYPE=Debug CXX_FLAGS="-Qunused-arguments" CFLAGS="-Qunused-arguments" CCACHE_CPP2=1 OPENMP=Off
+#       os: linux
+#       compiler: clang
+# ## clang tests class and TOPP tests: without gui and without address sanitizer (debug build)
+#     - env: ENABLE_STYLE_TESTING=OFF WITH_GUI=OFF ENABLE_TOPP_TESTING=OFF ENABLE_CLASS_TESTING=ON ADDRESS_SANITIZER=Off BUILD_TYPE=Debug CXX_FLAGS="-Qunused-arguments" CFLAGS="-Qunused-arguments" CCACHE_CPP2=1 OPENMP=Off
+#       os: linux
+#       compiler: clang
+# 
+# ## clang tests class and TOPP tests: without gui and without address sanitizer (release build)
+#     - env: ENABLE_STYLE_TESTING=OFF WITH_GUI=ON ENABLE_TOPP_TESTING=ON ENABLE_CLASS_TESTING=ON ADDRESS_SANITIZER=Off BUILD_TYPE=Release CXX_FLAGS="-Qunused-arguments" CFLAGS="-Qunused-arguments" CCACHE_CPP2=1 OPENMP=Off
+#       os: linux
+#       compiler: clang
+#
 ### OS X tests
 #    - env: ENABLE_STYLE_TESTING=OFF WITH_GUI=OFF ENABLE_TOPP_TESTING=ON ENABLE_CLASS_TESTING=OFF ADDRESS_SANITIZER=Off BUILD_TYPE=Release
 #      os: osx

AUTHORS

@@ -8,14 +8,18 @@ the authors tag in the respective file header.
  - Alexandra Scherbart
  - Alexandra Zerck
  - Andreas Bertsch
+ - Andreas Simon
  - Anton Pervukhin
  - Bastian Blank
  - Chris Bauer
  - Chris Bielow
+ - Christian Ehrlich
  - Clemens Groepl
  - Cornelia Friedle
  - Daniel Jameson
+ - Darren Kessner
  - David Wojnar
+ - Dilek Dere
  - Dimitri Schachmann
  - Erhan Kenar
  - Eugen Netz
@@ -33,24 +37,30 @@ the authors tag in the respective file header.
  - Holger Plattfaut
  - Immanuel Luhn
  - Johan Teleman
+ - Johannes Junker
  - Johannes Veit
  - Julianus Pfeuffer
  - Katharina Albers
  - Knut Reinert
  - Lars Nilse
+ - Leon Bichmann
  - Lucia Espona
  - Lukas Mueller
+ - Lukas Zimmermann
  - Marcel Schilling
  - Marc Sturm
  - Markus Mueller
  - Martin Langwisch
  - Mathias Walzer
+ - Matthew The
  - Nico Pfeifer
  - Ole Schulz-Trieglaff
+ - Oliver Alka
  - Oliver Kohlbacher
  - Peter Kunszt
  - Petra Gutenbrunner
  - Rene Hussong
+ - Samuel Wein
  - Sandro Andreotti
  - Steffen Sass
  - Stephan Aiche

CMakeLists.txt

@@ -94,7 +94,7 @@ list(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake/Windows")
 #------------------------------------------------------------------------------
 
 set(OPENMS_PACKAGE_VERSION_MAJOR "2")
-set(OPENMS_PACKAGE_VERSION_MINOR "2")
+set(OPENMS_PACKAGE_VERSION_MINOR "3")
 set(OPENMS_PACKAGE_VERSION_PATCH "0")
 
 #------------------------------------------------------------------------------
@@ -184,6 +184,11 @@ if(ADDRESS_SANITIZER)
   include(cmake/AddressSanitizer.cmake)
 endif()
 
