From a5d34b968ab9beee8713a424af654b5c39c988cb Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Fri, 7 Apr 2017 09:04:49 +0200
Subject: [PATCH] debian directory
---
debian/changelog | 0
debian/compat | 1 +
debian/control | 16 ++++
debian/control.cmake | 16 ++++
debian/copyright | 7 ++
debian/rules | 82 +++++++++++++++++++
debian/xtpcpp.install | 2 +
.../protein_list_view/proteintablemodel.cpp | 52 ++++++++----
src/gui/protein_list_view/proteintablemodel.h | 4 +
src/utils/types.h | 19 +++++
10 files changed, 181 insertions(+), 18 deletions(-)
create mode 100644 debian/changelog
create mode 100644 debian/compat
create mode 100644 debian/control
create mode 100644 debian/control.cmake
create mode 100644 debian/copyright
create mode 100755 debian/rules
create mode 100644 debian/xtpcpp.install
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 000000000..e69de29bb
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 000000000..ec635144f
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 000000000..0040eb756
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,16 @@
+Source: xtpcpp
+Maintainer: Olivier Langella <Olivier.Langella@moulon.inra.fr>
+Homepage: http://pappso.inra.fr/bioinfo
+Section: libs
+Priority: optional
+Build-Depends: debhelper (>= 9), cmake (>= 2.6), libqt4-dev (>= 4.8), libpappsomspp-dev (= 0.2.32-3), libpwiz-dev, libodsstream-dev
+Standards-Version: 3.9.4
+
+Package: xtpcpp
+Architecture: any
+Multi-Arch: same
+Depends: ${shlibs:Depends},
+ ${misc:Depends}, libpappsomspp-qt4 (= 0.2.32-3), libpwiz3,
+ libodsstream-qt4, libqt4-gui, libqt4-svg, libqt4-xml
+Pre-Depends: ${misc:Pre-Depends}
+Description: C++ version of X!TandemPipeline
diff --git a/debian/control.cmake b/debian/control.cmake
new file mode 100644
index 000000000..77d5b7ba6
--- /dev/null
+++ b/debian/control.cmake
@@ -0,0 +1,16 @@
+Source: xtpcpp
+Maintainer: Olivier Langella <Olivier.Langella@moulon.inra.fr>
+Homepage: http://pappso.inra.fr/bioinfo
+Section: libs
+Priority: optional
+Build-Depends: debhelper (>= 9), cmake (>= 2.6), libqt4-dev (>= 4.8), libpappsomspp-dev (= @LIBPAPPSOMSPP_VERSION@), libpwiz-dev, libodsstream-dev
+Standards-Version: 3.9.4
+
+Package: xtpcpp
+Architecture: any
+Multi-Arch: same
+Depends: ${shlibs:Depends},
+ ${misc:Depends}, libpappsomspp-qt4 (= @LIBPAPPSOMSPP_VERSION@), libpwiz3,
+ libodsstream-qt4, libqt4-gui, libqt4-svg, libqt4-xml
+Pre-Depends: ${misc:Pre-Depends}
+Description: C++ version of X!TandemPipeline
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 000000000..142f7326f
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,7 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: xtpcpp
+Source: https://sourcesup.renater.fr/projects/xtandempipeline/
+
+Files: *
+Copyright: Olivier Langella <Olivier.Langella@moulon.inra.fr>
+License: GPL-3.0+
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 000000000..f3f4eaaae
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,82 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+export DESTDIR=$(CURDIR)/debian/tmp
+
+#%:
+# dh $@ --buildsystem=cmake --parallel
+
+configure: configure-stamp
+configure-stamp:
+ cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release .
+ dh_testdir
+ # Add here commands to configure the package.
+
+ touch configure-stamp
+
+
+build: build-stamp
+
+build-stamp: configure-stamp
+ dh_testdir
+
+ # Add here commands to compile the package.
+ $(MAKE)
+ #$(MAKE) doc
+ #docbook-to-man debian/beads.sgml > beads.1
+
+ touch $@
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp configure-stamp CMakeCache.txt
+
+ # Add here commands to clean up after the build process.
+ -$(MAKE) clean
+
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_prep
+ dh_installdirs
+
+ $(MAKE) DESTDIR=$(DESTDIR) install
+
+
+# Build architecture-independent files here.
+binary-indep: build install
+# We have nothing to do by default.
+
+# Build architecture-dependent files here.
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_installexamples
+ dh_install --sourcedir=$(DESTDIR) --list-missing
+# dh_install
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install configure
diff --git a/debian/xtpcpp.install b/debian/xtpcpp.install
new file mode 100644
index 000000000..d4c8f6803
--- /dev/null
+++ b/debian/xtpcpp.install
@@ -0,0 +1,2 @@
+usr/bin/xtpcpp
+usr/share/applications/xtpcpp.desktop
diff --git a/src/gui/protein_list_view/proteintablemodel.cpp b/src/gui/protein_list_view/proteintablemodel.cpp
index f09913a09..85b9831b8 100644
--- a/src/gui/protein_list_view/proteintablemodel.cpp
+++ b/src/gui/protein_list_view/proteintablemodel.cpp
@@ -28,6 +28,21 @@
#include <QDebug>
#include <pappsomspp/pappsoexception.h>
#include "proteinlistwindow.h"
+#include "../../utils/types.h"
+
+ProteinTableModel::columnMap ProteinTableModel::_column_assignment = {
+ (std::int8_t)ProteinListColumn::checked,
+ (std::int8_t)ProteinListColumn::group,
+ (std::int8_t)ProteinListColumn::accession,
+ (std::int8_t)ProteinListColumn::description,
+ (std::int8_t)ProteinListColumn::evalue,
+ (std::int8_t)ProteinListColumn::spectrum,
+ (std::int8_t)ProteinListColumn::specific_spectrum,
+ (std::int8_t)ProteinListColumn::sequence,
+ (std::int8_t)ProteinListColumn::specific_sequence,
+ (std::int8_t)ProteinListColumn::coverage,
+ (std::int8_t)ProteinListColumn::pai,
+};
IdentificationGroup * ProteinTableModel::getIdentificationGroup() {
return _p_identification_group;
@@ -132,54 +147,55 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
if (_p_identification_group == nullptr) {
return QVariant();
}
- if (col == 0) {
+ switch (_column_assignment[col]) {
+ case (std::int8_t)ProteinListColumn::checked:
return QVariant();
- }
+ break;
- if (col == 1) {
+ case (std::int8_t)ProteinListColumn::group:
pappso::GrpProtein * p_grp_prot = _p_identification_group->getProteinMatchList().at(row)->getGrpProteinSp().get();
if (p_grp_prot != nullptr) return p_grp_prot->getGroupingId();
return QVariant();
+ break;
}
-
- if (col == 2) {
- return _p_identification_group->getProteinMatchList().at(row)->getProteinXtpSp().get()->getAccession();
+ if (_column_assignment[col] == (std::int8_t) ProteinListColumn::accession ) {
+ return QVariant(_p_identification_group->getProteinMatchList().at(row)->getProteinXtpSp().get()->getAccession());
}
- if (col == 3) {
- return _p_identification_group->getProteinMatchList().at(row)->getProteinXtpSp().get()->getDescription();
+ if (_column_assignment[col] == (std::int8_t) ProteinListColumn::description ) {
+ return _p_identification_group->getProteinMatchList().at(row)->getProteinXtpSp().get()->getDescription();
}
- if (col == 4) {
+ if (_column_assignment[col] == (std::int8_t) ProteinListColumn::evalue ) {
return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getEvalue());
-
}
-
- if (col == 5) {//spectrum
+ if (_column_assignment[col] == (std::int8_t) ProteinListColumn::spectrum ) {
return QVariant ((qreal) _p_identification_group->getProteinMatchList().at(row)->countValidAndCheckedSpectrum());
}
- if (col == 6) {//specific
+
+ if (_column_assignment[col] == (std::int8_t) ProteinListColumn::specific_spectrum ) {
GroupingGroup * p_groupin_group = _p_identification_group->getProteinMatchList().at(row)->getGroupingGroupSp().get();
if (p_groupin_group != nullptr) {
return QVariant ((qreal) p_groupin_group->countSpecificSpectrum(_p_identification_group->getProteinMatchList().at(row)));
}
}
- if (col == 7) {//sequence
+
+ if (_column_assignment[col] == (std::int8_t) ProteinListColumn::sequence ) {
return QVariant ((qreal) _p_identification_group->getProteinMatchList().at(row)->countUniqueSequence());
}
- if (col == 8) {//specific sequence
+ if (_column_assignment[col] == (std::int8_t) ProteinListColumn::specific_sequence ) {
GroupingGroup * p_groupin_group = _p_identification_group->getProteinMatchList().at(row)->getGroupingGroupSp().get();
if (p_groupin_group != nullptr) {
return QVariant ((qreal) p_groupin_group->countSpecificSequence(_p_identification_group->getProteinMatchList().at(row)));
}
}
- if (col == 9) {
+ if (_column_assignment[col] == (std::int8_t) ProteinListColumn::coverage ) {
return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getCoverage());
}
- if (col == 10) {
+
+ if (_column_assignment[col] == (std::int8_t) ProteinListColumn::pai ) {
return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getPAI());
}
-
return QVariant();
}
return QVariant();
diff --git a/src/gui/protein_list_view/proteintablemodel.h b/src/gui/protein_list_view/proteintablemodel.h
index ecb7aafbc..17f3b5d38 100644
--- a/src/gui/protein_list_view/proteintablemodel.h
+++ b/src/gui/protein_list_view/proteintablemodel.h
@@ -45,6 +45,8 @@ public:
void setIdentificationGroup(IdentificationGroup * p_identification_group);
IdentificationGroup * getIdentificationGroup();
+ using columnMap = std::int8_t[20];
+
public slots:
void onProteinDataChanged();
private :
@@ -53,6 +55,8 @@ private :
IdentificationGroup * _p_identification_group = nullptr;
ProteinListWindow * _p_protein_list_window;
QStringList _columns;
+
+ static columnMap _column_assignment;
};
#endif // PROTEINTABLEMODEL_H
diff --git a/src/utils/types.h b/src/utils/types.h
index bc7c3b7f7..3bf0931e2 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -36,4 +36,23 @@ enum class GroupingType {
SampleScan ///< X!TandemPipeline algo
};
+
+/** \def ProteinListColumn list of available fields to display in protein list
+ *
+ */
+
+enum class ProteinListColumn {
+ checked, ///< manual checked
+ group, ///< group id
+ accession, ///< accession
+ description, ///< protein description
+ evalue, ///< Evalue
+ spectrum, ///< spectrum count
+ specific_spectrum, ///< specific spectrum count
+ sequence, ///< unique sequence count
+ specific_sequence, ///< specific unique sequence
+ coverage, ///< protein coverage
+ pai, ///< PAI
+};
+
#endif /* _TYPES_H_ */
--
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