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Commit a4f022f5 authored by Langella Olivier's avatar Langella Olivier
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near release

parents e2d5eb31 9060c2b5
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src/CMakeLists.txt
+ 4
− 4
View file @ a4f022f5
......@@ -13,10 +13,10 @@ SET(xtpcpp_RCCS xtpcpp.qrc)
#FIND_PACKAGE(Boost REQUIRED)
#INCLUDE_DIRECTORIES( ${Boost_INCLUDE_DIRS})
FIND_PACKAGE( Qt5 COMPONENTS Core Gui Svg Xml REQUIRED )
FIND_PACKAGE( Qt5 COMPONENTS Core Gui Svg Xml PrintSupport REQUIRED )
QT5_ADD_RESOURCES(xtpcpp_RCC_SRCS ${xtpcpp_RCCS})
FIND_PACKAGE( QCustomPlot REQUIRED )
FIND_PACKAGE( Odsstream REQUIRED ) #ODSSTREAM_INCLUDE_DIR AND ODSSTREAM_LIBRARY
#SET (ODSSTREAM_DIR "/home/olivier/eclipse/git/cpp_libodsstream")
#SET (ODSSTREAM_INCLUDE_DIR "${ODSSTREAM_DIR}/src")
......@@ -232,8 +232,8 @@ 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}
Qt5::Gui Qt5::Xml Qt5::Svg)
TARGET_LINK_LIBRARIES(xtpcpp ${PAPPSOMSPP_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)
......
src/gui/project_view/project_view.ui
+ 93
− 63
View file @ a4f022f5
......@@ -216,70 +216,92 @@
<item row="0" column="0">
<layout class="QVBoxLayout" name="verticalLayout_5">
<item>
<layout class="QFormLayout" name="formLayout_2">
<item row="0" column="0">
<layout class="QFormLayout" name="formLayout_3"/>
</item>
<item row="1" column="0">
<widget class="QLabel" name="label_2">
<property name="text">
<string>mean</string>
</property>
</widget>
</item>
<item row="2" column="0">
<widget class="QLabel" name="label_4">
<property name="text">
<string>median</string>
</property>
</widget>
</item>
<item row="3" column="0">
<widget class="QLabel" name="label_5">
<property name="text">
<string>standard deviation</string>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QComboBox" name="precision_unit_combobox">
<item>
<property name="text">
<string>ppm</string>
</property>
</item>
<item>
<property name="text">
<string>dalton</string>
<widget class="QWidget" name="widget" native="true">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<layout class="QVBoxLayout" name="verticalLayout_7">
<item>
<layout class="QFormLayout" name="formLayout_2">
<property name="sizeConstraint">
<enum>QLayout::SetMinimumSize</enum>
</property>
</item>
</widget>
</item>
<item row="1" column="1">
<widget class="QLabel" name="mass_precision_mean_label">
<property name="text">
<string>0</string>
</property>
</widget>
</item>
<item row="2" column="1">
<widget class="QLabel" name="mass_precision_median_label">
<property name="text">
<string>0</string>
</property>
</widget>
</item>
<item row="3" column="1">
<widget class="QLabel" name="mass_precision_sd_label">
<property name="toolTip">
<string>Mass deviation is computed on all valid and checked proteins but not decoy</string>
</property>
<property name="text">
<string>0</string>
</property>
</widget>
</item>
</layout>
<item row="0" column="1">
<widget class="QComboBox" name="precision_unit_combobox">
<item>
<property name="text">
<string>ppm</string>
</property>
</item>
<item>
<property name="text">
<string>dalton</string>
</property>
</item>
</widget>
</item>
<item row="1" column="0">
<widget class="QLabel" name="label_2">
<property name="text">
<string>mean</string>
</property>
</widget>
</item>
<item row="1" column="1">
<widget class="QLabel" name="mass_precision_mean_label">
<property name="text">
<string>0</string>
</property>
</widget>
</item>
<item row="2" column="0">
<widget class="QLabel" name="label_4">
<property name="text">
<string>median</string>
</property>
</widget>
</item>
<item row="2" column="1">
<widget class="QLabel" name="mass_precision_median_label">
<property name="text">
<string>0</string>
</property>
</widget>
</item>
<item row="3" column="0">
<widget class="QLabel" name="label_5">
<property name="text">
<string>standard deviation</string>
</property>
</widget>
</item>
<item row="3" column="1">
<widget class="QLabel" name="mass_precision_sd_label">
<property name="toolTip">
<string>Mass deviation is computed on all valid and checked proteins but not decoy</string>
</property>
<property name="text">
<string>0</string>
</property>
</widget>
</item>
</layout>
</item>
</layout>
</widget>
</item>
<item>
<widget class="QCustomPlot" name="mass_histogram_widget" native="true">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Expanding">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
</widget>
</item>
</layout>
</item>
......@@ -301,6 +323,14 @@
</widget>
<widget class="QStatusBar" name="statusbar"/>
</widget>
<customwidgets>
<customwidget>
<class>QCustomPlot</class>
<extends>QWidget</extends>
<header>qcustomplot.h</header>
<container>1</container>
</customwidget>
</customwidgets>
<resources/>
<connections>
<connection>
......
