From ff39eb29b77efb31b8ae7d1d4d42cddbf6151213 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Mon, 29 May 2017 16:30:05 +0200
Subject: [PATCH] new ptm island group object
---
src/CMakeLists.txt | 1 +
src/grouping/ptm/ptmgroupingexperiment.cpp | 3 ++
src/grouping/ptm/ptmgroupingexperiment.h | 3 ++
src/grouping/ptm/ptmislandgroup.cpp | 45 +++++++++++++++++++
src/grouping/ptm/ptmislandgroup.h | 50 ++++++++++++++++++++++
5 files changed, 102 insertions(+)
create mode 100644 src/grouping/ptm/ptmislandgroup.cpp
create mode 100644 src/grouping/ptm/ptmislandgroup.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 34d6ea67..59eeff83 100644
--- a/src/CMakeLists.txt
+++ b/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
diff --git a/src/grouping/ptm/ptmgroupingexperiment.cpp b/src/grouping/ptm/ptmgroupingexperiment.cpp
index 17654749..3810beec 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.cpp
+++ b/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;
}
+
diff --git a/src/grouping/ptm/ptmgroupingexperiment.h b/src/grouping/ptm/ptmgroupingexperiment.h
index d34fad8e..3ae765f9 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.h
+++ b/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
diff --git a/src/grouping/ptm/ptmislandgroup.cpp b/src/grouping/ptm/ptmislandgroup.cpp
new file mode 100644
index 00000000..d2006630
--- /dev/null
+++ b/src/grouping/ptm/ptmislandgroup.cpp
@@ -0,0 +1,45 @@
+/**
+ * \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()
+{
+
+}
diff --git a/src/grouping/ptm/ptmislandgroup.h b/src/grouping/ptm/ptmislandgroup.h
new file mode 100644
index 00000000..106c9ac7
--- /dev/null
+++ b/src/grouping/ptm/ptmislandgroup.h
@@ -0,0 +1,50 @@
+/**
+ * \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
--
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