Commit fc112332 authored by Langella Olivier's avatar Langella Olivier
Browse files

using pwiz xic extractor without MsRunXic object

parent a30ba4d4
......@@ -230,7 +230,7 @@ void XicBox::setPeptideEvidenceInMsRun(const PeptideEvidence * p_peptide_evidenc
}
void XicBox::setXic(std::vector< pappso::MsRunXicSp> xic_sp_list) {
void XicBox::setXic(std::vector< pappso::XicSp> xic_sp_list) {
qDebug() << "XicBox::setXic begin " << xic_sp_list.size();
ui->xic_widget->clear();
for (int i=0; i < xic_sp_list.size(); i++) {
......
......@@ -35,7 +35,6 @@
#include "../../../utils/types.h"
#include "../../../core/peptideevidence.h"
#include "../xicwindow.h"
#include <pappsomspp/xicextractor/msrunxic.h>
#include <pappsomspp/peptide/peptidenaturalisotopelist.h>
#include <qcustomplot.h>
......@@ -71,7 +70,7 @@ signals :
private slots:
void remove();
void reExtractXic();
void setXic(std::vector< pappso::MsRunXicSp> xic_sp_list);
void setXic(std::vector< pappso::XicSp> xic_sp_list);
void setIsotopeMassList(std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list);
void error(QString error_message);
void extractXicInOtherMsRun();
......
......@@ -39,7 +39,7 @@ void XicWorkerThread::doXicLoad(MsRunSp p_msrun, std::vector<pappso::mz> mz_list
for (pappso::mz mass:mz_list) {
mass_list.push_back(pappso::MassRange(mass, precision));
}
std::vector<pappso::MsRunXicSp> xic_sp_list = SpectrumStore::getXicSpFromMsRunSp(p_msrun.get(), mass_list, method);
std::vector<pappso::XicSp> xic_sp_list = SpectrumStore::getXicSpFromMsRunSp(p_msrun.get(), mass_list, method);
emit xicLoaded(xic_sp_list);
......
......@@ -29,10 +29,10 @@
#ifndef XICWORKERTHREAD_H
#define XICWORKERTHREAD_H
#include <pappsomspp/xicextractor/msrunxic.h>
#include <pappsomspp/peptide/peptidenaturalisotopelist.h>
#include<QObject>
#include "../../core/msrun.h"
#include <pappsomspp/xic/xic.h>
class XicWorkerThread : public QObject
{
......@@ -44,7 +44,7 @@ public slots:
void doComputeIsotopeMassList(pappso::PeptideSp peptide_sp, unsigned int charge, pappso::PrecisionP precision, double minimum_isotope_pattern_ratio);
signals:
void xicLoaded(std::vector<pappso::MsRunXicSp> xic_sp_list);
void xicLoaded(std::vector<pappso::XicSp> xic_sp_list);
void isotopeMassListComputed(std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list);
void operationFailed(QString error);
......
......@@ -39,7 +39,7 @@ int main(int argc, char *argv[])
qRegisterMetaType<TandemRunBatch>("TandemRunBatch");
qRegisterMetaType<std::vector<pappso::mz>>("std::vector<pappso::mz>");
qRegisterMetaType<pappso::PrecisionP>("pappso::PrecisionP");
qRegisterMetaType<std::vector<pappso::MsRunXicSp>>("std::vector<pappso::MsRunXicSp>");
qRegisterMetaType<std::vector<pappso::XicSp>>("std::vector<pappso::XicSp>");
qRegisterMetaType<pappso::PeptideSp>("pappso::PeptideSp");
qRegisterMetaType<pappso::XicExtractMethod>("pappso::XicExtractMethod");
qRegisterMetaType<pappso::SpectrumSp>("pappso::SpectrumSp");
......
......@@ -160,7 +160,7 @@ void ComparBaseSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
}
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ ;
/*
if (!_first_cell_coordinate.isEmpty()) {
QString last_cell_coordinate = _p_writer->getOdsCellCoordinate();
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " << _first_cell_coordinate<< " " << last_cell_coordinate;
......@@ -168,7 +168,7 @@ void ComparBaseSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
_p_writer->addColorScale(color_scale);
_first_cell_coordinate = "";
}
*/
_p_writer->writeLine();
_p_writer->writeLine();
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " end";
......
