From cafd9651cda4bf0563d55d8f1a6ba3e734530c5d Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Sat, 1 Apr 2017 12:14:00 +0200
Subject: [PATCH] trying to update valid protein status
---
src/core/project.cpp | 4 +-
src/core/project.h | 1 +
src/core/proteinmatch.cpp | 44 ++++++------
src/core/proteinmatch.h | 4 +-
.../peptide_list_view/peptidelistwindow.cpp | 2 +
.../peptidetableproxymodel.cpp | 1 +
src/gui/project_view/projectwindow.cpp | 4 ++
src/gui/project_view/projectwindow.h | 1 +
src/gui/protein_view/protein_detail_view.ui | 70 +++++++++++++------
src/gui/protein_view/proteinwindow.cpp | 1 +
10 files changed, 85 insertions(+), 47 deletions(-)
diff --git a/src/core/project.cpp b/src/core/project.cpp
index 7c09d5e3..ff0b7c75 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -48,7 +48,9 @@ PeptideStore & Project::getPeptideStore() {
ProteinStore & Project::getProteinStore() {
return _protein_store;
}
-
+const AutomaticFilterParameters & Project::getAutomaticFilterParameters() const {
+ return _automatic_filter_parameters;
+}
void Project::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
_automatic_filter_parameters = automatic_filter_parameters;
for (auto & p_id_group : _identification_goup_list) {
diff --git a/src/core/project.h b/src/core/project.h
index 677f54ad..5f64afb9 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -52,6 +52,7 @@ public:
/** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
* */
void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
+ const AutomaticFilterParameters & getAutomaticFilterParameters() const;
void startGrouping();
const GroupingType getGroupingType() const;
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index e00020a3..98b5a7ee 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -42,7 +42,7 @@ ProteinMatch::~ProteinMatch()
}
void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
- qDebug() <<"ProteinMatch::updateAutomaticFilters begin " ;
+ qDebug() <<"ProteinMatch::updateAutomaticFilters begin " ;
_proxy_valid = false;
unsigned int number_of_valid_peptides =0;
bool cross_sample = automatic_filter_parameters.getFilterCrossSamplePeptideNumber();
@@ -69,12 +69,14 @@ void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & auto
}
}
+ if (number_of_valid_peptides > 0) {
- if (number_of_valid_peptides < automatic_filter_parameters.getFilterMinimumPeptidePerMatch()) {
- }
- else {
- if (_evalue <= automatic_filter_parameters.getFilterProteinEvalue()) {
- _proxy_valid = true;
+ if (number_of_valid_peptides < automatic_filter_parameters.getFilterMinimumPeptidePerMatch()) {
+ }
+ else {
+ if (getEvalue() <= automatic_filter_parameters.getFilterProteinEvalue()) {
+ _proxy_valid = true;
+ }
}
}
qDebug() <<"ProteinMatch::updateAutomaticFilters end " << number_of_valid_peptides ;
@@ -270,7 +272,7 @@ pappso::pappso_double ProteinMatch::getPAI(const pappso::MsRunIdSp & sp_msrun_id
const QString ProteinMatch::getHtmlSequence() const
{
- size_t prot_size = _protein_sp.get()->size();
+ size_t prot_size = _protein_sp.get()->size();
//qDebug() << "ProteinMatch::getCoverage begin prot_size=" << prot_size << " " << _protein_sp.get()-//>getSequence();
if (prot_size == 0) return 0;
bool cover_bool[prot_size] = {false};
@@ -287,21 +289,21 @@ const QString ProteinMatch::getHtmlSequence() const
}
QString sequence = getProteinXtpSp().get()->getSequence();
QString sequence_html;
- for (unsigned int i=0; i < prot_size; i++) {
-
- if(cover_bool[i]) {
- sequence_html.append(QString("<span style=\"background-color:yellow;\">%1").arg(sequence[i]));
- i++;
- for (;i < prot_size; i++) {
- if(cover_bool[i]) {
- sequence_html.append(sequence[i]);
- }
- else {
- sequence_html.append(QString("</span>%1").arg(sequence[i]));
- break;
- }
+ for (unsigned int i=0; i < prot_size; i++) {
+
+ if(cover_bool[i]) {
+ sequence_html.append(QString("<span style=\"background-color:yellow;\">%1").arg(sequence[i]));
+ i++;
+ for (; i < prot_size; i++) {
+ if(cover_bool[i]) {
+ sequence_html.append(sequence[i]);
}
- sequence_html.append(QString("</span>"));
+ else {
+ sequence_html.append(QString("</span>%1").arg(sequence[i]));
+ break;
+ }
+ }
+ sequence_html.append(QString("</span>"));
}
else {
sequence_html.append(sequence[i]);
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index ec757235..49cc8fca 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -98,12 +98,12 @@ public:
const pappso::GrpProteinSp & getGrpProteinSp() const;
const GroupingGroupSp & getGroupingGroupSp() const;
-protected :
-
/** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
