From 8daacc98c00e72dc1609143b88d413e538674ada Mon Sep 17 00:00:00 2001
From: "Filippo Rusconi (Uploading Debian Developer)" <lopippo@debian.org>
Date: Fri, 4 Nov 2022 11:43:53 +0100
Subject: [PATCH 1/6] Import new versions from the qt6olivier branch.
---
src/pappsomspp/msfile/msfileaccessor.cpp | 9 +-
src/pappsomspp/peptide/peptide.cpp | 16 +
src/pappsomspp/peptide/peptide.h | 11 +-
.../peptide/peptidenaturalisotope.h | 2 +-
.../peptide/peptidenaturalisotopeaverage.cpp | 34 ++
.../peptide/peptidenaturalisotopeaverage.h | 11 +-
.../detection/tracedetectioninterface.h | 11 +-
.../detection/tracedetectionmoulon.cpp | 5 +-
.../detection/tracedetectionmoulon.h | 3 +-
.../detection/tracedetectionzivy.cpp | 5 +-
.../processing/detection/tracedetectionzivy.h | 17 +-
.../processing/detection/tracepeak.cpp | 53 +++
.../processing/detection/tracepeak.h | 54 ++-
src/pappsomspp/psm/features/psmfeatures.cpp | 313 +++++++++++++++++-
src/pappsomspp/psm/features/psmfeatures.h | 103 +++++-
src/pappsomspp/psm/peakionisotopematch.cpp | 60 +++-
src/pappsomspp/psm/peakionisotopematch.h | 12 +
src/pappsomspp/psm/peakionmatch.cpp | 54 +++
src/pappsomspp/psm/peakionmatch.h | 39 +--
.../psm/peptideisotopespectrummatch.cpp | 110 ++++--
.../psm/peptideisotopespectrummatch.h | 28 +-
src/pappsomspp/psm/peptidespectrummatch.h | 2 +-
.../psm/xtandem/xtandemhyperscore.cpp | 8 +-
src/pappsomspp/trace/trace.cpp | 29 ++
src/pappsomspp/trace/trace.h | 8 +-
src/pappsomspp/vendors/tims/timsframebase.cpp | 65 ++++
src/pappsomspp/vendors/tims/timsframebase.h | 11 +
.../massspectrumwidget/massspectrumwidget.cpp | 13 +-
.../massspectrumwidget/massspectrumwidget.h | 2 +-
.../widget/massspectrumwidget/qcpspectrum.cpp | 12 +-
.../widget/plotwidget/basetraceplotwidget.cpp | 3 -
src/pappsomspp/widget/xicwidget/qcpxic.cpp | 28 +-
src/pappsomspp/widget/xicwidget/qcpxic.h | 2 +-
src/pappsomspp/widget/xicwidget/xicwidget.cpp | 6 +-
src/pappsomspp/widget/xicwidget/xicwidget.h | 2 +-
src/pappsomspp/xic/xic.cpp | 4 +
src/pappsomspp/xic/xic.h | 1 +
.../xicextractor/msrunxicextractorfactory.cpp | 3 -
tests/test_psm.cpp | 242 +++++++++++++-
tests/test_xic.cpp | 67 ++--
40 files changed, 1234 insertions(+), 224 deletions(-)
diff --git a/src/pappsomspp/msfile/msfileaccessor.cpp b/src/pappsomspp/msfile/msfileaccessor.cpp
index caeab30ae..f37ef669e 100644
--- a/src/pappsomspp/msfile/msfileaccessor.cpp
+++ b/src/pappsomspp/msfile/msfileaccessor.cpp
@@ -7,7 +7,7 @@
#include "msfileaccessor.h"
#include "pwizmsfilereader.h"
-//#include "timsmsfilereader.h"
+#include "timsmsfilereader.h"
#include "xymsfilereader.h"
@@ -16,8 +16,8 @@
#include "../utils.h"
#include "../msrun/msrunid.h"
#include "../msrun/private/pwizmsrunreader.h"
-//#include "../msrun/private/timsmsrunreader.h"
-//#include "../msrun/private/timsmsrunreaderms2.h"
+#include "../msrun/private/timsmsrunreader.h"
+#include "../msrun/private/timsmsrunreaderms2.h"
#include "../msrun/xymsrunreader.h"
@@ -260,8 +260,6 @@ MsFileAccessor::buildMsRunReaderSPtr(
QObject::tr("unable to build a reader for %1 : unknown file format")
.arg(QFileInfo(ms_run_id.get()->getFileName()).absoluteFilePath())));
}
-#if 0
-// Remove this section because it cripples my work on Qt6 build
else if(file_format == MzFormat::brukerTims)
{
@@ -278,7 +276,6 @@ MsFileAccessor::buildMsRunReaderSPtr(
qDebug() << "by default, build a TimsMsRunReader.";
return std::make_shared<TimsMsRunReader>(ms_run_id);
}
-#endif
else
{
qDebug() << "Returning a PwizMsRunReader .";
diff --git a/src/pappsomspp/peptide/peptide.cpp b/src/pappsomspp/peptide/peptide.cpp
index db6deba79..28745eea1 100644
--- a/src/pappsomspp/peptide/peptide.cpp
+++ b/src/pappsomspp/peptide/peptide.cpp
@@ -39,6 +39,22 @@
namespace pappso
{
+bool
+peptideIonTypeIsComplement(PeptideIon ion_type_ref, PeptideIon ion_type)
+{
+ if(peptideIonIsNter(ion_type))
+ std::swap(ion_type_ref, ion_type);
+ if(peptideIonIsNter(ion_type))
+ return false;
+ if((ion_type_ref == PeptideIon::b) && (ion_type == PeptideIon::y))
+ return true;
+ if((ion_type_ref == PeptideIon::ao) && (ion_type == PeptideIon::yo))
+ return true;
+ if((ion_type_ref == PeptideIon::bstar) && (ion_type == PeptideIon::ystar))
+ return true;
+
+ return false;
+}
bool
peptideIonIsNter(PeptideIon ion_type)
diff --git a/src/pappsomspp/peptide/peptide.h b/src/pappsomspp/peptide/peptide.h
index 82db6a9f5..22fd740ca 100644
--- a/src/pappsomspp/peptide/peptide.h
+++ b/src/pappsomspp/peptide/peptide.h
@@ -52,14 +52,21 @@ enum class PeptideDirection : std::int8_t
/** \brief tells if an ion is Nter
* \param ion_type the ion to test
*/
-bool peptideIonIsNter(PeptideIon ion_type);
+PMSPP_LIB_DECL bool peptideIonIsNter(PeptideIon ion_type);
+
+/** \brief tells if an ion type is the complement ion of the other
+ * \param ion_type_ref the ion type reference
+ * \param ion_type the ion to test
+ */
+PMSPP_LIB_DECL bool peptideIonTypeIsComplement(PeptideIon ion_type_ref,
+ PeptideIon ion_type);
/** \brief get the direction of a peptide ion
* \param ion_type the ion to test
* \return the peptide direction
*/
-PeptideDirection getPeptideIonDirection(PeptideIon ion_type);
+PMSPP_LIB_DECL PeptideDirection getPeptideIonDirection(PeptideIon ion_type);
enum class PeptideIonNter
{
diff --git a/src/pappsomspp/peptide/peptidenaturalisotope.h b/src/pappsomspp/peptide/peptidenaturalisotope.h
index b55eaeb38..bce9b9602 100644
--- a/src/pappsomspp/peptide/peptidenaturalisotope.h
+++ b/src/pappsomspp/peptide/peptidenaturalisotope.h
@@ -48,7 +48,7 @@ class PMSPP_LIB_DECL PeptideNaturalIsotope : public PeptideInterface
PeptideNaturalIsotope(const PeptideInterfaceSp &peptide,
const std::map<Isotope, int> &map_isotope);
PeptideNaturalIsotope(const PeptideNaturalIsotope &other);
- ~PeptideNaturalIsotope();
+ virtual ~PeptideNaturalIsotope();
virtual unsigned int size() const override;
virtual const QString getSequence() const override;
diff --git a/src/pappsomspp/peptide/peptidenaturalisotopeaverage.cpp b/src/pappsomspp/peptide/peptidenaturalisotopeaverage.cpp
index 6d54a05b1..90a4deac1 100644
--- a/src/pappsomspp/peptide/peptidenaturalisotopeaverage.cpp
+++ b/src/pappsomspp/peptide/peptidenaturalisotopeaverage.cpp
@@ -29,6 +29,28 @@
namespace pappso
{
+
+
+PeptideNaturalIsotopeAverage::PeptideNaturalIsotopeAverage(
+ const PeptideInterfaceSp &peptide,
+ unsigned int isotopeNumber,
+ unsigned int charge,
+ PrecisionPtr precision)
+ : mcsp_peptideSp(peptide),
+ m_isotopeLevel(isotopeNumber),
+ m_isotopeRank(1),
+ m_z(charge),
+ mp_precision(precision)
+{
+
+ m_peptideNaturalIsotopeSpList.clear();
+
+ double diffC13 = ((double)isotopeNumber * DIFFC12C13) / (double)charge;
+
+ m_averageMz = peptide.get()->getMz(charge) + diffC13;
+ m_abundanceRatio = 0;
+}
+
PeptideNaturalIsotopeAverage::PeptideNaturalIsotopeAverage(
const PeptideInterfaceSp &peptide,
unsigned int askedIsotopeRank,
@@ -161,6 +183,7 @@ PeptideNaturalIsotopeAverage::PeptideNaturalIsotopeAverage(
: mcsp_peptideSp(other.mcsp_peptideSp), mp_precision(other.mp_precision)
{
+ qDebug();
m_peptideNaturalIsotopeSpList = other.m_peptideNaturalIsotopeSpList;
m_averageMz = other.m_averageMz;
@@ -168,6 +191,7 @@ PeptideNaturalIsotopeAverage::PeptideNaturalIsotopeAverage(
m_isotopeLevel = other.m_isotopeLevel;
m_isotopeRank = other.m_isotopeRank;
m_z = other.m_z;
+ qDebug();
}
PeptideNaturalIsotopeAverage::~PeptideNaturalIsotopeAverage()
@@ -237,4 +261,14 @@ PeptideNaturalIsotopeAverage::isEmpty() const
return (m_peptideNaturalIsotopeSpList.size() == 0);
}
+QString
+PeptideNaturalIsotopeAverage::toString() const
+{
+ return QString("%1 l%2 mz%3 z%4 N%5")
+ .arg(getPeptideInterfaceSp().get()->getSequence())
+ .arg(getPeptideInterfaceSp().get()->size())
+ .arg(getMz())
+ .arg(getCharge())
+ .arg(getIsotopeNumber());
+}
} // namespace pappso
diff --git a/src/pappsomspp/peptide/peptidenaturalisotopeaverage.h b/src/pappsomspp/peptide/peptidenaturalisotopeaverage.h
index c84556e4c..c06ca0232 100644
--- a/src/pappsomspp/peptide/peptidenaturalisotopeaverage.h
+++ b/src/pappsomspp/peptide/peptidenaturalisotopeaverage.h
@@ -42,6 +42,14 @@ typedef std::shared_ptr<const PeptideNaturalIsotopeAverage>
class PMSPP_LIB_DECL PeptideNaturalIsotopeAverage
{
public:
+ /** @brief fast constructor
+ * simple isotope build, not computing isotope ratio
+ */
+ PeptideNaturalIsotopeAverage(const PeptideInterfaceSp &peptide,
+ unsigned int isotopeNumber,
+ unsigned int charge,
+ PrecisionPtr precision);
+
PeptideNaturalIsotopeAverage(const PeptideInterfaceSp &peptide,
unsigned int askedIsotopeRank,
unsigned int isotopeLevel,
@@ -54,7 +62,7 @@ class PMSPP_LIB_DECL PeptideNaturalIsotopeAverage
PrecisionPtr precision);
PeptideNaturalIsotopeAverage(const PeptideNaturalIsotopeAverage &other);
- ~PeptideNaturalIsotopeAverage();
+ virtual ~PeptideNaturalIsotopeAverage();
PeptideNaturalIsotopeAverageSp makePeptideNaturalIsotopeAverageSp() const;
pappso_double getMz() const;
@@ -67,6 +75,7 @@ class PMSPP_LIB_DECL PeptideNaturalIsotopeAverage
PrecisionPtr getPrecision() const;
virtual bool matchPeak(pappso_double peak_mz) const final;
bool isEmpty() const;
+ virtual QString toString() const;
private:
void recursiveDepletion(std::vector<PeptideNaturalIsotopeSp> &v_isotope_list,
diff --git a/src/pappsomspp/processing/detection/tracedetectioninterface.h b/src/pappsomspp/processing/detection/tracedetectioninterface.h
index 52aa045bd..114c9cd85 100644
--- a/src/pappsomspp/processing/detection/tracedetectioninterface.h
+++ b/src/pappsomspp/processing/detection/tracedetectioninterface.h
@@ -43,8 +43,15 @@ class TraceDetectionSinkInterface
class TraceDetectionInterface
{
public:
- virtual void detect(const Trace &xic,
- TraceDetectionSinkInterface &sink) const = 0;
+ /** @brief detect peaks on a trace
+ * @param trace the trace to detect peaks on
+ * @param sink the object to store peaks or stream it
+ * @param remove_peak_base if true, removes the area under the base of the
+ * peak
+ */
+ virtual void detect(const Trace &trace,
+ TraceDetectionSinkInterface &sink,
+ bool remove_peak_base) const = 0;
};
diff --git a/src/pappsomspp/processing/detection/tracedetectionmoulon.cpp b/src/pappsomspp/processing/detection/tracedetectionmoulon.cpp
index 2fb3ed76f..a3c275c7b 100644
--- a/src/pappsomspp/processing/detection/tracedetectionmoulon.cpp
+++ b/src/pappsomspp/processing/detection/tracedetectionmoulon.cpp
@@ -84,7 +84,8 @@ TraceDetectionMoulon::getTicStop() const
void
TraceDetectionMoulon::detect(const Trace &xic,
- TraceDetectionSinkInterface &sink) const
+ TraceDetectionSinkInterface &sink,
+ bool remove_peak_base) const
{
Trace xic_smoothed(xic);
@@ -138,7 +139,7 @@ TraceDetectionMoulon::detect(const Trace &xic,
if(banked)
{
- TracePeak peak(it_begin, it + 1);
+ TracePeak peak(it_begin, it + 1, remove_peak_base);
sink.setTracePeak(peak);
}
banked = false;
diff --git a/src/pappsomspp/processing/detection/tracedetectionmoulon.h b/src/pappsomspp/processing/detection/tracedetectionmoulon.h
index d144048c4..22dd6d402 100644
--- a/src/pappsomspp/processing/detection/tracedetectionmoulon.h
+++ b/src/pappsomspp/processing/detection/tracedetectionmoulon.h
@@ -56,7 +56,8 @@ class PMSPP_LIB_DECL TraceDetectionMoulon : public TraceDetectionInterface
void detect(const Trace &xic,
- TraceDetectionSinkInterface &sink) const override;
+ TraceDetectionSinkInterface &sink,
+ bool remove_peak_base) const override;
};
diff --git a/src/pappsomspp/processing/detection/tracedetectionzivy.cpp b/src/pappsomspp/processing/detection/tracedetectionzivy.cpp
index db3dd951d..e72c72ecd 100644
--- a/src/pappsomspp/processing/detection/tracedetectionzivy.cpp
+++ b/src/pappsomspp/processing/detection/tracedetectionzivy.cpp
@@ -107,7 +107,8 @@ TraceDetectionZivy::getDetectionThresholdOnMaxmin() const
void
TraceDetectionZivy::detect(const Trace &xic,
- TraceDetectionSinkInterface &sink) const
+ TraceDetectionSinkInterface &sink,
+ bool remove_peak_base) const
{
// detect peak positions on close curve : a peak is an intensity value
@@ -214,7 +215,7 @@ TraceDetectionZivy::detect(const Trace &xic,
// peak.setMaxXicElement(*maxYDataPoint(it, xic_position));
// areaTrace()
- TracePeak peak(it, xic_position);
+ TracePeak peak(it, xic_position, remove_peak_base);
sink.setTracePeak(peak);
// }
//++i;
