From 17adc62be0a446237436860527f487867dc1727b Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 26 Oct 2017 17:16:13 +0200
Subject: [PATCH] building new xpip file
---
src/CMakeLists.txt | 5 +-
.../identificationdatasource.cpp | 7 +
.../identificationdatasource.h | 5 +
src/core/msrun.cpp | 5 +
src/core/msrun.h | 4 +
src/gui/main.ui | 23 +++
src/gui/mainwindow.cpp | 43 ++++-
src/gui/mainwindow.h | 1 +
src/output/xpip.cpp | 150 +++++++++++++-----
src/output/xpip.h | 14 +-
src/utils/identificationdatasourcestore.cpp | 2 +
src/utils/types.h | 20 +--
12 files changed, 222 insertions(+), 57 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 4db3e0c0..8dd1aeed 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -85,8 +85,6 @@ SET(CPP_FILES
input/xpipsaxhandler.cpp
input/xtandemparamsaxhandler.cpp
input/xtandemsaxhandler.cpp
- output/masschroqml.cpp
- output/proticdbml.cpp
output/ods/comparbasesheet.cpp
output/ods/comparspecificspectrasheet.cpp
output/ods/comparspectrasheet.cpp
@@ -100,6 +98,9 @@ SET(CPP_FILES
output/ods/samplesheet.cpp
output/ods/simplesheet.cpp
output/ods/spectrasheet.cpp
+ output/masschroqml.cpp
+ output/proticdbml.cpp
+ output/xpip.cpp
utils/fastafilestore.cpp
utils/identificationdatasourcestore.cpp
utils/groupstore.cpp
diff --git a/src/core/identification_sources/identificationdatasource.cpp b/src/core/identification_sources/identificationdatasource.cpp
index c49f027c..ca74c073 100644
--- a/src/core/identification_sources/identificationdatasource.cpp
+++ b/src/core/identification_sources/identificationdatasource.cpp
@@ -37,6 +37,7 @@ IdentificationDataSource::IdentificationDataSource(const IdentificationDataSourc
{
_ms_run_sp = other._ms_run_sp;
_resource_name = other._resource_name;
+ _xml_id = other._xml_id;
}
IdentificationDataSource::~IdentificationDataSource()
@@ -44,6 +45,12 @@ IdentificationDataSource::~IdentificationDataSource()
}
+void IdentificationDataSource::setXmlId(const QString xmlid) {
+ _xml_id = xmlid;
+}
+const QString & IdentificationDataSource::getXmlId() const {
+ return _xml_id;
+}
bool IdentificationDataSource::operator==(const IdentificationDataSource& other) const
{
diff --git a/src/core/identification_sources/identificationdatasource.h b/src/core/identification_sources/identificationdatasource.h
index f99f8720..7d23ac48 100644
--- a/src/core/identification_sources/identificationdatasource.h
+++ b/src/core/identification_sources/identificationdatasource.h
@@ -43,6 +43,10 @@ public:
IdentificationDataSource(const IdentificationDataSource& other);
~IdentificationDataSource();
bool operator==(const IdentificationDataSource& other) const;
+
+
+ void setXmlId(const QString xmlid);
+ const QString & getXmlId() const;
/** @brief URL or filename containing identification data
* */
@@ -108,6 +112,7 @@ protected :
IdentificationEngine _engine = IdentificationEngine::unknown;
private :
//static std::map<QString, pappso::MsRunIdSp> _map_msrunidsp;
+ QString _xml_id;
QString _version;
MsRunSp _ms_run_sp = nullptr;
std::map<IdentificationEngineParam, QVariant> _params;
diff --git a/src/core/msrun.cpp b/src/core/msrun.cpp
index 390f27a0..206abdab 100644
--- a/src/core/msrun.cpp
+++ b/src/core/msrun.cpp
@@ -85,6 +85,11 @@ MzFormat MsRun::getMzFormat() const {
void MsRun::setMsRunStatistics(MsRunStatistics param, const QVariant& value) {
_param_stats.insert(std::pair<MsRunStatistics, QVariant>(param, value));
}
+
+const std::map<MsRunStatistics, QVariant> & MsRun::getMsRunStatisticsMap() const {
+ return _param_stats;
+}
+
const QVariant MsRun::getMsRunStatistics(MsRunStatistics param) const {
try {
return _param_stats.at(param);
