From c48bf6039a3e3d22a7e28b04b3da056e56a4bf81 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Thu, 1 Jun 2017 13:33:05 +0200
Subject: [PATCH] direct output for tsv spectral count
---
src/gui/main.ui | 23 +++++++++++++
src/gui/mainwindow.cpp | 54 +++++++++++++++++++++++++++---
src/gui/mainwindow.h | 1 +
src/output/ods/comparbasesheet.cpp | 8 +++--
4 files changed, 80 insertions(+), 6 deletions(-)
diff --git a/src/gui/main.ui b/src/gui/main.ui
index 088de361..b21bdc63 100644
--- a/src/gui/main.ui
+++ b/src/gui/main.ui
@@ -41,6 +41,7 @@
<addaction name="actionMassChroQ"/>
<addaction name="actionSpreadsheet"/>
<addaction name="actionProticDb"/>
+ <addaction name="action_spectral_counting_mcq"/>
</widget>
<addaction name="actionLoad_results"/>
<addaction name="actionLoad"/>
@@ -108,6 +109,11 @@
<string>PROTICdb</string>
</property>
</action>
+ <action name="action_spectral_counting_mcq">
+ <property name="text">
+ <string>Spectral Counting mcq</string>
+ </property>
+ </action>
</widget>
<resources>
<include location="../xtpcpp.qrc"/>
@@ -257,6 +263,22 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>action_spectral_counting_mcq</sender>
+ <signal>triggered()</signal>
+ <receiver>Main</receiver>
+ <slot>doActionSpectralCountingMcq()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>-1</x>
+ <y>-1</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>231</x>
+ <y>191</y>
+ </hint>
+ </hints>
+ </connection>
</connections>
<slots>
<slot>selectXpipFile()</slot>
@@ -268,5 +290,6 @@
<slot>doActionModifications()</slot>
<slot>doActionLabelingMethods()</slot>
<slot>doActionFasta()</slot>
+ <slot>doActionSpectralCountingMcq()</slot>
</slots>
</ui>
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index c2568e55..76b615e8 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -31,9 +31,21 @@
#include "ui_main.h"
#include <pappsomspp/pappsoexception.h>
#include <pappsomspp/fasta/fastaoutputstream.h>
+#include <odsstream/tsvoutputstream.h>
#include "../utils/utils.h"
#include "workerthread.h"
+#include "output/ods/comparspectrasheet.h"
+class TsvNoSheetOutput: public TsvOutputStream {
+public :
+ TsvNoSheetOutput(QTextStream & otxtstream):TsvOutputStream(otxtstream) {
+ }
+ ~TsvNoSheetOutput() {
+ }
+
+ virtual void writeSheet(const QString & sheetName) override {
+ }
+};
MainWindow::MainWindow(QWidget *parent):
QMainWindow(parent),
@@ -60,11 +72,11 @@ MainWindow::MainWindow(QWidget *parent):
//QDockWidget *dock = new QDockWidget(tr("Protein List"), this);
//dock->setWidget(_protein_list_window);
//addDockWidget(Qt::RightDockWidgetArea, dock);
-
+
qRegisterMetaType<ProjectSp>("ProjectSp");
qRegisterMetaType<AutomaticFilterParameters>("AutomaticFilterParameters");
qRegisterMetaType<GroupingType>("GroupingType");
-
+
#if QT_VERSION >= 0x050000
// Qt5 code
/*
@@ -263,6 +275,40 @@ void MainWindow::doActionSpreadsheet() {
qDebug() << "MainWindow::doActionSpreadsheet end";
}
+void MainWindow::doActionSpectralCountingMcq()
+{
+ qDebug() << "MainWindow::doActionSpectralCountingMcq begin";
+
+ QSettings settings;
+ QString default_location = settings.value("path/scmcqfile", "").toString();
+