......@@ -331,10 +331,10 @@ pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunSp(MsRun * msrun, unsign
}
std::vector<pappso::MsRunXicSp> SpectrumStore::getXicSpFromMsRunSp(MsRun * p_msrun, const std::vector<pappso::MassRange> & mass_range_list, pappso::XicExtractMethod method) {
std::vector<pappso::XicSp> SpectrumStore::getXicSpFromMsRunSp(MsRun * p_msrun, const std::vector<pappso::MassRange> & mass_range_list, pappso::XicExtractMethod method) {
qDebug() << "SpectrumStore::getXicSpFromMsRunSp begin" ;
pappso::MsRunXicExtractorFactory::getInstance().setTmpDir("/tmp");
std::vector<pappso::MsRunXicSp> xic_sp_list;
std::vector<pappso::XicSp> xic_sp_list;
if (p_msrun == nullptr) {
qDebug() << "SpectrumStore::getXicSpFromMsRunSp ERROR p_msrun == nullptr " ;
throw pappso::ExceptionNotFound(QObject::tr("SpectrumStore::getXicSpFromMsRunSp ERROR p_msrun == nullptr"));
......@@ -346,14 +346,14 @@ std::vector<pappso::MsRunXicSp> SpectrumStore::getXicSpFromMsRunSp(MsRun * p_msr
if (p_msdatafile != nullptr) {
auto it = _map_msrun_msrunxicextractor.find(p_msrun);
if (it == _map_msrun_msrunxicextractor.end()) {
pappso::MsRunXicExtractorSp extractor = pappso::MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorDiskSp(*p_msrun);
pappso::MsRunXicExtractorSp extractor = pappso::MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorPwizSp(*p_msrun);
_map_msrun_msrunxicextractor.insert(std::pair<MsRun *, pappso::MsRunXicExtractorSp>(p_msrun, extractor));
extractor->setXicExtractMethod(method);
return extractor.get()->getMsRunXicSpList(mass_range_list);
return extractor.get()->getXicSpList(mass_range_list);
}
it->second.get()->setXicExtractMethod(method);
return it->second.get()->getMsRunXicSpList(mass_range_list);
return it->second.get()->getXicSpList(mass_range_list);
}
return (xic_sp_list);
}
......@@ -43,7 +43,7 @@ class MSDataFile;
class SpectrumStore {
public:
static pappso::SpectrumSp getSpectrumSpFromMsRunSp(MsRun * p_msrun, unsigned int scan_num);
static std::vector<pappso::MsRunXicSp> getXicSpFromMsRunSp(MsRun * p_msrun, const std::vector<pappso::MassRange> & mass_range_list, pappso::XicExtractMethod method);
static std::vector<pappso::XicSp> getXicSpFromMsRunSp(MsRun * p_msrun, const std::vector<pappso::MassRange> & mass_range_list, pappso::XicExtractMethod method);
/** @brief try to find MS run statistics
*/
static void checkMsRunStatistics(MsRun *);
......
# cd buildwin64
# cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=../win64/work.cmake ..
set(ODSSTREAM_QT5_FOUND 1)
set(ODSSTREAM_INCLUDE_DIR "/home/langella/developpement/git/libodsstream/src")
set(ODSSTREAM_QT5_LIBRARY "/home/langella/developpement/git/libodsstream/cbuild/src/libodsstream-qt5.so")
set(PAPPSOMSPP_QT5_FOUND 1)
set(PAPPSOMSPP_WIDGET_QT5_FOUND 1)
set(PAPPSOMSPP_INCLUDE_DIR "/home/langella/developpement/git/pappsomspp/src")
set(PAPPSOMSPP_QT5_LIBRARY "/home/langella/developpement/git/pappsomspp/cbuild/src/libpappsomspp-qt5.so")
set(PAPPSOMSPP_WIDGET_QT5_LIBRARY "/home/langella/developpement/git/pappsomspp/cbuild/src/pappsomspp/widget/libpappsomspp-widget-qt5.so")
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment