debian directory

debian/compat

+9

debian/control

+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

debian/control.cmake

+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

debian/copyright

+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+

debian/rules

+#!/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

debian/xtpcpp.install

+usr/bin/xtpcpp
+usr/share/applications/xtpcpp.desktop

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();

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

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_ */