forgotten files added

src/grouping/ptm/ptminterface.cpp

+/**
+ * \file grouping/ptm/ptminterface.cpp
+ * \date 15/06/2020
+ * \author Olivier Langella
+ * \brief PTM interface
+ */
+
+/*******************************************************************************
+ * Copyright (c) 2020 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ *     XTPcpp is free software: you can redistribute it and/or modify
+ *     it under the terms of the GNU General Public License as published by
+ *     the Free Software Foundation, either version 3 of the License, or
+ *     (at your option) any later version.
+ *
+ *     XTPcpp is distributed in the hope that it will be useful,
+ *     but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *     GNU General Public License for more details.
+ *
+ *     You should have received a copy of the GNU General Public License
+ *     along with XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+
+
+#include "ptminterface.h"
+
+PtmInterface::PtmInterface()
+{
+}
+
+PtmInterface::PtmInterface(const PtmInterface &other)
+{
+}
+
+PtmInterface::~PtmInterface()
+{
+}

src/grouping/ptm/ptminterface.h

+/**
+ * \file grouping/ptm/ptminterface.h
+ * \date 15/06/2020
+ * \author Olivier Langella
+ * \brief PTM interface
+ */
+
+/*******************************************************************************
+ * Copyright (c) 2020 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ *     XTPcpp is free software: you can redistribute it and/or modify
+ *     it under the terms of the GNU General Public License as published by
+ *     the Free Software Foundation, either version 3 of the License, or
+ *     (at your option) any later version.
+ *
+ *     XTPcpp is distributed in the hope that it will be useful,
+ *     but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *     GNU General Public License for more details.
+ *
+ *     You should have received a copy of the GNU General Public License
+ *     along with XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+
+#pragma once
+
+#include <vector>
+#include <pappsomspp/amino_acid/aamodification.h>
+
+#include "../../core/peptidematch.h"
+#include "../../core/proteinmatch.h"
+
+
+/**
+ * @brief Interface to describe a post translational modification
+ */
+class PtmInterface
+{
+  public:
+  /**
+   * Default constructor
+   */
+  PtmInterface();
+
+  /**
+   * Copy constructor
+   *
+   * @param other TODO
+   */
+  PtmInterface(const PtmInterface &other);
+
+  /**
+   * Destructor
+   */
+  virtual ~PtmInterface();
+
+
+  virtual std::size_t
+  countPeptideMatchPtm(const PeptideMatch &peptide_match) const = 0;
+
+  virtual std::vector<unsigned int>
+  getPtmPositions(const PeptideMatch &peptide_match) const = 0;
+
+
+  virtual std::vector<unsigned int>
+  getPtmPositions(const ProteinMatch *protein_match) const = 0;
+
+
+  protected:
+  struct ModificationAndAa
+  {
+    pappso::AaModificationP modification;
+    std::vector<char> aa_list;
+  };
+
+
+  std::vector<ModificationAndAa> m_modificationList;
+};