diff --git a/src/pappsomspp/processing/detection/tracedetectionzivy.h b/src/pappsomspp/processing/detection/tracedetectionzivy.h
index 3ec699efa..a2a44be3a 100644
--- a/src/pappsomspp/processing/detection/tracedetectionzivy.h
+++ b/src/pappsomspp/processing/detection/tracedetectionzivy.h
@@ -35,12 +35,6 @@ namespace pappso
class PMSPP_LIB_DECL TraceDetectionZivy : public TraceDetectionInterface
{
- private:
- FilterMorphoMean m_smooth;
- FilterMorphoMinMax m_minMax;
- FilterMorphoMaxMin m_maxMin;
- pappso_double m_detectionThresholdOnMinMax;
- pappso_double m_detectionThresholdOnMaxMin;
public:
TraceDetectionZivy(unsigned int smoothing_half_window_length,
@@ -65,7 +59,16 @@ class PMSPP_LIB_DECL TraceDetectionZivy : public TraceDetectionInterface
pappso_double getDetectionThresholdOnMaxmin() const;
void detect(const Trace &xic,
- TraceDetectionSinkInterface &sink) const override;
+ TraceDetectionSinkInterface &sink,
+ bool remove_peak_base) const override;
+
+
+ private:
+ FilterMorphoMean m_smooth;
+ FilterMorphoMinMax m_minMax;
+ FilterMorphoMaxMin m_maxMin;
+ pappso_double m_detectionThresholdOnMinMax;
+ pappso_double m_detectionThresholdOnMaxMin;
};
} // namespace pappso
diff --git a/src/pappsomspp/processing/detection/tracepeak.cpp b/src/pappsomspp/processing/detection/tracepeak.cpp
index 68c04b32f..5bb4c0128 100644
--- a/src/pappsomspp/processing/detection/tracepeak.cpp
+++ b/src/pappsomspp/processing/detection/tracepeak.cpp
@@ -31,6 +31,7 @@ namespace pappso
TracePeak::TracePeak()
{
}
+
TracePeak::TracePeak(std::vector<DataPoint>::const_iterator it_begin,
std::vector<DataPoint>::const_iterator it_end)
{
@@ -41,6 +42,24 @@ TracePeak::TracePeak(std::vector<DataPoint>::const_iterator it_begin,
m_area = areaTrace(it_begin, it_end);
}
+TracePeak::TracePeak(std::vector<DataPoint>::const_iterator it_begin,
+ std::vector<DataPoint>::const_iterator it_end,
+ bool remove_base)
+{
+
+ m_left = *it_begin;
+ m_right = *(it_end - 1);
+ m_max = *maxYDataPoint(it_begin, it_end);
+ m_area = areaTrace(it_begin, it_end);
+ if(remove_base)
+ {
+ // remove the base of this peak
+ m_area -= std::min(m_left.y, m_right.y) * (m_right.x - m_left.x);
+ if(m_area < 0)
+ m_area = 0;
+ }
+}
+
TracePeak::TracePeak(const TracePeak &other)
{
m_area = other.m_area;
@@ -117,4 +136,38 @@ TracePeak::containsRt(pappso::pappso_double rt) const
return (false);
}
+
+const DataPoint &
+TracePeak::getMaxXicElement() const
+{
+ return m_max;
+}
+
+const DataPoint &
+TracePeak::getLeftBoundary() const
+{
+ return m_left;
+}
+
+
+bool
+TracePeak::operator==(const TracePeak &other) const
+{
+ return ((m_area == other.m_area) && (m_max == other.m_max) &&
+ (m_left == other.m_left) && (m_right == other.m_right));
+}
+
+TracePeak &
+TracePeak::operator=(const TracePeak &other)
+{
+ if(this == &other)
+ return *this;
+
+ m_area = other.m_area;
+ m_max = other.m_max;
+ m_left = other.m_left;
+ m_right = other.m_right;
+
+ return *this;
+}
} // namespace pappso
diff --git a/src/pappsomspp/processing/detection/tracepeak.h b/src/pappsomspp/processing/detection/tracepeak.h
index 372359260..abfbafb4d 100644
--- a/src/pappsomspp/processing/detection/tracepeak.h
+++ b/src/pappsomspp/processing/detection/tracepeak.h
@@ -38,18 +38,22 @@ typedef std::shared_ptr<const TracePeak> TracePeakCstSPtr;
* */
class PMSPP_LIB_DECL TracePeak
{
- protected:
- pappso_double m_area = 0;
- DataPoint m_max;
- DataPoint m_left;
- DataPoint m_right;
-
public:
TracePeak();
/** @brief construct a peak given a trace, begin and end x coordinate
*/
TracePeak(std::vector<DataPoint>::const_iterator it_begin,
std::vector<DataPoint>::const_iterator it_end);
+
+ /** @brief construct a peak given a trace, begin and end x coordinate
+ *
+ * @param it_begin begining of trace
+ * @param it_end end of trace
+ * @param remove_base if true, remove the base peak signal
+ */
+ TracePeak(std::vector<DataPoint>::const_iterator it_begin,
+ std::vector<DataPoint>::const_iterator it_end,
+ bool remove_base);
TracePeak(const TracePeak &other);
~TracePeak();
@@ -57,50 +61,34 @@ class PMSPP_LIB_DECL TracePeak
TracePeakCstSPtr makeTracePeakCstSPtr() const;
DataPoint &getMaxXicElement();
- const DataPoint &
- getMaxXicElement() const
- {
- return m_max;
- };
+ const DataPoint &getMaxXicElement() const;
void setMaxXicElement(const DataPoint &max);
DataPoint &getLeftBoundary();
- const DataPoint &
- getLeftBoundary() const
- {
- return m_left;
- };
+ const DataPoint &getLeftBoundary() const;
void setLeftBoundary(const DataPoint &left);
DataPoint &getRightBoundary();
const DataPoint &getRightBoundary() const;
void setRightBoundary(const DataPoint &right);
pappso_double getArea() const;
+
+
void setArea(pappso_double area);
bool containsRt(pappso::pappso_double rt) const;
- bool
- operator==(const TracePeak &other) const
- {
- return ((m_area == other.m_area) && (m_max == other.m_max) &&
- (m_left == other.m_left) && (m_right == other.m_right));
- };
+ bool operator==(const TracePeak &other) const;
- TracePeak &
- operator=(const TracePeak &other)
- {
- if(this == &other)
- return *this;
+ TracePeak &operator=(const TracePeak &other);
- m_area = other.m_area;
- m_max = other.m_max;
- m_left = other.m_left;
- m_right = other.m_right;
- return *this;
- }
+ protected:
+ pappso_double m_area = 0;
+ DataPoint m_max;
+ DataPoint m_left;
+ DataPoint m_right;
};
diff --git a/src/pappsomspp/psm/features/psmfeatures.cpp b/src/pappsomspp/psm/features/psmfeatures.cpp
index ecb34f06f..fd8b4923b 100644
--- a/src/pappsomspp/psm/features/psmfeatures.cpp
+++ b/src/pappsomspp/psm/features/psmfeatures.cpp
@@ -28,24 +28,26 @@
#include "psmfeatures.h"
#include <memory>
+#include <cmath>
using namespace pappso;
-PsmFeatures::PsmFeatures()
+PsmFeatures::PsmFeatures(PrecisionPtr ms2precision, double minimumMz)
{
- m_ms2precision = PrecisionFactory::getDaltonInstance(0.02);
+ m_ms2precision = ms2precision;
m_ionList.push_back(PeptideIon::y);
m_ionList.push_back(PeptideIon::b);
+
+ msp_filterKeepGreater =
+ std::make_shared<FilterResampleKeepGreater>(minimumMz);
+
msp_filterChargeDeconvolution =
std::make_shared<FilterChargeDeconvolution>(m_ms2precision);
msp_filterMzExclusion = std::make_shared<FilterMzExclusion>(
PrecisionFactory::getPrecisionPtrFractionInstance(m_ms2precision, 0.5));
-
- // TODO compute number of matched complementary peaks having m/z compatible
- // with the precursor
}
PsmFeatures::~PsmFeatures()
@@ -53,24 +55,80 @@ PsmFeatures::~PsmFeatures()
}
void
-PsmFeatures::setPeptideSpectrumCharge(pappso::PeptideSp peptideSp,
+PsmFeatures::setPeptideSpectrumCharge(const pappso::PeptideSp peptideSp,
const MassSpectrum *p_spectrum,
unsigned int parent_charge)
{
+ m_peakIonPairs.clear();
+ msp_peptide = peptideSp;
MassSpectrum spectrum(*p_spectrum);
- msp_filterChargeDeconvolution.get()->filter(spectrum);
- msp_filterMzExclusion.get()->filter(spectrum);
+ msp_filterKeepGreater.get()->filter(spectrum);
+ // msp_filterChargeDeconvolution.get()->filter(spectrum);
+ // msp_filterMzExclusion.get()->filter(spectrum);
+
+ msp_peptideSpectrumMatch =
+ std::make_shared<PeptideIsotopeSpectrumMatch>(spectrum,
+ peptideSp,
+ parent_charge,
+ m_ms2precision,
+ m_ionList,
+ (unsigned int)1,
+ 0);
+
+ msp_peptideSpectrumMatch.get()->dropPeaksLackingMonoisotope();
+ m_spectrumSumIntensity = spectrum.sumY();
+
+
+ qDebug() << " accumulate";
+ std::vector<double> delta_list;
+
+
+ // TODO compute number of matched complementary peaks having m/z compatible
+ // with the precursor
- unsigned int max_charge = parent_charge;
- if(parent_charge > 1)
+ m_precursorTheoreticalMz = peptideSp.get()->getMz(parent_charge);
+ m_precursorTheoreticalMass = peptideSp.get()->getMass();
+ m_parentCharge = parent_charge;
+
+
+ findComplementIonPairs(peptideSp);
+
+
+ for(const pappso::PeakIonIsotopeMatch &peak_ion :
+ msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList())
{
- max_charge = parent_charge - 1;
+ delta_list.push_back(
+ peak_ion.getPeptideFragmentIonSp().get()->getMz(peak_ion.getCharge()) -
+ peak_ion.getPeak().x);
}
+ pappso::pappso_double sum =
+ std::accumulate(delta_list.begin(), delta_list.end(), 0);
- msp_peptideSpectrumMatch = std::make_shared<PeptideSpectrumMatch>(
- spectrum, peptideSp, max_charge, m_ms2precision, m_ionList);
+ qDebug() << " delta_list.size()=" << delta_list.size();
+ m_matchedMzDiffMean = 0;
+ m_matchedMzDiffMedian = 0;
+ m_matchedMzDiffSd = 0;
+ if(delta_list.size() > 0)
+ {
+ m_matchedMzDiffMean = sum / ((pappso::pappso_double)delta_list.size());
- m_spectrumSumIntensity = spectrum.sumY();
+ std::sort(delta_list.begin(), delta_list.end());
+ m_matchedMzDiffMedian = delta_list[(delta_list.size() / 2)];
+
+
+ qDebug() << " sd";
+ m_matchedMzDiffSd = 0;
+ for(pappso::pappso_double val : delta_list)
+ {
+ // sd = sd + ((val - mean) * (val - mean));
+ m_matchedMzDiffSd += std::pow((val - m_matchedMzDiffMean), 2);
+ }
+ m_matchedMzDiffSd = m_matchedMzDiffSd / delta_list.size();
+ m_matchedMzDiffSd = std::sqrt(m_matchedMzDiffSd);
+ }
+ else
+ {
+ }
}
@@ -88,7 +146,7 @@ PsmFeatures::getIntensityOfMatchedIon(PeptideIon ion_type)
return sum;
}
double
-PsmFeatures::getTotalIntensityOfMatchedIons()
+PsmFeatures::getTotalIntensityOfMatchedIons() const
{
double sum = 0;
for(const PeakIonMatch &peak_ion_match : *msp_peptideSpectrumMatch.get())
@@ -99,7 +157,230 @@ PsmFeatures::getTotalIntensityOfMatchedIons()
}
double
-PsmFeatures::getTotalIntensity()
+PsmFeatures::getTotalIntensity() const
{
return m_spectrumSumIntensity;
}
+
+std::size_t
+pappso::PsmFeatures::countMatchedIonComplementPairs() const
+{
+ return m_peakIonPairs.size();
+}
+
+const std::vector<
+ std::pair<pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch>> &
+pappso::PsmFeatures::getPeakIonPairs() const
+{
+ return m_peakIonPairs;
+}
+
+double
+pappso::PsmFeatures::getTotalIntensityOfMatchedIonComplementPairs() const
+{
+
+ double sum = 0;
+ for(auto &peak_pairs : m_peakIonPairs)
+ {
+ sum += peak_pairs.first.getPeak().y;
+ sum += peak_pairs.second.getPeak().y;
+ }
+ return sum;
+}
+
+double
+pappso::PsmFeatures::getMatchedMzDiffSd() const
+{
+ return m_matchedMzDiffSd;
+}
+
+double
+pappso::PsmFeatures::getMatchedMzDiffMean() const
+{
+ return m_matchedMzDiffMean;
+}
+
+
+std::size_t
+pappso::PsmFeatures::getNumberOfMatchedIons() const
+{
+ return msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList().size();
+}
+
+std::size_t
+pappso::PsmFeatures::getMaxConsecutiveIon(pappso::PeptideIon ion_type)
+{
+ std::size_t max = 0;
+ auto peak_ion_match_list =
+ msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList();
+
+ peak_ion_match_list.erase(
+ std::remove_if(
+ peak_ion_match_list.begin(),
+ peak_ion_match_list.end(),
+ [ion_type](const PeakIonIsotopeMatch &a) {
+ if(a.getPeptideIonType() != ion_type)
+ return true;
+ if(a.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber() > 0)
+ return true;
+ return false;
+ }),
+ peak_ion_match_list.end());
+
+ peak_ion_match_list.sort(
+ [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) {
+ if(a.getCharge() < b.getCharge())
+ return true;
+ if(a.getPeptideIonType() < b.getPeptideIonType())
+ return true;
+ if(a.getPeptideFragmentIonSp().get()->size() <
+ b.getPeptideFragmentIonSp().get()->size())
+ return true;
+ return false;
+ });
+
+ unsigned int charge = 0;
+ std::size_t size = 0;
+ std::size_t count = 0;
+ for(std::list<PeakIonIsotopeMatch>::iterator it = peak_ion_match_list.begin();
+ it != peak_ion_match_list.end();
+ it++)
+ {
+ qDebug()
+ << it->toString() << max << " " << it->getPeak().x << " "
+ << it->getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber();
+ count++;
+ if((charge != it->getCharge()) ||
+ (size != (it->getPeptideFragmentIonSp().get()->size() - 1)))
+ {
+ count = 1;
+ charge = it->getCharge();
+ }
+ if(max < count)
+ max = count;
+
+ size = it->getPeptideFragmentIonSp().get()->size();
+ }
+
+ return max;
+}
+
+std::size_t
+pappso::PsmFeatures::getAaSequenceCoverage(pappso::PeptideIon ion_type)
+{
+ std::vector<bool> covered;
+ covered.resize(msp_peptide.get()->size(), false);
+
+ for(auto &peak : msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList())
+ {
+ if(peak.getPeptideIonType() == ion_type)
+ {
+ covered[peak.getPeptideFragmentIonSp().get()->size() - 1] = true;
+ }
+ }
+ return std::count(covered.begin(), covered.end(), true);
+}
+