diff --git a/src/core/msrun.h b/src/core/msrun.h
index ce038fc8..fcba9f99 100644
--- a/src/core/msrun.h
+++ b/src/core/msrun.h
@@ -67,6 +67,10 @@ public:
/** \brief get MS run statistics
*/
virtual const QVariant getMsRunStatistics(MsRunStatistics param) const;
+
+ /** \brief get MS run statistics map
+ */
+ virtual const std::map<MsRunStatistics, QVariant> & getMsRunStatisticsMap() const;
private :
QString _xml_id;
diff --git a/src/gui/main.ui b/src/gui/main.ui
index 0fd652b6..b7bcf935 100644
--- a/src/gui/main.ui
+++ b/src/gui/main.ui
@@ -74,6 +74,7 @@
<addaction name="action_xtandem_run"/>
<addaction name="actionLoad_results"/>
<addaction name="actionLoad"/>
+ <addaction name="action_save_project"/>
<addaction name="separator"/>
<addaction name="menu_export_files"/>
<addaction name="separator"/>
@@ -160,6 +161,11 @@
<string>&X!Tandem run</string>
</property>
</action>
+ <action name="action_save_project">
+ <property name="text">
+ <string>Save project</string>
+ </property>
+ </action>
</widget>
<resources>
<include location="../xtpcpp.qrc"/>
@@ -405,6 +411,22 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>action_save_project</sender>
+ <signal>triggered()</signal>
+ <receiver>Main</receiver>
+ <slot>doActionSaveProject()</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>
@@ -419,5 +441,6 @@
<slot>doActionSpectralCountingMcq()</slot>
<slot>doActionAbout()</slot>
<slot>doActionTandemRun()</slot>
+ <slot>doActionSaveProject()</slot>
</slots>
</ui>
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index 73698b60..169b28a3 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -36,6 +36,7 @@
#include "../utils/utils.h"
#include "workerthread.h"
#include "output/ods/comparspectrasheet.h"
+#include "output/xpip.h"
class TsvNoSheetOutput: public TsvOutputStream {
public :
@@ -71,6 +72,7 @@ MainWindow::MainWindow(QWidget *parent):
ui->menu_export_files->setDisabled(true);
ui->centralwidget->layout()->addWidget(_project_window);
_project_window->hide();
+ ui->action_save_project->setDisabled(true);
ui->default_display_widget->show();
//_protein_list_window = new ProteinListWindow(this);
//QDockWidget *dock = new QDockWidget(tr("Protein List"), this);
@@ -133,9 +135,9 @@ void MainWindow::doDisplayJobFinished(QString message) {
qDebug() << "MainWindow::doDisplayJobFinished " << message;
hideWaitingMessage();
QMessageBox::information(this,
- tr("job finished"), message);
-
-
+ tr("job finished"), message);
+
+
}
void MainWindow::doDisplayLoadingMessage(QString message) {
@@ -237,10 +239,11 @@ void MainWindow::doProjectReady(ProjectSp project_sp) {
ui->menu_export_files->setDisabled(false);
ui->menu_edit->setDisabled(false);
-
-
+
+
_project_window->show();
ui->default_display_widget->hide();
+ ui->action_save_project->setDisabled(false);
qDebug() << "MainWindow::doProjectReady end";
}
@@ -307,6 +310,36 @@ void MainWindow::selectXpipFile() {
}
+
+void MainWindow::doActionSaveProject() {
+ try {
+ QMessageBox::warning(this,
+ tr("Experimental feature"), "WARNING : project files export is not ready");
+ QSettings settings;
+ QString default_location = settings.value("path/xpipfile", "").toString();
+
+
+ QString filename = QFileDialog::getSaveFileName(this, tr("Save XPIP file"),
+ QString("%1/untitled.xpip").arg(default_location),
+ tr("XPIP (*.xpip)"));
+
+ if (filename.isEmpty()) {
+ return;
+ }
+
+ settings.setValue("path/xpipfile", QFileInfo(filename).absolutePath());
+
+ Xpip xpip_file(filename);
+ xpip_file.write(_project_sp);
+ xpip_file.close();
+
+ }
+ catch (pappso::PappsoException & error) {
