Merge branch 'master' of forgemia.inra.fr:pappso/xtpcpp into master

CMakeLists.txt

@@ -149,6 +149,7 @@ endif(CMAKE_INSTALL_PREFIX)
 
 # Subdirectories
 add_subdirectory(src)
+add_subdirectory(doc)
 
 if(UNIX)
     # Doxygen

doc/CMakeLists.txt

+message("")
+message(STATUS "${BoldGreen}Starting configuration for the doc material for ${CMAKE_PROJECT_NAME} ${ColourReset}")
+message("")
+
+# The UNIX man pages
+if(UNIX AND NOT APPLE)
+
+	message(STATUS "Going to generate the man pages.")
+
+	execute_process(COMMAND docbook-to-man xtpcpp.xml
+		OUTPUT_FILE	${CMAKE_BINARY_DIR}/xtpcpp
+		WORKING_DIRECTORY	${CMAKE_CURRENT_SOURCE_DIR})
+
+endif(UNIX AND NOT APPLE)
+
+
+###############
+# install stuff
+
+# The history and licence files.
+
+message("Installing the doc files in ${DOC_DIR}")
+
+# The man page.
+if(UNIX AND NOT APPLE)
+	install(FILES ${CMAKE_BINARY_DIR}/xtpcpp
+		${CMAKE_BINARY_DIR}/xtpcpp
+		DESTINATION ${CMAKE_INSTALL_PREFIX}/share/man/man1)
+endif()
+
+
+
+message("")
+message(STATUS "${BoldGreen}Finished configuration of the doc material.${ColourReset}")
+message("")
+

doc/xtpcpp.xml

+<?xml version="1.0"?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN"
+[
+<!ENTITY progname "xtpcpp">
+<!ENTITY progName "xtpcpp">
+]>
+
+<refentry>
+
+	<refentryinfo>
+		<date>2020 november 6</date>
+	</refentryinfo>
+
+	<refmeta>
+		<refentrytitle>
+			<application>&progName;</application>
+		</refentrytitle>
+		<manvolnum>1</manvolnum>
+		<refmiscinfo>&progName; proteomic software for peptides and proteins identification and quantification</refmiscinfo>
+	</refmeta>
+
+	<refnamediv>
+		<refname>
+			<application>&progName;</application>
+		</refname>
+
+		<refpurpose>
+			Open xtpcpp project file (.xpip extensions)
+		</refpurpose>
+	</refnamediv>
+
+	<refsynopsisdiv>
+
+		<cmdsynopsis>
+			<command>&progname;</command>
+			<arg><option><replaceable class="parameter">options</replaceable></option></arg>
+			<arg><option><replaceable class="parameter">filename ...</replaceable></option></arg>
+		</cmdsynopsis>
+
+	</refsynopsisdiv>
+
+	<refsect1>
+		<title>DESCRIPTION</title>
+		<para>
+
+			This manual page documents briefly the <command>&progName;</command> software. 
+
+			This program can be used to load MS/MS identification engine results. It includes
+            peptide filtering, grouping algorithms, data visualization, peptide quantification using XICs.
+
+		</para>
+
+ </refsect1>
+
+ <refsect1>
+	 <title>OPTIONS</title>
+	 <variablelist>
+
+		 <varlistentry>
+			 <term><option>-h | --help</option></term>
+			 <listitem>
+				 <para>
+					 Displays detailed usage information and exits.
+				 </para>
+			 </listitem>
+		 </varlistentry>
+
+		 <varlistentry>
+			 <term><option>-v | --version</option></term>
+			 <listitem>
+				 <para>
+					 Print the version of the software program.
+				 </para>
+			 </listitem>
+		 </varlistentry>
+
+		 <varlistentry>
+			 <term><replaceable class="parameter">filename</replaceable></term>
+			 <listitem>
+				 <para>
+					 X!TandemPipeline project file to be opened.
+				 </para>
+			 </listitem>      
+		 </varlistentry>
+
+	 </variablelist>
+ </refsect1>
+
+ <refsect1>
+	 <title>Bibliographic reference to be cited</title>
+	 <para>
+		 Langella O, Valot B, Balliau T, Blein-Nicolas M, Bonhomme L, Zivy M. (2017) X!TandemPipeline: A Tool to Manage Sequence Redundancy for Protein Inference and Phosphosite Identification. J. Proteome Res., 2 (16) 494-503 
+	 </para>
+ </refsect1>
+</refentry>
+

src/gui/ptm_island_list_view/ptmislandproxymodel.cpp

@@ -65,7 +65,8 @@ PtmIslandProxyModel::~PtmIslandProxyModel()
 
 bool
 PtmIslandProxyModel::filterAcceptsColumn(int source_column,
-                                         const QModelIndex &source_parent) const
+                                         const QModelIndex &source_parent
+                                         [[maybe_unused]]) const
 {
   return m_column_display[source_column];
 }
@@ -202,7 +203,8 @@ PtmIslandProxyModel::onTableClicked(const QModelIndex &index)
   int row = source_index.row();
   int col = source_index.column();
 
-  PtmIslandSp ptm_island_sp = _p_ptm_island_table_model->getPtmGroupingExperiment()
+  PtmIslandSp ptm_island_sp =
+    _p_ptm_island_table_model->getPtmGroupingExperiment()
       ->getPtmIslandList()
       .at(row);