From 91fd327224bd516ffbc1d1dd6c97d024db35ca32 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Tue, 2 Jan 2018 16:25:44 +0100
Subject: [PATCH] using new spectrum widget
---
src/CMakeLists.txt | 22 +-
.../edit_modifications/editmodifications.cpp | 2 +-
.../peptide_detail_view.ui | 87 ++--
src/gui/peptide_detail_view/peptidewindow.cpp | 80 ++-
src/gui/peptide_detail_view/peptidewindow.h | 2 -
.../spectrum_widget/overlaywidget.cpp | 148 ------
.../spectrum_widget/overlaywidget.h | 103 ----
.../spectrum_widget/qspectrumwidget.cpp | 103 ----
.../spectrum_widget/qspectrumwidget.h | 69 ---
.../spectrum_widget/spectrumpainter.cpp | 471 ------------------
.../spectrum_widget/spectrumpainter.h | 119 -----
src/gui/project_view/projectwindow.cpp | 2 +-
12 files changed, 98 insertions(+), 1110 deletions(-)
delete mode 100644 src/gui/peptide_detail_view/spectrum_widget/overlaywidget.cpp
delete mode 100644 src/gui/peptide_detail_view/spectrum_widget/overlaywidget.h
delete mode 100644 src/gui/peptide_detail_view/spectrum_widget/qspectrumwidget.cpp
delete mode 100644 src/gui/peptide_detail_view/spectrum_widget/qspectrumwidget.h
delete mode 100644 src/gui/peptide_detail_view/spectrum_widget/spectrumpainter.cpp
delete mode 100644 src/gui/peptide_detail_view/spectrum_widget/spectrumpainter.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 78e9cbc05..0e6e3ffb5 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -32,7 +32,19 @@ FIND_PACKAGE( Pappsomspp REQUIRED )
# SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
# SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
# SET (PAPPSOMSPP_QT5_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt5.so")
+# SET (PAPPSOMSPP_WIDGET_QT5_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/pappsomspp/widget/libpappsomspp-widget-qt5.so")
# SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt4.so")
+IF (PAPPSOMSPP_QT5_FOUND)
+ELSE (PAPPSOMSPP_QT5_FOUND)
+ MESSAGE("PAPPSOms++ library not found")
+ MESSAGE("did you apt-get install libpappsomspp-dev ?")
+ENDIF (PAPPSOMSPP_QT5_FOUND)
+
+IF (PAPPSOMSPP_WIDGET_QT5_FOUND)
+ELSE (PAPPSOMSPP_WIDGET_QT5_FOUND)
+ MESSAGE("PAPPSOms++ widget library not found")
+ MESSAGE("did you apt-get install libpappsomspp-widget-dev ?")
+ENDIF (PAPPSOMSPP_WIDGET_QT5_FOUND)
set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake_modules)
@@ -80,7 +92,6 @@ SET(CPP_FILES
grouping/ptm/ptmislandgroup.cpp
grouping/ptm/ptmislandsubgroup.cpp
grouping/ptm/ptmsamplescan.cpp
- gui/peptide_detail_view/spectrum_widget/spectrumpainter.cpp
input/condorqxmlsaxhandler.cpp
input/identificationpwizreader.cpp
input/xpipsaxhandler.cpp
@@ -128,8 +139,6 @@ SET(XTPCPP_SRCS
./gui/load_results_dialog/loadresultsdialog.cpp
./gui/mainwindow.cpp
./gui/peptide_detail_view/peptidewindow.cpp
- ./gui/peptide_detail_view/spectrum_widget/overlaywidget.cpp
- ./gui/peptide_detail_view/spectrum_widget/qspectrumwidget.cpp
./gui/peptide_list_view/peptidelistwindow.cpp
./gui/peptide_list_view/peptidetablemodel.cpp
./gui/peptide_list_view/peptidetableproxymodel.cpp
@@ -185,8 +194,6 @@ SET(XTPCPP_MOC_HDRS
./gui/load_results_dialog/loadresultsdialog.h
./gui/mainwindow.h
./gui/peptide_detail_view/peptidewindow.h
- ./gui/peptide_detail_view/spectrum_widget/overlaywidget.h
- ./gui/peptide_detail_view/spectrum_widget/qspectrumwidget.h
./gui/peptide_list_view/peptidelistwindow.h
./gui/peptide_list_view/peptidetablemodel.h
./gui/peptide_list_view/peptidetableproxymodel.h
@@ -223,8 +230,7 @@ MESSAGE("XTPCPP_SRCS: ${XTPCPP_SRCS}")
ADD_EXECUTABLE(xtpcpp main.cpp ${CPP_FILES} ${XTPCPP_SRCS} ${GUI_UI_HDRS} ${XTPCPP_MOC_SRCS} ${xtpcpp_RCC_SRCS})
target_include_directories (xtpcpp PUBLIC ${Pwiz_INCLUDE_DIR} ${PAPPSOMSPP_INCLUDE_DIR} ${ODSSTREAM_INCLUDE_DIR}
-${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR}
-${CMAKE_CURRENT_BINARY_DIR}/gui/peptide_detail_view/spectrum_widget ${CMAKE_CURRENT_SOURCE_DIR}/gui/peptide_detail_view/spectrum_widget)
+${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR} )
target_compile_definitions(xtpcpp PUBLIC ${QT_DEFINITIONS})
SET_TARGET_PROPERTIES(xtpcpp
@@ -233,7 +239,7 @@ target_compile_definitions(xtpcpp PUBLIC ${QT_DEFINITIONS})
#COMPILE_DEFINITIONS "${QT_DEFINITIONS}"
#INCLUDE_DIRECTORIES "${QT_INCLUDE_DIR} ${QT_QTCORE_INCLUDE_DIR}"
)
-TARGET_LINK_LIBRARIES(xtpcpp ${PAPPSOMSPP_QT5_LIBRARY} ${Pwiz_LIBRARY} ${ODSSTREAM_QT5_LIBRARY} ${QCustomPlot_LIBRARIES}
+TARGET_LINK_LIBRARIES(xtpcpp ${PAPPSOMSPP_QT5_LIBRARY} ${PAPPSOMSPP_WIDGET_QT5_LIBRARY} ${Pwiz_LIBRARY} ${ODSSTREAM_QT5_LIBRARY} ${QCustomPlot_LIBRARIES}
Qt5::Gui Qt5::Xml Qt5::Svg Qt5::PrintSupport)
INSTALL(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/xtpcpp DESTINATION bin)
diff --git a/src/gui/edit_modifications/editmodifications.cpp b/src/gui/edit_modifications/editmodifications.cpp
index 5eb3e1ace..ad688acd0 100644
--- a/src/gui/edit_modifications/editmodifications.cpp
+++ b/src/gui/edit_modifications/editmodifications.cpp
@@ -102,7 +102,7 @@ void EditModifications::ItemClicked (QModelIndex index )
qDebug() << "EditModifications::ItemClicked data=" << index.data().toString();
qDebug() << "EditModifications::ItemClicked acc=" << _p_modification_str_li->data(index,Qt::UserRole).toString();
qDebug() << "EditModifications::ItemClicked str=" << _p_modification_str_li->data(index,Qt::DisplayRole).toString();
- pappso::AaModificationP modification = AaModification::getInstance(index.data(Qt::UserRole).toString());
+ pappso::AaModificationP modification = pappso::AaModification::getInstance(index.data(Qt::UserRole).toString());
setSelectedModification(modification);
setReplaceModification(nullptr);
}
diff --git a/src/gui/peptide_detail_view/peptide_detail_view.ui b/src/gui/peptide_detail_view/peptide_detail_view.ui
index 14e90e9e7..d0fd5c081 100644
--- a/src/gui/peptide_detail_view/peptide_detail_view.ui
+++ b/src/gui/peptide_detail_view/peptide_detail_view.ui
@@ -7,7 +7,7 @@
<x>0</x>
<y>0</y>
<width>826</width>
- <height>404</height>
+ <height>430</height>
</rect>
</property>
<property name="windowTitle">
@@ -127,31 +127,31 @@
<item>
<layout class="QVBoxLayout" name="verticalLayout_9">
<item>
- <widget class="QWidget" name="file_not_found">
- <layout class="QFormLayout" name="file_not_found_layout">
- <item row="0" column="0">
