From ef4569e315f7bc4432ea59c8255cd692f7d8e23c Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Tue, 21 Mar 2017 16:25:54 +0100
Subject: [PATCH] new interface to handle grouping
---
src/CMakeLists.txt | 1 +
src/core/identificationgroup.cpp | 2 ++
src/core/identificationgroup.h | 6 ++---
src/grouping/groupingexperiment.cpp | 34 ++++++++++++++++++++++++++
src/grouping/groupingexperiment.h | 37 +++++++++++++++++++++++++++++
5 files changed, 77 insertions(+), 3 deletions(-)
create mode 100644 src/grouping/groupingexperiment.cpp
create mode 100644 src/grouping/groupingexperiment.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 6bc611419..5385f2566 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -63,6 +63,7 @@ SET(CPP_FILES
core/identification_sources/identificationdatasource.cpp
core/identification_sources/identificationxtandemfile.cpp
files/xpipfile.cpp
+ grouping/groupingexperiment.cpp
input/xpipsaxhandler.cpp
utils/peptidestore.cpp
utils/readspectrum.cpp
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index c8d345bb0..87ab4a8bd 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -44,6 +44,8 @@ void IdentificationGroup::updateAutomaticFilters(const AutomaticFilterParameters
p_protein_match->updateAutomaticFilters(automatic_filter_parameters);
}
+ if (_p_grp_experiment != nullptr) {
+ }
}
void IdentificationGroup::addProteinMatch(ProteinMatch * protein_match) {
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index dc448a6d7..e981318a4 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -21,11 +21,11 @@
* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
******************************************************************************/
#include <memory>
-#include <pappsomspp/grouping/grpexperiment.h>
#include <QFileInfo>
#include "proteinmatch.h"
#include <pappsomspp/msrun/msrunid.h>
+#include "grouping/groupingexperiment.h"
#ifndef IDENTIFICATIONGROUP_H
#define IDENTIFICATIONGROUP_H
@@ -50,9 +50,9 @@ public:
/** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
* */
void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
-
- pappso::GrpExperiment * _p_grp_experiment= nullptr;
private :
+ GroupingExperiment * _p_grp_experiment= nullptr;
+
Project * _p_project;
std::vector<ProteinMatch *> _protein_match_list;
diff --git a/src/grouping/groupingexperiment.cpp b/src/grouping/groupingexperiment.cpp
new file mode 100644
index 000000000..717e7580f
--- /dev/null
+++ b/src/grouping/groupingexperiment.cpp
@@ -0,0 +1,34 @@
+
+/*******************************************************************************
+* 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 "groupingexperiment.h"
+
+GroupingExperiment::GroupingExperiment()
+{
+
+}
+
+GroupingExperiment::~GroupingExperiment()
+{
+
+}
diff --git a/src/grouping/groupingexperiment.h b/src/grouping/groupingexperiment.h
new file mode 100644
index 000000000..f473f2c6b
--- /dev/null
+++ b/src/grouping/groupingexperiment.h
@@ -0,0 +1,37 @@
+
+/*******************************************************************************
+* 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 GROUPINGEXPERIMENT_H
+#define GROUPINGEXPERIMENT_H
+
+class GroupingExperiment
+{
+public:
+ GroupingExperiment();
+ ~GroupingExperiment();
+
+
+};
+
+#endif // GROUPINGEXPERIMENT_H
--
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