diff --git a/src/pappsomspp/vendors/tims/timsdata.cpp b/src/pappsomspp/vendors/tims/timsdata.cpp
index 778196d9a598bf9cbca782c431553b358e03de14..32049a491fb7e66fd04f721bdf6de35b6668f5e6 100644
--- a/src/pappsomspp/vendors/tims/timsdata.cpp
+++ b/src/pappsomspp/vendors/tims/timsdata.cpp
@@ -613,7 +613,7 @@ TimsData::getPrecursorsFromMzRtCharge(int charge,
QSqlDatabase qdb = openDatabaseConnection();
QSqlQuery q = qdb.exec(
QString(
- "SELECT Frames.time, Precursors.MonoisotopicMz, Precursors.Charge, "
+ "SELECT Frames.Time, Precursors.MonoisotopicMz, Precursors.Charge, "
"Precursors.Id, Frames.Id, PasefFrameMsMsInfo.ScanNumBegin, "
"PasefFrameMsMsInfo.scanNumEnd "
"FROM Frames "
@@ -622,7 +622,7 @@ TimsData::getPrecursorsFromMzRtCharge(int charge,
"WHERE Precursors.Charge == %1 "
"AND Precursors.MonoisotopicMz > %2 -0.01 "
"AND Precursors.MonoisotopicMz < %2 +0.01 "
- "AND Frames.Time >= %3 "
+ "AND Frames.Time >= %3 -1 "
"AND Frames.Time < %3 +1; ")
.arg(charge)
.arg(mz_val)
diff --git a/src/pappsomspp/vendors/tims/xicextractor/timsdirectxicextractor.cpp b/src/pappsomspp/vendors/tims/xicextractor/timsdirectxicextractor.cpp
index 9e58942bf6a26ef41da32688bef5ddfccf9b2523..9e6acb4c1db19dd0d5c29dfaf9e4a53129a048fa 100644
--- a/src/pappsomspp/vendors/tims/xicextractor/timsdirectxicextractor.cpp
+++ b/src/pappsomspp/vendors/tims/xicextractor/timsdirectxicextractor.cpp
@@ -105,7 +105,7 @@ TimsDirectXicExtractor::extractTimsXicList(
frame_sptr.get()->extractTimsXicListInRtRange(
itXicListbegin, itXicListend, m_xicExtractMethod);
- qInfo() << "" << frame_sptr.get()->getId();
+ qDebug() << "" << frame_sptr.get()->getId();
}
qDebug();
}
diff --git a/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.cpp b/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.cpp
index ed22e8c2d570b84c55f4a10281b1e6d15792307a..c2a79237dc9df6ea6a480211b7a613b3fed82467 100644
--- a/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.cpp
+++ b/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.cpp
@@ -318,7 +318,6 @@ MassSpectrumWidget::plot()
}
else
{
-
_peak_ion_isotope_match_list.sort(
[](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) {
return a.getPeak().y > b.getPeak().y;
@@ -455,3 +454,12 @@ MassSpectrumWidget::computeIsotopeMassList()
}
}
}
+
+void
+pappso::MassSpectrumWidget::highlightPrecursorPeaks(double precursor_mz)
+{
+ if(_ms_level > 1)
+ {
+ _custom_plot->highlightPrecursorPeaks(precursor_mz, _p_ms2_precision);
+ }
+}
diff --git a/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.h b/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.h
index fab9f4783b0cac315786a22df39c291d8f7f49d0..ca240734b2e47ea2eb735b40d942303d064c4e29 100644
--- a/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.h
+++ b/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.h
@@ -68,6 +68,7 @@ class PMSPP_LIB_DECL MassSpectrumWidget : public GraphicDeviceWidget
bool savePdf(const QString &fileName, int width = 0, int height = 0);
void toQPaintDevice(QPaintDevice *device, const QSize &size) override;
+ void highlightPrecursorPeaks(double precursor_mz);
// void setIsotopeMassList(std::vector<pappso::PeptideNaturalIsotopeAverageSp>
// & isotope_mass_list);
diff --git a/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.cpp b/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.cpp
index e95b622e13b2cc46ec7672b6567e6f7571069490..117c801607d3e90d3ceea37aebccfc09425bb09f 100644
--- a/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.cpp
+++ b/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.cpp
@@ -68,6 +68,12 @@ QCPSpectrum::QCPSpectrum(MassSpectrumWidget *parent, bool visible)
_p_peak_bars_isotope->setPen(QPen(red, 1));
_p_peak_bars_isotope->setBrush(QBrush(red));
+ mp_peak_bars_precursor = new QCPBars(xAxis, yAxis);
+ mp_peak_bars_precursor->setWidthType(QCPBars::WidthType::wtAbsolute);
+ mp_peak_bars_precursor->setWidth(_bar_width * 1.5);
+ mp_peak_bars_precursor->setPen(QPen(Qt::cyan, 1));
+ mp_peak_bars_precursor->setVisible(true);
+
connect(this->xAxis,
SIGNAL(rangeChanged(QCPRange)),
this,
@@ -458,3 +464,28 @@ QCPSpectrum::addMs1IsotopePattern(
total_intensity);
}
}
+
+void
+pappso::QCPSpectrum::highlightPrecursorPeaks(double precursor_mz,
+ PrecisionPtr ms2_precision)
+{
+ MzRange range(precursor_mz, ms2_precision);
+
+ for(const DataPoint &peak : *_p_spectrum)
+ {
+ if((peak.x > range.lower()) && (peak.x < range.upper()))