- <widget class="QLabel" name="mz_data_dir_label">
- <property name="text">
- <string>TextLabel</string>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QPushButton" name="select_dir">
- <property name="text">
- <string>set mz data directory</string>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
+ <widget class="QWidget" name="file_not_found" native="true">
+ <layout class="QFormLayout" name="file_not_found_layout">
+ <item row="0" column="0">
+ <widget class="QLabel" name="mz_data_dir_label">
+ <property name="text">
+ <string>TextLabel</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QPushButton" name="select_dir">
+ <property name="text">
+ <string>set mz data directory</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout_2">
<item>
<layout class="QHBoxLayout" name="horizontalLayout_4">
<item>
- <widget class="QSpectrumWidget" name="spectrumWidget" native="true">
+ <widget class="pappso::SpectrumWidget" name="spectrum_widget" native="true">
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Expanding">
<horstretch>0</horstretch>
@@ -340,7 +340,7 @@
<x>0</x>
<y>0</y>
<width>826</width>
- <height>23</height>
+ <height>25</height>
</rect>
</property>
</widget>
@@ -348,29 +348,14 @@
</widget>
<customwidgets>
<customwidget>
- <class>QSpectrumWidget</class>
+ <class>pappso::SpectrumWidget</class>
<extends>QWidget</extends>
- <header>qspectrumwidget.h</header>
+ <header>pappsomspp/widget/spectrumwidget/spectrumwidget.h</header>
+ <container>1</container>
</customwidget>
</customwidgets>
<resources/>
<connections>
- <connection>
- <sender>select_dir</sender>
- <signal>clicked()</signal>
- <receiver>PeptideDetailView</receiver>
- <slot>chooseDefaultMzDataDir()</slot>
- <hints>
- <hint type="sourcelabel">
- <x>371</x>
- <y>101</y>
- </hint>
- <hint type="destinationlabel">
- <x>838</x>
- <y>384</y>
- </hint>
- </hints>
- </connection>
<connection>
<sender>pushButton</sender>
<signal>clicked()</signal>
@@ -394,8 +379,8 @@
<slot>doMsmsPrecisionValueChanged(double)</slot>
<hints>
<hint type="sourcelabel">
- <x>804</x>
- <y>325</y>
+ <x>801</x>
+ <y>346</y>
</hint>
<hint type="destinationlabel">
<x>870</x>
@@ -426,8 +411,8 @@
<slot>doSaveSvg()</slot>
<hints>
<hint type="sourcelabel">
- <x>729</x>
- <y>348</y>
+ <x>813</x>
+ <y>392</y>
</hint>
<hint type="destinationlabel">
<x>866</x>
@@ -435,6 +420,22 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>select_dir</sender>
+ <signal>clicked()</signal>
+ <receiver>PeptideDetailView</receiver>
+ <slot>chooseDefaultMzDataDir()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>373</x>
+ <y>117</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>977</x>
+ <y>204</y>
+ </hint>
+ </hints>
+ </connection>
</connections>
<slots>
<slot>chooseDefaultMzDataDir()</slot>
diff --git a/src/gui/peptide_detail_view/peptidewindow.cpp b/src/gui/peptide_detail_view/peptidewindow.cpp
index c500a83d4..415e08c83 100644
--- a/src/gui/peptide_detail_view/peptidewindow.cpp
+++ b/src/gui/peptide_detail_view/peptidewindow.cpp
@@ -45,17 +45,17 @@ void SpectrumSpLoaderThread::doLoadSpectrumSp (PeptideEvidence * p_peptide_evide
}
catch (pappso::ExceptionNotFound & error) {
- qDebug() << "SpectrumSpLoaderThread::doLoadSpectrumSp error " << error.qwhat();
+ qDebug() << "SpectrumSpLoaderThread::doLoadSpectrumSp error " << error.qwhat();
emit spectrumSpReady(spectrum, error.qwhat(), QString(""));
}
-
+
catch (pappso::PappsoException & error) {
qDebug() << "SpectrumSpLoaderThread::doLoadSpectrumSp error " << error.qwhat();
emit spectrumSpReady(spectrum, QString(""), error.qwhat());
}
-
+
catch (std::exception & error) {
- qDebug() << "SpectrumSpLoaderThread::doLoadSpectrumSp error " << error.what();
+ qDebug() << "SpectrumSpLoaderThread::doLoadSpectrumSp error " << error.what();
emit spectrumSpReady(spectrum, QString(""), QString(error.what()));
}
qDebug() << "SpectrumSpLoaderThread::doLoadSpectrumSp end";
@@ -68,8 +68,6 @@ PeptideWindow::PeptideWindow(ProjectWindow *parent):
qDebug() << "PeptideWindow::PeptideWindow begin";
_p_project_window = parent;
ui->setupUi(this);
-
- _p_spectrum_overlay = new LoadingOverlay(ui->spectrumWidget);
/*
*/
SpectrumSpLoaderThread * worker = new SpectrumSpLoaderThread;
@@ -85,13 +83,16 @@ PeptideWindow::PeptideWindow(ProjectWindow *parent):
ui->precision_spinbox->setValue(precision);
if (unit == "dalton") {
- _p_precision = Precision::getDaltonInstance(precision);
+ _p_precision = pappso::Precision::getDaltonInstance(precision);
} else {
- _p_precision = Precision::getPpmInstance(precision);
+ _p_precision = pappso::Precision::getPpmInstance(precision);
}
ui->file_not_found->setVisible(false);
+
+ //ui->spectrum_widget->setIonList();
+
qRegisterMetaType<pappso::SpectrumSp>("pappso::SpectrumSp");
#if QT_VERSION >= 0x050000
// Qt5 code
@@ -99,7 +100,7 @@ PeptideWindow::PeptideWindow(ProjectWindow *parent):
connect (this, &PeptideWindow::loadSpectrumSp, worker,&SpectrumSpLoaderThread::doLoadSpectrumSp);
connect (worker, &SpectrumSpLoaderThread::spectrumSpReady, this,&PeptideWindow::doSpectrumSpReady);
- connect (_p_spectrum_overlay,&LoadingOverlay::mzChanged, this, &PeptideWindow::setMz);
+ connect (ui->spectrum_widget,&pappso::SpectrumWidget::mzChanged, this, &PeptideWindow::setMz);
#else
// Qt4 code
connect (_p_project_window, SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
@@ -115,7 +116,6 @@ PeptideWindow::PeptideWindow(ProjectWindow *parent):
PeptideWindow::~PeptideWindow()
{
- delete _p_spectrum_overlay;
delete ui;
}
@@ -144,8 +144,6 @@ void PeptideWindow::updateDisplay() {
ui->mz_label->setText(QString::number(_p_peptide_evidence->getPeptideXtpSp().get()->getMz(_p_peptide_evidence->getCharge()), 'f', 4));
ui->expmz_label->setText(QString::number(_p_peptide_evidence->getExperimentalMz(), 'f', 4));
ui->delta_label->setText(QString::number(_p_peptide_evidence->getDeltaMass(), 'g', 4));
-
-
}
catch (pappso::PappsoException exception_pappso) {
QMessageBox::warning(this,
@@ -176,9 +174,8 @@ void PeptideWindow::chooseDefaultMzDataDir() {
qDebug() << "PeptideWindow::chooseDefaultMzDataDir begin";
- _p_spectrum_overlay->displayLoadingMessage();
ui->file_not_found->setVisible(false);
- ui->spectrumWidget->setVisible(true);
+ ui->spectrum_widget->setVisible(true);