+#------------------------------------------------------------------------------
+# Enable fingerid_test
+#------------------------------------------------------------------------------
+option(ENABLE_FINGERID_TEST "Enable test for fingerid (SiriusAdapter)" OFF)
+
 #------------------------------------------------------------------------------
 # Enable Coverage
 #------------------------------------------------------------------------------
@@ -248,14 +253,15 @@ if("${PACKAGE_TYPE}" STREQUAL "dmg")
                          "This disables codesigning and might lead to problems with Gatekeeper on target machines.")
   else()
     ## CPack has a special variable for it.
-    set(CPACK_BUNDLE_APPLE_CERT_APP ${SIGNING_IDENTITY})
+    set(CPACK_BUNDLE_APPLE_CERT_APP "${SIGNING_IDENTITY}")
   endif()
 endif()
 
 #------------------------------------------------------------------------------
 # Output directories
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${OPENMS_HOST_BINARY_DIRECTORY}/lib")
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${OPENMS_HOST_BINARY_DIRECTORY}/bin")
+set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY "${OPENMS_HOST_BINARY_DIRECTORY}/lib")
 set(OPENMS_BINARY_DIR "${OPENMS_HOST_BINARY_DIRECTORY}/bin")
 set(OPENMS_WIN32_DLL_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
 

CONTRIBUTING.md

@@ -2,7 +2,7 @@ Help us to make OpenMS better and become part of the OpenMS open-source communit
 
 This document is displayed because you either opened an issue or you want to provide your code as a pull request for inclusion into OpenMS. Please take a look at the appropriate section below to find some details on how we handle this process.
 
-#Reporting an Issue:
+# Reporting an Issue:
 
 You most likely came here to:
   - report bugs or annoyances
@@ -21,7 +21,7 @@ If you found a bug, e.g. an OpenMS tool crashes during data processing, it is es
 If you are an official OpenMS team meber:
   - label your issue using github labels (e.g. as: question, defect) that indicate the type of issue and which components of OpenMS (blue labels) are affected. The severity is usually assigned by OpenMS maintainers and used internally to e.g. indicate if a bug is a blocker for a new release.
 
-#Opening a Pull Request
+# Opening a Pull Request
 
 You probably came here to open a pull request that:
   - implements new features and tools or
@@ -34,10 +34,10 @@ Before getting started we recommend taking a look at our GitHub-Wiki: https://gi
 There you will find information on:
  - coding conventions
  - testing
- - additional documentation for developers. 
+ - additional documentation for developers 
 
 The section on "Development model" will give details on how to incorporate your contributions into the OpenMS code base. A core developer will review your changes to the main development branch (develop) and approve them (or ask for modifications). You may indicate the prefered reviewer(s) by adding links to them in a comment section (e.g., @cbielow @hendrikweisser @hroest @jpfeuffer @timosachsenberg)
 
-Also consider getting in contact with the core developers early. They might provide additional guidance and valuable information on how your specific aim is achieved. This might give you a head start in, for example, developing novel tools or algorithms. 
+Also consider getting in contact with the core developers early. They might provide additional guidance and valuable information on how your specific aim is achieved. This might give you a head start in, for example, developing novel tools or algorithms.
 
 Happy coding!

License.txt

@@ -46,6 +46,12 @@ The respective license files for the contrib libraries
 can be found in the "contrib" package root directory or online
 (see below).
 
+SeqAn
+  - URL:
+  https://www.seqan.de/
+  - License:
+  https://github.com/seqan/seqan/blob/master/LICENSE
+
 libSVM
   - URL:
   http://www.csie.ntu.edu.tw/~cjlin/libsvm/
@@ -76,12 +82,6 @@ Boost (headers)
   - License:
   http://www.boost.org/more/license_info.html
 
-Comet
-  - URL:
-  http://comet-ms.sourceforge.net/
-  - License:
-  http://www.apache.org/licenses/LICENSE-2.0.html
-
 ZLib
   - URL:
   http://www.zlib.net
@@ -94,11 +94,36 @@ BZ2Lib
   - License:
   http://www.bzip.org/1.0.5/bzip2-manual-1.0.5.html
 
