From 32646ed54c52bb0194bf9b20f3efa9d887648384 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Wed, 29 Mar 2017 17:02:42 +0200
Subject: [PATCH] display not valid peptides, warning : bug counting valid
peptides per msrun
---
src/CMakeLists.txt | 4 ++--
src/core/proteinmatch.cpp | 12 ++++++++----
src/gui/peptide_list_view/peptidetablemodel.cpp | 9 ++++++++-
src/gui/protein_list_view/proteinlistwindow.cpp | 5 ++++-
src/gui/protein_list_view/proteinlistwindow.h | 2 +-
5 files changed, 23 insertions(+), 9 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 2f5d3bbc..46172223 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -29,8 +29,8 @@ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5
#sudo apt-get install libpappsomspp-dev
#FIND_PACKAGE( Pappsomspp REQUIRED )
-SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
-# SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
+# SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
+ SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt4.so")
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index eae99e21..fc62465f 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -63,19 +63,23 @@ void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & auto
else {
std::pair<std::map<const pappso::MsRunId*, unsigned int>::iterator,bool> ret = _count_per_msrun.insert(std::pair<const pappso::MsRunId*, unsigned int>(p_peptide_match->getMsRunIdSp().get(),0));
ret.first->second +=1;
- if (ret.first->second > _number_of_valid_peptides) {
- _number_of_valid_peptides = ret.first->second;
- }
}
}
}
}
+ for (auto && pair_msrun_count : _count_per_msrun) {
+ if (pair_msrun_count.second > _number_of_valid_peptides) {
+ _number_of_valid_peptides = pair_msrun_count.second;
+ }
+ }
//update protein evalue ?
- if (_number_of_valid_peptides >= automatic_filter_parameters.getFilterMinimumPeptidePerMatch()) {
+ if (_number_of_valid_peptides < automatic_filter_parameters.getFilterMinimumPeptidePerMatch()) {
+ }
+ else {
if (_evalue <= automatic_filter_parameters.getFilterProteinEvalue()) {
_proxy_valid = true;
}
diff --git a/src/gui/peptide_list_view/peptidetablemodel.cpp b/src/gui/peptide_list_view/peptidetablemodel.cpp
index adb38945..65e5bbc1 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.cpp
+++ b/src/gui/peptide_list_view/peptidetablemodel.cpp
@@ -24,6 +24,7 @@
#include "peptidetablemodel.h"
#include <QDebug>
+#include <QColor>
#include <pappsomspp/grouping/grppeptide.h>
@@ -145,6 +146,12 @@ QVariant PeptideTableModel::data(const QModelIndex &index, int role ) const {
}
}
break;
+ case Qt::BackgroundRole:
+ if (_p_protein_match->getPeptideMatchList().at(row)->isValid() == false)
+ {
+ return QVariant(QColor("grey"));
+ }
+ break;
case Qt::DisplayRole:
if (_p_protein_match == nullptr) {
}
@@ -203,5 +210,5 @@ bool PeptideTableModel::acceptRow(int source_row) {
if (_p_protein_match->getPeptideMatchList().at(source_row)->isValid()) {
return true;
}
- return false;
+ return true;
}
diff --git a/src/gui/protein_list_view/proteinlistwindow.cpp b/src/gui/protein_list_view/proteinlistwindow.cpp
index 00348a5a..6fe75065 100644
--- a/src/gui/protein_list_view/proteinlistwindow.cpp
+++ b/src/gui/protein_list_view/proteinlistwindow.cpp
@@ -188,7 +188,10 @@ void ProteinListWindow::setIdentificationGroup(IdentificationGroup * p_identific
}
void ProteinListWindow::updateStatusBar() {
+ if (_p_identification_group == nullptr) {
+ }
+ else {
ui->statusbar->showMessage(tr("proteins %1 valid, %2 checked, %3 displayed").arg(_p_identification_group->countValid()).arg(_p_identification_group->countValidAndChecked()).arg(_p_proxy_model->rowCount()));
-
+ }
}
diff --git a/src/gui/protein_list_view/proteinlistwindow.h b/src/gui/protein_list_view/proteinlistwindow.h
index 268939d4..4ce0985f 100644
--- a/src/gui/protein_list_view/proteinlistwindow.h
+++ b/src/gui/protein_list_view/proteinlistwindow.h
@@ -74,7 +74,7 @@ protected :
private:
- IdentificationGroup * _p_identification_group;
+ IdentificationGroup * _p_identification_group=nullptr;
Ui::ProteinView *ui;
ProteinTableModel * _protein_table_model_p = nullptr;
ProteinTableProxyModel * _p_proxy_model = nullptr;
--
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