emit loadSpectrumSp(_p_peptide_evidence);
ui->statusbar->showMessage(tr("loading spectrum"));
@@ -195,18 +192,16 @@ void PeptideWindow::openInPeptideViewer() {
myProcess->start(program, arguments);
}
-void PeptideWindow::doSpectrumSpReady(SpectrumSp spectrum_sp, QString error, QString fatal_error) {
+void PeptideWindow::doSpectrumSpReady(pappso::SpectrumSp spectrum_sp, QString error, QString fatal_error) {
qDebug() << "PeptideWindow::doSpectrumSpReady begin error=" << error << " fatal_error=" << fatal_error;
- _p_spectrum_overlay->hideLoadingMessage();
if ((error.isEmpty()) && (fatal_error.isEmpty())) {
ui->statusbar->showMessage(tr(""));
- pappso::QualifiedSpectrum spectrum_copy;
- spectrum_copy.setPrecursorCharge(_p_peptide_evidence->getCharge());
- spectrum_copy.setOriginalSpectrumSp(spectrum_sp);
-
- ui->spectrumWidget->setQualifiedSpectrum(spectrum_copy);
+ ui->spectrum_widget->setMsLevel(2);
+ ui->spectrum_widget->setSpectrumSp(spectrum_sp);
ui->file_not_found->setVisible(false);
- ui->spectrumWidget->setVisible(true);
+ ui->spectrum_widget->setVisible(true);
+
+ ui->spectrum_widget->plot();
_spectrum_is_ready = true;
}
if (!error.isEmpty()) {
@@ -219,14 +214,14 @@ void PeptideWindow::doSpectrumSpReady(SpectrumSp spectrum_sp, QString error, QSt
ui->mz_data_dir_label->setText(path);
ui->file_not_found->setVisible(true);
- ui->spectrumWidget->setVisible(false);
+ ui->spectrum_widget->setVisible(false);
_spectrum_is_ready = false;
}
if (!fatal_error.isEmpty()) {
//fatal_error
QMessageBox::warning(this,
- tr("Oops! an error occurred in XTPCPP. Dont Panic :"), fatal_error);
+ tr("Oops! an error occurred in XTPCPP. Dont Panic :"), fatal_error);
ui->statusbar->showMessage(tr("ERROR reading spectrum"));
QSettings settings;
QString path = settings.value("path/mzdatadir", "").toString();
@@ -234,7 +229,7 @@ void PeptideWindow::doSpectrumSpReady(SpectrumSp spectrum_sp, QString error, QSt
ui->mz_data_dir_label->setText(path);
ui->file_not_found->setVisible(true);
- ui->spectrumWidget->setVisible(false);
+ ui->spectrum_widget->setVisible(false);
_spectrum_is_ready = false;
}
qDebug() << "PeptideWindow::doSpectrumSpReady end";
@@ -242,24 +237,26 @@ void PeptideWindow::doSpectrumSpReady(SpectrumSp spectrum_sp, QString error, QSt
}
void PeptideWindow::setPeptideEvidence(PeptideEvidence * p_peptide_evidence) {
- qDebug() << "PeptideWindow::setPeptideMatch begin";
+ qDebug() << "PeptideWindow::setPeptideEvidence begin";
_p_peptide_evidence = p_peptide_evidence;
_spectrum_is_ready = false;
- qDebug() << "PeptideWindow::setPeptideMatch emit loadSpectrumSp(_p_peptide_match)";
+ qDebug() << "PeptideWindow::setPeptideEvidence emit loadSpectrumSp(_p_peptide_match)";
emit loadSpectrumSp(_p_peptide_evidence);
- _p_spectrum_overlay->displayLoadingMessage();
ui->file_not_found->setVisible(false);
- ui->spectrumWidget->setVisible(true);
+ ui->spectrum_widget->setVisible(true);
ui->statusbar->showMessage(tr("loading spectrum"));
pappso::PeptideSp peptide = _p_peptide_evidence->getPeptideXtpSp();
- ui->spectrumWidget->setPrecision(_p_precision);
- ui->spectrumWidget->setPeptideSp(peptide);
+ ui->spectrum_widget->setMs2Precision(_p_precision);
+ ui->spectrum_widget->setPeptideCharge(_p_peptide_evidence->getCharge());
+ ui->spectrum_widget->setMaximumIsotopeLevel(3);
+ ui->spectrum_widget->setPeptideSp(peptide);
+ ui->spectrum_widget->plot();
updateDisplay();
- qDebug() << "PeptideWindow::setPeptideMatch end";
+ qDebug() << "PeptideWindow::setPeptideEvidence end";
}
void PeptideWindow::doMsmsPrecisionUnitChanged(QString unit) {
@@ -270,11 +267,12 @@ void PeptideWindow::doMsmsPrecisionUnitChanged(QString unit) {
if (unit == "dalton") {
- _p_precision = Precision::getDaltonInstance(precision);
+ _p_precision = pappso::Precision::getDaltonInstance(precision);
} else {
- _p_precision = Precision::getPpmInstance(precision);
+ _p_precision = pappso::Precision::getPpmInstance(precision);
}
- ui->spectrumWidget->setPrecision(_p_precision);
+ ui->spectrum_widget->setMs2Precision(_p_precision);
+ ui->spectrum_widget->plot();
settings.setValue("peptideview/precision_unit", unit);
@@ -289,11 +287,12 @@ void PeptideWindow::doMsmsPrecisionValueChanged(double precision_value) {
if (unit == "dalton") {
- _p_precision = Precision::getDaltonInstance(precision);
+ _p_precision = pappso::Precision::getDaltonInstance(precision);
} else {
- _p_precision = Precision::getPpmInstance(precision);
+ _p_precision = pappso::Precision::getPpmInstance(precision);
}
- ui->spectrumWidget->setPrecision(_p_precision);
+ ui->spectrum_widget->setMs2Precision(_p_precision);
+ ui->spectrum_widget->plot();
settings.setValue("peptideview/precision_value", precision);
}
@@ -329,11 +328,8 @@ void PeptideWindow::doSaveSvg() {
generator.setViewBox(QRect(0, 0, 1200, 500));
generator.setTitle(tr("%1 SVG spectrum generator").arg(SOFTWARE_NAME));
generator.setDescription(tr("This is an annotated SVG spectrum"));
- QPainter painter;
- painter.begin(&generator);
- ui->spectrumWidget->paint(painter);
- painter.end();
+ ui->spectrum_widget->toQPaintDevice(&generator);
//emit operateXpipFile(filename);
}
catch (pappso::PappsoException & error) {
diff --git a/src/gui/peptide_detail_view/peptidewindow.h b/src/gui/peptide_detail_view/peptidewindow.h
index 419cd3b39..5a9f88b2a 100644
--- a/src/gui/peptide_detail_view/peptidewindow.h
+++ b/src/gui/peptide_detail_view/peptidewindow.h
@@ -30,7 +30,6 @@
#include <pappsomspp/spectrum/spectrum.h>
#include "../../core/peptidematch.h"
#include "../../core/identificationgroup.h"
-#include "spectrum_widget/overlaywidget.h"
class ProjectWindow;
@@ -93,7 +92,6 @@ private:
PeptideEvidence * _p_peptide_evidence = nullptr;
pappso::PrecisionP _p_precision;
- LoadingOverlay * _p_spectrum_overlay;
bool _spectrum_is_ready=false;
};
diff --git a/src/gui/peptide_detail_view/spectrum_widget/overlaywidget.cpp b/src/gui/peptide_detail_view/spectrum_widget/overlaywidget.cpp
deleted file mode 100644
index 2ee85c70a..000000000
--- a/src/gui/peptide_detail_view/spectrum_widget/overlaywidget.cpp
+++ /dev/null
@@ -1,148 +0,0 @@
-
-/*******************************************************************************
-* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of PAPPSOms-tools.