+ QString filename = QFileDialog::getSaveFileName(this, tr("Save spectral count TSV text file"),
+ QString("%1/untitled.tsv").arg(default_location),
+ tr("TSV (*.tsv)"));
+
+ if (filename.isEmpty()) {
+ return;
+ }
+
+ settings.setValue("path/scmcqfile", QFileInfo(filename).absolutePath());
+
+
+
+ QFile outFile;
+ outFile.setFileName(filename);
+ outFile.open(QIODevice::WriteOnly);
+ QTextStream * p_outputStream = new QTextStream(&outFile);
+ TsvNoSheetOutput* p_writer = new TsvNoSheetOutput(*p_outputStream);
+ ComparSpectraSheet spectra_sheet(nullptr, p_writer, _project_sp.get());
+ spectra_sheet.writeSheet();
+
+ p_writer->close();
+ delete p_writer;
+ delete p_outputStream;
+ outFile.close();
+ qDebug() << "MainWindow::doActionSpectralCountingMcq end";
+}
+
void MainWindow::doActionFasta() {
try {
@@ -324,7 +370,7 @@ void MainWindow::doActionMassChroQ() {
}
settings.setValue("path/mcqfile", QFileInfo(filename).absolutePath());
-
+
showWaitingMessage(tr("Writing %1 XPIP file").arg(QFileInfo(filename).fileName()));
emit operateWritingMassChroqFile(filename, _project_sp);
//emit operateXpipFile(filename);
@@ -352,7 +398,7 @@ void MainWindow::doActionProticDb() {
}
settings.setValue("path/proticfile", QFileInfo(filename).absolutePath());
-
+
showWaitingMessage(tr("Writing %1 PROTICdbML file").arg(QFileInfo(filename).fileName()));
emit operateWritingProticFile(filename, _project_sp);
//emit operateXpipFile(filename);
diff --git a/src/gui/mainwindow.h b/src/gui/mainwindow.h
index 956d8cf3..362df421 100644
--- a/src/gui/mainwindow.h
+++ b/src/gui/mainwindow.h
@@ -71,6 +71,7 @@ public slots:
void doOperationFailed(QString);
void doOperationFinished();
void doGroupingFinished();
+ void doActionSpectralCountingMcq();
//void peptideEdited(QString peptideStr);
// void setColor(const QColor &color);
// void setShape(Shape shape);
diff --git a/src/output/ods/comparbasesheet.cpp b/src/output/ods/comparbasesheet.cpp
index acf60e13..338a6967 100644
--- a/src/output/ods/comparbasesheet.cpp
+++ b/src/output/ods/comparbasesheet.cpp
@@ -70,7 +70,7 @@ void ComparBaseSheet::writeHeaders(IdentificationGroup * p_ident) {
});
- _p_writer->writeLine();
+ //_p_writer->writeLine();
_p_writer->writeCell("Group ID");
_p_writer->writeCell("Subgroup ID");
//_p_writer->setCellAnnotation("MS sample name (MS run)");
@@ -95,9 +95,13 @@ void ComparBaseSheet::writeProteinMatch(const ProteinMatch * p_protein_match) {
unsigned int subgroup_number = p_protein_match->getGrpProteinSp().get()->getSubGroupNumber();
unsigned int rank_number = p_protein_match->getGrpProteinSp().get()->getRank();
- _p_ods_export->setEvenOrOddStyle(group_number, _p_writer);
+ if (_p_ods_export != nullptr) {
+ _p_ods_export->setEvenOrOddStyle(group_number, _p_writer);
+ }
_p_writer->writeCell(pappso::Utils::getLexicalOrderedString(group_number));
+ if (_p_ods_export != nullptr) {
_p_ods_export->setEvenOrOddStyle(subgroup_number, _p_writer);
+ }
_p_writer->writeCell(pappso::Utils::getLexicalOrderedString(subgroup_number));
_p_writer->clearTableCellStyleRef();
_p_writer->writeCell(p_protein_match->getGrpProteinSp().get()->getGroupingId());
--
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