+std::size_t
+pappso::PsmFeatures::getComplementPairsAaSequenceCoverage()
+{
+
+ std::vector<bool> covered;
+ covered.resize(msp_peptide.get()->size(), false);
+
+ for(auto &peak_pair : m_peakIonPairs)
+ {
+ std::size_t pos =
+ peak_pair.first.getPeptideFragmentIonSp().get()->size() - 1;
+ covered[pos] = true;
+ covered[pos + 1] = true;
+ }
+ return std::count(covered.begin(), covered.end(), true);
+}
+
+
+double
+pappso::PsmFeatures::getMaxIntensityPeakIonMatch(
+ pappso::PeptideIon ion_type) const
+{
+ std::list<pappso::PeakIonIsotopeMatch> peak_ion_type =
+ msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList();
+
+ peak_ion_type.remove_if([ion_type](const PeakIonIsotopeMatch &a) {
+ return (a.getPeptideIonType() != ion_type);
+ });
+ auto peak_it = std::max_element(
+ peak_ion_type.begin(),
+ peak_ion_type.end(),
+ [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) {
+ return (a.getPeak().y < b.getPeak().y);
+ });
+
+ if(peak_it == peak_ion_type.end())
+ return 0;
+ return peak_it->getPeak().y;
+}
+
+double
+pappso::PsmFeatures::getMaxIntensityMatchedIonComplementPairPrecursorMassDelta()
+ const
+{
+ auto peak_it = std::max_element(
+ m_peakIonPairs.begin(),
+ m_peakIonPairs.end(),
+ [](const std::pair<pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch>
+ &a,
+ const std::pair<pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch>
+ &b) {
+ return ((a.first.getPeak().y + a.second.getPeak().y) <
+ (b.first.getPeak().y + b.second.getPeak().y));
+ });
+
+ if(peak_it == m_peakIonPairs.end())
+ return 0;
+
+ return getIonPairPrecursorMassDelta(*peak_it);
+}
+
+double
+pappso::PsmFeatures::getIonPairPrecursorMassDelta(
+ const std::pair<pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch>
+ &ion_pair) const
+{
+ qDebug() << m_precursorTheoreticalMz << " " << ion_pair.first.getPeak().x
+ << " " << ion_pair.second.getPeak().x << " "
+ << ion_pair.second.getCharge() << " " << ion_pair.first.getCharge()
+ << " " << m_parentCharge;
+ double diff =
+ (m_precursorTheoreticalMass + (MHPLUS * ion_pair.first.getCharge())) /
+ ion_pair.first.getCharge();
+
+
+ return (diff - (ion_pair.first.getPeak().x + ion_pair.second.getPeak().x -
+ ((MHPLUS * ion_pair.first.getCharge())) /
+ ion_pair.first.getCharge()));
+}
+
+
+void
+pappso::PsmFeatures::findComplementIonPairs(const pappso::PeptideSp &peptideSp)
+{
+ std::size_t peptide_size = peptideSp.get()->size();
+ std::vector<PeakIonIsotopeMatch> ion_isotope_list(
+ msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList().begin(),
+ msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList().end());
+ for(const pappso::PeakIonIsotopeMatch &peak_ion_ext : ion_isotope_list)
+ {
+ if(peptideIonIsNter(peak_ion_ext.getPeptideIonType()))
+ {
+ auto it = findComplementIonType(ion_isotope_list.begin(),
+ ion_isotope_list.end(),
+ peak_ion_ext,
+ peptide_size);
+ if(it != ion_isotope_list.end())
+ { // contains the complementary ion
+ m_peakIonPairs.push_back({peak_ion_ext, *it});
+ }
+ }
+ }
+}
diff --git a/src/pappsomspp/psm/features/psmfeatures.h b/src/pappsomspp/psm/features/psmfeatures.h
index 734714524..69d6eea99 100644
--- a/src/pappsomspp/psm/features/psmfeatures.h
+++ b/src/pappsomspp/psm/features/psmfeatures.h
@@ -32,7 +32,8 @@
#include "../../peptide/peptidefragmention.h"
#include "../../processing/filters/filterchargedeconvolution.h"
#include "../../processing/filters/filterexclusionmz.h"
-#include "../peptidespectrummatch.h"
+#include "../../processing/filters/filterresample.h"
+#include "../peptideisotopespectrummatch.h"
namespace pappso
{
@@ -42,33 +43,119 @@ namespace pappso
class PMSPP_LIB_DECL PsmFeatures
{
public:
- /**
- * Default constructor
+ /** @brief compute psm features
+ * @param ms2precision precision of mass measurements for MS2 fragments
+ * @param minimumMz ignore mz values under this threshold
*/
- PsmFeatures();
+ PsmFeatures(PrecisionPtr ms2precision, double minimumMz);
/**
* Destructor
*/
~PsmFeatures();
- void setPeptideSpectrumCharge(pappso::PeptideSp peptideSp,
+ void setPeptideSpectrumCharge(const pappso::PeptideSp peptideSp,
const MassSpectrum *p_spectrum,
unsigned int parent_charge);
+ /** @brief get the sum of intensity of a specific ion
+ * @param ion_type ion species (y, b, ...)
+ */
double getIntensityOfMatchedIon(PeptideIon ion_type);
- double getTotalIntensity();
- double getTotalIntensityOfMatchedIons();
+
+ /** @brief sum of all peak intensities (matched or not)
+ */
+ double getTotalIntensity() const;
+
+
+ /** @brief sum of matched peak intensities
+ */
+ double getTotalIntensityOfMatchedIons() const;
+
+ /** @brief number of matched ions (peaks)
+ */
+ std::size_t getNumberOfMatchedIons() const;
+
+ /** @brief count the number of matched ion complement
+ *
+ * matched ion complement are ions with a sum compatible to the precursor mass
+ *
+ */
+ std::size_t countMatchedIonComplementPairs() const;
+
+ /** @brief intensity of matched ion complement
+ */
+ double getTotalIntensityOfMatchedIonComplementPairs() const;
+
+ const std::vector<
+ std::pair<pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch>> &
+ getPeakIonPairs() const;
+
+
+ /** @brief get mean deviation of matched peak mass delta
+ */
+ double getMatchedMzDiffMean() const;
+
+
+ /** @brief get standard deviation of matched peak mass delta
+ */
+ double getMatchedMzDiffSd() const;
+
+
+ /** @brief get the precursor mass delta of the maximum intensity pair of
+ * complement ions
+ */
+ double getMaxIntensityMatchedIonComplementPairPrecursorMassDelta() const;
+
+
+ /** @brief get the maximum consecutive fragments of one ion type
+ * @param ion_type ion species (y, b, ...)
+ */
+ std::size_t getMaxConsecutiveIon(PeptideIon ion_type);
+
+ /** @brief number of amino acid covered by matched ions
+ */
+ std::size_t getAaSequenceCoverage(PeptideIon ion_type);
+
+
+ /** @brief number of amino acid covered by matched complement pairs of ions
+ */
+ std::size_t getComplementPairsAaSequenceCoverage();
+
+ double getMaxIntensityPeakIonMatch(PeptideIon ion_type) const;
+
+
+ double getIonPairPrecursorMassDelta(
+ const std::pair<pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch>
+ &ion_pair) const;
+
+
+ private:
+ void findComplementIonPairs(const pappso::PeptideSp &peptideSp);
private:
std::shared_ptr<FilterChargeDeconvolution> msp_filterChargeDeconvolution;
std::shared_ptr<FilterMzExclusion> msp_filterMzExclusion;
+ std::shared_ptr<FilterResampleKeepGreater> msp_filterKeepGreater;
- std::shared_ptr<PeptideSpectrumMatch> msp_peptideSpectrumMatch;
+ std::shared_ptr<PeptideIsotopeSpectrumMatch> msp_peptideSpectrumMatch;
+ pappso::PeptideSp msp_peptide;
PrecisionPtr m_ms2precision;
std::list<PeptideIon> m_ionList;
double m_spectrumSumIntensity;
+
+ double m_precursorTheoreticalMz;
+ double m_precursorTheoreticalMass;
+ unsigned int m_parentCharge = 1;
+
+ std::vector<
+ std::pair<pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch>>
+ m_peakIonPairs;
+
+ double m_matchedMzDiffMean = 0;
+ double m_matchedMzDiffMedian = 0;
+ double m_matchedMzDiffSd = 0;
};
} // namespace pappso
diff --git a/src/pappsomspp/psm/peakionisotopematch.cpp b/src/pappsomspp/psm/peakionisotopematch.cpp
index f80c30b66..cf33efa73 100644
--- a/src/pappsomspp/psm/peakionisotopematch.cpp
+++ b/src/pappsomspp/psm/peakionisotopematch.cpp
@@ -26,6 +26,42 @@
namespace pappso
{
+std::vector<PeakIonIsotopeMatch>::iterator
+findComplementIonType(std::vector<PeakIonIsotopeMatch>::iterator begin,
+ std::vector<PeakIonIsotopeMatch>::iterator end,
+ const PeakIonIsotopeMatch &peak_ion,
+ std::size_t peptide_size)
+{
+
+ return std::find_if(
+ begin,
+ end,
+ [peak_ion, peptide_size](const PeakIonIsotopeMatch &to_compare) {
+ if(to_compare.getCharge() == peak_ion.getCharge())
+ {
+ if((to_compare.getPeptideFragmentIonSp().get()->size() +
+ peak_ion.getPeptideFragmentIonSp().get()->size()) == peptide_size)
+ {
+ if(peptideIonTypeIsComplement(to_compare.getPeptideIonType(),
+ peak_ion.getPeptideIonType()))
+ {
+ if(to_compare.getPeptideNaturalIsotopeAverageSp()
+ .get()
+ ->getIsotopeNumber() ==
+ peak_ion.getPeptideNaturalIsotopeAverageSp()
+ .get()
+ ->getIsotopeNumber())
+ {
+ return true;
+ }
+ }
+ }
+ }
+
+ return false;
+ });
+}
+
PeakIonIsotopeMatch::PeakIonIsotopeMatch(
const DataPoint &peak,
@@ -34,12 +70,20 @@ PeakIonIsotopeMatch::PeakIonIsotopeMatch(
: PeakIonMatch(peak, ion_sp, naturalIsotopeAverageSp.get()->getCharge()),
_naturalIsotopeAverageSp(naturalIsotopeAverageSp)
{
+ qDebug();
}
PeakIonIsotopeMatch::PeakIonIsotopeMatch(const PeakIonIsotopeMatch &other)
- : PeakIonMatch(other),
- _naturalIsotopeAverageSp(other._naturalIsotopeAverageSp)
+ : PeakIonMatch(other)
{
+ _naturalIsotopeAverageSp = other._naturalIsotopeAverageSp;
+}
+
+
+PeakIonIsotopeMatch::PeakIonIsotopeMatch(PeakIonIsotopeMatch &&other)
+ : PeakIonMatch(std::move(other))
+{
+ _naturalIsotopeAverageSp = other._naturalIsotopeAverageSp;
}
PeakIonIsotopeMatch::~PeakIonIsotopeMatch()
@@ -55,11 +99,21 @@ PeakIonIsotopeMatch::getPeptideNaturalIsotopeAverageSp() const
PeakIonIsotopeMatch &
PeakIonIsotopeMatch::operator=(const PeakIonIsotopeMatch &other)
{
-
+ PeakIonMatch::operator =(other);
_naturalIsotopeAverageSp = other._naturalIsotopeAverageSp;
return *this;
}
+QString
+PeakIonIsotopeMatch::toString() const
+{
+ return QString("%1isotope%2r%3mz%4")
+ .arg(PeakIonMatch::toString())
+ .arg(_naturalIsotopeAverageSp.get()->getIsotopeNumber())
+ .arg(_naturalIsotopeAverageSp.get()->getIsotopeRank())
+ .arg(getPeak().x);
+}
+
} // namespace pappso
diff --git a/src/pappsomspp/psm/peakionisotopematch.h b/src/pappsomspp/psm/peakionisotopematch.h
index 838c28e9b..ef79d1709 100644
--- a/src/pappsomspp/psm/peakionisotopematch.h
+++ b/src/pappsomspp/psm/peakionisotopematch.h
@@ -33,6 +33,16 @@ namespace pappso
class PeakIonIsotopeMatch;
typedef std::shared_ptr<const PeakIonIsotopeMatch> PeakIonIsotopeMatchCstSPtr;
+
+/** @brief find the first element containing the complementary ion
+ * complementary ion of y1 is b(n-1) for instance
+ * */
+PMSPP_LIB_DECL std::vector<PeakIonIsotopeMatch>::iterator
+findComplementIonType(std::vector<PeakIonIsotopeMatch>::iterator begin,
+ std::vector<PeakIonIsotopeMatch>::iterator end,
+ const PeakIonIsotopeMatch &peak_ion,
+ std::size_t peptide_size);
+
class PMSPP_LIB_DECL PeakIonIsotopeMatch : public PeakIonMatch
{
public:
@@ -41,6 +51,7 @@ class PMSPP_LIB_DECL PeakIonIsotopeMatch : public PeakIonMatch
const PeptideNaturalIsotopeAverageSp &naturalIsotopeAverageSp,
const PeptideFragmentIonSp &ion_sp);
PeakIonIsotopeMatch(const PeakIonIsotopeMatch &other);
+ PeakIonIsotopeMatch(PeakIonIsotopeMatch &&other);
virtual ~PeakIonIsotopeMatch();
virtual const PeptideNaturalIsotopeAverageSp &
@@ -48,6 +59,7 @@ class PMSPP_LIB_DECL PeakIonIsotopeMatch : public PeakIonMatch
PeakIonIsotopeMatch &operator=(const PeakIonIsotopeMatch &other);
+ virtual QString toString() const;
private:
PeptideNaturalIsotopeAverageSp _naturalIsotopeAverageSp;
diff --git a/src/pappsomspp/psm/peakionmatch.cpp b/src/pappsomspp/psm/peakionmatch.cpp
index 8419e6d6a..8344074ee 100644
--- a/src/pappsomspp/psm/peakionmatch.cpp
+++ b/src/pappsomspp/psm/peakionmatch.cpp
@@ -44,9 +44,63 @@ PeakIonMatch::PeakIonMatch(const PeakIonMatch &other)
{
}
+PeakIonMatch::PeakIonMatch(PeakIonMatch &&other)
+ : _peak(std::move(other._peak)),
+ _ion_sp(other._ion_sp),
+ _charge(std::move(other._charge))
+{
+}
+
PeakIonMatch::~PeakIonMatch()
{
}
+PeakIonMatch &
+PeakIonMatch::operator=(const PeakIonMatch &other)
+{
+ _peak = other._peak;
+ _ion_sp = other._ion_sp;
+ _charge = other._charge;
+
+ return *this;
+}
+
+const PeptideFragmentIonSp &
+PeakIonMatch::getPeptideFragmentIonSp() const
+{
+ return _ion_sp;
+}
+
+const DataPoint &
+PeakIonMatch::getPeak() const
+{
+ return _peak;
+}
+
+unsigned int
+PeakIonMatch::getCharge() const
+{
+ return _charge;
+}
+
+PeptideIon
+PeakIonMatch::getPeptideIonType() const
+{
+ return _ion_sp.get()->getPeptideIonType();
+}
+
+PeptideDirection
+PeakIonMatch::getPeptideIonDirection() const
+{
+ return _ion_sp.get()->getPeptideFragmentSp().get()->getPeptideIonDirection();
+}
+
+QString
+PeakIonMatch::toString() const
+{
+ return QString("%1").arg(
+ _ion_sp.get()->getCompletePeptideIonName(getCharge()));
+}
+
} // namespace pappso
