[refactor] moved percolator in file functionality into library

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

@@ -0,0 +1,80 @@
+// --------------------------------------------------------------------------
+//                   OpenMS -- Open-Source Mass Spectrometry
+// --------------------------------------------------------------------------
+// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
+// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
+//
+// 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: Timo Sachsenberg $
+// $Authors: Timo Sachsenberg $
+// --------------------------------------------------------------------------
+
+#pragma once
+
+#include <OpenMS/METADATA/PeptideIdentification.h>
+#include <OpenMS/FORMAT/TextFile.h>
+
+#include <vector>
+
+namespace OpenMS
+{
+
+  /**
+     @brief Class for storing Percolator tab-delimited input files.
+
+  */
+  class OPENMS_DLLAPI PercolatorInfile
+  {
+    public:
+      static void store(const String& pin_file, 
+        const std::vector<PeptideIdentification>& peptide_ids, 
+        const StringList& feature_set, 
+        const std::string& enz, 
+        int min_charge, 
+        int max_charge);
+
+      // uses spectrum_reference, if empty uses spectrum_id, if also empty fall back to using index
+      static String getScanIdentifier(const PeptideIdentification& pid, size_t index);
+
+    protected:
+
+      //id <tab> label <tab> scannr <tab> calcmass <tab> expmass <tab> feature1 <tab> ... <tab> featureN <tab> peptide <tab> proteinId1 <tab> .. <tab> proteinIdM
+      static TextFile preparePin_(
+        const std::vector<PeptideIdentification>& peptide_ids, 
+        const StringList& feature_set, 
+        const std::string& enz, 
+        int min_charge, 
+        int max_charge);
+
+
+      static Int getScanNumber_(const String& scan_identifier);
+
+      static bool isEnz_(const char& n, const char& c, const std::string& enz);
+
+      static Size countEnzymatic_(const String& peptide, const std::string& enz);
+
+  };
+} // namespace OpenMS

src/openms/include/OpenMS/FORMAT/sources.cmake

@@ -74,6 +74,7 @@ PepNovoInfile.h
 PepNovoOutfile.h
 PepXMLFile.h
 PepXMLFileMascot.h
+PercolatorInfile.h
 PercolatorOutfile.h
 ProtXMLFile.h
 QcMLFile.h