+Eigen
+ - URL:
+ http://eigen.tuxfamily.org/
+ - License:
+ https://www.mozilla.org/en-US/MPL/2.0/
+
+Geometric Tools (Wildmagic)
+ - URL:
+ https://www.geometrictools.com/
+ - License:
+ http://www.boost.org/LICENSE_1_0.txt
+
+SQLite:
+ - URL:
+ https://www.sqlite.org/
+ - License:
+ https://www.sqlite.org/copyright.html
+
+Kiss FFT
+`- URL:
+ https://sourceforge.net/projects/kissfft/
+ - License:
+ https://sourceforge.net/p/kissfft/code/ci/default/tree/COPYING
+
+
 ---------------------   Search engines:  ------------------------
 
 OMSSA
   - URL:
-  http://pubchem.ncbi.nlm.nih.gov/omssa/
+  ftp://ftp.ncbi.nlm.nih.gov/pub/lewisg/omssa
   - License:
   Public Domain
 
@@ -116,16 +141,15 @@ X!Tandem:
 
 MyriMatch:
   - URL and source code:
-  http://fenchurch.mc.vanderbilt.edu/software.php
+  https://www.ncbi.nlm.nih.gov/pubmed/17269722
   - License:
   http://www.apache.org/licenses/LICENSE-2.0.txt
 
 MSGF+:
   - URL and source code:
-  http://proteomics.ucsd.edu/Software/MSGFPlus/ 
+  https://github.com/sangtaekim/msgfplus
   - License:
-  http://sourceforge.net/p/open-ms/code/HEAD/tree/THIRDPARTY/All/
-  MSGFPlus/LICENSE.txt
+  https://github.com/sangtaekim/msgfplus/blob/master/LICENSE.txt
 
 Fido:
   - URL and source code:
@@ -138,3 +162,24 @@ LuciPhOr2:
   http://luciphor2.sourceforge.net/
   - License:
   http://www.apache.org/licenses/LICENSE-2.0
+
+SpectraST:
+  - URL and source code:
+ https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/
+ trans_proteomic_pipeline/src/Search/SpectraST/ 
+  - License:
+  https://www.gnu.org/licenses/gpl.html
+  https://www.gnu.org/copyleft/lesser.html
+
+SIRIUS:
+  - URL:
+  https://bio.informatik.uni-jena.de/software/sirius/
+  - License:
+  https://www.gnu.org/licenses/gpl
+
+Comet:
+  - URL and source code:
+  https://sourceforge.net/projects/comet-ms/
+  - License:
+  http://www.apache.org/licenses/LICENSE-2.0.html
+

cmake/MacOSX/TOPP_bash_profile

@@ -57,11 +57,11 @@ else
   export PATH=${OPENMS_TOPP_PATH}/INIFileEditor.app/Contents/MacOS/:${PATH}
   export PATH=${OPENMS_TOPP_PATH}/TOPPAS.app/Contents/MacOS/:${PATH}
   ## also the search engines
-  for folder in ${OPENMS_TOPP_PATH}/TOPP/SEARCHENGINES/*/ ; do
+  for folder in ${OPENMS_DATA_PATH}/THIRDPARTY/*/ ; do
     export PATH=$folder:$PATH
   done
-  ## and finally topp
-  export PATH=${OPENMS_TOPP_PATH}/TOPP:${PATH}
+  ## and finally the bin folder
+  export PATH=${OPENMS_TOPP_PATH}/bin:${PATH}
 fi
 
 ## EOF

cmake/MacOSX/fixdmg.sh

@@ -9,9 +9,9 @@
 # <wait 1-2min>
 # defaults write com.apple.Finder AppleShowAllFiles FALSE && killall Finder
 
-DISK_NAME=OpenMS-2.2.0-Darwin
+DISK_NAME=OpenMS-2.3.0-Darwin
 DMG_NAME=${DISK_NAME}.dmg
-OPENMS_NAME=OpenMS-2.2.0
+OPENMS_NAME=OpenMS-2.3.0
 backgroundPictureName=.background.png
 LICENSE=${PWD}/_CPack_Packages/Darwin/DragNDrop/sla.r
 

cmake/compiler_flags.cmake

@@ -130,6 +130,9 @@ elseif ("${CMAKE_C_COMPILER_ID}" MATCHES "Clang")
                   -Wno-c++98-compat-pedantic
                   # These are warnings of moderate severity, which are disabled
                   # for now until we are down to a reasonable size of warnings.
+                  -Wno-unknown-warning-option
+                  -Wno-double-promotion
+                  -Wno-unused-template
                   -Wno-conversion
                   -Wno-float-equal
                   -Wno-switch-enum