diff --git a/src/pappsomspp/psm/peakionmatch.h b/src/pappsomspp/psm/peakionmatch.h
index 287461e4d..f0f09291f 100644
--- a/src/pappsomspp/psm/peakionmatch.h
+++ b/src/pappsomspp/psm/peakionmatch.h
@@ -43,39 +43,22 @@ class PMSPP_LIB_DECL PeakIonMatch
const PeptideFragmentIonSp &ion_sp,
unsigned int charge);
PeakIonMatch(const PeakIonMatch &other);
+ PeakIonMatch(PeakIonMatch &&other);
virtual ~PeakIonMatch();
- virtual const PeptideFragmentIonSp &
- getPeptideFragmentIonSp() const
- {
- return _ion_sp;
- };
+ PeakIonMatch &operator=(const PeakIonMatch &other);
- const DataPoint &
- getPeak() const
- {
- return _peak;
- };
+ virtual const PeptideFragmentIonSp &getPeptideFragmentIonSp() const;
- unsigned int
- getCharge() const
- {
- return _charge;
- };
+ const DataPoint &getPeak() const;
+
+ unsigned int getCharge() const;
+
+ PeptideIon getPeptideIonType() const;
+ PeptideDirection getPeptideIonDirection() const;
+
+ virtual QString toString() const;
- PeptideIon
- getPeptideIonType() const
- {
- return _ion_sp.get()->getPeptideIonType();
- };
- PeptideDirection
- getPeptideIonDirection() const
- {
- return _ion_sp.get()
- ->getPeptideFragmentSp()
- .get()
- ->getPeptideIonDirection();
- };
private:
DataPoint _peak;
diff --git a/src/pappsomspp/psm/peptideisotopespectrummatch.cpp b/src/pappsomspp/psm/peptideisotopespectrummatch.cpp
index 93702f1b0..ec9dac65a 100644
--- a/src/pappsomspp/psm/peptideisotopespectrummatch.cpp
+++ b/src/pappsomspp/psm/peptideisotopespectrummatch.cpp
@@ -32,7 +32,7 @@ PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch(
const PeptideSp &peptideSp,
unsigned int parent_charge,
PrecisionPtr precision,
- std::list<PeptideIon> ion_type_list,
+ const std::list<PeptideIon> &ion_type_list,
unsigned int max_isotope_number,
[[maybe_unused]] unsigned int max_isotope_rank)
: _precision(precision)
@@ -40,6 +40,7 @@ PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch(
try
{
+ _peak_ion_match_list.clear();
qDebug() << "PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch "
"begin max_isotope_number="
<< max_isotope_number;
@@ -47,32 +48,26 @@ PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch(
qDebug() << "PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch "
"peak_list spectrum.size="
<< spectrum.size();
- std::list<DataPoint> peak_list(spectrum.begin(), spectrum.end());
-
- qDebug() << "PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch "
- "ion_type_list";
+ std::vector<DataPoint> peak_list(spectrum.begin(), spectrum.end());
for(auto ion_type : ion_type_list)
{
auto ion_list = fragmentIonList.getPeptideFragmentIonSp(ion_type);
- qDebug() << "PeptideIsotopeSpectrumMatch::"
- "PeptideIsotopeSpectrumMatch fragmentIonList";
for(unsigned int charge = 1; charge <= parent_charge; charge++)
{
for(auto &&ion : ion_list)
{
- unsigned int askedIsotopeRank = 1;
for(unsigned int isotope_number = 0;
isotope_number <= max_isotope_number;
isotope_number++)
{
- PeptideNaturalIsotopeAverage isotopeIon(ion,
- askedIsotopeRank,
- isotope_number,
- charge,
- precision);
+ PeptideNaturalIsotopeAverage isotopeIon(
+ ion, isotope_number, charge, precision);
+
+ qDebug()
+ << isotope_number << " " << isotopeIon.toString();
- std::list<DataPoint>::iterator it_peak =
+ std::vector<DataPoint>::iterator it_peak =
getBestPeakIterator(peak_list, isotopeIon);
if(it_peak != peak_list.end())
{
@@ -81,13 +76,14 @@ PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch(
isotopeIon.makePeptideNaturalIsotopeAverageSp(),
ion));
peak_list.erase(it_peak);
+
+ qDebug() << isotope_number << " "
+ << _peak_ion_match_list.back().toString();
}
}
}
}
}
- qDebug()
- << "PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch end";
}
catch(PappsoException &exception_pappso)
{
@@ -120,7 +116,7 @@ PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch(
PrecisionPtr precision)
: _precision(precision)
{
- qDebug() << "PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch begin";
+ qDebug() << " begin";
if(v_peptideIsotopeList.size() != v_peptideIonList.size())
{
throw PappsoException(
@@ -132,11 +128,11 @@ PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch(
auto isotopeIt = v_peptideIsotopeList.begin();
auto ionIt = v_peptideIonList.begin();
- std::list<DataPoint> peak_list(spectrum.begin(), spectrum.end());
+ std::vector<DataPoint> peak_list(spectrum.begin(), spectrum.end());
while(isotopeIt != v_peptideIsotopeList.end())
{
- std::list<DataPoint>::iterator it_peak =
+ std::vector<DataPoint>::iterator it_peak =
getBestPeakIterator(peak_list, *(isotopeIt->get()));
if(it_peak != peak_list.end())
{
@@ -147,7 +143,7 @@ PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch(
isotopeIt++;
ionIt++;
}
- qDebug() << "PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch end";
+ qDebug() << " end";
}
@@ -156,6 +152,7 @@ PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch(
: _precision(other._precision),
_peak_ion_match_list(other._peak_ion_match_list)
{
+ qDebug();
}
PeptideIsotopeSpectrumMatch::~PeptideIsotopeSpectrumMatch()
@@ -163,15 +160,15 @@ PeptideIsotopeSpectrumMatch::~PeptideIsotopeSpectrumMatch()
}
-std::list<DataPoint>::iterator
+std::vector<DataPoint>::iterator
PeptideIsotopeSpectrumMatch::getBestPeakIterator(
- std::list<DataPoint> &peak_list,
+ std::vector<DataPoint> &peak_list,
const PeptideNaturalIsotopeAverage &ion) const
{
// qDebug();
- std::list<DataPoint>::iterator itpeak = peak_list.begin();
- std::list<DataPoint>::iterator itend = peak_list.end();
- std::list<DataPoint>::iterator itselect = peak_list.end();
+ std::vector<DataPoint>::iterator itpeak = peak_list.begin();
+ std::vector<DataPoint>::iterator itend = peak_list.end();
+ std::vector<DataPoint>::iterator itselect = peak_list.end();
pappso_double best_intensity = 0;
@@ -197,5 +194,68 @@ PeptideIsotopeSpectrumMatch::getPeakIonIsotopeMatchList() const
return _peak_ion_match_list;
}
+std::size_t
+PeptideIsotopeSpectrumMatch::size() const
+{
+ return _peak_ion_match_list.size();
+}
+PeptideIsotopeSpectrumMatch::const_iterator
+PeptideIsotopeSpectrumMatch::begin() const
+{
+ return _peak_ion_match_list.begin();
+}
+PeptideIsotopeSpectrumMatch::const_iterator
+PeptideIsotopeSpectrumMatch::end() const
+{
+ return _peak_ion_match_list.end();
+}
+void
+PeptideIsotopeSpectrumMatch::dropPeaksLackingMonoisotope()
+{
+ qDebug();
+ _peak_ion_match_list.sort(
+ [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) {
+ if(a.getPeptideIonType() < b.getPeptideIonType())
+ return true;
+ if(a.getPeptideFragmentIonSp().get()->size() <
+ b.getPeptideFragmentIonSp().get()->size())
+ return true;
+ if(a.getCharge() < b.getCharge())
+ return true;
+ if(a.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber() <
+ b.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber())
+ return true;
+ return false;
+ });
+ PeptideIon ion_type = PeptideIon::b;
+ std::size_t nserie = 0;
+ std::size_t isotopeserie = 0;
+ unsigned int charge = 0;
+ for(std::list<PeakIonIsotopeMatch>::iterator it =
+ _peak_ion_match_list.begin();
+ it != _peak_ion_match_list.end();
+ it++)
+ {
+ if((nserie != it->getPeptideFragmentIonSp().get()->size()) ||
+ (ion_type != it->getPeptideIonType()) || (charge != it->getCharge()))
+ {
+ ion_type = it->getPeptideIonType();
+ isotopeserie = 0;
+ nserie = it->getPeptideFragmentIonSp().get()->size();
+ charge = it->getCharge();
+ }
+ if(isotopeserie <=
+ it->getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber())
+ {
+ isotopeserie =
+ it->getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber();
+ }
+ else
+ {
+ it = _peak_ion_match_list.erase(it);
+ }
+ }
+ qDebug();
+}
} // namespace pappso
diff --git a/src/pappsomspp/psm/peptideisotopespectrummatch.h b/src/pappsomspp/psm/peptideisotopespectrummatch.h
index 6c2297feb..8a627a817 100644
--- a/src/pappsomspp/psm/peptideisotopespectrummatch.h
+++ b/src/pappsomspp/psm/peptideisotopespectrummatch.h
@@ -53,7 +53,7 @@ class PMSPP_LIB_DECL PeptideIsotopeSpectrumMatch
const PeptideSp &peptide_sp,
unsigned int parent_charge,
PrecisionPtr precision,
- std::list<PeptideIon> ion_list,
+ const std::list<PeptideIon> &ion_type_list,
unsigned int max_isotope_number,
unsigned int max_isotope_rank);
PeptideIsotopeSpectrumMatch(
@@ -63,32 +63,22 @@ class PMSPP_LIB_DECL PeptideIsotopeSpectrumMatch
PrecisionPtr precision);
PeptideIsotopeSpectrumMatch(const PeptideIsotopeSpectrumMatch &other);
- ~PeptideIsotopeSpectrumMatch();
+ virtual ~PeptideIsotopeSpectrumMatch();
const std::list<PeakIonIsotopeMatch> &getPeakIonIsotopeMatchList() const;
typedef std::list<PeakIonIsotopeMatch>::const_iterator const_iterator;
- unsigned int
- size() const
- {
- return _peak_ion_match_list.size();
- }
- const_iterator
- begin() const
- {
- return _peak_ion_match_list.begin();
- }
- const_iterator
- end() const
- {
- return _peak_ion_match_list.end();
- }
+ std::size_t size() const;
+ const_iterator begin() const;
+ const_iterator end() const;
+
+ void dropPeaksLackingMonoisotope();
private:
- virtual std::list<DataPoint>::iterator
- getBestPeakIterator(std::list<DataPoint> &peak_list,
+ virtual std::vector<DataPoint>::iterator
+ getBestPeakIterator(std::vector<DataPoint> &peak_list,
const PeptideNaturalIsotopeAverage &ion) const;
PrecisionPtr _precision;
diff --git a/src/pappsomspp/psm/peptidespectrummatch.h b/src/pappsomspp/psm/peptidespectrummatch.h
index 59ee54ea1..88ad0c261 100644
--- a/src/pappsomspp/psm/peptidespectrummatch.h
+++ b/src/pappsomspp/psm/peptidespectrummatch.h
@@ -61,7 +61,7 @@ class PMSPP_LIB_DECL PeptideSpectrumMatch
PrecisionPtr precision);
PeptideSpectrumMatch(const PeptideSpectrumMatch &other);
- ~PeptideSpectrumMatch();
+ virtual ~PeptideSpectrumMatch();
bool contains(const PeptideFragmentIon *peptideFragmentIonSp,
unsigned int z) const;
diff --git a/src/pappsomspp/psm/xtandem/xtandemhyperscore.cpp b/src/pappsomspp/psm/xtandem/xtandemhyperscore.cpp
index 743e723dd..2f0072887 100644
--- a/src/pappsomspp/psm/xtandem/xtandemhyperscore.cpp
+++ b/src/pappsomspp/psm/xtandem/xtandemhyperscore.cpp
@@ -262,9 +262,11 @@ XtandemHyperscore::getHyperscore() const
{
try
{
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
- << " _proto_hyperscore=" << _proto_hyperscore;
- return (log10(_proto_hyperscore) * 4);
+ qDebug() << " _proto_hyperscore=" << _proto_hyperscore;
+ double hyperscore = (log10(_proto_hyperscore) * 4);
+ if(hyperscore < 0)
+ return 0;
+ return hyperscore;
}
catch(PappsoException &exception_pappso)
{
diff --git a/src/pappsomspp/trace/trace.cpp b/src/pappsomspp/trace/trace.cpp
index 8ae85b2fb..8b2352b6f 100644
--- a/src/pappsomspp/trace/trace.cpp
+++ b/src/pappsomspp/trace/trace.cpp
@@ -323,6 +323,35 @@ areaTrace(std::vector<DataPoint>::const_iterator begin,
}
+double
+areaTraceMinusBase(std::vector<DataPoint>::const_iterator begin,
+ std::vector<DataPoint>::const_iterator end)
+{
+
+ if(begin == end)
+ return 0;
+ auto previous = begin;
+ auto next = begin + 1;
+ auto last = next;
+ double area = 0;
+ while(next != end)
+ {
+ last = next;
+ area += ((next->x - previous->x) * (previous->y + next->y)) / (double)2;
+ previous++;
+ next++;
+ }
+ if(area > 0)
+ {
+ // remove base peak area
+ area -= (((last->y + begin->y) * (last->x - begin->x)) / 2);
+ if(area < 0)
+ return 0;
+ }
+ return area;
+}
+
+
Trace
flooredLocalMaxima(std::vector<DataPoint>::const_iterator begin,
std::vector<DataPoint>::const_iterator end,
diff --git a/src/pappsomspp/trace/trace.h b/src/pappsomspp/trace/trace.h
index 76c3f4476..7b34b8876 100644
--- a/src/pappsomspp/trace/trace.h
+++ b/src/pappsomspp/trace/trace.h
@@ -126,7 +126,6 @@ quantileYTrace(std::vector<DataPoint>::const_iterator begin,
PMSPP_LIB_DECL double areaTrace(std::vector<DataPoint>::const_iterator begin,
std::vector<DataPoint>::const_iterator end);
-
PMSPP_LIB_DECL Trace
flooredLocalMaxima(std::vector<DataPoint>::const_iterator begin,
std::vector<DataPoint>::const_iterator end,
@@ -210,14 +209,17 @@ class PMSPP_LIB_DECL Trace : public std::vector<DataPoint>
virtual Trace &filter(const FilterInterface &filter) final;
QString toString() const;
+ /** @brief find datapoint with exactly x value
+ */
+ std::vector<DataPoint>::const_iterator
+ dataPointCstIteratorWithX(pappso_double value) const;
+
protected:
//! Return a reference to the DataPoint instance that has its y member equal
//! to \p value.
// const DataPoint &dataPointWithX(pappso_double value) const;
std::size_t dataPointIndexWithX(pappso_double value) const;
std::vector<DataPoint>::iterator dataPointIteratorWithX(pappso_double value);
- std::vector<DataPoint>::const_iterator
- dataPointCstIteratorWithX(pappso_double value) const;
};
diff --git a/src/pappsomspp/vendors/tims/timsframebase.cpp b/src/pappsomspp/vendors/tims/timsframebase.cpp
index 833706352..4754caa94 100644
--- a/src/pappsomspp/vendors/tims/timsframebase.cpp
+++ b/src/pappsomspp/vendors/tims/timsframebase.cpp
@@ -492,4 +492,69 @@ TimsFrameBase::getScanIntensities(std::size_t scanNum) const
"ERROR unable to getScanIntensities in TimsFrameBase for scan number %1")
.arg(scanNum));
}
+
+Trace
+TimsFrameBase::getIonMobilityTraceByMzIndexRange(
+ std::size_t mz_index_lower_bound,
+ std::size_t mz_index_upper_bound,
+ XicExtractMethod method) const
+{
+ Trace im_trace;
+ DataPoint data_point;
+ for(quint32 i = 0; i < m_scanNumber; i++)
+ {
+ data_point.x = i;
+ data_point.y = 0;
+ qDebug() << "m_scanNumber=" << m_scanNumber << " i=" << i;
+ std::vector<quint32> index_list = getScanIndexList(i);
+ auto it_lower = std::find_if(index_list.begin(),
+ index_list.end(),
+ [mz_index_lower_bound](quint32 to_compare) {
+ if(to_compare < mz_index_lower_bound)
+ {
+ return false;
+ }
+ return true;
+ });
+
+
+ if(it_lower == index_list.end())
+ {
+ }
+ else
+ {
+
+
+ auto it_upper =
+ std::find_if(index_list.begin(),
+ index_list.end(),
+ [mz_index_upper_bound](quint32 to_compare) {
+ if(mz_index_upper_bound >= to_compare)
+ {
+ return false;
+ }
+ return true;
+ });
+ std::vector<quint32> intensity_list = getScanIntensities(i);
+ for(int j = std::distance(index_list.begin(), it_lower);
+ j < std::distance(index_list.begin(), it_upper);
+ j++)
+ {
+ if(method == XicExtractMethod::sum)
+ {
+ data_point.y += intensity_list[j];
+ }
+ else
+ {
+ data_point.y =
+ std::max((double)intensity_list[j], data_point.y);
+ }
+ }
+ }
+ im_trace.push_back(data_point);
+ }
+ qDebug();
+ return im_trace;
+}
+// namespace pappso
} // namespace pappso
diff --git a/src/pappsomspp/vendors/tims/timsframebase.h b/src/pappsomspp/vendors/tims/timsframebase.h
index 36e8158a4..ba9476ca5 100644
--- a/src/pappsomspp/vendors/tims/timsframebase.h
+++ b/src/pappsomspp/vendors/tims/timsframebase.h
@@ -213,6 +213,17 @@ class TimsFrameBase
*/
virtual std::vector<quint32> getScanIntensities(std::size_t scanNum) const;
+ /** @brief get a mobility trace cumulating intensities inside the given mass
+ * index range
+ * @param mz_index_lower_bound raw mass index lower bound
+ * @param mz_index_upper_bound raw mass index upper bound
+ * @param method max or sum intensities
+ */
+ virtual Trace
+ getIonMobilityTraceByMzIndexRange(std::size_t mz_index_lower_bound,
+ std::size_t mz_index_upper_bound,
+ XicExtractMethod method) const;
+
protected:
/** @brief total number of scans contained in this frame
diff --git a/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.cpp b/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.cpp
index a2dfd20c9..2297de9c5 100644
--- a/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.cpp
+++ b/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.cpp
@@ -202,7 +202,9 @@ MassSpectrumWidget::peptideAnnotate()
_max_isotope_number,
_max_isotope_rank);
- _peak_ion_isotope_match_list = psm_match.getPeakIonIsotopeMatchList();
+ _peak_ion_isotope_match_list = std::list<PeakIonIsotopeMatch>(
+ psm_match.getPeakIonIsotopeMatchList().begin(),
+ psm_match.getPeakIonIsotopeMatchList().end());
}
else
{
@@ -318,11 +320,17 @@ MassSpectrumWidget::plot()
}
else
{
+ qDebug();
_peak_ion_isotope_match_list.sort(
[](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) {
- return a.getPeak().y > b.getPeak().y;
+ qDebug() << a.getPeak().y << " > ";
+ qDebug() << b.getPeak().y << " . ";
+ return (a.getPeak().y > b.getPeak().y);
});
+ qDebug();
unsigned int i = 0;
+
+ qDebug();
for(const PeakIonIsotopeMatch &peak_ion_match :
_peak_ion_isotope_match_list)
{
@@ -358,6 +366,7 @@ MassSpectrumWidget::plot()
}
}
+ qDebug();
_custom_plot->replot();
qDebug();
}
diff --git a/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.h b/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.h
index 29b6528ce..112beb401 100644
--- a/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.h
+++ b/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.h
@@ -1,5 +1,5 @@
/**
- * \file pappsomspp/widget/spectrumwidget/massspectrumwidget.h
+ * \file pappsomspp/widget/massspectrumwidget/massspectrumwidget.h
* \date 22/12/2017
* \author Olivier Langella
* \brief plot a sectrum and annotate with peptide
diff --git a/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.cpp b/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.cpp
index 12c82a750..00fea9913 100644
--- a/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.cpp
+++ b/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.cpp
@@ -300,8 +300,8 @@ QCPSpectrum::mousePressEvent(QMouseEvent *event)
<< xAxis->pixelToCoord(event->x()) << " "
<< yAxis->pixelToCoord(event->y());*/
_click = true;
- _old_x = event->x();
- _old_y = yAxis->pixelToCoord(event->y());
+ _old_x = event->position().x();
+ _old_y = yAxis->pixelToCoord(event->position().y());
if(_old_y < 0)
_old_y = 0;
/* qDebug() << "QCPSpectrum::mousePressEvent end";*/
@@ -318,13 +318,13 @@ QCPSpectrum::mouseReleaseEvent(QMouseEvent *event [[maybe_unused]])
void
QCPSpectrum::mouseMoveEvent(QMouseEvent *event)
{
- pappso::pappso_double x = xAxis->pixelToCoord(event->x());
+ pappso::pappso_double x = xAxis->pixelToCoord(event->position().x());
if(_click)
{
/* qDebug() << "QCPSpectrum::mouseMoveEvent begin "
<< xAxis->pixelToCoord(event->x()) << " "
<< yAxis->pixelToCoord(event->y());*/
- pappso::pappso_double y = yAxis->pixelToCoord(event->y());
+ pappso::pappso_double y = yAxis->pixelToCoord(event->position().y());
if(y < 0)
{
y = 0;
@@ -339,9 +339,9 @@ QCPSpectrum::mouseMoveEvent(QMouseEvent *event)
else
{
this->xAxis->moveRange(xAxis->pixelToCoord(_old_x) -
- xAxis->pixelToCoord(event->x()));
+ xAxis->pixelToCoord(event->position().x()));
}
- _old_x = event->x();
+ _old_x = event->position().x();
_old_y = y;
replot();
// qDebug() << "QCPSpectrum::mouseMoveEvent end";
diff --git a/src/pappsomspp/widget/plotwidget/basetraceplotwidget.cpp b/src/pappsomspp/widget/plotwidget/basetraceplotwidget.cpp
index 772ea7951..a8be4eaf2 100644
--- a/src/pappsomspp/widget/plotwidget/basetraceplotwidget.cpp
+++ b/src/pappsomspp/widget/plotwidget/basetraceplotwidget.cpp
@@ -132,7 +132,6 @@ BaseTracePlotWidget::setGraphData(QCPGraph *graph_p,
QVector<double> key_qvector;
QVector<double> value_qvector;
-#pragma GCC warning "Filippo Rusconi: Please check if the bug was fixed in Qt"
#if 0
// Now replace the graph's data. Note that the data are
@@ -204,8 +203,6 @@ BaseTracePlotWidget::addTrace(const pappso::Trace &trace, const QColor &color)
QVector<double> key_qvector;
QVector<double> value_qvector;
-#pragma GCC warning "Filippo Rusconi: Please check if the bug was fixed in Qt"
-
#if 0
// Now replace the graph's data. Note that the data are
// inherently sorted (true below).
diff --git a/src/pappsomspp/widget/xicwidget/qcpxic.cpp b/src/pappsomspp/widget/xicwidget/qcpxic.cpp
index 387b8d34f..86e9b4510 100644
--- a/src/pappsomspp/widget/xicwidget/qcpxic.cpp
+++ b/src/pappsomspp/widget/xicwidget/qcpxic.cpp
@@ -103,13 +103,11 @@ QCPXic::keyReleaseEvent(QKeyEvent *event)
void
QCPXic::mousePressEvent(QMouseEvent *event)
{
- qDebug() << "QCPXic::mousePressEvent begin "
- << xAxis->pixelToCoord(event->x()) << " "
- << yAxis->pixelToCoord(event->y());
+ qDebug() << " begin ";
_mouse_move = false;
_click = true;
- _old_x = event->x();
- _old_y = yAxis->pixelToCoord(event->y());
+ _old_x = event->position().x();
+ _old_y = yAxis->pixelToCoord(event->position().y());
if(_old_y < 0)
{
_old_y = 0;
@@ -123,8 +121,8 @@ void
QCPXic::mouseReleaseEvent(QMouseEvent *event)
{
qDebug() << "QCPXic::mouseReleaseEvent begin "
- << xAxis->pixelToCoord(event->x()) << " "
- << yAxis->pixelToCoord(event->y());
+ << xAxis->pixelToCoord(event->position().x()) << " "
+ << yAxis->pixelToCoord(event->position().y());
_click = false;
if(_mouse_move)
{
@@ -140,13 +138,13 @@ void
QCPXic::mouseMoveEvent(QMouseEvent *event)
{
_mouse_move = true;
- pappso::pappso_double x = xAxis->pixelToCoord(event->x());
+ pappso::pappso_double x = xAxis->pixelToCoord(event->position().x());
if(_click)
{
qDebug() << "QCPXic::mouseMoveEvent begin "
- << xAxis->pixelToCoord(event->x()) << " "
- << yAxis->pixelToCoord(event->y());
- pappso::pappso_double y = yAxis->pixelToCoord(event->y());
+ << xAxis->pixelToCoord(event->position().x()) << " "
+ << yAxis->pixelToCoord(event->position().y());
+ pappso::pappso_double y = yAxis->pixelToCoord(event->position().y());
if(y < 0)
{
y = 0;
@@ -161,9 +159,9 @@ QCPXic::mouseMoveEvent(QMouseEvent *event)
else
{
this->xAxis->moveRange(xAxis->pixelToCoord(_old_x) -
- xAxis->pixelToCoord(event->x()));
+ xAxis->pixelToCoord(event->position().x()));
}
- _old_x = event->x();
+ _old_x = event->position().x();
_old_y = y;
replot();
qDebug() << "QCPXic::mouseMoveEvent end";
@@ -179,7 +177,7 @@ QCPXic::mouseMoveEvent(QMouseEvent *event)
}
}
-void
+QCPGraph *
QCPXic::addXicP(const Xic *xic_p)
{
@@ -207,6 +205,8 @@ QCPXic::addXicP(const Xic *xic_p)
if(_intensity_range.upper < xic_p->maxYDataPoint().y)
_intensity_range.upper = xic_p->maxYDataPoint().y;
}
+
+ return graph_xic;
}
diff --git a/src/pappsomspp/widget/xicwidget/qcpxic.h b/src/pappsomspp/widget/xicwidget/qcpxic.h
index a585ecfd7..a0be5db48 100644
--- a/src/pappsomspp/widget/xicwidget/qcpxic.h
+++ b/src/pappsomspp/widget/xicwidget/qcpxic.h
@@ -49,7 +49,7 @@ class QCPXic : public QCustomPlot
protected:
void clear();
void rescale();
- void addXicP(const Xic *xic_p);
+ QCPGraph *addXicP(const Xic *xic_p);
void addMsMsEvent(const Xic *xic_p, pappso::pappso_double rt);
void
addXicPeakList(const Xic *xic_p,
diff --git a/src/pappsomspp/widget/xicwidget/xicwidget.cpp b/src/pappsomspp/widget/xicwidget/xicwidget.cpp
index 538ba9dd7..4593c1a3f 100644
--- a/src/pappsomspp/widget/xicwidget/xicwidget.cpp
+++ b/src/pappsomspp/widget/xicwidget/xicwidget.cpp
@@ -63,11 +63,11 @@ XicWidget::addMsMsEvent(const Xic *xic_p, pappso::pappso_double rt)
_qcp_xic->addMsMsEvent(xic_p, rt);
_map_xic_msms_event[xic_p] = rt;
}
-void
-XicWidget::addXicSp(XicCstSPtr &xic_sp)
+QCPGraph *
+XicWidget::addXicSp(XicCstSPtr xic_sp)
{
_xic_sp_list.push_back(xic_sp);
- _qcp_xic->addXicP(xic_sp.get());
+ return _qcp_xic->addXicP(xic_sp.get());
}
const QString &
diff --git a/src/pappsomspp/widget/xicwidget/xicwidget.h b/src/pappsomspp/widget/xicwidget/xicwidget.h
index 5038cc15a..fc0aa83c5 100644
--- a/src/pappsomspp/widget/xicwidget/xicwidget.h
+++ b/src/pappsomspp/widget/xicwidget/xicwidget.h
@@ -52,7 +52,7 @@ class PMSPP_LIB_DECL XicWidget : public GraphicDeviceWidget
~XicWidget();
- void addXicSp(XicCstSPtr &xic_sp);
+ QCPGraph *addXicSp(XicCstSPtr xic_sp);
void addMsMsEvent(const Xic *xic_p, pappso::pappso_double rt);
void
addXicPeakList(const Xic *xic_p,
diff --git a/src/pappsomspp/xic/xic.cpp b/src/pappsomspp/xic/xic.cpp
index c3cfcd874..98fb683b7 100644
--- a/src/pappsomspp/xic/xic.cpp
+++ b/src/pappsomspp/xic/xic.cpp
@@ -40,6 +40,10 @@ Xic::Xic()
qDebug() << "Xic::Xic end";
}
+Xic::Xic(const Trace &other) : Trace(other)
+{
+}
+
Xic::~Xic()
{
}
diff --git a/src/pappsomspp/xic/xic.h b/src/pappsomspp/xic/xic.h
index 1b43e7519..34298c22c 100644
--- a/src/pappsomspp/xic/xic.h
+++ b/src/pappsomspp/xic/xic.h
@@ -44,6 +44,7 @@ class PMSPP_LIB_DECL Xic : public Trace
{
public:
Xic();
+ Xic(const Trace & other);
virtual ~Xic();
diff --git a/src/pappsomspp/xicextractor/msrunxicextractorfactory.cpp b/src/pappsomspp/xicextractor/msrunxicextractorfactory.cpp
index 5b15543ff..73d92ae86 100644
--- a/src/pappsomspp/xicextractor/msrunxicextractorfactory.cpp
+++ b/src/pappsomspp/xicextractor/msrunxicextractorfactory.cpp
@@ -72,8 +72,6 @@ MsRunXicExtractorInterfaceSp
MsRunXicExtractorFactory::buildMsRunXicExtractorSp(
MsRunReaderSPtr &msrun_reader) const
{
-#if 0
-// Remove this section because it cripples my work on Qt6 build
pappso::TimsMsRunReaderMs2 *tims2_reader =
dynamic_cast<pappso::TimsMsRunReaderMs2 *>(msrun_reader.get());
@@ -116,7 +114,6 @@ MsRunXicExtractorFactory::buildMsRunXicExtractorSp(
return (msrun_xic_extractor_sp);
}
return nullptr;
-#endif
}
diff --git a/tests/test_psm.cpp b/tests/test_psm.cpp
index 2150cd2b3..e495e4ac5 100644
--- a/tests/test_psm.cpp
+++ b/tests/test_psm.cpp
@@ -27,11 +27,14 @@
******************************************************************************/
// make test ARGS="-V -I 18,18"
+// ./tests/catch2-only-tests [psm] -s
+// ./tests/catch2-only-tests [psmfeature] -s
+#include <algorithm>
-#define CATCH_CONFIG_MAIN
#include <catch2/catch.hpp>
#include <pappsomspp/mzrange.h>
#include <pappsomspp/psm/peptidespectrummatch.h>
+#include <pappsomspp/psm/features/psmfeatures.h>
#include <iostream>
#include <iomanip>
#include <set>
@@ -83,5 +86,242 @@ TEST_CASE("psm test suite.", "[psm]")
spectrum_simple, peptide_sp, 2, precision, ion_list);
test_count = psmb.countTotalMatchedIons();
REQUIRE(test_count == 0);
+
+
+ precision = PrecisionFactory::getDaltonInstance(0.02);
+ PeptideIsotopeSpectrumMatch psm_iso(
+ spectrum_simple, peptide_sp, 2, precision, ion_list, 2, 0);
+