src/gui/project_view/projectwindow.cpp
+ 38
− 0
View file @ a4f022f5
......@@ -35,6 +35,8 @@
#include <numeric>
#include "../workerthread.h"
#include "../../core/labeling/labelingmethod.h"
#include "../../../utils/utils.h"
#include <qcustomplot.h>
......@@ -65,6 +67,26 @@ ProjectWindow::ProjectWindow(MainWindow *parent):
_p_waiting_message_dialog = new WaitingMessageDialog(this);
ui->mass_histogram_widget->xAxis->setLabel("mass delta");
ui->mass_histogram_widget->yAxis->setLabel("count");
ui->mass_histogram_widget->setInteractions(QCP::iRangeDrag | QCP::iRangeZoom );
ui->mass_histogram_widget->axisRects().at(0)->setRangeDrag(Qt::Horizontal);
ui->mass_histogram_widget->axisRects().at(0)->setRangeZoom(Qt::Horizontal);
//legend->setVisible(false);
ui->mass_histogram_widget->legend->setFont(QFont("Helvetica",9));
// set locale to english, so we get english decimal separator:
//setLocale(QLocale(QLocale::English, QLocale::UnitedKingdom));
setFocusPolicy(Qt::ClickFocus);
QCPGraph * p_graph = ui->mass_histogram_widget->addGraph();
//p_graph->setName("raw xic");
//QPen pen;
//pen.setColor(getNewColors());
//graph()->setPen(pen);
//graph()->setName(lineNames.at(i-QCPGraph::lsNone));
p_graph->setLineStyle(QCPGraph::LineStyle::lsStepCenter);
//p_graph->setScatterStyle(QCPScatterStyle(QCPScatterStyle::ssDisc, 2.0));
#if QT_VERSION >= 0x050000
// Qt5 code
......@@ -277,6 +299,22 @@ void ProjectWindow::computeMassPrecision() {
ui->mass_precision_mean_label->setText(QString::number(mean,'f',10));
ui->mass_precision_median_label->setText(QString::number(median,'f',10));
ui->mass_precision_sd_label->setText(QString::number(sd,'f',10));
std::vector< std::pair<pappso::pappso_double, size_t >> histogram = Utils::getHistogram(delta_list, 100);
// generate some data:
QVector<double> x, y;
for (std::pair<pappso::pappso_double, size_t > & mass_pair: histogram)
{
x.push_back(mass_pair.first);
y.push_back(mass_pair.second);
}
QCPGraph * p_graph = ui->mass_histogram_widget->graph();
p_graph->setData(x,y);
p_graph->rescaleAxes(true);
ui->mass_histogram_widget->rescaleAxes();
ui->mass_histogram_widget->replot();
}
catch (pappso::PappsoException exception_pappso) {
ui->mass_precision_mean_label->setText("0");
......
src/utils/utils.cpp
+ 28
− 14
View file @ a4f022f5
#include "utils.h"
#include <pappsomspp/exception/exceptionnotfound.h>
#include <pappsomspp/mass_range.h>
#include <cmath>
const QUrl Utils::getOlsUrl(QString psimod_accession) {
......@@ -9,7 +10,7 @@ const QUrl Utils::getOlsUrl(QString psimod_accession) {
return url;
}
const QString Utils::getXmlDouble(pappso::pappso_double number){
const QString Utils::getXmlDouble(pappso::pappso_double number) {
return QString::number(number,'g',6);
}
......@@ -37,20 +38,33 @@ const QString Utils::getDatabaseName(ExternalDatabase database) {
}
std::vector<size_t> Utils::getHistogram(std::vector<pappso::pappso_double> data_values, unsigned int number_of_class) {
std::vector<size_t> histogram(number_of_class);
std::sort(data_values.begin(), data_values.end());
pappso::pappso_double min = *data_values.begin();
pappso::pappso_double max = *(data_values.end()-1);
pappso::pappso_double offset = (max-min)/ (pappso::pappso_double) number_of_class;
for (pappso::pappso_double value :data_values) {
histogram[(value /offset )] = value;
std::vector<std::pair<pappso::pappso_double, size_t>> Utils::getHistogram(std::vector<pappso::pappso_double> data_values, unsigned int number_of_class) {
std::vector<std::pair<pappso::pappso_double, size_t>> histogram(number_of_class+1);
try {
qDebug() << "Utils::getHistogram begin";
std::sort(data_values.begin(), data_values.end());
pappso::pappso_double min = *data_values.begin();
pappso::pappso_double max = *(data_values.end()-1);
pappso::pappso_double total = std::abs(max-min);
pappso::pappso_double offset = (total/ (pappso::pappso_double) number_of_class);
qDebug() << "Utils::getHistogram number_of_class offset=" << offset;
for (unsigned int i= 0; i < histogram.size(); i++) {
histogram[i] = std::pair<pappso::pappso_double, size_t> {(min + (offset * i) + (offset/2)), 0};
qDebug() << "Utils::getHistogram x=" << histogram[i].first;
}
qDebug() << "Utils::getHistogram data_values";
for (pappso::pappso_double value :data_values) {
//qDebug() << "Utils::getHistogram value=" << value;
unsigned int i = std::abs((value-min)/offset );
qDebug() << "Utils::getHistogram i=" << i << " size=" << histogram.size();
histogram.at(i).second++;
}
}
catch (std::exception exception_std) {
throw pappso::PappsoException(QObject::tr("Utils::getHistogram error %1").arg(exception_std.what()));
}
qDebug() << "Utils::getHistogram end";
return histogram;
}
......
src/utils/utils.h
+ 1
− 1
View file @ a4f022f5
......@@ -35,7 +35,7 @@ public:
static const QString getDatabaseName(ExternalDatabase database);
static const QString getXmlDouble(pappso::pappso_double number);
static pappso::AaModificationP guessAaModificationPbyMonoisotopicMassDelta(pappso::mz mass);
static std::vector<size_t> getHistogram(std::vector<pappso::pappso_double> data_values, unsigned int number_of_class);
static std::vector<std::pair<pappso::pappso_double, size_t>> getHistogram(std::vector<pappso::pappso_double> data_values, unsigned int number_of_class);
};
......
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