-*
-* PAPPSOms-tools is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* PAPPSOms-tools is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
-#include "overlaywidget.h"
-#include <QDebug>
-
-
-
-void LoadingOverlay::paintLoadingMessage(QPainter &painter) {
-
- if (_is_loading) {
- //p.fillRect(rect(), QColor(100, 100, 100, 128));
- painter.setPen(QColor(200, 200, 255, 255));
- painter.setFont(QFont("arial,helvetica", 48));
- painter.drawText(rect(), "Loading...", Qt::AlignHCenter | Qt::AlignVCenter);
- }
-}
-void LoadingOverlay::displayLoadingMessage() {
- _is_loading= true;
-}
-void LoadingOverlay::hideLoadingMessage() {
- _is_loading= false;
-}
-void LoadingOverlay::paintEvent(QPaintEvent *) {
- QPainter painter;
-
- painter.begin(this);
- painter.setRenderHint(QPainter::Antialiasing);
- qDebug() << "LoadingOverlay::paintEvent _is_loading="<< _is_loading;
- if (_is_loading) {
- paintLoadingMessage(painter);
- }
- else {
- paintUserSelectedZone(painter);
- }
- painter.end();
-}
-void LoadingOverlay::mousePressEvent(QMouseEvent * event) {
-
- qDebug() << " LoadingOverlay::mousePressEvent";
-
- _pressed = true;
- _first_point.first = event->x();
- _first_point.second = event->y();
- _current_mouse_mz = _p_spectrum_widget->getSpectrumPainter().getMzFromLocalPosX(event->x());
-
- _second_point.first = 0;
- emit mzChanged(_current_mouse_mz);
- update();
-}
-
-
-void LoadingOverlay::mouseReleaseEvent(QMouseEvent * event) {
-
- qDebug() << " LoadingOverlay::mouseReleaseEvent";
- _pressed = false;
- // _press_mz = _spectrum_painter.getMzFromLocalPosX(event->x());
- //_second_point.first = event->x();
- //_second_point.second = event->y();
- if (_second_point.first > 0) {
- mz min = _p_spectrum_widget->getSpectrumPainter().getMzFromLocalPosX(_first_point.first);
- mz max = _p_spectrum_widget->getSpectrumPainter().getMzFromLocalPosX(_second_point.first);
- if (max < min) {
- swap(min,max);
- }
- pappso_double max_intensity = _p_spectrum_widget->getSpectrumPainter().getIntensityFromLocalPosY(_second_point.second);
- _p_spectrum_widget->getSpectrumPainter().setMinMz(min);
- _p_spectrum_widget->getSpectrumPainter().setMaxMz(max);
- _p_spectrum_widget->getSpectrumPainter().setMaxIntensity(max_intensity);
- }
- else {
- _p_spectrum_widget->getSpectrumPainter().setMaxMz(0);
- }
- _second_point.first = 0;
- update();
-
-}
-void LoadingOverlay::mouseMoveEvent(QMouseEvent * event) {
- qDebug() << "LoadingOverlay::mouseMoveEvent" << event->x();
- mz new_mz = _p_spectrum_widget->getSpectrumPainter().getMzFromLocalPosX(event->x());
-
- if (_pressed) {
- int min = _p_spectrum_widget->getSpectrumPainter().getMarginLeft();
- _second_point.first = event->x();
- if (_second_point.first < min) {
- _second_point.first = min;
- }
- int max = this->size().width();
- if (_second_point.first > max) {
- _second_point.first = max;
- }
- _second_point.second = event->y();
-
- if (_second_point.second < 0) {
- _second_point.second = 0;
- }
-
- max = _p_spectrum_widget->getSpectrumPainter().getLocalPosYFromIntensity(0);
- if (_second_point.second > max) {
- _second_point.second = max;
- }
-
- _first_point.second = _p_spectrum_widget->getSpectrumPainter().getLocalPosYFromIntensity(0);
- }
- // if (_current_mouse_mz != new_mz) {
- _current_mouse_mz = new_mz;
- qDebug() << "LoadingOverlay::mouseMoveEvent emit mzChanged(_current_mouse_mz)" ;
- emit mzChanged(_current_mouse_mz);
-
- // if (_press_mz > 0) {
- update();
-
- // }
- // }
-}
-
-
-void LoadingOverlay::paintUserSelectedZone(QPainter & painter) {
- if (_second_point.first > 0) {
- painter.setPen(QColor("red"));
- QRect rect(_first_point.first, _first_point.second, _second_point.first-_first_point.first, _second_point.second-_first_point.second);
- painter.drawRect(rect);
-
- // show the classname of the widget
- QBrush translucentBrush(QColor(255,246,240, 100));
- painter.fillRect(rect, translucentBrush);
- }
-
-}
diff --git a/src/gui/peptide_detail_view/spectrum_widget/overlaywidget.h b/src/gui/peptide_detail_view/spectrum_widget/overlaywidget.h
deleted file mode 100644
index 0b264f154..000000000
--- a/src/gui/peptide_detail_view/spectrum_widget/overlaywidget.h
+++ /dev/null
@@ -1,103 +0,0 @@
-
-/*******************************************************************************
-* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of PAPPSOms-tools.
-*
-* PAPPSOms-tools is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* PAPPSOms-tools is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
-
-#ifndef OVERLAYWIDGET_H
-#define OVERLAYWIDGET_H
-#include <QApplication>
-#include <QMainWindow>
-#include <QResizeEvent>
-#include <QPainter>
-
-#include "qspectrumwidget.h"
-
-class OverlayWidget : public QWidget
-{
-public:
- explicit OverlayWidget(QWidget * parent = 0) : QWidget(parent) {
- if (parent) {
- parent->installEventFilter(this);
- raise();
- }
- }
-protected:
- //! Catches resize and child events from the parent widget
- bool eventFilter(QObject * obj, QEvent * ev) {
- if (obj == parent()) {
- if (ev->type() == QEvent::Resize) {
- QResizeEvent * rev = static_cast<QResizeEvent*>(ev);
- resize(rev->size());
- }
- else if (ev->type() == QEvent::ChildAdded) {
- raise();
- }
- }
- return QWidget::eventFilter(obj, ev);
- }
- //! Tracks parent widget changes
- bool event(QEvent* ev) {
- if (ev->type() == QEvent::ParentAboutToChange) {
- if (parent()) parent()->removeEventFilter(this);
- }
- else if (ev->type() == QEvent::ParentChange) {
- if (parent()) {
- parent()->installEventFilter(this);
- raise();
- }
- }
- return QWidget::event(ev);
- }
-};
-
-class LoadingOverlay : public OverlayWidget
-{
- Q_OBJECT
-public:
- LoadingOverlay(QSpectrumWidget * parent) : OverlayWidget(parent) {
- // setAttribute(Qt::WA_TranslucentBackground);
- _p_spectrum_widget =parent;
- setMouseTracking(true);
- }
- void displayLoadingMessage();
- void hideLoadingMessage();
-protected:
- void paintEvent(QPaintEvent *) override;
- void mouseReleaseEvent(QMouseEvent * event) override;
- void mousePressEvent(QMouseEvent * event) override;
- void mouseMoveEvent(QMouseEvent * event) override;
-signals:
- void mzChanged(double mz);
-private :
- void paintLoadingMessage(QPainter & painter);
- void paintUserSelectedZone(QPainter & painter);
-private:
- bool _pressed = false;
- QSpectrumWidget * _p_spectrum_widget;
- mz _current_mouse_mz;
- bool _is_loading=false;
-
- std::pair<int, int> _first_point;
- std::pair<int, int> _second_point;
-
-};
-
-#endif // OVERLAYWIDGET_H
diff --git a/src/gui/peptide_detail_view/spectrum_widget/qspectrumwidget.cpp b/src/gui/peptide_detail_view/spectrum_widget/qspectrumwidget.cpp
deleted file mode 100644
index 0d3eec469..000000000
--- a/src/gui/peptide_detail_view/spectrum_widget/qspectrumwidget.cpp
+++ /dev/null
@@ -1,103 +0,0 @@
-
-/*******************************************************************************
-* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of PAPPSOms-tools.
