PercolatorAdapter has been changed by Timo reverted to proper parsing…

.gitignore

@@ -17,3 +17,6 @@ OpenMS.config
 OpenMS.creator
 OpenMS.files
 OpenMS.includes
+.DS_Store
+src/.DS_Store
+src/openms/.DS_Store

cmake/knime_package_support.cmake

@@ -118,6 +118,8 @@ add_custom_target(
   COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=MSGFPlusAdapter -DPARAM=executable -D CTD_PATH=${CTD_PATH} -P ${SCRIPT_DIRECTORY}remove_parameter_from_ctd.cmake
   # LuciPhorAdapter
   COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=LuciphorAdapter -DPARAM=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
   # 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
@@ -265,6 +267,8 @@ elseif(NOT EXISTS ${SEARCH_ENGINES_DIRECTORY}/Fido)
   message(FATAL_ERROR "The given search engine directory seems to have an invalid layout (Fido is missing). ${FOLDER_STRUCTURE_MESSAGE}")
 elseif(NOT EXISTS ${SEARCH_ENGINES_DIRECTORY}/LuciPHOr2)
   message(FATAL_ERROR "The given search engine directory seems to have an invalid layout (LuciPHOr2 is missing). ${FOLDER_STRUCTURE_MESSAGE}")
+elseif(NOT EXISTS ${SEARCH_ENGINES_DIRECTORY}/Percolator)
+  message(FATAL_ERROR "The given search engine directory seems to have an invalid layout (Percolator is missing). Please check use the one from the SVN.")
 elseif(NOT APPLE AND NOT EXISTS ${SEARCH_ENGINES_DIRECTORY}/MyriMatch)
   message(FATAL_ERROR "The given search engine directory seems to have an invalid layout (MyriMatch is missing). ${FOLDER_STRUCTURE_MESSAGE}")
 endif()

doc/doxygen/public/TOPP.doxygen

@@ -139,6 +139,7 @@
   - @subpage TOPP_PeptideIndexer - Refreshes the protein references for all peptide hits.
   - @subpage TOPP_PhosphoScoring - Scores potential phosphorylation sites in order to localize the most probable sites.
   - @subpage TOPP_ProteinInference - Infer proteins from a list of (high-confidence) peptides.
+  - @subpage TOPP_PercolatorAdapter - Applies the percolator algorithm to protein/peptide identifications.
 
   <b>Targeted Experiments</b>
   - @subpage TOPP_InclusionExclusionListCreator - Creates inclusion and/or exclusion lists for LC-MS/MS experiments.

doc/doxygen/public/UTILS.doxygen

@@ -78,6 +78,8 @@
   - @subpage UTILS_RNPxl - Tool for RNP cross linking experiment analysis.
   - @subpage UTILS_SequenceCoverageCalculator - Prints information about idXML files.
   - @subpage UTILS_SpecLibCreator - Creates an MSP-formatted spectral library.
+  - @subpage UTILS_PSMFeatureExtractor - Creates search engine specific features for PercolatorAdapter input.
+
 
   <b>Quantitation</b>
   - @subpage UTILS_ERPairFinder - Evaluate pair ratios on enhanced resolution (zoom) scans.

