From 7c3309b2cf6fc4c9d89a8cbc14e23beb7c2399f4 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Mon, 3 Apr 2017 11:25:38 +0200
Subject: [PATCH] highlight peptide is OK
---
src/CMakeLists.txt | 4 +--
src/core/proteinmatch.cpp | 49 +++++++++++++++++++++++---
src/core/proteinmatch.h | 17 ++++++---
src/gui/project_view/projectwindow.cpp | 2 ++
src/gui/project_view/projectwindow.h | 1 +
src/gui/protein_view/proteinwindow.cpp | 8 +++++
src/gui/protein_view/proteinwindow.h | 1 +
7 files changed, 72 insertions(+), 10 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index ced3b3bd..a40d8a47 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 013d1968..091f7ac5 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -27,6 +27,10 @@
#include <set>
+QColor ProteinMatch::_color_peptide_background = QColor("yellow");
+QColor ProteinMatch::_color_highlighted_peptide_background = QColor("#ff7878");
+
+
ProteinMatch::ProteinMatch()
{
@@ -41,6 +45,14 @@ ProteinMatch::~ProteinMatch()
}
}
+bool ProteinMatch::contains(PeptideMatch * peptide_match) const {
+ if (peptide_match == nullptr) return false;
+ for (auto & p_peptide_match : _peptide_match_list) {
+ if (p_peptide_match == peptide_match) return true;
+ }
+ return false;
+}
+
void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
qDebug() <<"ProteinMatch::updateAutomaticFilters begin " ;
_proxy_valid = false;
@@ -273,12 +285,23 @@ pappso::pappso_double ProteinMatch::getPAI(const pappso::MsRunIdSp & sp_msrun_id
}
-const QString ProteinMatch::getHtmlSequence() const
+const QString ProteinMatch::getHtmlSequence(PeptideMatch * peptide_match_to_locate) const
{
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};
+ bool highlight_bool[prot_size] = {false};
+ if (this->contains(peptide_match_to_locate)) {
+ size_t size = peptide_match_to_locate->getPeptideXtpSp().get()->size();
+ size_t offset = peptide_match_to_locate->getStart();
+ if (offset >= 0) {
+ for (size_t i=0; (i < size) && (offset < prot_size) ; i++,offset++) {
+ highlight_bool[offset] = true;
+ }
+ }
+ }
+
for (auto & p_peptide_match : _peptide_match_list) {
if (p_peptide_match->isValidAndChecked()) {
size_t size = p_peptide_match->getPeptideXtpSp().get()->size();
@@ -293,11 +316,29 @@ 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]));
+ if(highlight_bool[i]) {
+ sequence_html.append(QString("<span style=\"background-color:%2;\">%1").arg(sequence[i]).arg(_color_highlighted_peptide_background.name()));
+ i++;
+ for (; i < prot_size; i++) {
+ if(highlight_bool[i]) {
+ sequence_html.append(sequence[i]);
+ }
+ else {
+ sequence_html.append(QString("</span>"));
+ i--;
+ break;
+ }
+ }
+ sequence_html.append(QString("</span>"));
+ }
+ else if(cover_bool[i]) {
+ sequence_html.append(QString("<span style=\"background-color:%2;\">%1").arg(sequence[i]).arg(_color_peptide_background.name()));
i++;
for (; i < prot_size; i++) {
+ if (highlight_bool[i]) {
+ i--;
+ break;
+ }
if(cover_bool[i]) {
sequence_html.append(sequence[i]);
}
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index 49cc8fca..c2693248 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -21,6 +21,7 @@
* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
******************************************************************************/
+#include <QColor>
#include <vector>
#include <pappsomspp/types.h>
#include "proteinxtp.h"
@@ -48,7 +49,7 @@ public:
/** @brief compute protein Evalue overall samples
* */
pappso::pappso_double getEvalue() const;
-
+
/** @brief compute protein Evalue within samples
* */
pappso::pappso_double getEvalue(const pappso::MsRunIdSp & sp_msrun_id) const;
