From dac373514e2527cb98a8ccce9d56d9008a998294 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Sat, 1 Apr 2017 22:54:33 +0200
Subject: [PATCH] reading spectrum
---
.../identificationdatasource.cpp | 7 ++
.../identificationdatasource.h | 2 +-
.../identificationxtandemfile.cpp | 2 +-
src/gui/peptide_detail_view/peptidewindow.cpp | 20 ++++-
src/gui/peptide_detail_view/peptidewindow.h | 2 +
src/gui/project_view/projectwindow.cpp | 14 +++-
src/utils/readspectrum.cpp | 78 ++++++++++++++++++-
src/utils/readspectrum.h | 17 ++--
8 files changed, 130 insertions(+), 12 deletions(-)
diff --git a/src/core/identification_sources/identificationdatasource.cpp b/src/core/identification_sources/identificationdatasource.cpp
index b8dcb46ba..02b348175 100644
--- a/src/core/identification_sources/identificationdatasource.cpp
+++ b/src/core/identification_sources/identificationdatasource.cpp
@@ -24,6 +24,7 @@
#include "identificationxtandemfile.h"
#include <pappsomspp/pappsoexception.h>
#include <QFileInfo>
+#include "../../utils/readspectrum.h"
IdentificationDataSource::MapIdentificationDataSources IdentificationDataSource::_map_identification_data_sources = []
@@ -86,3 +87,9 @@ void IdentificationDataSource::setMsRunSp (pappso::MsRunIdSp ms_run_sp) {
pappso::MsRunIdSp IdentificationDataSource::getMsRunSp () const {
return (_ms_run_sp);
}
+
+
+pappso::SpectrumSp IdentificationDataSource::getSpectrumSp(unsigned int scan_number) const {
+ pappso::SpectrumSp spectrum_sp = SpectrumStore::getSpectrumSpFromMsRunIdSp(_ms_run_sp, scan_number);
+ return spectrum_sp;
+}
diff --git a/src/core/identification_sources/identificationdatasource.h b/src/core/identification_sources/identificationdatasource.h
index 6b90eff21..ebac8d5c8 100644
--- a/src/core/identification_sources/identificationdatasource.h
+++ b/src/core/identification_sources/identificationdatasource.h
@@ -46,7 +46,7 @@ public:
pappso::MsRunIdSp getMsRunSp () const;
/** @brief get the spectrum with scan number
* */
- virtual pappso::SpectrumSp getSpectrumSp(unsigned int scan_number) const = 0;
+ virtual pappso::SpectrumSp getSpectrumSp(unsigned int scan_number) const;
protected :
QString _resource_name;
diff --git a/src/core/identification_sources/identificationxtandemfile.cpp b/src/core/identification_sources/identificationxtandemfile.cpp
index 41b4d0e32..ec3b44cb2 100644
--- a/src/core/identification_sources/identificationxtandemfile.cpp
+++ b/src/core/identification_sources/identificationxtandemfile.cpp
@@ -41,6 +41,6 @@ bool IdentificationXtandemFile::operator==(const IdentificationXtandemFile& othe
}
pappso::SpectrumSp IdentificationXtandemFile::getSpectrumSp(unsigned int scan_number) const {
- pappso::SpectrumSp spectrum_sp;
+ pappso::SpectrumSp spectrum_sp = IdentificationDataSource::getSpectrumSp(scan_number);
return spectrum_sp;
}
diff --git a/src/gui/peptide_detail_view/peptidewindow.cpp b/src/gui/peptide_detail_view/peptidewindow.cpp
index 9f68d3b54..638bcdc3d 100644
--- a/src/gui/peptide_detail_view/peptidewindow.cpp
+++ b/src/gui/peptide_detail_view/peptidewindow.cpp
@@ -25,7 +25,9 @@
#include "../project_view/projectwindow.h"
#include "ui_peptide_detail_view.h"
#include <pappsomspp/pappsoexception.h>
+#include <pappsomspp/spectrum/qualifiedspectrum.h>
#include <QMessageBox>
+#include <QSettings>
PeptideWindow::PeptideWindow(ProjectWindow *parent):
QMainWindow(parent),
@@ -36,6 +38,15 @@ PeptideWindow::PeptideWindow(ProjectWindow *parent):
/*
*/
+ QSettings settings;
+ QString unit = settings.value("peptideview/precision_unit", "dalton").toString();
+ pappso::mz precision = settings.value("peptideview/precision_value", "0.2").toDouble();
+
+ if (unit == "dalton") {
+ _p_precision = Precision::getDaltonInstance(precision);