-*
-* PAPPSOms-tools is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* PAPPSOms-tools is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
-
-#include "qspectrumwidget.h"
-#include <QStyleOption>
-#include <pappsomspp/peptide/peptidefragmentionlistbase.h>
-#include <pappsomspp/peptide/peptidestrparser.h>
-
-
-QSpectrumWidget::QSpectrumWidget(QWidget *parent)
- : QWidget(parent)
-{
- qDebug() << "QSpectrumWidget::QSpectrumWidget begin";
- //_ion_list = PeptideFragmentIonListBase::getCIDionList();
-
- //_peptide_sp = PeptideStrParser::parseString("AIADGSLLDLLR");
-
- //_spectrum_sp = readSpectrum("../../pappsomspp/test/data/peaklist_15046.mgf", 0, _zmax).makeSpectrumSp();
-
- unsigned int zmax=3;
-
- _spectrum_painter.setPeptideSp(Peptide("A").makePeptideSp());
- // _spectrum_painter.setSpectrumSp(Spectrum().makeSpectrumSp());
-
- _spectrum_painter.setParentIonCharge(zmax);
- _spectrum_painter.setIonList(PeptideFragmentIonListBase::getCIDionList());
- //_spectrum_painter.setPrecision(_p_precision);
-
-
- setMouseTracking(true);
-
- //SvgSpectrum svgspectrum(_peptide_sp, _spectrum_sp, _zmax, _precision, _ion_list);
-
- _spectrum_painter.setMarginLeft(60);
- _spectrum_painter.setMarginTop(15);
- _spectrum_painter.setMarginBottom(20);
- _spectrum_painter.setFontPointSize(10);
-
- qDebug() << "QSpectrumWidget::QSpectrumWidget end";
-
-}
-QSpectrumWidget::~QSpectrumWidget()
-{
-
-}
-
-void QSpectrumWidget::setPrecision(pappso::PrecisionP p_precision) {
- qDebug() << "QSpectrumWidget::setPrecision";
- _spectrum_painter.setPrecision(p_precision);
- update();
-}
-
-void QSpectrumWidget::setPeptideSp(pappso::PeptideSp & peptide_sp) {
- _spectrum_painter.setPeptideSp(peptide_sp);
- update();
-}
-void QSpectrumWidget::setQualifiedSpectrum(pappso::QualifiedSpectrum spectrum) {
-
- _spectrum_painter.setQualifiedSpectrum(spectrum);
- update();
-
-}
-
-void QSpectrumWidget::paintEvent(QPaintEvent * /* event */)
-{
- QPainter painter;
- painter.begin(this);
- painter.setRenderHint(QPainter::Antialiasing);
- paint(painter);
- painter.end();
-}
-
-void QSpectrumWidget::paint(QPainter &painter)
-{
- //painter.drawLine(QLine(0, 35, 200, 35));
- _spectrum_painter.paint(painter, this->size().width(), this->size().height());
-}
-
-void QSpectrumWidget::setIsotopeMassList(std::vector<pappso::PeptideNaturalIsotopeAverageSp> & isotopeMassList) {
- _spectrum_painter.setIsotopeMassList(isotopeMassList);
- update();
-}
-
diff --git a/src/gui/peptide_detail_view/spectrum_widget/qspectrumwidget.h b/src/gui/peptide_detail_view/spectrum_widget/qspectrumwidget.h
deleted file mode 100644
index 913442664..000000000
--- a/src/gui/peptide_detail_view/spectrum_widget/qspectrumwidget.h
+++ /dev/null
@@ -1,69 +0,0 @@
-
-/*******************************************************************************
-* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of PAPPSOms-tools.
-*
-* PAPPSOms-tools is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* PAPPSOms-tools is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
-
-#ifndef QSPECTRUMWIDGET_H
-#define QSPECTRUMWIDGET_H
-
-#include <QWidget>
-#include <QPainter>
-#include <QMouseEvent>
-#include <pappsomspp/spectrum/qualifiedspectrum.h>
-#include <pappsomspp/peptide/peptide.h>
-#include <pappsomspp/peptide/peptidefragmention.h>
-#include "spectrumpainter.h"
-
-using namespace pappso;
-
-class QSpectrumWidget: public QWidget
-{
- Q_OBJECT
-public:
- QSpectrumWidget(QWidget *parent = 0);
- ~QSpectrumWidget();
-
- void paint(QPainter &painter);
-
- pappso_double getCanvasWidth() const {return _spectrum_painter.getCanvasWidth();};
- void setPeptideSp(pappso::PeptideSp & peptide_sp);
- void setPrecision(pappso::PrecisionP p_precision);
- void setIsotopeMassList(std::vector<pappso::PeptideNaturalIsotopeAverageSp> & isotopeMassList);
-
- SpectrumPainter & getSpectrumPainter() {return _spectrum_painter;};
-
-
-public slots:
- void setQualifiedSpectrum(pappso::QualifiedSpectrum spectrum);
-
- // void setColor(const QColor &color);
- // void setShape(Shape shape);
-signals:
- void mzChanged(double mz);
-
-protected:
- void paintEvent(QPaintEvent *event) override;
-
-private :
- SpectrumPainter _spectrum_painter;
-};
-
-#endif // QSPECTRUMWIDGET_H
diff --git a/src/gui/peptide_detail_view/spectrum_widget/spectrumpainter.cpp b/src/gui/peptide_detail_view/spectrum_widget/spectrumpainter.cpp
deleted file mode 100644
index c06787724..000000000
--- a/src/gui/peptide_detail_view/spectrum_widget/spectrumpainter.cpp
+++ /dev/null
@@ -1,471 +0,0 @@
-
-/*******************************************************************************
-* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of PAPPSOms-tools.