+ viewError(tr("Error while writing XPIP file :\n%1").arg(error.qwhat()));
+ }
+
+}
+
void MainWindow::doActionSpreadsheet() {
qDebug() << "MainWindow::doActionSpreadsheet begin";
try {
diff --git a/src/gui/mainwindow.h b/src/gui/mainwindow.h
index d0ab7b21..40212223 100644
--- a/src/gui/mainwindow.h
+++ b/src/gui/mainwindow.h
@@ -74,6 +74,7 @@ public slots:
void doActionTandemRun();
void doActionSpreadsheet();
void doActionModifications();
+ void doActionSaveProject();
void doDisplayLoadingMessage(QString message);
void doDisplayLoadingMessagePercent(QString message, int value);
void doDisplayJobFinished(QString message);
diff --git a/src/output/xpip.cpp b/src/output/xpip.cpp
index e9a836e2..662bf0c9 100644
--- a/src/output/xpip.cpp
+++ b/src/output/xpip.cpp
@@ -28,6 +28,8 @@
******************************************************************************/
#include "xpip.h"
+#include "../config.h"
+#include <QDateTime>
#include <pappsomspp/pappsoexception.h>
Xpip::Xpip(const QString & out_filename)
@@ -81,35 +83,36 @@ void Xpip::write(ProjectSp sp_project) {
//xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd"
_output_stream->writeAttribute("http://www.w3.org/2001/XMLSchema-instance","schemaLocation","http://pappso.inra.fr/xsd/xpip/4.0 http://pappso.inra.fr/xsd/xpip-4.0.xsd");
-
- //<information Data_Type="combi" match_number="6807"/>
- // _output_stream->writeStartElement("information");
- // _output_stream->writeAttribute("Data_Type","combi");
- // _output_stream->writeEndElement();
-
- //<filter_params pep_evalue="0.01" prot_evalue="-2.0" pep_number="2" filter_to_all="false" database_filter="/gorgone/pappso/jouy/raw/2013_Orbitrap/2013_07_04_Chanat/contaminants_standarts.fasta"/>
- _output_stream->writeStartElement("filter_params");
- _output_stream->writeAttribute("pep_evalue","combi");
- _output_stream->writeAttribute("prot_evalue","combi");
- _output_stream->writeAttribute("pep_number","combi");
- _output_stream->writeAttribute("filter_to_all","combi");
- _output_stream->writeEndElement();
-
- <identifications>
- <identification>
- <modifs_list_mass>
+
+ //<information Data_Type="combi" match_number="6807"/>
+ // _output_stream->writeStartElement("information");
+ // _output_stream->writeAttribute("Data_Type","combi");
+ // _output_stream->writeEndElement();
+ writeDescription();
+
+ //<filter_params pep_evalue="0.01" prot_evalue="-2.0" pep_number="2" filter_to_all="false" database_filter="/gorgone/pappso/jouy/raw/2013_Orbitrap/2013_07_04_Chanat/contaminants_standarts.fasta"/>
+ //const AutomaticFilterParameters & getAutomaticFilterParameters() const;
+ writeFilterParameters(_sp_project.get()->getAutomaticFilterParameters());
+
+ writeMsrunList(_sp_project.get()->getMsRunStore());
+ writeIdentificationDataSourceList(_sp_project.get()->getIdentificationDataSourceStore());
+ /*
+ <identifications>
+ <identification>
+ <modifs_list_mass>
<modifs_mass modvalue="-18.01056"/>
- <modifs_mass modvalue="-17.02655"/>
- <modifs_mass modvalue="15.99491"/>
- <modifs_mass modvalue="42.01057"/>
- <modifs_mass modvalue="42.01056"/>
- <modifs_mass modvalue="57.02146"/>
- </modifs_list_mass>
- <samples>
- <sample value="20120906_balliau_extract_1_A01_urnb-1"/>
- <sample value="20120906_balliau_extract_1_A02_urzb-1"/>
- </samples>
- //<masschroq>
+ <modifs_mass modvalue="-17.02655"/>
+ <modifs_mass modvalue="15.99491"/>
+ <modifs_mass modvalue="42.01057"/>
+ <modifs_mass modvalue="42.01056"/>
+ <modifs_mass modvalue="57.02146"/>
+ </modifs_list_mass>
+ <samples>
+ <sample value="20120906_balliau_extract_1_A01_urnb-1"/>
+ <sample value="20120906_balliau_extract_1_A02_urzb-1"/>
+ </samples>