+ std::list<PeakIonIsotopeMatch> peak_ion_isotope_match_list =
+ psm_iso.getPeakIonIsotopeMatchList();
+
+ for(auto peak : peak_ion_isotope_match_list)
+ {
+ qDebug() << peak.toString() << " "
+ << peak.getPeptideNaturalIsotopeAverageSp().get();
+ }
+ REQUIRE(peak_ion_isotope_match_list.size() == 19);
+
+ psm_iso.dropPeaksLackingMonoisotope();
+ peak_ion_isotope_match_list = psm_iso.getPeakIonIsotopeMatchList();
+ for(auto peak : peak_ion_isotope_match_list)
+ {
+ qDebug() << peak.toString() << " "
+ << peak.getPeptideNaturalIsotopeAverageSp().get();
+ }
+ REQUIRE(peak_ion_isotope_match_list.size() == 19);
+
+ qDebug() << peak_ion_isotope_match_list.size();
+ peak_ion_isotope_match_list.sort(
+ [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) {
+ qDebug() << a.getPeak().y << " > ";
+ qDebug() << b.getPeak().y << " . ";
+ return (a.getPeak().y > b.getPeak().y);
+ });
+
+
+ spectrum_simple = readMgf(
+ QString(CMAKE_SOURCE_DIR).append("/tests/data/peaklist_15046.mgf"));
+
+ peptide_sp = Peptide("AIADGSLLDLLR").makePeptideSp();
+
+
+ precision = PrecisionFactory::getDaltonInstance(0.02);
+ qDebug();
+ PeptideIsotopeSpectrumMatch psm_iso_check(
+ spectrum_simple, peptide_sp, 2, precision, ion_list, 2, 0);
+
+ qDebug();
+ peak_ion_isotope_match_list = psm_iso_check.getPeakIonIsotopeMatchList();
+
+ REQUIRE(peak_ion_isotope_match_list.size() == 39);
+ qDebug();
+
+ for(auto &peak : peak_ion_isotope_match_list)
+ {
+ qDebug() << peak.toString() << " "
+ << peak.getPeptideNaturalIsotopeAverageSp().get();
+ }
+
+
+ peak_ion_isotope_match_list.sort(
+ [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) {
+ if(a.getPeptideIonType() < b.getPeptideIonType())
+ return true;
+ if(a.getPeptideFragmentIonSp().get()->size() <
+ b.getPeptideFragmentIonSp().get()->size())
+ return true;
+ if(a.getCharge() < b.getCharge())
+ return true;
+ if(a.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber() <
+ b.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber())
+ return true;
+ return false;
+ });
+
+
+ auto it = peak_ion_isotope_match_list.begin();
+ REQUIRE(it->toString().toStdString() == "b2+isotope0r1mz185.128");
+ it++;
+ REQUIRE(it->toString().toStdString() == "b3+isotope0r1mz256.165");
+
+ for(auto peak : peak_ion_isotope_match_list)
+ {
+ qDebug() << peak.toString() << " "
+ << peak.getPeptideNaturalIsotopeAverageSp().get();
+ }
+
+ psm_iso_check.dropPeaksLackingMonoisotope();
+ peak_ion_isotope_match_list = psm_iso_check.getPeakIonIsotopeMatchList();
+
+ for(auto peak : peak_ion_isotope_match_list)
+ {
+ qDebug() << peak.toString() << " "
+ << peak.getPeptideNaturalIsotopeAverageSp().get();
+ }
+ REQUIRE(peak_ion_isotope_match_list.size() == 39);
+ }
+}
+
+
+TEST_CASE("psm features test suite.", "[psmfeature]")
+{
+ // Set the debugging message formatting pattern.
+ qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
+
+ SECTION("..:: readMgf ::..", "[psm]")
+ {
+ cout << std::endl << "..:: readMgf ::.." << std::endl;
+ // bool refine_spectrum_synthesis = false;
+
+ MassSpectrum spectrum_simple =
+ readMgf(QString(CMAKE_SOURCE_DIR).append("/tests/data/scan_2016.mgf"));
+ //.applyCutOff(150).takeNmostIntense(100).applyDynamicRange(100);
+
+
+ Peptide peptide("EDKPQPPPEGR");
+ PeptideSp peptide_sp(peptide.makePeptideSp());
+ // peptide_sp.get()->addAaModification(AaModification::getInstance("MOD:00397"),
+ // 0);
+
+ PsmFeatures features(PrecisionFactory::getDaltonInstance(0.02), 150);
+
+ features.setPeptideSpectrumCharge(peptide_sp, &spectrum_simple, 3);
+
+ REQUIRE(features.getTotalIntensity() == Approx(248641.8659667977));
+ REQUIRE(features.getIntensityOfMatchedIon(PeptideIon::b) ==
+ Approx(1751.5864257813).epsilon(0.001));
+ REQUIRE(features.getIntensityOfMatchedIon(PeptideIon::y) ==
+ Approx(57112.2947998047).epsilon(0.001));
+
+
+ REQUIRE(features.countMatchedIonComplementPairs() == 0);
+
+
+ /*
+ <group id="15968" mh="1275.731419" z="2" rt="PT2843.58S" expect="1.7e-04"
+ label="GRMZM5G815453_P01 P00874 Ribulose bisphosphate carboxylase large chain
+ Precursor..." type="model" sumI="6.08" maxI="111642" fI="1116.42" act="0" >
+ <protein expect="-191.8" id="15968.1" uid="49237" label="GRMZM5G815453_P01
+ P00874 Ribulose bisphosphate carboxylase large chain Precursor..." sumI="8.97"
+ > <note label="description">GRMZM5G815453_P01 P00874 Ribulose bisphosphate
+ carboxylase large chain Precursor (RuBisCO large subunit)(EC 4.1.1.39)
+ seq=translation; coord=Pt:56824..58323:1; parent_transcript=GRMZM5G815453_T01;
+ parent_gene=GRMZM5G815453</note> <file type="peptide"
+ URL="/gorgone/pappso/formation/TD/Database/Genome_Z_mays_5a.fasta"/> <peptide
+ start="1" end="483"> <domain id="15968.1.1" start="347" end="357"
+ expect="1.7e-04" mh="1275.7311" delta="0.0003" hyperscore="29.0"
+ nextscore="10.8" y_score="10.5" y_ions="8" b_score="3.8" b_ions="1" pre="EGER"
+ post="DDFI" seq="EITLGFVDLLR" missed_cleavages="0">
+ </domain>
+ </peptide>
+ */
+ spectrum_simple =
+ readMgf(QString(CMAKE_SOURCE_DIR).append("/tests/data/scan_15968.mgf"));
+
+
+ peptide_sp = Peptide("EITLGFVDLLR").makePeptideSp();
+
+ features.setPeptideSpectrumCharge(peptide_sp, &spectrum_simple, 2);
+
+
+ REQUIRE(
+ features.getMaxIntensityMatchedIonComplementPairPrecursorMassDelta() ==
+ Approx(-0.0036778069).epsilon(0.00001));
+ REQUIRE(features.countMatchedIonComplementPairs() == 3);
+
+ REQUIRE(features.getPeakIonPairs().size() == 3);
+
+ REQUIRE(features.getPeakIonPairs()[0].first.toString().toStdString() ==
+ "b2+isotope0r1mz243.134");
+ REQUIRE(features.getPeakIonPairs()[0].second.toString().toStdString() ==
+ "y9+isotope0r1mz1033.61");
+
+ REQUIRE(features.getPeakIonPairs()[1].first.toString().toStdString() ==
+ "b6+isotope0r1mz661.367");
+ REQUIRE(features.getPeakIonPairs()[1].second.toString().toStdString() ==
+ "y5+isotope0r1mz615.383");
+
+ REQUIRE(features.getPeakIonPairs()[2].first.toString().toStdString() ==
+ "b7+isotope0r1mz760.435");
+ REQUIRE(features.getPeakIonPairs()[2].second.toString().toStdString() ==
+ "y4+isotope0r1mz516.315");
+
+
+ REQUIRE(
+ features.getIonPairPrecursorMassDelta(features.getPeakIonPairs()[0]) ==
+ Approx(-0.0036778069).epsilon(0.001));
+ REQUIRE(
+ features.getIonPairPrecursorMassDelta(features.getPeakIonPairs()[1]) ==
+ Approx(-0.0118262069).epsilon(0.001));
+ REQUIRE(
+ features.getIonPairPrecursorMassDelta(features.getPeakIonPairs()[2]) ==
+ Approx(-0.0114600069).epsilon(0.001));
+
+
+ REQUIRE(features.getMaxConsecutiveIon(PeptideIon::y) == 9);
+ REQUIRE(features.getMaxConsecutiveIon(PeptideIon::b) == 2);
+ REQUIRE(features.getMaxConsecutiveIon(PeptideIon::a) == 0);
+
+
+ spectrum_simple = readMgf(
+ QString(CMAKE_SOURCE_DIR).append("/tests/data/peaklist_15046.mgf"));
+
+ peptide_sp = Peptide("AIADGSLLDLLR").makePeptideSp();
+
+ features.setPeptideSpectrumCharge(peptide_sp, &spectrum_simple, 2);
+ REQUIRE(features.getMaxConsecutiveIon(PeptideIon::y) == 10);
+ REQUIRE(features.getMaxConsecutiveIon(PeptideIon::b) == 3);
+ REQUIRE(features.getAaSequenceCoverage(PeptideIon::y) == 10);
+ REQUIRE(features.getAaSequenceCoverage(PeptideIon::b) == 5);
+
+
+ REQUIRE(features.getIntensityOfMatchedIon(PeptideIon::y) ==
+ Approx(863068.6967769999));
+ REQUIRE(features.getMaxIntensityPeakIonMatch(PeptideIon::y) ==
+ Approx(114514.0625));
+
+ REQUIRE(features.getIntensityOfMatchedIon(PeptideIon::b) ==
+ Approx(254791.342651));
+ REQUIRE(features.getMaxIntensityPeakIonMatch(PeptideIon::b) ==
+ Approx(161016.984375));
+
+
+ // SeqCoverComplementPeaks
+ REQUIRE(features.getComplementPairsAaSequenceCoverage() == 5);
+ REQUIRE(((double)features.getComplementPairsAaSequenceCoverage() /
+ (double)peptide_sp.get()->size()) == Approx(5.0 / 12.0));
+ REQUIRE(((double)0 / (double)peptide_sp.get()->size()) == Approx(0));
+
+
+ REQUIRE((features.getTotalIntensityOfMatchedIonComplementPairs() /
+ features.getTotalIntensity()) == Approx(0.1727291768));
+
+ REQUIRE((features.getTotalIntensityOfMatchedIonComplementPairs() <
+ features.getTotalIntensity()));
+
+ REQUIRE(
+ features.getMaxIntensityMatchedIonComplementPairPrecursorMassDelta() ==
+ Approx(0.0008592852).epsilon(0.00001));
}
}
diff --git a/tests/test_xic.cpp b/tests/test_xic.cpp
index 8a12c625e..4bea25662 100644
--- a/tests/test_xic.cpp
+++ b/tests/test_xic.cpp
@@ -313,15 +313,15 @@ TEST_CASE("XIC test suite.", "[XIC]")
xicprm_test);
INFO("readOdsXic OK");
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ qDebug();
TraceDetectionZivy _zivy(2, 3, 3, 5000, 6000);
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ qDebug();
TraceDetectionMaxSink max_peak_tic;
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ qDebug();
try
{
- _zivy.detect(xicprm_test, max_peak_tic);
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _zivy.detect(xicprm_test, max_peak_tic, true);
+ qDebug();
}
catch(PappsoException &error)
{
@@ -339,41 +339,41 @@ TEST_CASE("XIC test suite.", "[XIC]")
OdsDocWriter writer(&fileods);
TracePeakOdsWriterSink ods_sink(writer);
- _zivy.detect(xicprm_test, ods_sink);
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _zivy.detect(xicprm_test, ods_sink, true);
+ qDebug();
writer.close();
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ qDebug();
fileods.close();
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ qDebug();
Xic realxic_test;
readOdsXic(QString(CMAKE_SOURCE_DIR).append("/tests/data/xic/real_xic.ods"),
realxic_test);
INFO("readOdsXic OK");
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ qDebug();
QFile realfileods(
QString(CMAKE_SOURCE_DIR).append("/tests/data/xic/real_xic_detect.ods"));
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ qDebug();
OdsDocWriter realwriter(&realfileods);
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ qDebug();
TracePeakOdsWriterSink real_ods_sink(realwriter);
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ qDebug();
//_zivy.setSink(&max_peak_tic);
TraceDetectionZivy _zivyb(2, 4, 3, 30000, 50000);
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ qDebug();
try
{
- _zivyb.detect(realxic_test, real_ods_sink);
+ _zivyb.detect(realxic_test, real_ods_sink, true);
}
catch(PappsoException &error)
{
INFO("error TraceDetectionZivy : " << error.qwhat().toStdString());
throw error;
}
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ qDebug();
realwriter.close();
realfileods.close();
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ qDebug();
QFile realfilemoulondetectods(
QString(CMAKE_SOURCE_DIR)
@@ -383,7 +383,7 @@ TEST_CASE("XIC test suite.", "[XIC]")
TraceDetectionMoulon moulon(4, 60000, 40000);
- moulon.detect(realxic_test, real_detect_moulonods_sink);
+ moulon.detect(realxic_test, real_detect_moulonods_sink, true);
realdetectmoulonwriter.close();
realfilemoulondetectods.close();
@@ -453,25 +453,25 @@ TEST_CASE("test operations on tracepeaklist", "[tracepeaklist]")
Xic empty_xic;
TraceDetectionZivy _zivy(2, 3, 3, 5000, 6000);
TracePeakList peak_list;
- _zivy.detect(empty_xic, peak_list);
+ _zivy.detect(empty_xic, peak_list, true);
REQUIRE(peak_list.size() == 0);
empty_xic.resize(2);
fill(empty_xic.begin(), empty_xic.end(), DataPoint(1, 1));
- _zivy.detect(empty_xic, peak_list);
+ _zivy.detect(empty_xic, peak_list, true);
REQUIRE(peak_list.size() == 0);
empty_xic.resize(3);
fill(empty_xic.begin(), empty_xic.end(), DataPoint(1, 1));
- _zivy.detect(empty_xic, peak_list);
+ _zivy.detect(empty_xic, peak_list, true);
REQUIRE(peak_list.size() == 0);
empty_xic.resize(4);
fill(empty_xic.begin(), empty_xic.end(), DataPoint(1, 1));
- _zivy.detect(empty_xic, peak_list);
+ _zivy.detect(empty_xic, peak_list, true);
REQUIRE(peak_list.size() == 0);
@@ -484,7 +484,7 @@ TEST_CASE("test operations on tracepeaklist", "[tracepeaklist]")
i++;
}
- _zivy.detect(empty_xic, peak_list);
+ _zivy.detect(empty_xic, peak_list, true);
REQUIRE(peak_list.size() == 0);
@@ -497,7 +497,7 @@ TEST_CASE("test operations on tracepeaklist", "[tracepeaklist]")
i++;
}
- _zivy.detect(empty_xic, peak_list);
+ _zivy.detect(empty_xic, peak_list, true);
REQUIRE(peak_list.size() == 0);
}
SECTION("test for masschroq issue#15", "[tracepeaklist]")
@@ -512,7 +512,7 @@ TEST_CASE("test operations on tracepeaklist", "[tracepeaklist]")
TraceDetectionZivy zivy15(2, 4, 3, 5000, 3000);
TracePeakList peak_list;
qDebug();
- zivy15.detect(xic, peak_list);
+ zivy15.detect(xic, peak_list, true);
qDebug();
REQUIRE(peak_list.size() == 0);
}
@@ -528,8 +528,23 @@ TEST_CASE("test operations on tracepeaklist", "[tracepeaklist]")
readOdsXic(QString(CMAKE_SOURCE_DIR).append("/tests/data/xic/real_xic.ods"),
xicprm_test);
+ TracePeak peak(
+ xicprm_test.begin() + 9079, xicprm_test.begin() + 9142, false);
+
+ REQUIRE(peak.getArea() == Approx(96163224.06));
+
+ TracePeak peak_nobase(
+ xicprm_test.begin() + 9079, xicprm_test.begin() + 9142, true);
+
+ REQUIRE(peak_nobase.getArea() == Approx(76281621.60));
+
+ REQUIRE(
+ peak_nobase.getLeftBoundary().y *
+ (peak_nobase.getRightBoundary().x - peak_nobase.getLeftBoundary().x) ==
+ Approx(peak.getArea() - peak_nobase.getArea()));
+
INFO("readOdsXic OK");
- REQUIRE_NOTHROW(_zivy.detect(xicprm_test, peak_list));
+ REQUIRE_NOTHROW(_zivy.detect(xicprm_test, peak_list, true));
REQUIRE(peak_list.size() == 64);
--
GitLab
From 40780727f82d0b3e40c0e9cf38ff16ef5e95156f Mon Sep 17 00:00:00 2001
From: "Filippo Rusconi (Uploading Debian Developer)" <lopippo@debian.org>
Date: Mon, 7 Nov 2022 17:12:45 +0100
Subject: [PATCH 2/6] Import last version from qt6olivier.