cmake/install_macros.cmake

@@ -140,7 +140,7 @@ endmacro()
 macro(install_thirdparty_folder foldername)
   if(EXISTS ${SEARCH_ENGINES_DIRECTORY}/${foldername})
     install(DIRECTORY             ${SEARCH_ENGINES_DIRECTORY}/${foldername}
-            DESTINATION           ${INSTALL_BIN_DIR}/SEARCHENGINES
+            DESTINATION           ${INSTALL_SHARE_DIR}/THIRDPARTY
             COMPONENT             ${foldername}
             FILE_PERMISSIONS      OWNER_EXECUTE OWNER_WRITE OWNER_READ
                                   GROUP_READ GROUP_EXECUTE

cmake/knime/binaries_lnx.ini

@@ -1,6 +1,7 @@
 OPENMS_DATA_PATH=$ROOT/share/OpenMS
-PATH=$ROOT/bin/:$ROOT/bin/Fido:$ROOT/bin/Comet:$ROOT/bin/OMSSA:$ROOT/bin/MyriMatch:$ROOT/bin/XTandem:$ROOT/../../../jre/bin/java:${PATH}
+PATH=$ROOT/bin/:$ROOT/bin/Fido:$ROOT/bin/Comet:$ROOT/bin/OMSSA:$ROOT/bin/MyriMatch:$ROOT/bin/XTandem:$ROOT/bin/Percolator:$ROOT/bin/SpectraST:$ROOT/../../../jre/bin/java:${PATH}
 LD_LIBRARY_PATH=$ROOT/lib/:${LD_LIBRARY_PATH}
 MSGFPLUS_PATH=$ROOT/bin/MSGFPlus/MSGFPlus.jar
 LUCIPHOR_PATH=$ROOT/bin/LuciPHOr2/luciphor2.jar
+SIRIUS_PATH=$ROOT/bin/Sirius/sirius
 OPENMS_DISABLE_UPDATE_CHECK=ON

cmake/knime/binaries_mac.ini

@@ -1,5 +1,6 @@
 OPENMS_DATA_PATH=$ROOT/share/OpenMS
-PATH=$ROOT/bin/:$ROOT/bin/Fido:$ROOT/bin/Comet:$ROOT/bin/OMSSA:$ROOT/bin/XTandem:$ROOT/../../../jre/Home/bin
+PATH=$ROOT/bin/:$ROOT/bin/Fido:$ROOT/bin/Comet:$ROOT/bin/OMSSA:$ROOT/bin/XTandem:$ROOT/bin/Percolator:$ROOT/bin/SpectraST:$ROOT/../../../jre/Home/bin
 MSGFPLUS_PATH=$ROOT/bin/MSGFPlus/MSGFPlus.jar
 LUCIPHOR_PATH=$ROOT/bin/LuciPHOr2/luciphor2.jar
+SIRIUS_PATH=$ROOT/bin/Sirius/sirius
 OPENMS_DISABLE_UPDATE_CHECK=ON

