From e0594bd8e4d2d8ce2b6c1ed0b80e55297a619d7d Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Tue, 9 May 2017 17:20:21 +0200
Subject: [PATCH] store mz format
---
src/core/msrun.cpp | 12 +++++++++---
src/core/msrun.h | 1 +
src/utils/readspectrum.cpp | 19 ++++++++++++++++---
src/utils/readspectrum.h | 2 ++
src/utils/types.h | 2 ++
5 files changed, 30 insertions(+), 6 deletions(-)
diff --git a/src/core/msrun.cpp b/src/core/msrun.cpp
index 57ee5eb02..52a6c8998 100644
--- a/src/core/msrun.cpp
+++ b/src/core/msrun.cpp
@@ -49,9 +49,9 @@ MsRun::~MsRun() {
}
- const QString & MsRun::getSampleName() const {
- return _name;
- }
+const QString & MsRun::getSampleName() const {
+ return _name;
+}
void MsRun::setFilename(const QString filename) {
_location = filename;
@@ -69,3 +69,9 @@ const QString & MsRun::getFilename() const {
MzFormat MsRun::getMzFormat() const {
return _mz_format;
}
+
+
+void MsRun::setMzFormat(MzFormat mz_format) {
+ _mz_format = mz_format;
+}
+
diff --git a/src/core/msrun.h b/src/core/msrun.h
index 25ad79b76..a389390a0 100644
--- a/src/core/msrun.h
+++ b/src/core/msrun.h
@@ -54,6 +54,7 @@ public:
const QString & getXmlId() const;
MzFormat getMzFormat() const;
+ void setMzFormat(MzFormat mz_format);
private :
QString _xml_id;
QString _location;
diff --git a/src/utils/readspectrum.cpp b/src/utils/readspectrum.cpp
index b04825222..4bece5340 100644
--- a/src/utils/readspectrum.cpp
+++ b/src/utils/readspectrum.cpp
@@ -27,6 +27,7 @@
#include <QSettings>
#include <QFileInfo>
#include <QDir>
+#include <QString>
#include <pappsomspp/spectrum/spectrum.h>
#include <pappsomspp/exception/exceptionnotfound.h>
@@ -58,6 +59,20 @@ pwiz::msdata::MSDataFile * getPwizMSDataFile(const QString & filename) {
return dataFile;
}
+MzFormat getPwizMSDataFileFormat(pwiz::msdata::MSDataFile * p_ms_data_file) {
+ pwiz::msdata::CVID native_id_format = pwiz::msdata::id::getDefaultNativeIDFormat(*p_ms_data_file);
+ if (native_id_format == pwiz::cv::CVID::MS_Mascot_MGF_format) {
+ return MzFormat::MGF;
+ }
+ if (native_id_format == pwiz::cv::CVID::MS_mzML_format) {
+ return MzFormat::mzML;
+ }
+ if (native_id_format == pwiz::cv::CVID::MS_ISB_mzXML_format) {
+ return MzFormat::mzXML;
+ }
+ throw pappso::PappsoException(QObject::tr(" pwiz::msdata::CVID native_id_format %1 not found").arg(native_id_format));
+ return MzFormat::unknown;
+}
SpectrumSp getSpectrumSpFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, unsigned int scan_num, unsigned int & precursor_charge_state) {
@@ -75,9 +90,6 @@ SpectrumSp getSpectrumSpFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_
else {
// turn our scan numbers into navtieId strings for pwiz
native_id_format = pwiz::msdata::id::getDefaultNativeIDFormat(*p_ms_data_file);
- if (native_id_format == pwiz::cv::CVID::MS_Mascot_MGF_format) {
- scan_num = scan_num-1;
- }
string nativeScanId = pwiz::msdata::id::translateScanNumberToNativeID(native_id_format, QString("%1").arg(scan_num).toStdString());
spectrum_index = spectrum_list_ptr.get()->find(nativeScanId);
}
@@ -202,6 +214,7 @@ pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunSp(MsRunSp msrun, unsign
}
msrun.get()->setFilename(mz_file);
p_msdatafile = getPwizMSDataFile(mz_file);
+ msrun.get()->setMzFormat(getPwizMSDataFileFormat(p_msdatafile));
_map_msrun_msdatafile.insert(std::pair<MsRunSp, pwiz::msdata::MSDataFile *>(msrun, p_msdatafile));
}
else {
diff --git a/src/utils/readspectrum.h b/src/utils/readspectrum.h
index 89eee5bf7..1643e3942 100644
--- a/src/utils/readspectrum.h
+++ b/src/utils/readspectrum.h
@@ -36,6 +36,8 @@ pwiz::msdata::MSDataFile * getPwizMSDataFile(const QString & filename);
pappso::SpectrumSp getSpectrumSpFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, unsigned int scan_num, unsigned int & precursor_charge_state);
+MzFormat getPwizMSDataFileFormat(pwiz::msdata::MSDataFile * p_ms_data_file);
+
class SpectrumStore {
public:
static pappso::SpectrumSp getSpectrumSpFromMsRunSp(MsRunSp msrun, unsigned int scan_num);
diff --git a/src/utils/types.h b/src/utils/types.h
index 7244df994..432f5e157 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -66,8 +66,10 @@ enum class GroupingType {
*/
enum class MzFormat {
+ unknown, ///< unknown format
mzML, ///< mzML
mzXML, ///< mzXML
+ MGF, ///< Mascot format
};
/** \def ValidationState
--
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