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

@@ -0,0 +1,203 @@
+// --------------------------------------------------------------------------
+//                   OpenMS -- Open-Source Mass Spectrometry
+// --------------------------------------------------------------------------
+// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
+// ETH Zurich, and Freie Universitaet Berlin 2002-2015.
+//
+// This software is released under a three-clause BSD license:
+//  * Redistributions of source code must retain the above copyright
+//    notice, this list of conditions and the following disclaimer.
+//  * Redistributions in binary form must reproduce the above copyright
+//    notice, this list of conditions and the following disclaimer in the
+//    documentation and/or other materials provided with the distribution.
+//  * Neither the name of any author or any participating institution
+//    may be used to endorse or promote products derived from this software
+//    without specific prior written permission.
+// For a full list of authors, refer to the file AUTHORS.
+// --------------------------------------------------------------------------
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
+// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// --------------------------------------------------------------------------
+// $Maintainer: Mathias Walzer $
+// $Authors: Mathias Walzer, Matthew The $
+// --------------------------------------------------------------------------
+
+#ifndef OPENMS_ANALYSIS_ID_TOPPERC_H
+#define OPENMS_ANALYSIS_ID_TOPPERC_H
+
+#include <vector>
+#include <iostream>
+#include <cmath>
+#include <string>
+#include <map>
+#include <algorithm>
+#include <limits>
+
+#include <OpenMS/CONCEPT/Types.h>
+#include <OpenMS/KERNEL/StandardTypes.h>
+#include <OpenMS/FORMAT/FileHandler.h>
+#include <OpenMS/DATASTRUCTURES/DataValue.h>
+
+#include <boost/lexical_cast.hpp>
+
+namespace OpenMS
+{
+    /**
+        @brief Percolator feature set and integration helper
+
+        This class contains functions to handle (compute, aggregate, integrate)
+        Percolator features. This includes the calculation or extraction of
+        Percolator features for the specific search engine usage, preparation for
+        PercolatorApater usage and result reintegration and in the case of
+        multiple search engine incorporation of different features.
+    */
+
+    class OPENMS_DLLAPI PercolatorFeatureSetHelper
+    {
+
+    public:
+        /**
+         * @brief concatMULTISEPeptideIds
+         * @param all_peptide_ids PeptideIdentification vector to append to
+         * @param new_peptide_ids PeptideIdentification vector to be appended
+         * @param search_engine search engine to depend on for feature creation
+         *
+         * Appends a vector of PeptideIdentification to another and registers concatenation Percolator features depending on given search engine.
+         */
+        static void concatMULTISEPeptideIds(std::vector<PeptideIdentification>& all_peptide_ids, std::vector<PeptideIdentification>& new_peptide_ids, String search_engine);
+
+        /**
+         * @brief mergeMULTISEPeptideIds
+         * @param all_peptide_ids PeptideIdentification vector to be merged into
+         * @param new_peptide_ids PeptideIdentification vector to merge
+         * @param search_engine search engine to create features from their scores
+         *
+         * Merges a vector of PeptideIdentification into another and registers merge Percolator features depending on given search engine.
+         */
+        static void mergeMULTISEPeptideIds(std::vector<PeptideIdentification>& all_peptide_ids, std::vector<PeptideIdentification>& new_peptide_ids, String search_engine);
+
+        /**
+         * @brief mergeMULTISEProteinIds
+         * @param all_protein_ids ProteinIdentification vector to be merged into
+         * @param new_protein_ids ProteinIdentification vector to merge
+         *
+         * Concatenates SearchParameter of multiple search engine runs and merges PeptideEvidences, registers the created Percolator features
+         */
+        static void mergeMULTISEProteinIds(std::vector<ProteinIdentification>& all_protein_ids, std::vector<ProteinIdentification>& new_protein_ids);
+
+
+        /**
+         * @brief addMSGFFeatures
+         * @param peptide_ids PeptideIdentification vector to create Percolator features in
+         * @param feature_set register of added features
+         *
+         * Creates and adds MSGF+ specific Percolator features and registers them in feature_set
+         */
+        static void addMSGFFeatures(std::vector<PeptideIdentification>& peptide_ids, StringList& feature_set);
+
+        /**
+         * @brief addXTANDEMFeatures
+         * @param peptide_ids PeptideIdentification vector to create Percolator featrues in
+         * @param feature_set register of added features
+         *
+         * Creates and adds X!Tandem specific Percolator features and registers them in feature_set
+         */
+        static void addXTANDEMFeatures(std::vector<PeptideIdentification>& peptide_ids, StringList& feature_set);
+
+        /**
+         * @brief addCOMETFeatures
+         * @param peptide_ids PeptideIdentification vector to create Percolator featrues in
+         * @param feature_set register of added features
+         *
+         * Creates and adds Comet specific Percolator features and registers them in feature_set
+         */
+        static void addCOMETFeatures(std::vector<PeptideIdentification>& peptide_ids, StringList& feature_set);
+
+        /**
+         * @brief addMASCOTFeatures
+         * @param peptide_ids PeptideIdentification vector to create Percolator featrues in
+         * @param feature_set register of added features
+         *
+         * Creates and adds Mascot specific Percolator features and registers them in feature_set
+         */
+        static void addMASCOTFeatures(std::vector<PeptideIdentification>& peptide_ids, StringList& feature_set);
+
+        /**
+         * @brief addMULTISEFeatures
+         * @param peptide_ids PeptideIdentification vector to create Percolator featrues in
+         * @param search_engines_used the list of search engines to be considered
+         * @param feature_set register of added features
+         * @param complete_only will only add features for PeptideIdentifications where all given search engines identified something
+         * @param limits_imputation
+         *
+         * Adds multiple search engine specific Percolator features and registers them in feature_set
+         */
+        static void addMULTISEFeatures(std::vector<PeptideIdentification>& peptide_ids, StringList& search_engines_used, StringList& feature_set, bool complete_only = true, bool limits_imputation = false);
+
+        /**
+         * @brief addCONCATSEFeatures
+         * @param peptide_id_list PeptideIdentification vector to create Percolator featrues in
+         * @param search_engines_used the list of search engines to be considered
+         * @param feature_set register of added features
+         *
+         * Adds multiple search engine specific Percolator features and registers them in feature_set
+        */
+        static void addCONCATSEFeatures(std::vector<PeptideIdentification>& peptide_id_list, StringList& search_engines_used, StringList& feature_set);
+
+        /**
+         * @brief checkExtraFeatures
+         * @param psms the vector of PeptideHit to be checked
+         * @param extra_features the list of requested extra features
+         *
+         * checks and removes requested extra Percolator features that are actually unavailable (to compute)
+         */
+        static void checkExtraFeatures(const std::vector<PeptideHit> &psms, StringList& extra_features);
+
+
+    protected:
+        PercolatorFeatureSetHelper();
+        virtual ~PercolatorFeatureSetHelper();
+
+        /// Rescales the fragment features to penalize features calculated by few ions, adapted from MSGFtoPercolator
+        static double rescaleFragmentFeature_(double featureValue, int NumMatchedMainIons);
+
+        /// helper functin for assigning the frequently occurring feature delta score
+        static void assignDeltaScore_(std::vector<PeptideHit>& hits, String score_ref, String output_ref);
+
+        /// gets the scan identifer to merge by
+        static String getScanMergeKey_(std::vector<PeptideIdentification>::iterator it, std::vector<PeptideIdentification>::iterator start);
+
+        /// For accession dependent sorting of ProteinHits
+        struct lq_ProteinHit
+        {
+          inline bool operator() (const ProteinHit& h1, const ProteinHit& h2)
+          {
+            return (h1.getAccession() < h2.getAccession());
+          }
+        };
+
+        /// For accession dependent sorting of PeptideEvidences
+        struct lq_PeptideEvidence
+        {
+          inline bool operator() (const PeptideEvidence& h1, const PeptideEvidence& h2)
+          {
+            return (h1.getProteinAccession() < h2.getProteinAccession());
+          }
+        };
+
+    };
+
+} //namespace OpenMS
+
+#endif //OPENMS_ANALYSIS_ID_PERCOLATORFEATURESETHELPER_H
+

src/openms/include/OpenMS/ANALYSIS/ID/sources.cmake

@@ -23,6 +23,7 @@ MetaboliteSpectralMatching.h
 PeptideProteinResolution.h
 ProtonDistributionModel.h
 PeptideIndexing.h
+PercolatorFeatureSetHelper.h
 )
 
 ### add path to the filenames

src/openms/include/OpenMS/FORMAT/FileTypes.h

@@ -102,6 +102,7 @@ namespace OpenMS
       MRM,                ///< SpectraST MRM List
       PSMS,               ///< Percolator tab-delimited output (PSM level)
       PARAMXML,           ///< internal format for writing and reading parameters (also used as part of CTD)
+      PIN,                ///< Percolator tab-delimited input (PSM level)
       SIZE_OF_TYPE        ///< No file type. Simply stores the number of types
     };