+ //<masschroq>
+ */
// <rawdata><!-- time_values_dir="directory" to read retention time corrections-->
_output_stream->writeStartElement("rawdata");
_output_stream->writeComment("time_values_dir=\"directory\" to read retention time corrections");
@@ -135,16 +138,87 @@ void Xpip::write(ProjectSp sp_project) {
_output_stream->writeEndElement();
- writeGroups();
- writeProteinList();
- writePeptideList();
- writeIsotopeLabelList();
- writeAlignments();
- writeQuantificationMethods();
- _output_stream->writeStartElement("quantification");
- writeQuantificationResults();
- writeQuantificationTraces();
- writeQuantify();
+ _output_stream->writeEndDocument();
+}
+void Xpip::writeDoubleAttribute(const QString & attribute, pappso::pappso_double value) {
+ _output_stream->writeAttribute(attribute,QString::number(value, 'f', 10));
+
+}
+void Xpip::writeBooleanAttribute(const QString & attribute, bool value) {
+ if (value) {
+ _output_stream->writeAttribute(attribute,"true");
+ }
+ else {
+ _output_stream->writeAttribute(attribute,"false");
+ }
+
+}
+void Xpip::writeFilterParameters(const AutomaticFilterParameters & filters) {
+
+ _output_stream->writeStartElement("filter_params");
+ writeDoubleAttribute("pep_evalue",filters.getFilterPeptideEvalue());
+ writeDoubleAttribute("prot_evalue",filters.getFilterProteinEvalue());
+ _output_stream->writeAttribute("pep_number",QString("%1").arg(filters.getFilterMinimumPeptidePerMatch()));
+ writeBooleanAttribute("cross_sample",filters.getFilterCrossSamplePeptideNumber());
+ _output_stream->writeEndElement();
+}
+
+void Xpip::writeDescription() {
+
+ _output_stream->writeStartElement("description");
+ _output_stream->writeAttribute("version",XTPCPP_VERSION);
+ writeBooleanAttribute("combine",_sp_project.get()->isCombineMode());
+ _output_stream->writeAttribute("date",QDateTime::currentDateTime().toString( Qt::ISODate));
+ _output_stream->writeEndElement();
+}
+
+
+void Xpip::writeIdentificationDataSourceList(const IdentificationDataSourceStore & ident_store) {
+
+ _output_stream->writeStartElement("identification_source_list");
+ for (const IdentificationDataSourceSp ident_source_sp : ident_store.getIdentificationDataSourceList()) {
+ _output_stream->writeStartElement("identification_source");
+ _output_stream->writeAttribute("id",ident_source_sp.get()->getXmlId());
+ _output_stream->writeAttribute("msrun_id",ident_source_sp.get()->getMsRunSp().get()->getXmlId());
+ //_output_stream->writeAttribute("format",QString("%1").arg(static_cast<std::int8_t>(ident_source_sp.get()->getIdentFormat())));
+ _output_stream->writeAttribute("path",ident_source_sp.get()->getResourceName());
+
+ _output_stream->writeAttribute("engine",QString("%1").arg(static_cast<std::int8_t>(ident_source_sp.get()->getIdentificationEngine())));
+ _output_stream->writeAttribute("version",ident_source_sp.get()->getIdentificationEngineVersion());
+
+ _output_stream->writeEndElement();
+ }
_output_stream->writeEndElement();
+
}
+void Xpip::writeMsrunList(const MsRunStore & msrun_store) {
+
+ _output_stream->writeStartElement("msrun_list");
+ for (const MsRunSp msrun_sp : msrun_store.getMsRunList()) {
+ _output_stream->writeStartElement("msrun");
+ _output_stream->writeAttribute("id",msrun_sp.get()->getXmlId());
+ _output_stream->writeAttribute("name",msrun_sp.get()->getSampleName());
+ _output_stream->writeAttribute("format",QString("%1").arg(static_cast<std::int8_t>(msrun_sp.get()->getMzFormat())));
+ QFileInfo mz_info(msrun_sp.get()->getFilename());
+ if (mz_info.exists()) {
+ _output_stream->writeAttribute("path",msrun_sp.get()->getFilename());
+ }
