new ptm island group object

src/CMakeLists.txt

@@ -70,6 +70,7 @@ SET(CPP_FILES
   grouping/groupingpeptidemass.cpp
   grouping/ptm/ptmgroupingexperiment.cpp
   grouping/ptm/ptmisland.cpp
+  grouping/ptm/ptmislandgroup.cpp
   grouping/ptm/ptmislandsubgroup.cpp
   gui/peptide_detail_view/spectrum_widget/spectrumpainter.cpp
   input/xpipsaxhandler.cpp

src/grouping/ptm/ptmgroupingexperiment.cpp

@@ -72,6 +72,8 @@ PtmGroupingExperiment::~PtmGroupingExperiment()
 
 }
 
+void PtmGroupingExperiment::startGrouping() {
+}
 void PtmGroupingExperiment::addPtmIsland(PtmIslandSp ptm_island_sp) {
     if (std::none_of(_ptm_island_subgroup_list.begin(), _ptm_island_subgroup_list.end(), [ptm_island_sp](PtmIslandSubgroupSp element) {
     return element.get()->mergePtmIslandSp(ptm_island_sp);
@@ -134,3 +136,4 @@ std::vector<unsigned int> PtmGroupingExperiment::getPtmPositions(const ProteinMa
     position_list.erase(last, position_list.end());
     return position_list;
 }
+

src/grouping/ptm/ptmgroupingexperiment.h

@@ -34,6 +34,7 @@
 #include <pappsomspp/amino_acid/aamodification.h>
 #include "ptmisland.h"
 #include "ptmislandsubgroup.h"
+#include "ptmislandgroup.h"
 
 class PtmGroupingExperiment
 {
@@ -42,6 +43,7 @@ public:
     ~PtmGroupingExperiment();
     
     void addProteinMatch(const ProteinMatch* p_protein_match);
+    void startGrouping();
 
 private:
     std::vector<unsigned int> getPtmPositions(const ProteinMatch * protein_match) const;
@@ -52,6 +54,7 @@ private:
     std::list<pappso::AaModificationP> _modification_list;
     ValidationState _peptide_validation_state = ValidationState::validAndChecked;
     std::vector<PtmIslandSubgroupSp> _ptm_island_subgroup_list;
+    std::vector<PtmIslandGroupSp> _ptm_island_group_list;
 };
 
 #endif // PTMGROUPINGEXPERIMENT_H

src/grouping/ptm/ptmislandgroup.cpp

+/**
+ * \file grouping/ptm/ptmislandgroup.cpp
+ * \date 29/5/2017
+ * \author Olivier Langella
+ * \brief object to group subgroups of ptmislands sharing at least one protein
+ */
+
+/*******************************************************************************
+* Copyright (c) 2017 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/>.
+*
+* Contributors:
+*     Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#include "ptmislandgroup.h"
+
+PtmIslandGroup::PtmIslandGroup()
+{
+
+}
+
+PtmIslandGroup::PtmIslandGroup(const PtmIslandGroup& other)
+{
+
+}
+
+PtmIslandGroup::~PtmIslandGroup()
+{
+
+}

src/grouping/ptm/ptmislandgroup.h

+/**
+ * \file grouping/ptm/ptmislandgroup.h
+ * \date 29/5/2017
+ * \author Olivier Langella
+ * \brief object to group subgroups of ptmislands sharing at least one protein
+ */
+
+/*******************************************************************************
+* Copyright (c) 2017 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/>.
+*
+* Contributors:
+*     Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#ifndef PTMISLANDGROUP_H
+#define PTMISLANDGROUP_H
+
+#include <memory>
+
+class PtmIslandGroup;
+
+/** \brief shared pointer on a Peptide object
+ */
+typedef std::shared_ptr<PtmIslandGroup> PtmIslandGroupSp;
+
+
+class PtmIslandGroup
+{
+public:
+    PtmIslandGroup();
+    PtmIslandGroup(const PtmIslandGroup& other);
+    ~PtmIslandGroup();
+};
+
+#endif // PTMISLANDGROUP_H