-*
-* PAPPSOms-tools is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* PAPPSOms-tools is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
-#include "spectrumpainter.h"
-
-#include <QDebug>
-#include <cmath>
-
-SpectrumPainter::SpectrumPainter()
-{
- _p_precision = pappso::Precision::getDaltonInstance(0.5);
-}
-
-SpectrumPainter::~SpectrumPainter()
-{
- //delete _p_precision;
-}
-void SpectrumPainter::setFontPointSize(int point_size) {
- _font_point_size = point_size;
-}
-
-void SpectrumPainter::setMarginLeft(pappso_double margin) {
- _margin_left = margin;
-}
-void SpectrumPainter::setMarginTop(pappso_double margin) {
- _margin_top = margin;
-}
-void SpectrumPainter::setMarginBottom(pappso_double margin) {
- _margin_bottom = margin;
-}
-
-void SpectrumPainter::setQualifiedSpectrum(pappso::QualifiedSpectrum & spectrum) {
- _ms_level = spectrum.getMsLevel();
- setSpectrumSp(spectrum.getOriginalSpectrumSp());
- setParentIonCharge(spectrum.getPrecursorCharge());
-}
-
-void SpectrumPainter::setPeptideSp(const pappso::PeptideSp & peptide_sp) {
- _peptide_sp = peptide_sp;
- _is_isotope = false;
- _peptide_fragment_ion_isotope_list.clear();
-
- PeptideFragmentIonListBase peptide_ion_list(peptide_sp, _ion_list);
-
- _peptide_fragment_ion_list.clear();
- _peptide_fragment_ion_charge_list.clear();
-
- for (auto ion_type: _ion_list) {
- auto ion_list = peptide_ion_list.getPeptideFragmentIonSp(ion_type);
-
- for (unsigned int charge=1; charge <= _parent_ion_charge; charge++) {
- for (auto && ion : ion_list) {
- _peptide_fragment_ion_list.push_back(ion);
- _peptide_fragment_ion_charge_list.push_back(charge);
- }
- }
- }
-}
-
-void SpectrumPainter::setIsotopeMassList(std::vector<pappso::PeptideNaturalIsotopeAverageSp> & isotopeMassList) {
- // list of isotope to display on MS level 1 spectrum
- _isotope_mass_list = isotopeMassList;
-}
-
-void SpectrumPainter::setPeptideFragmentIonList(const std::vector<PeptideFragmentIonSp> & peptide_fragment_ion_list, const std::vector<unsigned int> & peptide_fragment_ion_charge_list) {
- _peptide_fragment_ion_list = peptide_fragment_ion_list;
- _peptide_fragment_ion_charge_list = peptide_fragment_ion_charge_list;
- _is_isotope = false;
-}
-
-void SpectrumPainter::setPeptideFragmentIonIsotopeList(const std::vector<PeptideNaturalIsotopeAverageSp> & peptide_fragment_ion_isotope_list, const std::vector<PeptideFragmentIonSp> & peptide_fragment_ion_list) {
- _peptide_fragment_ion_list = peptide_fragment_ion_list;
- _peptide_fragment_ion_isotope_list = _peptide_fragment_ion_isotope_list;
- _is_isotope = true;
-}
-
-void SpectrumPainter::setSpectrumSp(const pappso::SpectrumSp & spectrum_sp) {
- _spectrum_sp = spectrum_sp;
- _max_mz = 0;
-}
-void SpectrumPainter::setParentIonCharge(unsigned int parent_ion_charge) {
- _parent_ion_charge = parent_ion_charge;
-}
-void SpectrumPainter::setIonList(const list< PeptideIon > & ion_list) {
- _ion_list = ion_list;
-}
-void SpectrumPainter::setPrecision(PrecisionP precision) {
- qDebug() << "SpectrumPainter::setPrecision begin " << precision->toString();
- _p_precision =precision;
- //_precision._precision = precision._precision;
-}
-
-
-int SpectrumPainter::getLocalPosYFromIntensity(pappso_double intensity) const {
- return getY(intensity);
-}
-
-pappso_double SpectrumPainter::getIntensityFromLocalPosY(pappso_double y) const {
- return ((_spectrum_height-(y-_margin_top))/_spectrum_height)*_max_int;
- //(((_spectrum_height-y)-_margin_top)/_spectrum_height)*_max_int;
-}
-
-mz SpectrumPainter::getMzFromLocalPosX(pappso_double x) const {
- mz mz = (x - _margin_left - _padding);
- mz = (mz / _spectrum_width) * (_max_mz - _min_mz);
- mz = mz + _min_mz;
- qDebug() << " pos.x=" << x << " mz=" << mz;
- if (mz < _min_mz) return 0;
- if (mz > _max_mz) return 0;
- return mz;
-}
-
-
-
-pappso_double SpectrumPainter::getX(pappso_double x) const {
-
- return ((_spectrum_width / (_max_mz - _min_mz)) * (x - _min_mz)) + _margin_left + _padding;
-}
-
-
-
-pappso_double SpectrumPainter::getY(pappso_double x) const {
-
- return ((_max_int - x) * ( _spectrum_height/_max_int)) + _margin_top;
-}
-
-bool SpectrumPainter::peakInPsm(pappso::PeptideSpectrumMatch* p_psm, pappso::PeptideIsotopeSpectrumMatch* p_psm_isotope, mz mz) {
- if (_is_isotope) {
- for (auto it = p_psm_isotope->begin() ; it != p_psm_isotope->end(); it++) {
- if (it->getPeak().mz == mz) {
- return true;
- }
- }
- }
- else {
- for (auto it = p_psm->begin() ; it != p_psm->end(); it++) {
- if (it->getPeak().mz == mz) {
- return true;
- }
- }
- }
- return false;
-}
-
-void SpectrumPainter::convertPsmToSpectrum(Spectrum * spectrum_text_draw, pappso::PeptideSpectrumMatch* p_psm, pappso::PeptideIsotopeSpectrumMatch* p_psm_isotope) {
- if (_is_isotope) {
- for (auto it = p_psm_isotope->begin() ; it != p_psm_isotope->end(); it++) {
- spectrum_text_draw->push_back(it->getPeak());
- }
- }
- else {
- for (auto it = p_psm->begin() ; it != p_psm->end(); it++) {
- spectrum_text_draw->push_back(it->getPeak());
- }
- }
-}
-
-
-//http://stackoverflow.com/questions/24831484/how-to-align-qpainter-drawtext-around-a-point-not-a-rectangle
-void drawText(QPainter & painter, qreal x, qreal y, Qt::Alignment flags,
- const QString & text, QRectF * boundingRect = 0)
-{
- const qreal size = 32767.0;
- QPointF corner(x, y - size);
- if (flags & Qt::AlignHCenter) corner.rx() -= size/2.0;
- else if (flags & Qt::AlignRight) corner.rx() -= size;
- if (flags & Qt::AlignVCenter) corner.ry() += size/2.0;
- else if (flags & Qt::AlignTop) corner.ry() += size;
- else flags |= Qt::AlignBottom;
- QRectF rect(corner, QSizeF(size, size));
- painter.drawText(rect, flags, text, boundingRect);
-}
-
-void drawText(QPainter & painter, const QPointF & point, Qt::Alignment flags,
- const QString & text, QRectF * boundingRect = 0)
-{
- drawText(painter, point.x(), point.y(), flags, text, boundingRect);
-}
-
-bool spectrumContainsMz(const Spectrum & spectrum, const Peak & peak) {
- std::vector<Peak>::const_iterator it_peak;
- for (it_peak = spectrum.begin() ; it_peak != spectrum.end(); it_peak++) {
- if (peak.mz== it_peak->mz) return true;
- }
- return false;
-}
-
-int NumDigits(int n) {
- int digits = 0;
- if (n <= 0) {
- n = -n;
- ++digits;
- }
- while (n) {
- n /= 10;
- ++digits;
- }
- return digits;
-}
-
-
-
-void SpectrumPainter::paint(QPainter & painter, pappso_double width, pappso_double height) {
- qDebug() << "SpectrumPainter::paint begin";
- //if (_peptide_sp.get() == nullptr) return;
- //painter.drawLine(QLine(0, 35, 2000, 35));
- _canvas_height = height;
- _spectrum_height = height - _margin_bottom - _margin_top;
- _canvas_width = width;
- _spectrum_width = width - _margin_left - (_padding*2);
-
- QFont font = painter.font() ;
-
- /* twice the size than the current font size */
- font.setPointSize(_font_point_size);
-
- /* set the modified font to the painter */
- painter.setFont(font);