---
CMakeLists.txt | 13 ++++++
src/CMakeLists.txt | 34 +++++++-------
src/pappsomspp/obo/obopsimodterm.cpp | 37 ++++++++++++++++
src/pappsomspp/obo/obopsimodterm.h | 11 +++--
src/pappsomspp/vendors/tims/timsdata.cpp | 56 ++++++++++++++----------
src/pappsomspp/vendors/tims/timsdata.h | 6 +--
tests/CMakeLists.txt | 46 ++++++++++---------
tests/test_psm.cpp | 4 +-
tests/widget/main.cpp | 1 +
9 files changed, 136 insertions(+), 72 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index be95412d7..c69c962bd 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -85,6 +85,11 @@ add_definitions(-Wall)
message(STATUS "${BoldGreen}Setting definition -Wextra.${ColourReset}")
add_definitions(-Wextra)
+if(WARN_AS_ERROR)
+ message(STATUS "${BoldYellow}Setting definition -Werror.${ColourReset}")
+ add_definitions(-Werror)
+endif()
+
message(STATUS "${BoldRed}CMAKE_SOURCE_DIR: ${CMAKE_SOURCE_DIR}${ColourReset}")
@@ -180,6 +185,14 @@ message(STATUS "Boost_INCLUDES: ${Boost_INCLUDE_DIRS}")
message(STATUS "Boost_LIB_DIRS: ${Boost_LIBRARY_DIRS}")
+# QCustomPlotQt6
+if(QCustomPlotQt6_FOUND)
+else (QCustomPlotQt6_FOUND)
+ set(QCustomPlotQt6_DIR ${CMAKE_MODULE_PATH})
+ find_package(QCustomPlotQt6 REQUIRED)
+endif(QCustomPlotQt6_FOUND)
+
+
if(Alglib_FOUND)
else (Alglib_FOUND)
set(Alglib_DIR ${CMAKE_MODULE_PATH})
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 4babea01b..806a0883f 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -57,7 +57,7 @@ set(CPP_FILES
pappsomspp/processing/filters/filterceilingamplitudepercentage.cpp
pappsomspp/processing/filters/filterlowintensitysignalremoval.cpp
- #pappsomspp/processing/tandemwrapper/tandemwrapperrun.cpp
+ pappsomspp/processing/tandemwrapper/tandemwrapperrun.cpp
pappsomspp/processing/tandemwrapper/wraptandeminput.cpp
pappsomspp/processing/tandemwrapper/wraptandemresults.cpp
pappsomspp/processing/tandemwrapper/xtandempresetreader.cpp
@@ -90,7 +90,7 @@ set(CPP_FILES
pappsomspp/msfile/msfilereader.cpp
pappsomspp/msfile/mzformatenumstr.cpp
pappsomspp/msfile/pwizmsfilereader.cpp
- #pappsomspp/msfile/timsmsfilereader.cpp
+ pappsomspp/msfile/timsmsfilereader.cpp
pappsomspp/msfile/xymsfilereader.cpp
pappsomspp/msrun/alignment/msrunretentiontime.cpp
@@ -102,9 +102,9 @@ set(CPP_FILES
pappsomspp/msrun/msrunid.cpp
pappsomspp/msrun/msrunreader.cpp
pappsomspp/msrun/private/pwizmsrunreader.cpp
- #pappsomspp/msrun/private/timsmsrunreader.cpp
- #pappsomspp/msrun/private/timsmsrunreaderms2.cpp
- #pappsomspp/msrun/private/timsmsrunreaderms2selected.cpp
+ pappsomspp/msrun/private/timsmsrunreader.cpp
+ pappsomspp/msrun/private/timsmsrunreaderms2.cpp
+ pappsomspp/msrun/private/timsmsrunreaderms2selected.cpp
pappsomspp/msrun/xiccoord/xiccoord.cpp
pappsomspp/msrun/xiccoord/xiccoordtims.cpp
pappsomspp/msrun/xymsrunreader.cpp
@@ -159,18 +159,18 @@ set(CPP_FILES
pappsomspp/trace/maptrace.cpp
pappsomspp/trace/trace.cpp
- #pappsomspp/vendors/tims/mzcalibration/mzcalibrationinterface.cpp
- #pappsomspp/vendors/tims/mzcalibration/mzcalibrationmodel1.cpp
- #pappsomspp/vendors/tims/mzcalibration/mzcalibrationstore.cpp
- #pappsomspp/vendors/tims/xicextractor/timsdirectxicextractor.cpp
- #pappsomspp/vendors/tims/xicextractor/timsxicextractorinterface.cpp
- #pappsomspp/vendors/tims/timsbindec.cpp
- #pappsomspp/vendors/tims/timsdata.cpp
- #pappsomspp/vendors/tims/timsframe.cpp
- #pappsomspp/vendors/tims/timsframerawdatachunck.cpp
- #pappsomspp/vendors/tims/timsframebase.cpp
- #pappsomspp/vendors/tims/timsframetype1.cpp
- #pappsomspp/vendors/tims/timsms2centroidfilter.cpp
+ pappsomspp/vendors/tims/mzcalibration/mzcalibrationinterface.cpp
+ pappsomspp/vendors/tims/mzcalibration/mzcalibrationmodel1.cpp
+ pappsomspp/vendors/tims/mzcalibration/mzcalibrationstore.cpp
+ pappsomspp/vendors/tims/xicextractor/timsdirectxicextractor.cpp
+ pappsomspp/vendors/tims/xicextractor/timsxicextractorinterface.cpp
+ pappsomspp/vendors/tims/timsbindec.cpp
+ pappsomspp/vendors/tims/timsdata.cpp
+ pappsomspp/vendors/tims/timsframe.cpp
+ pappsomspp/vendors/tims/timsframerawdatachunck.cpp
+ pappsomspp/vendors/tims/timsframebase.cpp
+ pappsomspp/vendors/tims/timsframetype1.cpp
+ pappsomspp/vendors/tims/timsms2centroidfilter.cpp
pappsomspp/xic/xic.cpp
pappsomspp/xic/qualifiedxic.cpp
diff --git a/src/pappsomspp/obo/obopsimodterm.cpp b/src/pappsomspp/obo/obopsimodterm.cpp
index 2dd6a04f9..b126743b4 100644
--- a/src/pappsomspp/obo/obopsimodterm.cpp
+++ b/src/pappsomspp/obo/obopsimodterm.cpp
@@ -47,6 +47,43 @@ QRegularExpression OboPsiModTerm::m_findExactPsiModLabel(
QRegularExpression OboPsiModTerm::m_findRelatedPsiMsLabel(
"^(.*)\\sRELATED\\sPSI-MS-label\\s\\[\\]$");
+
+OboPsiModTerm::OboPsiModTerm()
+{
+}
+
+OboPsiModTerm::~OboPsiModTerm()
+{
+}
+OboPsiModTerm::OboPsiModTerm(const OboPsiModTerm &other)
+{
+ m_accession = other.m_accession;
+ m_name = other.m_name;
+ m_definition = other.m_definition;
+ m_psiModLabel = other.m_psiModLabel;
+ m_psiMsLabel = other.m_psiMsLabel;
+ m_diffFormula = other.m_diffFormula;
+ m_origin = other.m_origin;
+
+ m_diffMono = other.m_diffMono;
+}
+
+OboPsiModTerm &
+OboPsiModTerm::operator=(const OboPsiModTerm &other)
+{
+ m_accession = other.m_accession;
+ m_name = other.m_name;
+ m_definition = other.m_definition;
+ m_psiModLabel = other.m_psiModLabel;
+ m_psiMsLabel = other.m_psiMsLabel;
+ m_diffFormula = other.m_diffFormula;
+ m_origin = other.m_origin;
+
+ m_diffMono = other.m_diffMono;
+ return *this;
+}
+
+
bool
OboPsiModTerm::isValid() const
{
diff --git a/src/pappsomspp/obo/obopsimodterm.h b/src/pappsomspp/obo/obopsimodterm.h
index f312dc77c..884b7c868 100644
--- a/src/pappsomspp/obo/obopsimodterm.h
+++ b/src/pappsomspp/obo/obopsimodterm.h
@@ -33,10 +33,10 @@ class PMSPP_LIB_DECL OboPsiModTerm
friend OboPsiMod;
public:
- OboPsiModTerm() = default;
- ~OboPsiModTerm() = default;
- OboPsiModTerm(const OboPsiModTerm &) = default;
- OboPsiModTerm &operator=(const OboPsiModTerm &) = default;
+ OboPsiModTerm();
+ virtual ~OboPsiModTerm();
+ OboPsiModTerm(const OboPsiModTerm &);
+ OboPsiModTerm &operator=(const OboPsiModTerm &);
bool isValid() const;
@@ -49,7 +49,7 @@ class PMSPP_LIB_DECL OboPsiModTerm
QString m_diffFormula;
QString m_origin;
- double m_diffMono;
+ double m_diffMono = 0;
private:
void parseLine(const QString &line);
@@ -63,5 +63,4 @@ class PMSPP_LIB_DECL OboPsiModTerm
} // namespace pappso
-
extern int oboPsiModTermMetaTypeId;
diff --git a/src/pappsomspp/vendors/tims/timsdata.cpp b/src/pappsomspp/vendors/tims/timsdata.cpp
index 75dde4a84..c72ccc367 100644
--- a/src/pappsomspp/vendors/tims/timsdata.cpp
+++ b/src/pappsomspp/vendors/tims/timsdata.cpp
@@ -966,7 +966,7 @@ void
TimsData::getQualifiedMs1MassSpectrumByPrecursorId(
const MsRunIdCstSPtr &msrun_id,
QualifiedMassSpectrum &mass_spectrum,
- SpectrumDescr &spectrum_descr,
+ const SpectrumDescr &spectrum_descr,
bool want_binary_data)
{
@@ -1410,7 +1410,7 @@ void
TimsData::getQualifiedMs2MassSpectrumByPrecursorId(
const MsRunIdCstSPtr &msrun_id,
QualifiedMassSpectrum &mass_spectrum,
- SpectrumDescr &spectrum_descr,
+ const SpectrumDescr &spectrum_descr,
bool want_binary_data)
{
try
@@ -1799,9 +1799,10 @@ pappso::TimsData::ms2ReaderSpectrumCollectionByMsLevel(
std::function<std::vector<QualifiedMassSpectrum>(
- pappso::TimsData::SpectrumDescr &)>
- generate_spectrum = [itself, msrun_id, pointer_handler, ms_level](
- pappso::TimsData::SpectrumDescr &spectrum_descr)
+ const pappso::TimsData::SpectrumDescr &)>
+ map_function_generate_spectrum =
+ [itself, msrun_id, pointer_handler, ms_level](
+ const pappso::TimsData::SpectrumDescr &spectrum_descr)
-> std::vector<QualifiedMassSpectrum> {
std::vector<QualifiedMassSpectrum> mass_spectrum_list;
itself->ms2ReaderGenerateMS1MS2Spectrum(msrun_id,
@@ -1814,28 +1815,35 @@ pappso::TimsData::ms2ReaderSpectrumCollectionByMsLevel(
return mass_spectrum_list;
};
+ std::function<void(
+ std::size_t,
+ const std::vector<QualifiedMassSpectrum> &qualified_spectrum_list)>
+ reduce_function_spectrum_list =
+ [pointer_handler, local_filepath](
+ std::size_t res,
+ const std::vector<QualifiedMassSpectrum> &qualified_spectrum_list) {
+ for(auto &qualified_spectrum : qualified_spectrum_list)
+ {
+ pointer_handler->setQualifiedMassSpectrum(qualified_spectrum);
+ }
+
+ if(pointer_handler->shouldStop())
+ {
+ qDebug() << "The operation was cancelled. Breaking the loop.";
+ throw ExceptionInterrupted(
+ QObject::tr("reading TimsTOF job on %1 cancelled by the user")
+ .arg(local_filepath));
+ }
+ res++;
+ };
+
+
QFuture<std::size_t> res;
res = QtConcurrent::mappedReduced<std::size_t>(
spectrum_description_list.begin(),
spectrum_description_list.end(),
- generate_spectrum,
- [pointer_handler, res, local_filepath](
- std::size_t &result,
- std::vector<QualifiedMassSpectrum> qualified_spectrum_list) {
- for(auto &qualified_spectrum : qualified_spectrum_list)
- {
- pointer_handler->setQualifiedMassSpectrum(qualified_spectrum);
- }
-
- if(pointer_handler->shouldStop())
- {
- qDebug() << "The operation was cancelled. Breaking the loop.";
- throw ExceptionInterrupted(
- QObject::tr("reading TimsTOF job cancelled by the user :\n%1")
- .arg(local_filepath));
- }
- result++;
- },
+ map_function_generate_spectrum,
+ reduce_function_spectrum_list,
QtConcurrent::OrderedReduce);
res.waitForFinished();
}
@@ -1849,7 +1857,7 @@ pappso::TimsData::ms2ReaderGenerateMS1MS2Spectrum(
const MsRunIdCstSPtr &msrun_id,
std::vector<QualifiedMassSpectrum> &qualified_mass_spectrum_list,
pappso::SpectrumCollectionHandlerInterface &handler,
- pappso::TimsData::SpectrumDescr &spectrum_descr,
+ const pappso::TimsData::SpectrumDescr &spectrum_descr,
unsigned int ms_level)
{
diff --git a/src/pappsomspp/vendors/tims/timsdata.h b/src/pappsomspp/vendors/tims/timsdata.h
index de8a19f83..2434f8aa2 100644
--- a/src/pappsomspp/vendors/tims/timsdata.h
+++ b/src/pappsomspp/vendors/tims/timsdata.h
@@ -129,13 +129,13 @@ class PMSPP_LIB_DECL TimsData
void
getQualifiedMs2MassSpectrumByPrecursorId(const MsRunIdCstSPtr &msrun_id,
QualifiedMassSpectrum &mass_spectrum,
- SpectrumDescr &spectrum_descr,
+ const SpectrumDescr &spectrum_descr,
bool want_binary_data);
void
getQualifiedMs1MassSpectrumByPrecursorId(const MsRunIdCstSPtr &msrun_id,
QualifiedMassSpectrum &mass_spectrum,
- SpectrumDescr &spectrum_descr,
+ const SpectrumDescr &spectrum_descr,
bool want_binary_data);