src/grouping/ptm/ptmphospho.cpp

+/**
+ * \file grouping/ptm/ptmphospho.cpp
+ * \date 15/06/2020
+ * \author Olivier Langella
+ * \brief PTM phosphorylation
+ */
+
+/*******************************************************************************
+ * Copyright (c) 2020 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ *     XTPcpp is free software: you can redistribute it and/or modify
+ *     it under the terms of the GNU General Public License as published by
+ *     the Free Software Foundation, either version 3 of the License, or
+ *     (at your option) any later version.
+ *
+ *     XTPcpp is distributed in the hope that it will be useful,
+ *     but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *     GNU General Public License for more details.
+ *
+ *     You should have received a copy of the GNU General Public License
+ *     along with XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+
+#include "ptmphospho.h"
+
+PtmPhospho::PtmPhospho()
+{
+
+  // phospho :
+  m_modificationList.push_back(
+    {pappso::AaModification::getInstance("MOD:00696"), {}});
+  m_modificationList.push_back(
+    {pappso::AaModification::getInstance("MOD:00704"), {'S', 'T'}});
+}
+
+PtmPhospho::~PtmPhospho()
+{
+}
+
+
+std::size_t
+PtmPhospho::countPeptideMatchPtm(const PeptideMatch &peptide_match) const
+{
+
+  unsigned int number = 0;
+  for(const ModificationAndAa &modification : m_modificationList)
+    {
+      if(modification.aa_list.size() == 0)
+        {
+          number += peptide_match.getPeptideEvidence()
+                      ->getPeptideXtpSp()
+                      .get()
+                      ->getNumberOfModification(modification.modification);
+        }
+      else
+        {
+          number += peptide_match.getPeptideEvidence()
+                      ->getPeptideXtpSp()
+                      .get()
+                      ->countModificationOnAa(modification.modification,
+                                              modification.aa_list);
+        }
+    }
+  return number;
+}
+
+
+std::vector<unsigned int>
+PtmPhospho::getPtmPositions(const PeptideMatch &peptide_match) const
+{
+  std::vector<unsigned int> position_list;
+
+  for(const ModificationAndAa &modification : m_modificationList)
+    {
+      if(modification.aa_list.size() == 0)
+        {
+          for(unsigned int position :
+              peptide_match.getPeptideEvidence()
+                ->getPeptideXtpSp()
+                .get()
+                ->getModificationPositionList(modification.modification))
+            {
+              position_list.push_back(position);
+            }
+        }
+      else
+        {
+          for(unsigned int position :
+              peptide_match.getPeptideEvidence()
+                ->getPeptideXtpSp()
+                .get()
+                ->getModificationPositionList(modification.modification,
+                                              modification.aa_list))
+            {
+              position_list.push_back(position);
+            }
+        }
+    }
+
+  std::sort(position_list.begin(), position_list.end());
+  auto last = std::unique(position_list.begin(), position_list.end());
+  position_list.erase(last, position_list.end());
+  return position_list;
+}
+
+
+std::vector<unsigned int>
+PtmPhospho::getPtmPositions(const ProteinMatch *protein_match) const
+{
+  std::vector<unsigned int> position_list;
+
+  for(const PeptideMatch &peptide_match :
+      protein_match->getPeptideMatchList(ValidationState::validAndChecked))
+    {
+      unsigned int start = peptide_match.getStart();
+      std::vector<unsigned int> positionb_list =
+        this->getPtmPositions(peptide_match);
+      for(unsigned int position : positionb_list)
+        {
+          position_list.push_back(start + position);
+        }
+    }
+  std::sort(position_list.begin(), position_list.end());
+  auto last = std::unique(position_list.begin(), position_list.end());
+  position_list.erase(last, position_list.end());
+  return position_list;
+}

src/grouping/ptm/ptmphospho.h

+/**
+ * \file grouping/ptm/ptmphospho.h
+ * \date 15/06/2020
+ * \author Olivier Langella
+ * \brief PTM phosphorylation
+ */
+
+/*******************************************************************************
+ * Copyright (c) 2020 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ *     XTPcpp is free software: you can redistribute it and/or modify
+ *     it under the terms of the GNU General Public License as published by
+ *     the Free Software Foundation, either version 3 of the License, or
+ *     (at your option) any later version.
+ *
+ *     XTPcpp is distributed in the hope that it will be useful,
+ *     but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *     GNU General Public License for more details.
+ *
+ *     You should have received a copy of the GNU General Public License
+ *     along with XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+
+#pragma once
+
+#include "ptminterface.h"
+
+/**
+ * @todo write docs
+ */
+class PtmPhospho : public PtmInterface
+{
+  public:
+  /**
+   * Default constructor
+   */
+  PtmPhospho();
+
+  /**
+   * Destructor
+   */
+  ~PtmPhospho();
+
+  virtual std::size_t
+  countPeptideMatchPtm(const PeptideMatch &peptide_match) const override;
+
+  virtual std::vector<unsigned int>
+  getPtmPositions(const PeptideMatch &peptide_match) const override;
+
+  virtual std::vector<unsigned int>
+  getPtmPositions(const ProteinMatch *protein_match) const override;
+};