+ {
+ mp_peak_bars_precursor->addData(peak.x, peak.y);
+ QCPItemText *text_label = new QCPItemText(this);
+ text_label->setVisible(true);
+ text_label->setPositionAlignment(Qt::AlignBottom | Qt::AlignHCenter);
+ text_label->position->setType(QCPItemPosition::ptPlotCoords);
+ text_label->position->setCoords(
+ peak.x,
+ peak.y); // place position at center/top of axis rect
+ text_label->setFont(QFont(font().family(), 8));
+ text_label->setText("precursor");
+ text_label->setColor(Qt::cyan);
+ }
+ }
+}
diff --git a/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.h b/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.h
index 1540ca94d173fd99690a962053b7f0210870556e..199886df76708fb5876c4a56312d8554723bfe29 100644
--- a/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.h
+++ b/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.h
@@ -60,6 +60,7 @@ class QCPSpectrum : public QCustomPlot
&isotope_mass_list,
pappso_double intensity);
void addPeakIonIsotopeMatch(const PeakIonIsotopeMatch &peak_ion_match);
+ void highlightPrecursorPeaks(double precursor_mz, PrecisionPtr ms2_precision);
virtual void mouseMoveEvent(QMouseEvent *event) override;
virtual void mousePressEvent(QMouseEvent *event) override;
virtual void mouseReleaseEvent(QMouseEvent *event) override;
@@ -83,6 +84,7 @@ class QCPSpectrum : public QCustomPlot
QCPRange _mass_delta_range;
QCPBars *_p_peak_bars;
QCPBars *_p_peak_bars_isotope;
+ QCPBars *mp_peak_bars_precursor;
std::map<PeptideIon, QCPBars *> _map_ion_type_bars;
QCPAxisRect *_p_delta_axis_rect;
QCPGraph *_p_delta_graph;
diff --git a/tests/test_timsxicextractor.cpp b/tests/test_timsxicextractor.cpp
index f3cc9d7f44bf40a5b8a73a7059f98abfad3fc4d4..99a30cd4babd8625b12747efbea67b0ab0ccdf50 100644
--- a/tests/test_timsxicextractor.cpp
+++ b/tests/test_timsxicextractor.cpp
@@ -42,6 +42,7 @@
#include <pappsomspp/processing/filters/filtersuitestring.h>
#include "config.h"
#include "common.h"
+#include <time.h>
using namespace pappso;
@@ -66,16 +67,16 @@ TEST_CASE("Extracting XIC from timsdata.", "[TimsXicExtractor]")
"200ngHeLaPASEF_2min_compressed.d/analysis.tdf",
"a1");
*/
- pappso::MsFileAccessor accessor(
- "/gorgone/pappso/jouy/raw/2021_Tims_TOF/20210126_HeLa/"
- "1-26-2021_1_QC_HeLa10ng_825.d/analysis.tdf",
- "a1");
- /*
+// pappso::MsFileAccessor accessor(
+// "/gorgone/pappso/jouy/raw/2021_Tims_TOF/20210126_HeLa/"
+// "1-26-2021_1_QC_HeLa10ng_825.d/analysis.tdf",
+// "a1");
+//
pappso::MsFileAccessor accessor(
"/data/test_tdf_quality/2-3-2021_1_HeLa10ng_871.d/analysis.tdf",
"a1");
-*/
+
accessor.setPreferedFileReaderType(pappso::MzFormat::brukerTims,
pappso::FileReaderType::tims_ms2);
@@ -95,24 +96,39 @@ TEST_CASE("Extracting XIC from timsdata.", "[TimsXicExtractor]")
pappso::TimsDataSp tims_data = tims2_reader->getTimsDataSPtr();
- std::vector<std::size_t> precursor_list = {3, 4, 5, 3000, 3001};
+ std::vector<std::size_t> precursor_list = {2159};
+ std::vector<pappso_double> mz_list = {466.738, 467.239};
std::vector<pappso::TimsXicStructure> xic_list;
+ std::vector<pappso::TimsXicStructure> xic_struct_list;
+ clock_t start = clock();
for(auto precursor_id : precursor_list)
{
xic_list.push_back(tims_data.get()->getTimsXicStructureFromPrecursorId(
- precursor_id, PrecisionFactory::getPpmInstance(10.0)));
+ precursor_id, PrecisionFactory::getPpmInstance(30.0)));
}
+ for(pappso::pappso_double mz : mz_list)
+ {
+ pappso::TimsXicStructure new_xic_struct =
+ pappso::TimsXicStructure(xic_list[0]);
+ new_xic_struct.mzRange =
+ pappso::MzRange(mz, PrecisionFactory::getPpmInstance(30.0));
+ new_xic_struct.xicSptr = std::make_shared<Xic>();
+ xic_struct_list.push_back(new_xic_struct);
+ }
tims_data.get()->extractXicListByTimsXicStructureList(
- xic_list, pappso::XicExtractMethod::sum, 100000);
-
- for(auto &&xic_struct : xic_list)
+ xic_struct_list, pappso::XicExtractMethod::sum, 100000);
+
+ qInfo() << QString("Time taken: %1\n").arg((double)(clock() - start)/CLOCKS_PER_SEC);
+ for(auto &&xic_struct : xic_struct_list)
{
REQUIRE(xic_struct.xicSptr.get() != nullptr);
- QFile fileods(QString("tims_xic_%1.ods").arg(xic_struct.precursorId));
+ QFile fileods(QString("/data/test_tdf_quality/tims_xic_%1_%2.ods")
+ .arg(xic_struct.precursorId)
+ .arg(xic_struct.mzRange.getMz()));
OdsDocWriter writer(&fileods);
writer.writeLine();
writer.writeCell("precursorId");