-
- if (_spectrum_sp.get() != nullptr) {
- const Spectrum & spectrum_int_draw = *_spectrum_sp.get();
- if (_max_mz == 0) {
- _min_mz = _spectrum_sp.get()->begin()->mz ;
- _max_mz = (--_spectrum_sp.get()->end())->mz ;
- _max_int = _spectrum_sp.get()->getMaxIntensity().intensity;
- }
- if (_max_int < 0) {
- _max_int = _spectrum_sp.get()->getMaxIntensity().intensity;
- }
- PeptideSpectrumMatch * p_psm = nullptr;
- PeptideIsotopeSpectrumMatch * p_psm_isotope = nullptr;
- if (_is_isotope) {
- p_psm_isotope = new PeptideIsotopeSpectrumMatch(spectrum_int_draw, _peptide_fragment_ion_isotope_list, _peptide_fragment_ion_list, _p_precision);
- }
- else {
- p_psm = new PeptideSpectrumMatch(spectrum_int_draw,_peptide_fragment_ion_list, _peptide_fragment_ion_charge_list, _p_precision);
- }
-
- //Spectrum spectrum_for_hyperscore = spectrumSp.get()->applyCutOff(150).takeNmostIntense(100).applyDynamicRange(100);
-
- //XtandemHyperscore hyperscore_withxtspectrum(spectrum_for_hyperscore, peptideSp,zmax, precision, ion_list,true);
- //Spectrum spectrum_remains = _spectrum_sp.get()->minus(psm);
- pappso_double stroke_width = 0.8;
-
- //painter.translate(-_min_mz,0);
- //painter.scale(0.1,0.5);
- painter.setPen(Qt::black);
- //painter.setClipRect(QRect(0, 0, _max_mz, _spectrum_height));
- //painter.fillRect(QRect(0, 0, _max_mz, _spectrum_height), Qt::white);
- //painter.drawRect(QRect(getX(_min_mz)-_padding, 0,getX(_max_mz)-_padding, _spectrum_height));
- painter.setPen(QPen(Qt::black, 1, Qt::SolidLine) );
- painter.drawLine(QLine(_margin_left, getY(0), _margin_left, getY(_max_int)));
- painter.drawLine(QLine(_margin_left-2, getY(_max_int), _margin_left+2, getY(_max_int)));
- drawText(painter, QPointF(_margin_left, getY(0)), Qt::AlignVCenter | Qt::AlignRight, "0 ");
- drawText(painter, QPointF(_margin_left, getY(_max_int)), Qt::AlignBottom | Qt::AlignHCenter, QString::number(_max_int, 'g', 2));
-
-
- unsigned long big_tic_int = pow10(NumDigits(_max_int));
-
- unsigned long delta = _max_int - 0;
- while (big_tic_int > 10) {
- if ((delta / big_tic_int) > 1) {
- break;
- }
- big_tic_int = big_tic_int / 10;
- }
- unsigned long small_tic_int = (unsigned long) floor(big_tic_int / 10);
-
- pappso_double begin_tic = (unsigned long) ((floor(0 / big_tic_int) + 1) * big_tic_int);
-
- painter.setPen(QPen(Qt::black, 3, Qt::SolidLine) );
- for (pappso_double ipos = begin_tic; ipos < _max_int; ipos += big_tic_int) {
- painter.drawLine(QLine(_margin_left-3, getY(ipos), _margin_left+3, getY(ipos)));
- drawText(painter, QPointF(_margin_left-3, getY(ipos)), Qt::AlignVCenter | Qt::AlignRight, QString::number(ipos, 'g', 2));
- //qDebug() << " ipos=" << ipos ;
- }
-
- //small tic
- painter.setPen(QPen(Qt::black, 1, Qt::SolidLine) );
- for (pappso_double ipos = 0; ipos < _max_int; ipos += small_tic_int) {
- painter.drawLine(QLine(_margin_left-1, getY(ipos), _margin_left+1, getY(ipos)));
- //qDebug() << " ipos=" << ipos ;
- }
-
- qDebug() << " NumDigits(_max_int)=" << NumDigits(_max_int) << " big_tic_int=" << big_tic_int << "_min_mz=" << _min_mz << " _max_mz=" << _max_mz ;
- if (_ms_level ==1) {
- std::vector<Peak>::const_iterator it_peak;
- PeptideNaturalIsotopeAverageSp precursor_peptide;
- MassRange * p_precursor_mass = nullptr;
- pappso_double monoisotope_intensity = 0;
- if (_isotope_mass_list.size() > 0) {
- precursor_peptide = _isotope_mass_list.at(0);
- p_precursor_mass = new MassRange(precursor_peptide.get()->getMz(), _p_precision);
- }
- for (it_peak = spectrum_int_draw.begin() ; it_peak != spectrum_int_draw.end(); it_peak++) {
- //draw all peaks in black
- painter.setPen(QPen(Qt::black, stroke_width, Qt::SolidLine) );
- pappso_double x = it_peak->mz;
-
- if (p_precursor_mass->contains(x)) {
- if (it_peak->intensity > monoisotope_intensity) {
- monoisotope_intensity = it_peak->intensity;
- }
- }
-
- if ((x > _min_mz) && ( x < _max_mz)) {
- //pappso_double y = _spectrum_height - it_peak->intensity;
- painter.drawLine(QLine(getX(x), getY(it_peak->intensity), getX(x),getY(0)));
- }
-
- // painter.setPen(Qt::black);
-
- }
- if (monoisotope_intensity > 0) {
- //draw isotope cluster
- std::vector<Peak> cluster;
- Peak peak;
- peak.mz = precursor_peptide.get()->getMz();
- peak.intensity = monoisotope_intensity;
- cluster.push_back(peak);
- pappso_double total_intensity = ((pappso_double)1.0 / precursor_peptide.get()->getIntensityRatio())*monoisotope_intensity;
- for (int j=1 ; j < _isotope_mass_list.size(); j++) {
- peak.mz = _isotope_mass_list.at(j).get()->getMz();
- peak.intensity = _isotope_mass_list.at(j).get()->getIntensityRatio() * total_intensity;
- cluster.push_back(peak);
- }
- for (it_peak = cluster.begin() ; it_peak != cluster.end(); it_peak++) {
- //draw all peaks in black
- painter.setPen(QPen(Qt::red, stroke_width, Qt::SolidLine) );
- pappso_double x = it_peak->mz;
-
- if (p_precursor_mass->contains(x)) {
- monoisotope_intensity = it_peak->intensity;
- }
-
- if ((x > _min_mz) && ( x < _max_mz)) {
- //pappso_double y = _spectrum_height - it_peak->intensity;
- //painter.drawLine(QLine(getX(x), getY(it_peak->intensity), getX(x),getY(0)));
- painter.drawRect(getX(x)-stroke_width,getY(0),3*stroke_width,getY(it_peak->intensity)-getY(0));
- }
-
- // painter.setPen(Qt::black);
-
- }
- }
- if (p_precursor_mass != nullptr) {
- delete p_precursor_mass;
- }
- }
- else {
-
- std::vector<Peak>::const_iterator it_peak;
- for (it_peak = spectrum_int_draw.begin() ; it_peak != spectrum_int_draw.end(); it_peak++) {
- if (peakInPsm(p_psm,p_psm_isotope, it_peak->mz)) {
- }
- else {
- //draw only non assigned peaks
- painter.setPen(QPen(Qt::black, stroke_width, Qt::SolidLine) );
- pappso_double x = it_peak->mz;
-
- if ((x > _min_mz) && ( x < _max_mz)) {
- //pappso_double y = _spectrum_height - it_peak->intensity;
- painter.drawLine(QLine(getX(x), getY(it_peak->intensity), getX(x),getY(0)));
- }
- }
- // painter.setPen(Qt::black);
-
- }
-//painter.rotate(45);
- if (_is_isotope) {
- p_psm_isotope = new PeptideIsotopeSpectrumMatch(spectrum_int_draw, _peptide_fragment_ion_isotope_list, _peptide_fragment_ion_list, _p_precision);
- }
- else {
-
- unsigned int draw_fragment_index = _peptide_fragment_ion_list.size();
- unsigned int write_ion_name = 10;
- Spectrum spectrum_text_draw;// = _spectrum_sp.get()->takeNmostIntense(write_ion_name);
- convertPsmToSpectrum(&spectrum_text_draw,p_psm,p_psm_isotope);
- spectrum_text_draw = spectrum_text_draw.takeNmostIntense(write_ion_name);
-
- qDebug() << "spectrum_text_draw.size()=" << spectrum_text_draw.size();
- for (int draw_fragment_index = (_peptide_fragment_ion_list.size()-1); draw_fragment_index>=0; draw_fragment_index--) {
- for (auto it_psm = p_psm->begin() ; it_psm != p_psm->end(); it_psm++) {
- if ((_peptide_fragment_ion_list[draw_fragment_index].get() == it_psm->getPeptideFragmentIonSp().get()) && (
- _peptide_fragment_ion_charge_list[draw_fragment_index] == it_psm->getCharge()
