From 7f6e14342779ed25c2c9fa6b41bddf3b5a92abdf Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Sun, 23 Jul 2017 08:20:09 +0200
Subject: [PATCH] new class to handle ptm sample scan ambiguity
---
src/CMakeLists.txt | 1 +
src/grouping/ptm/ptmisland.cpp | 6 ++++
src/grouping/ptm/ptmisland.h | 3 ++
src/grouping/ptm/ptmsamplescan.cpp | 39 +++++++++++++++++++++
src/grouping/ptm/ptmsamplescan.h | 55 ++++++++++++++++++++++++++++++
5 files changed, 104 insertions(+)
create mode 100644 src/grouping/ptm/ptmsamplescan.cpp
create mode 100644 src/grouping/ptm/ptmsamplescan.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 599cd606b..bdaca3a10 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -73,6 +73,7 @@ SET(CPP_FILES
grouping/ptm/ptmisland.cpp
grouping/ptm/ptmislandgroup.cpp
grouping/ptm/ptmislandsubgroup.cpp
+ grouping/ptm/ptmsamplescan.cpp
gui/peptide_detail_view/spectrum_widget/spectrumpainter.cpp
input/identificationpwizreader.cpp
input/xpipsaxhandler.cpp
diff --git a/src/grouping/ptm/ptmisland.cpp b/src/grouping/ptm/ptmisland.cpp
index 215df8a89..bdc27f1d0 100644
--- a/src/grouping/ptm/ptmisland.cpp
+++ b/src/grouping/ptm/ptmisland.cpp
@@ -169,3 +169,9 @@ bool PtmIsland::merge(PtmIslandSp ptm_island_sp) {
return true;
}
}
+
+std::vector<PtmSampleScanSp> PtmIsland::getPtmSampleScanSpList() const {
+ std::vector<PtmSampleScanSp> sample_scan_list;
+
+ return sample_scan_list;
+}
diff --git a/src/grouping/ptm/ptmisland.h b/src/grouping/ptm/ptmisland.h
index 9cc750b36..5e5f80e29 100644
--- a/src/grouping/ptm/ptmisland.h
+++ b/src/grouping/ptm/ptmisland.h
@@ -32,6 +32,7 @@
#include "../../core/proteinmatch.h"
#include "../../core/peptidematch.h"
+#include "ptmsamplescan.h"
#include <memory>
class PtmGroupingExperiment;
@@ -71,6 +72,8 @@ public:
unsigned int getStart() const;
unsigned int size() const;
+
+ std::vector<PtmSampleScanSp> getPtmSampleScanSpList() const;
private:
const ProteinMatch * _protein_match_p;
diff --git a/src/grouping/ptm/ptmsamplescan.cpp b/src/grouping/ptm/ptmsamplescan.cpp
new file mode 100644
index 000000000..8df90dec6
--- /dev/null
+++ b/src/grouping/ptm/ptmsamplescan.cpp
@@ -0,0 +1,39 @@
+/**
+ * \file grouping/ptm/ptmsamplescan.cpp
+ * \date 23/7/2017
+ * \author Olivier Langella
+ * \brief collection of PTM peptides sharing the same spectrum (sample scan)
+ */
+
+/*******************************************************************************
+* 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 "ptmsamplescan.h"
+
+PtmSampleScan::PtmSampleScan() {
+}
+
+PtmSampleScan::PtmSampleScan(const PtmSampleScan& other){
+}
+
+PtmSampleScan::~PtmSampleScan() {
+}
diff --git a/src/grouping/ptm/ptmsamplescan.h b/src/grouping/ptm/ptmsamplescan.h
new file mode 100644
index 000000000..1ce8a4eb1
--- /dev/null
+++ b/src/grouping/ptm/ptmsamplescan.h
@@ -0,0 +1,55 @@
+/**
+ * \file grouping/ptm/ptmsamplescan.h
+ * \date 23/7/2017
+ * \author Olivier Langella
+ * \brief collection of PTM peptides sharing the same spectrum (sample scan)
+ */
+
+/*******************************************************************************
+* 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 PTMSAMPLESCAN_H
+#define PTMSAMPLESCAN_H
+
+#include <memory>
+#include "../../core/peptidematch.h"
+
+class PtmSampleScan;
+
+/** \brief shared pointer on a PtmSampleScan object
+ */
+typedef std::shared_ptr<PtmSampleScan> PtmSampleScanSp;
+
+
+class PtmSampleScan
+{
+public:
+ PtmSampleScan();
+ PtmSampleScan(const PtmSampleScan& other);
+ ~PtmSampleScan();
+
+private:
+ std::vector<const PeptideMatch *> _peptide_match_list;
+
+};
+
+#endif // PTMSAMPLESCAN_H
--
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