+ } else {
+ _p_precision = Precision::getPpmInstance(precision);
+ }
#if QT_VERSION >= 0x050000
// Qt5 code
@@ -86,6 +97,13 @@ void PeptideWindow::updateDisplay() {
void PeptideWindow::setPeptideMatch(PeptideMatch * p_peptide_match) {
_p_peptide_match = p_peptide_match;
- SpectrumSp spectrum = _p_peptide_match->getIdentificationDataSource()->getSpectrumSp(_p_peptide_match->getScan());
+ SpectrumSp spectrum = _p_peptide_match->getIdentificationDataSource()->getSpectrumSp(_p_peptide_match->getScan());
+ pappso::QualifiedSpectrum spectrum_copy;
+ spectrum_copy.setOriginalSpectrumSp(spectrum);
+ ui->spectrumWidget->setQualifiedSpectrum(spectrum_copy);
+
+ pappso::PeptideSp peptide = p_peptide_match->getPeptideXtpSp();
+ ui->spectrumWidget->setPrecision(_p_precision);
+ ui->spectrumWidget->setPeptideSp(peptide);
updateDisplay();
}
diff --git a/src/gui/peptide_detail_view/peptidewindow.h b/src/gui/peptide_detail_view/peptidewindow.h
index 6253878af..cddfc11eb 100644
--- a/src/gui/peptide_detail_view/peptidewindow.h
+++ b/src/gui/peptide_detail_view/peptidewindow.h
@@ -25,6 +25,7 @@
#include <QMainWindow>
#include <QTextDocument>
+#include <pappsomspp/mass_range.h>
#include "../../core/peptidematch.h"
#include "../../core/identificationgroup.h"
@@ -53,6 +54,7 @@ private:
Ui::PeptideDetailView *ui;
ProjectWindow * _p_project_window;
PeptideMatch * _p_peptide_match = nullptr;
+ pappso::PrecisionP _p_precision;
};
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index b1f4fcc7a..57f6c18fe 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -116,7 +116,7 @@ void ProjectWindow::refreshGroup(IdentificationGroup * p_ident_group) {
}
else {
try {
- vector< MsRunIdSp > ms_run_list = p_ident_group->getMsRunIdSpList();
+ vector< pappso::MsRunIdSp > ms_run_list = p_ident_group->getMsRunIdSpList();
ui->sample_number_display->setText(QString("%1").arg(ms_run_list.size()));
ui->group_number_display->setText(QString("%1").arg(p_ident_group->countGroup()));
@@ -251,6 +251,18 @@ void ProjectWindow::setProjectSp(ProjectSp project_sp) {
_protein_list_window_collection.clear();
_p_current_protein_list_window = nullptr;
+ for (auto && p_window :_protein_detail_window_collection) {
+ delete p_window;
+ }
+ _protein_detail_window_collection.clear();
+ _p_current_protein_detail_window = nullptr;
+
+ for (auto && p_window :_peptide_detail_window_collection) {
+ delete p_window;
+ }
+ _peptide_detail_window_collection.clear();
+ _p_current_peptide_detail_window = nullptr;
+
_project_sp = project_sp;
refreshGroup(_project_sp.get()->getCurrentIdentificationGroupP());
//_protein_list_window->setIdentificationGroup(_project_sp.get()->getCurrentIdentificationGroupP());
diff --git a/src/utils/readspectrum.cpp b/src/utils/readspectrum.cpp
index 37944bff5..e44815461 100644
--- a/src/utils/readspectrum.cpp
+++ b/src/utils/readspectrum.cpp
@@ -24,6 +24,9 @@
#include "readspectrum.h"
#include <QDebug>
+#include <QSettings>
+#include <QFileInfo>
+#include <QDir>
#include <pappsomspp/spectrum/spectrum.h>
#include <pappsomspp/exception/exceptionnotfound.h>
@@ -40,7 +43,7 @@ using namespace pappso;
pwiz::msdata::MSDataFile * getPwizMSDataFile(const QString & filename) {
- qDebug() << "getPwizMSDataFile opening file " << filename ;
+ qDebug() << "getPwizMSDataFile opening file " << filename ;
std::string env;
env=setlocale(LC_ALL,"");
struct lconv * lc = localeconv ();
@@ -59,8 +62,8 @@ pwiz::msdata::MSDataFile * getPwizMSDataFile(const QString & filename) {
SpectrumSp getSpectrumSpFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, unsigned int scan_num, unsigned int & precursor_charge_state) {
if (p_ms_data_file == nullptr) {
- SpectrumSp empty;
- return (empty);
+ SpectrumSp empty;