- )) {
- painter.setPen(QPen(PeptideFragmentIon::getPeptideIonColor(it_psm->getPeptideIonType()), stroke_width, Qt::SolidLine) );
- pappso_double x = it_psm->getPeak().mz;
- if ((x > _min_mz) && ( x < _max_mz)) {
- //pappso_double y = _spectrum_height - it->getPeak().intensity;
- painter.drawLine(QLine(getX(x), getY(it_psm->getPeak().intensity), getX(x), getY(0)));
-
- if (spectrumContainsMz(spectrum_text_draw, it_psm->getPeak())) {
- qDebug() << "ion_name=" << it_psm->getPeptideFragmentIonSp().get()->getPeptideIonName() << " it_psm->getPeak().mz=" << QString::number(it_psm->getPeak().mz, 'g', 8) << " it_psm->getPeak().intensity=" << it_psm->getPeak().intensity;
- QString plusstr = "+";
- plusstr = plusstr.repeated(it_psm->getCharge());
- drawText(painter, QPointF(getX(x), getY(it_psm->getPeak().intensity)), Qt::AlignBottom | Qt::AlignHCenter, QString("%1%2%3").arg(it_psm->getPeptideFragmentIonSp().get()->getPeptideIonName()).arg(it_psm->getPeptideFragmentIonSp().get()->size()).arg(plusstr));
- }
- }
- //painter.setPen(Qt::black);
- }
-
- }
- }
- }
- }
-
- painter.setPen(QPen(Qt::black, stroke_width, Qt::SolidLine) );
- painter.drawLine(QLine(getX(_min_mz),getY(0), getX(_max_mz), getY(0)));
-
-
- big_tic_int = pow10(NumDigits(_max_mz));
-
- delta = _max_mz - _min_mz;
- while (big_tic_int > 10) {
- if ((delta / big_tic_int) > 2) {
- break;
- }
- big_tic_int = big_tic_int / 10;
- }
- small_tic_int = (unsigned long) floor(big_tic_int / 10);
-
- begin_tic = (unsigned long) ((floor(_min_mz / big_tic_int) + 1) * big_tic_int);
-
- painter.setPen(QPen(Qt::black, 2, Qt::SolidLine) );
- for (pappso_double ipos = begin_tic; ipos < _max_mz; ipos += big_tic_int) {
- painter.drawLine(QLine(getX(ipos), getY(0)+1, getX(ipos), getY(0)+3));
- drawText(painter, QPointF(getX(ipos), getY(0)+3), Qt::AlignTop | Qt::AlignHCenter, QString::number(ipos, 'f', 0));
- //qDebug() << " ipos=" << ipos ;
- }
-
- //small tic
- begin_tic = (unsigned long) ((floor(_min_mz / small_tic_int) + 1) * small_tic_int);
- painter.setPen(QPen(Qt::black, 1, Qt::SolidLine) );
- for (pappso_double ipos = begin_tic; ipos < _max_mz; ipos += small_tic_int) {
- painter.drawLine(QLine(getX(ipos), getY(0)+1, getX(ipos), getY(0)+1));
- //qDebug() << " ipos=" << ipos ;
- }
-
-
- //painter.scale(0.5,0.5);
- if (_is_isotope) {
- delete p_psm_isotope;
- }
- else {
- delete p_psm;
- }
-
-
- }
-
-}
diff --git a/src/gui/peptide_detail_view/spectrum_widget/spectrumpainter.h b/src/gui/peptide_detail_view/spectrum_widget/spectrumpainter.h
deleted file mode 100644
index 6d4b6f8a9..000000000
--- a/src/gui/peptide_detail_view/spectrum_widget/spectrumpainter.h
+++ /dev/null
@@ -1,119 +0,0 @@
-
-/*******************************************************************************
-* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of PAPPSOms-tools.
-*
-* PAPPSOms-tools is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* PAPPSOms-tools is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
-#ifndef SPECTRUMPAINTER_H
-#define SPECTRUMPAINTER_H
-
-#include <QPainter>
-#include <QPointF>
-#include <pappsomspp/peptide/peptide.h>
-#include <pappsomspp/spectrum/spectrum.h>
-#include <pappsomspp/peptide/peptidefragmentionlistbase.h>
-#include <pappsomspp/peptide/peptidenaturalisotopeaverage.h>
-#include <pappsomspp/psm/peptidespectrummatch.h>
-#include <pappsomspp/psm/peptideisotopespectrummatch.h>
-#include <pappsomspp/spectrum/qualifiedspectrum.h>
-
-using namespace pappso;
-
-class SpectrumPainter
-{
-public:
- SpectrumPainter();
- ~SpectrumPainter();
-
- void setPeptideSp(const pappso::PeptideSp & peptide_sp);
- void setSpectrumSp(const pappso::SpectrumSp & spectrum_sp);
- void setParentIonCharge(unsigned int parent_ion_charge);
- void setIonList(const list< PeptideIon > & ion_list);
- void setPrecision(PrecisionP precision);
- void setPeptideFragmentIonList(const std::vector<PeptideFragmentIonSp> & peptide_fragment_ion_list, const std::vector<unsigned int> & peptide_fragment_ion_charge_list);
- void setPeptideFragmentIonIsotopeList(const std::vector<PeptideNaturalIsotopeAverageSp> & peptide_fragment_ion_isotope_list, const std::vector<PeptideFragmentIonSp> & peptide_fragment_ion_list);
-
-
- void setIsotopeMassList(std::vector<pappso::PeptideNaturalIsotopeAverageSp> & isotopeMassList);
-
- mz getMzFromLocalPosX(pappso_double x) const;
- pappso_double getIntensityFromLocalPosY(pappso_double y) const;
- int getLocalPosYFromIntensity(pappso_double intensity) const;
-
- void paint(QPainter & painter, pappso_double width, pappso_double height);
- void setMarginLeft(pappso_double margin);
- void setFontPointSize(int point_size);
- void setMarginBottom(pappso_double margin);
- void setMarginTop(pappso_double margin);
-
- pappso_double getCanvasWidth() const {
- return _canvas_width;
- };
- pappso_double getMarginLeft() const {
- return _margin_left;
- };
- void setMinMz(mz mzX) {
- _min_mz = mzX;
- };
- void setMaxMz(mz mzX) {
- _max_mz = mzX;
- };
- void setMaxIntensity(pappso_double max_intensity) {
- _max_int = max_intensity;
- }
- void setQualifiedSpectrum(pappso::QualifiedSpectrum & spectrum);
-
-private :
- PrecisionP _p_precision = pappso::Precision::getDaltonInstance(0.5);
- std::list< PeptideIon > _ion_list;
- unsigned int _parent_ion_charge=3;
- SpectrumSp _spectrum_sp;
- PeptideSp _peptide_sp;
- std::vector<PeptideFragmentIonSp> _peptide_fragment_ion_list;
- std::vector<unsigned int> _peptide_fragment_ion_charge_list;
- std::vector<PeptideNaturalIsotopeAverageSp> _peptide_fragment_ion_isotope_list;
- std::vector< PeptideNaturalIsotopeAverageSp > _isotope_mass_list;
-
-private :
-
- bool _is_isotope = false;
- pappso_double _min_mz=0 ;
- pappso_double _max_mz=0 ;
- pappso_double _max_int = -1;
- pappso_double _canvas_height;
- pappso_double _canvas_width;
- pappso_double _spectrum_height = 500;
- pappso_double _spectrum_width = 1200;
- pappso_double _margin_top = 10;
- pappso_double _margin_bottom = 10;
- pappso_double _margin_left = 10;
- pappso_double _padding = 5;
- int _font_point_size = 12;
- unsigned int _ms_level;
-
-
-private :
- pappso_double getX(pappso_double x) const;
- pappso_double getY(pappso_double x) const;
- bool peakInPsm(pappso::PeptideSpectrumMatch* p_psm, pappso::PeptideIsotopeSpectrumMatch* p_psm_isotope, mz mz);
- void convertPsmToSpectrum(Spectrum * spectrum_text_draw, pappso::PeptideSpectrumMatch* p_psm, pappso::PeptideIsotopeSpectrumMatch* p_psm_isotope);
-};
-
-#endif // SPECTRUMPAINTER_H
-
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 939827d94..55fe94e8d 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -35,7 +35,7 @@
#include <numeric>
#include "../workerthread.h"
#include "../../core/labeling/labelingmethod.h"
-#include "../../../utils/utils.h"
+#include "../../utils/utils.h"
#include <qcustomplot.h>
--
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