* */
void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
+protected :
+
void setGroupingExperiment(GroupingExperiment * p_grp_experiment);
void setGroupInstance(GroupStore & group_store);
diff --git a/src/gui/peptide_list_view/peptidelistwindow.cpp b/src/gui/peptide_list_view/peptidelistwindow.cpp
index ed693ec9..c25b24f2 100644
--- a/src/gui/peptide_list_view/peptidelistwindow.cpp
+++ b/src/gui/peptide_list_view/peptidelistwindow.cpp
@@ -99,6 +99,8 @@ void PeptideListWindow::setProteinMatch(IdentificationGroup * p_identification_g
void PeptideListWindow::edited() {
qDebug() << "PeptideListWindow::edited begin";
//emit dataChanged(index, index);
+
+ _p_protein_match->updateAutomaticFilters(_project_window->getProjectP()->getAutomaticFilterParameters());
_project_window->doIdentificationGroupEdited(_p_identification_group);
//updateStatusBar();
diff --git a/src/gui/peptide_list_view/peptidetableproxymodel.cpp b/src/gui/peptide_list_view/peptidetableproxymodel.cpp
index 71db91f3..4326afaf 100644
--- a/src/gui/peptide_list_view/peptidetableproxymodel.cpp
+++ b/src/gui/peptide_list_view/peptidetableproxymodel.cpp
@@ -65,6 +65,7 @@ bool PeptideTableProxyModel::filterAcceptsRow(int source_row,
}
}
+ return true;
}
catch (pappso::PappsoException exception_pappso) {
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 45d9fa46..a0c28b9a 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -65,6 +65,10 @@ ProjectWindow::~ProjectWindow()
delete ui;
}
+
+Project * ProjectWindow::getProjectP() {
+ return _project_sp.get();
+}
void ProjectWindow::setDefaultProteinListWindow(ProteinListWindow* p_protein_list_window) {
qDebug() << "ProjectWindow::setDefaultProteinListWindow begin";
_p_current_protein_list_window = p_protein_list_window;
diff --git a/src/gui/project_view/projectwindow.h b/src/gui/project_view/projectwindow.h
index c82caf7b..56854003 100644
--- a/src/gui/project_view/projectwindow.h
+++ b/src/gui/project_view/projectwindow.h
@@ -45,6 +45,7 @@ class ProjectWindow: public QMainWindow {
public:
explicit ProjectWindow(MainWindow * parent = 0);
+ Project * getProjectP();
void setProjectSp(ProjectSp project_sp);
~ProjectWindow();
diff --git a/src/gui/protein_view/protein_detail_view.ui b/src/gui/protein_view/protein_detail_view.ui
index eb49e155..026af897 100644
--- a/src/gui/protein_view/protein_detail_view.ui
+++ b/src/gui/protein_view/protein_detail_view.ui
@@ -18,29 +18,53 @@
<item row="1" column="0">
<layout class="QVBoxLayout" name="verticalLayout">
<item>
- <widget class="QLabel" name="descriptionLabel">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Minimum">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>167</height>
- </size>
- </property>
- <property name="text">
- <string>TextLabel</string>
- </property>
- <property name="wordWrap">
- <bool>true</bool>
- </property>
- <property name="textInteractionFlags">
- <set>Qt::LinksAccessibleByMouse|Qt::TextSelectableByKeyboard|Qt::TextSelectableByMouse</set>
- </property>
- </widget>
+ <layout class="QHBoxLayout" name="horizontalLayout">
+ <item>
+ <widget class="QLabel" name="descriptionLabel">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Minimum">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>16777215</width>
+ <height>167</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>TextLabel</string>
+ </property>
+ <property name="wordWrap">
+ <bool>true</bool>
+ </property>
+ <property name="textInteractionFlags">
+ <set>Qt::LinksAccessibleByMouse|Qt::TextSelectableByKeyboard|Qt::TextSelectableByMouse</set>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QCheckBox" name="validCheckBox">
+ <property name="text">
+ <string>valid</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
</item>
<item>
<widget class="QTextEdit" name="sequenceTextEdit">
diff --git a/src/gui/protein_view/proteinwindow.cpp b/src/gui/protein_view/proteinwindow.cpp
index 5dc6e5de..8da3bcb8 100644
--- a/src/gui/protein_view/proteinwindow.cpp
+++ b/src/gui/protein_view/proteinwindow.cpp
@@ -63,6 +63,7 @@ void ProteinWindow::doIdentificationGroupGrouped(IdentificationGroup * p_identif
void ProteinWindow::updateDisplay() {
try {
+ if (_p_protein_match->isValid()) ui->validCheckBox->setCheckState(Qt::Checked);
ui->descriptionLabel->setText(_p_protein_match->getProteinXtpSp().get()->getAccession());
//ui->sequenceLabel->setText(_p_protein_match->getProteinXtpSp().get()->getSequence());
ui->sequenceTextEdit->setText(_p_protein_match->getHtmlSequence());
--
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