+ else {
+ _output_stream->writeAttribute("path",mz_info.completeBaseName());
+ }
+ const std::map<MsRunStatistics, QVariant> stats = msrun_sp.get()->getMsRunStatisticsMap();
+ if (stats.size() > 0) {
+ _output_stream->writeStartElement("stats");
+ for (const std::pair<MsRunStatistics, QVariant> stat_pair: stats) {
+ _output_stream->writeStartElement("stat");
+ _output_stream->writeAttribute("key",QString("%1").arg(static_cast<std::int8_t>(stat_pair.first)));
+ _output_stream->writeAttribute("value",stat_pair.second.toString());
+ _output_stream->writeEndElement();
+ }
+ _output_stream->writeEndElement();
+ }
+ _output_stream->writeEndElement();
+ }
+ _output_stream->writeEndElement();
+}
diff --git a/src/output/xpip.h b/src/output/xpip.h
index 2e2f190c..a6636dc7 100644
--- a/src/output/xpip.h
+++ b/src/output/xpip.h
@@ -37,13 +37,23 @@
class Xpip
{
- public:
+public:
Xpip(const QString & out_filename);
~Xpip();
void write(ProjectSp sp_project);
void close();
-
+
+private :
+ void writeFilterParameters(const AutomaticFilterParameters & filters);
+ void writeDescription();
+
+ void writeMsrunList(const MsRunStore & msrun_store);
+ void writeIdentificationDataSourceList(const IdentificationDataSourceStore & ident_store);
+ void writeDoubleAttribute(const QString & attribute, pappso::pappso_double value);
+ void writeBooleanAttribute(const QString & attribute, bool value);
+
+
private :
QFile * _output_file;
QXmlStreamWriter * _output_stream;
diff --git a/src/utils/identificationdatasourcestore.cpp b/src/utils/identificationdatasourcestore.cpp
index c675520b..c01d92ac 100644
--- a/src/utils/identificationdatasourcestore.cpp
+++ b/src/utils/identificationdatasourcestore.cpp
@@ -32,6 +32,7 @@
#include "../core/identification_sources/identificationxtandemfile.h"
#include "../core/identification_sources/identificationpwizfile.h"
#include <pappsomspp/pappsoexception.h>
+#include <pappsomspp/utils.h>
IdentificationDataSourceStore::IdentificationDataSourceStore()
{
@@ -68,6 +69,7 @@ IdentificationDataSourceSp IdentificationDataSourceStore::getInstance(const QStr
if (p_identfile == nullptr) {
throw pappso::PappsoException(QObject::tr("Identification resource %1 not recognized (null pointer)").arg(location));
}
+ p_identfile.get()->setXmlId(QString("ident%1").arg(pappso::Utils::getLexicalOrderedString(_map_identification_data_sources.size())));
_map_identification_data_sources.insert(std::pair< QString, IdentificationDataSourceSp >(location, p_identfile));
_map_identification_data_sources.insert(std::pair< QString, IdentificationDataSourceSp >(location_file.absoluteFilePath(), p_identfile));
diff --git a/src/utils/types.h b/src/utils/types.h
index 619d3b7c..68c5507b 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -43,11 +43,11 @@ enum class ExternalDatabase: std::int8_t {
/** \def IdentificationEngine identification engine
*
*/
-enum class IdentificationEngine {
- unknown, ///< X!Tandem
- XTandem, ///< X!Tandem
- mascot, ///< Mascot
- peptider ///< peptider
+enum class IdentificationEngine: std::int8_t {
+ unknown=0, ///< X!Tandem
+ XTandem=1, ///< X!Tandem
+ mascot=2, ///< Mascot
+ peptider=3 ///< peptider
};
/** \def PeptideMatchParam peptide match specific parameters
@@ -102,11 +102,11 @@ enum class GroupingType {
*
*/
-enum class MzFormat {
- unknown, ///< unknown format
- mzML, ///< mzML
- mzXML, ///< mzXML
- MGF, ///< Mascot format
+enum class MzFormat: std::int8_t {
+ unknown=0, ///< unknown format
+ mzML=1, ///< mzML
+ mzXML=2, ///< mzXML
+ MGF=3, ///< Mascot format
};
/** \def ValidationState
--
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