@@ -58,9 +59,10 @@ public:
* */
pappso::pappso_double getCoverage() const;
-/** @brief get coverage sequence (html representation)
- **/
- const QString getHtmlSequence() const;
+ /** @brief get coverage sequence (html representation)
+ * @param peptide_match_to_locate pointer to optional peptide match to locate on protein sequence
+ **/
+ const QString getHtmlSequence(PeptideMatch * peptide_match_to_locate = nullptr) const;
/** @brief compute Protein Abundance Index (PAI)
* overall sample PAI computation (Rappsilber et al. 2002)
@@ -102,6 +104,9 @@ public:
* */
void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
+ /** @brief tells if this protein match contains this peptides
+ */
+ bool contains(PeptideMatch * peptide_match) const;
protected :
void setGroupingExperiment(GroupingExperiment * p_grp_experiment);
@@ -113,6 +118,10 @@ private :
unsigned int countValidAndCheckedPeptideMassCharge(const pappso::MsRunIdSp & sp_msrun_id) const;
private:
+ static QColor _color_peptide_background;
+ static QColor _color_highlighted_peptide_background;
+
+
pappso::GrpProteinSp _sp_grp_protein;
GroupingGroupSp _sp_group;
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 57f6c18f..f631bb82 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -193,6 +193,8 @@ void ProjectWindow::doViewPeptideDetail(PeptideMatch * peptide_match) {
_p_current_peptide_detail_window->setPeptideMatch(peptide_match);
_p_current_peptide_detail_window->show();
+
+ emit peptideMatchSelected(peptide_match);
qDebug() << "ProjectWindow::doViewPeptideDetail end";
}
diff --git a/src/gui/project_view/projectwindow.h b/src/gui/project_view/projectwindow.h
index daae3dc4..1926e13d 100644
--- a/src/gui/project_view/projectwindow.h
+++ b/src/gui/project_view/projectwindow.h
@@ -57,6 +57,7 @@ public slots:
// void setShape(Shape shape);
signals:
void identificationGroupGrouped(IdentificationGroup * p_identification_group);
+ void peptideMatchSelected(PeptideMatch * peptide_match);
//void peptideChanged(pappso::PeptideSp peptide);
protected :
diff --git a/src/gui/protein_view/proteinwindow.cpp b/src/gui/protein_view/proteinwindow.cpp
index 1df41309..b683f168 100644
--- a/src/gui/protein_view/proteinwindow.cpp
+++ b/src/gui/protein_view/proteinwindow.cpp
@@ -48,6 +48,7 @@ ProteinWindow::ProteinWindow(ProjectWindow *parent):
#else
// Qt4 code
connect (_p_project_window, SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
+ connect (_p_project_window, SIGNAL(peptideMatchSelected(PeptideMatch*)), this,SLOT(doPeptideMatchSelected(PeptideMatch*)));
//connect(_protein_table_model_p, SIGNAL(layoutChanged()), this, SLOT(updateStatusBar()));
#endif
@@ -61,6 +62,13 @@ void ProteinWindow::doIdentificationGroupGrouped(IdentificationGroup * p_identif
updateDisplay();
}
+void ProteinWindow::doPeptideMatchSelected(PeptideMatch * peptide_match) {
+ if (_p_protein_match != nullptr) {
+ ui->sequenceTextEdit->setText(_p_protein_match->getHtmlSequence(peptide_match));
+
+ }
+}
+
void ProteinWindow::updateDisplay() {
try {
ui->validCheckBox->setCheckState(Qt::Unchecked);
diff --git a/src/gui/protein_view/proteinwindow.h b/src/gui/protein_view/proteinwindow.h
index 3dfeeda5..a9a14708 100644
--- a/src/gui/protein_view/proteinwindow.h
+++ b/src/gui/protein_view/proteinwindow.h
@@ -45,6 +45,7 @@ public:
public slots:
void doIdentificationGroupGrouped(IdentificationGroup * p_identification_group);
+ void doPeptideMatchSelected(PeptideMatch * peptide_match);
protected :
void updateDisplay();
--
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