cmake/knime/binaries_win.ini

@@ -1,6 +1,7 @@
 OPENMS_DATA_PATH=$ROOT\\share\\OpenMS\\
-PATH=$ROOT\\bin;$ROOT\\lib;$ROOT\\bin\\Fido;$ROOT\\bin\\Comet;$ROOT\\bin\\OMSSA;$ROOT\\bin\\MyriMatch;$ROOT\\bin\\XTandem;$ROOT\\..\\..\\..\\jre\\bin
-Path=$ROOT\\bin;$ROOT\\lib;$ROOT\\bin\\Fido;$ROOT\\bin\\Comet;$ROOT\\bin\\OMSSA;$ROOT\\bin\\MyriMatch;$ROOT\\bin\\XTandem;$ROOT\\..\\..\\..\\jre\\bin
+PATH=$ROOT\\bin;$ROOT\\lib;$ROOT\\bin\\Fido;$ROOT\\bin\\Comet;$ROOT\\bin\\OMSSA;$ROOT\\bin\\MyriMatch;$ROOT\\bin\\XTandem;$ROOT\\bin\\Percolator;$ROOT\\bin\\SpectraST;$ROOT\\..\\..\\..\\jre\\bin
+Path=$ROOT\\bin;$ROOT\\lib;$ROOT\\bin\\Fido;$ROOT\\bin\\Comet;$ROOT\\bin\\OMSSA;$ROOT\\bin\\MyriMatch;$ROOT\\bin\\XTandem;$ROOT\\bin\\Percolator;$ROOT\\bin\\SpectraST;$ROOT\\..\\..\\..\\jre\\bin
 MSGFPLUS_PATH=$ROOT\\bin\\MSGFPlus\\MSGFPlus.jar
 LUCIPHOR_PATH=$ROOT\\bin\\LuciPHOr2\\luciphor2.jar
+SIRIUS_PATH=$ROOT\\bin\\Sirius\\sirius-console-64.exe
 OPENMS_DISABLE_UPDATE_CHECK=ON

cmake/knime_package_support.cmake

@@ -122,6 +122,8 @@ add_custom_target(
   COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=CometAdapter -DPARAM=comet_executable -D CTD_PATH=${CTD_PATH} -P ${SCRIPT_DIRECTORY}remove_parameter_from_ctd.cmake
   # PercolatorAdapter
   COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=PercolatorAdapter -DPARAM=percolator_executable -D CTD_PATH=${CTD_PATH} -P ${SCRIPT_DIRECTORY}remove_parameter_from_ctd.cmake
+   # SiriusAdapter
+  COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=SiriusAdapter -DPARAM=executable -D CTD_PATH=${CTD_PATH} -P ${SCRIPT_DIRECTORY}remove_parameter_from_ctd.cmake
   # FidoAdapter
   COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=FidoAdapter -DPARAM=fido_executable -D CTD_PATH=${CTD_PATH} -P ${SCRIPT_DIRECTORY}remove_parameter_from_ctd.cmake
   COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=FidoAdapter -DPARAM=fidocp_executable -D CTD_PATH=${CTD_PATH} -P ${SCRIPT_DIRECTORY}remove_parameter_from_ctd.cmake

cmake/package_dragndrop_dmg.cmake

@@ -97,10 +97,11 @@ if (DEFINED CMAKE_VERSION AND NOT "${CMAKE_VERSION}" VERSION_LESS "3.5")
   set(CPACK_DMG_BACKGROUND_IMAGE ${PROJECT_SOURCE_DIR}/cmake/MacOSX/background.png)
   set(CPACK_DMG_FORMAT UDBZ) ## Try bzip2 to get slighlty smaller images
 
-  ## Sign the image. System keychain needs to be unlocked and include the ID used.
+  ## Sign the image. CPACK_BUNDLE_APPLE_CERT_APP needs to be unique and found in one of the
+  ## keychains in the search list (which needs to be unlocked).
   if (DEFINED CPACK_BUNDLE_APPLE_CERT_APP)
     add_custom_target(signed_dist
-      COMMAND codesign --deep --force --keychain /Library/Keychains/System.keychain --sign ${CPACK_BUNDLE_APPLE_CERT_APP} ${CPACK_PACKAGE_FILE_NAME}.dmg
+      COMMAND codesign --deep --force --sign ${CPACK_BUNDLE_APPLE_CERT_APP} ${CPACK_PACKAGE_FILE_NAME}.dmg
       WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
       COMMENT "Signing ${CPACK_PACKAGE_FILE_NAME}.dmg as ${CPACK_BUNDLE_APPLE_CERT_APP}"
       DEPENDS dist)

cmake/package_general.cmake

@@ -2,7 +2,7 @@
 #                   OpenMS -- Open-Source Mass Spectrometry
 # --------------------------------------------------------------------------
 # Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
-# ETH Zurich, and Freie Universitaet Berlin 2002-2016.
+# ETH Zurich, and Freie Universitaet Berlin 2002-2017.
 #
 # This software is released under a three-clause BSD license:
 #  * Redistributions of source code must retain the above copyright