+ return (empty);
}
const bool getBinaryData = true;
@@ -216,3 +219,72 @@ Spectrum readSpectrum(const QString & filename, unsigned int scan_num, unsigned
//qDebug() << " env=" << localeconv () << " lc->decimal_point " << lc->decimal_point;
return spectrum;
}
+
+
+std::map<pappso::MsRunIdSp, pwiz::msdata::MSDataFile *> create_map()
+{
+ std::map<pappso::MsRunIdSp, pwiz::msdata::MSDataFile *> m;
+ return m;
+}
+
+std::map<pappso::MsRunIdSp, pwiz::msdata::MSDataFile *> SpectrumStore::_map_msrun_msdatafile = create_map();
+
+
+const QString SpectrumStore::findMzFile(const QString &filename) {
+
+ QFileInfo file(filename);
+
+ if (file.exists()) {
+ return file.absoluteFilePath();
+ }
+
+ QString basename = file.baseName();
+ QString onlyfilename = file.fileName();
+ QSettings settings;
+ QString path = settings.value("path/mzdatadir", "/gorgone/pappso/formation/Janvier2014/TD/mzXML").toString();
+
+ QDir dir_search(path);
+
+ QFileInfoList files = dir_search.entryInfoList();
+ foreach (QFileInfo file, files) {
+ if (file.isDir()) {
+ qDebug() << "DIR: " << file.fileName();
+ } else {
+ qDebug() << "FILE: " << file.fileName();
+ if (onlyfilename == file.fileName()) {
+ return file.absoluteFilePath();
+ }
+ if (file.fileName().contains(onlyfilename)) {
+ return file.absoluteFilePath();
+ }
+ }
+ }
+ return QString();
+}
+
+pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunIdSp(pappso::MsRunIdSp msrun, unsigned int scan_num) {
+ pappso::SpectrumSp spectrum;
+ pwiz::msdata::MSDataFile * p_msdatafile = nullptr;
+ std::map<pappso::MsRunIdSp, pwiz::msdata::MSDataFile *>::iterator it_msdata = _map_msrun_msdatafile.find(msrun);
+ if (it_msdata == _map_msrun_msdatafile.end()) {
+ //not found
+
+ QString mz_file = findMzFile(msrun.get()->getFilename());
+ if (mz_file.isEmpty()) {
+ qDebug() << "SpectrumStore::getSpectrumSpFromMsRunIdSp ERROR file not found " << msrun.get()->getFilename();
+ return spectrum;
+ }
+ p_msdatafile = getPwizMSDataFile(mz_file);
+ _map_msrun_msdatafile.insert(std::pair<pappso::MsRunIdSp, pwiz::msdata::MSDataFile *>(msrun, p_msdatafile));
+ }
+ else {
+ p_msdatafile =it_msdata->second;
+ }
+ if (p_msdatafile == nullptr) {
+ return spectrum;
+ }
+ unsigned int precursor_charge_state;
+ spectrum = getSpectrumSpFromPwizMSDataFile(p_msdatafile, scan_num, precursor_charge_state);
+ return spectrum;
+
+}
diff --git a/src/utils/readspectrum.h b/src/utils/readspectrum.h
index da0cfeb53..919f7bd80 100644
--- a/src/utils/readspectrum.h
+++ b/src/utils/readspectrum.h
@@ -26,15 +26,22 @@
#include <QString>
#include <pappsomspp/spectrum/spectrum.h>
-
+#include <pappsomspp/msrun/msrunid.h>
#include <pwiz/data/msdata/MSDataFile.hpp>
+#include <map>
-using namespace pappso;
-
-Spectrum readSpectrum(const QString & filename, unsigned int scan_num,unsigned int & precursor_charge_state);
+pappso::Spectrum readSpectrum(const QString & filename, unsigned int scan_num,unsigned int & precursor_charge_state);
pwiz::msdata::MSDataFile * getPwizMSDataFile(const QString & filename);
-SpectrumSp getSpectrumSpFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, unsigned int scan_num, unsigned int & precursor_charge_state);
+pappso::SpectrumSp getSpectrumSpFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, unsigned int scan_num, unsigned int & precursor_charge_state);
+class SpectrumStore {
+public:
+ static pappso::SpectrumSp getSpectrumSpFromMsRunIdSp(pappso::MsRunIdSp msrun, unsigned int scan_num);
+private:
+ static const QString findMzFile(const QString &filename);
+private:
+ static std::map<pappso::MsRunIdSp, pwiz::msdata::MSDataFile *> _map_msrun_msdatafile;
+};
#endif // READSPECTRUM_H
--
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