/** @brief filter interface to apply just after raw MS2 specturm extraction
@@ -282,7 +282,7 @@ class PMSPP_LIB_DECL TimsData
const MsRunIdCstSPtr &msrun_id,
std::vector<QualifiedMassSpectrum> &qualified_mass_spectrum_list,
SpectrumCollectionHandlerInterface &handler,
- SpectrumDescr &spectrum_descr,
+ const SpectrumDescr &spectrum_descr,
unsigned int ms_level);
void fillSpectrumDescriptionWithSqlRecord(SpectrumDescr &spectrum_descr,
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index e24a4e403..fa0e3bf7a 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -32,6 +32,7 @@ if(MAKE_TESTS AND (WIN64 OR (UNIX AND NOT APPLE)))
find_package(Catch2 REQUIRED)
+
if(OdsStream_FOUND)
else (OdsStream_FOUND)
find_package(OdsStream REQUIRED)
@@ -150,17 +151,17 @@ if(MAKE_TESTS AND (WIN64 OR (UNIX AND NOT APPLE)))
target_link_libraries(test_fasta_reader Qt6::Core pappsomspp-shared)
add_test(test_fasta_reader "test_fasta_reader")
- add_executable(test_protein test_protein.cpp)
- target_link_libraries(test_protein Qt6::Core pappsomspp-shared)
- add_test(test_protein "test_protein")
+ #add_executable(test_protein test_protein.cpp)
+ #target_link_libraries(test_protein Qt6::Core pappsomspp-shared)
+ #add_test(test_protein "test_protein")
add_executable(test_massrange test_massrange.cpp)
target_link_libraries(test_massrange Qt6::Core pappsomspp-shared)
add_test(test_massrange "test_massrange")
- add_executable(test_peptide test_peptide.cpp)
- target_link_libraries(test_peptide Qt6::Core Qt6::Gui pappsomspp-shared)
- add_test(test_peptide "test_peptide")
+ #add_executable(test_peptide test_peptide.cpp)
+ #target_link_libraries(test_peptide Qt6::Core Qt6::Gui pappsomspp-shared)
+ #add_test(test_peptide "test_peptide")
add_executable(test_peptidenaturalisotopelist test_peptidenaturalisotopelist.cpp)
target_link_libraries(test_peptidenaturalisotopelist Qt6::Core Qt6::Gui pappsomspp-shared)
@@ -179,9 +180,9 @@ if(MAKE_TESTS AND (WIN64 OR (UNIX AND NOT APPLE)))
add_test(test_fragmentationcid "test_fragmentationcid")
#IF (FALSE)
- add_executable(test_big_hyperscore test_big_hyperscore.cpp ${CPP_TEST_FILES})
- target_link_libraries(test_big_hyperscore Qt6::Core Qt6::Gui Qt6::Xml pappsomspp-shared)
- add_test(test_big_hyperscore "test_big_hyperscore")
+ #add_executable(test_big_hyperscore test_big_hyperscore.cpp ${CPP_TEST_FILES})
+ #target_link_libraries(test_big_hyperscore Qt6::Core Qt6::Gui Qt6::Xml pappsomspp-shared)
+ #add_test(test_big_hyperscore "test_big_hyperscore")
#ENDIF(FALSE)
add_executable(test_rawmasslist test_rawmasslist.cpp)
@@ -189,32 +190,35 @@ if(MAKE_TESTS AND (WIN64 OR (UNIX AND NOT APPLE)))
add_test(test_rawmasslist "test_rawmasslist")
add_executable(test_isotope_with_spectrum common.cpp test_isotope_with_spectrum.cpp)
- target_link_libraries(test_isotope_with_spectrum Qt6::Core Qt6::Gui pappsomspp-shared ${Boost_LIBRARIES})
+ target_link_libraries(test_isotope_with_spectrum Qt6::Core Qt6::Gui
+ QuaZip::QuaZip pappsomspp-shared ${Boost_LIBRARIES})
add_test(test_isotope_with_spectrum "test_isotope_with_spectrum")
set(TEST_LIST ${TEST_LIST} test_isotope_with_spectrum)
add_executable(test_hyperscore common.cpp test_hyperscore.cpp)
- target_link_libraries(test_hyperscore Qt6::Core pappsomspp-shared Qt6::Gui ${Boost_LIBRARIES})
+ target_link_libraries(test_hyperscore Qt6::Core pappsomspp-shared Qt6::Gui
+ QuaZip::QuaZip ${Boost_LIBRARIES})
add_test(test_hyperscore "test_hyperscore")
set(TEST_LIST ${TEST_LIST} test_hyperscore)
add_executable(test_xtandem_spectrum common.cpp test_xtandem_spectrum.cpp)
- target_link_libraries(test_xtandem_spectrum Qt6::Core pappsomspp-shared Qt6::Gui ${Boost_LIBRARIES})
+ target_link_libraries(test_xtandem_spectrum Qt6::Core pappsomspp-shared
+ Qt6::Gui QuaZip::QuaZip ${Boost_LIBRARIES})
add_test(test_xtandem_spectrum "test_xtandem_spectrum")
set(TEST_LIST ${TEST_LIST} test_xtandem_spectrum)
add_executable(test_scan_15968 common.cpp test_scan_15968.cpp)
- target_link_libraries(test_scan_15968 Qt6::Core Qt6::Gui pappsomspp-shared ${Boost_LIBRARIES})
+ target_link_libraries(test_scan_15968 Qt6::Core Qt6::Gui pappsomspp-shared QuaZip::QuaZip ${Boost_LIBRARIES})
add_test(test_scan_15968 "test_scan_15968")
set(TEST_LIST ${TEST_LIST} test_scan_15968)
add_executable(test_psm common.cpp test_psm.cpp)
- target_link_libraries(test_psm Qt6::Core pappsomspp-shared Qt6::Gui Qt6::Concurrent ${Boost_LIBRARIES})
+ target_link_libraries(test_psm Qt6::Core pappsomspp-shared Qt6::Gui Qt6::Concurrent QuaZip::QuaZip ${Boost_LIBRARIES})
add_test(test_psm "test_psm")
set(TEST_LIST ${TEST_LIST} test_psm)
add_executable(test_xicextractor test_xicextractor.cpp)
- target_link_libraries(test_xicextractor Qt6::Core Qt6::Gui pappsomspp-shared ${Boost_LIBRARIES} OdsStream::Core)
+ target_link_libraries(test_xicextractor Qt6::Core Qt6::Gui pappsomspp-shared ${Boost_LIBRARIES} QuaZip::QuaZip OdsStream::Core)
add_test(test_xicextractor "test_xicextractor")
set(TEST_LIST ${TEST_LIST} test_xicextractor)
@@ -224,14 +228,14 @@ if(MAKE_TESTS AND (WIN64 OR (UNIX AND NOT APPLE)))
set(TEST_LIST ${TEST_LIST} test_msrunoutput)
- if(UNIX)
+ #if(UNIX)
- set_property(TEST catch2-only-tests test_big_hyperscore test_fasta_reader
- test_massrange test_peptidenaturalisotopelist test_peptidefragment
- test_fragmentationcid ${TEST_LIST} test_natural_isotope_average test_rawmasslist
- PROPERTY ENVIRONMENT "LD_LIBRARY_PATH=$ENV{LD_LIBRARY_PATH}:../src")
+ #set_property(TEST catch2-only-tests test_big_hyperscore test_fasta_reader
+ #test_massrange test_peptidenaturalisotopelist test_peptidefragment
+ #test_fragmentationcid ${TEST_LIST} test_natural_isotope_average test_rawmasslist
+ #PROPERTY ENVIRONMENT "LD_LIBRARY_PATH=$ENV{LD_LIBRARY_PATH}:../src")
- endif()
+ #endif()
if(WIN32)
set(ENV{PATH} "$ENV{PATH};..\\src")
diff --git a/tests/test_psm.cpp b/tests/test_psm.cpp
index e495e4ac5..1816cfece 100644
--- a/tests/test_psm.cpp
+++ b/tests/test_psm.cpp
@@ -29,8 +29,10 @@
// make test ARGS="-V -I 18,18"
// ./tests/catch2-only-tests [psm] -s
// ./tests/catch2-only-tests [psmfeature] -s
-#include <algorithm>
+#define CATCH_CONFIG_MAIN
+
+#include <algorithm>
#include <catch2/catch.hpp>
#include <pappsomspp/mzrange.h>
#include <pappsomspp/psm/peptidespectrummatch.h>
diff --git a/tests/widget/main.cpp b/tests/widget/main.cpp
index d18831695..e68322560 100644
--- a/tests/widget/main.cpp
+++ b/tests/widget/main.cpp
@@ -28,6 +28,7 @@
******************************************************************************/
#include <QApplication>
+#include <QIODevice>
#include <pappsomspp/pappsoexception.h>
#include "testwidgetgui.h"
--
GitLab
From 337e8e9931ee2aa006fe405cd6a8e5aedc1873eb Mon Sep 17 00:00:00 2001
From: "Filippo Rusconi (Uploading Debian Developer)" <lopippo@debian.org>
Date: Mon, 7 Nov 2022 17:24:40 +0100
Subject: [PATCH 3/6] Merge the debian/changelog from qt6olivier.
---
debian/changelog | 46 ++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 46 insertions(+)
diff --git a/debian/changelog b/debian/changelog
index a4b782d19..5787dfcbe 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -6,6 +6,52 @@ libpappsomspp (0.9.0-1) unstable; urgency=low
-- Filippo Rusconi <lopippo@debian.org> Thu, 22 Sep 2022 18:35:01 +0200
+libpappsomspp (0.8.60-1~bullseye+1) bullseye; urgency=medium
+
+ * bullseye backport
+
+ -- Olivier Langella <olivier.langella@u-psud.fr> Mon, 31 Oct 2022 09:06:33 +0100
+
+libpappsomspp (0.8.60-1) unstable; urgency=low
+
+ * Fix the distribution... was working too late at night...
+
+ -- Filippo Rusconi <lopippo@debian.org> Fri, 28 Oct 2022 10:20:12 +0200
+
+libpappsomspp (0.8.59-1) bullseye; urgency=low
+
+ * New upstream version.
+
+ * Incidentally, previous version was to fix a bug that was published in
+ betwwen the previous version and this one: (Closes: #1022934).
+
+ -- Filippo Rusconi <lopippo@debian.org> Fri, 28 Oct 2022 03:30:29 +0200
+
+libpappsomspp (0.8.58-1) bullseye; urgency=low
+
+ * New upstream version (see 0.8.57-1~bullseye+1).
+
+ * Standards-Version: 4.6.1.
+
+ * d/rules: Fix by Adrian Bunk to work around the excess precision of the x87
+ FPU that causes
+ https://buildd.debian.org/status/logs.php?pkg=libpappsomspp&arch=i386.
+
+ -- Filippo Rusconi <lopippo@debian.org> Thu, 27 Oct 2022 10:38:00 +0200
+
+libpappsomspp (0.8.57-1~bullseye+1) bullseye; urgency=medium
+
+ [ Olivier Langella ]
+ * avoid nullptr calls in custom plot widgets
+ * new tims frame widget color map
+ * better tdf handler
+ * new tests for protein , enzyme, psm, psmfeaures
+ * new psm feature API
+ [ Filippo Rusconi ]
+ * refactoring work to compile using Qt6
+
+ -- Olivier Langella <olivier.langella@u-psud.fr> Tue, 04 Oct 2022 17:02:43 +0200
+
libpappsomspp (0.8.56-1) unstable; urgency=low
* New version that implements features in the dt|rt,m/z color map realms.
--
GitLab
From 85006966037a47f65d8b54c8a1f7720265a31b54 Mon Sep 17 00:00:00 2001
From: "Filippo Rusconi (Uploading Debian Developer)" <lopippo@debian.org>
Date: Mon, 7 Nov 2022 17:25:44 +0100
Subject: [PATCH 4/6] Add dependency over zlib1g-dev.
---
debian/control | 1 +
1 file changed, 1 insertion(+)
diff --git a/debian/control b/debian/control
index f685fc065..23a624e0d 100644
--- a/debian/control
+++ b/debian/control
@@ -17,6 +17,7 @@ Build-Depends: debhelper-compat (= 12),
libsqlite3-dev,
libzstd-dev (>= 1.3.3),
liblzf-dev,
+ zlib1g-dev,
libboost-dev,
libboost-iostreams-dev,
libboost-thread-dev,
--
GitLab
From e906ca5b66ddd69b17f50f90fcd968bb29235d9c Mon Sep 17 00:00:00 2001
From: "Filippo Rusconi (Uploading Debian Developer)" <lopippo@debian.org>
Date: Mon, 7 Nov 2022 17:26:42 +0100
Subject: [PATCH 5/6] Add the fix for the i386 build.
---
debian/rules | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/debian/rules b/debian/rules
index e36ef89d1..a9a11dccb 100755
--- a/debian/rules
+++ b/debian/rules
@@ -11,6 +11,12 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
DPKG_EXPORT_BUILDFLAGS = 1
include /usr/share/dpkg/buildflags.mk
+ifneq (,$(filter $(DEB_HOST_ARCH_CPU), i386))
+ export DEB_CXXFLAGS_MAINT_APPEND += -ffloat-store
+endif
+
+
+
%:
dh $@ --buildsystem=cmake
--
GitLab
From 9cfce0edf4dc3030cf084d5d9cce827ad2210b7e Mon Sep 17 00:00:00 2001
From: "Filippo Rusconi (Uploading Debian Developer)" <lopippo@debian.org>
Date: Mon, 7 Nov 2022 17:34:51 +0100
Subject: [PATCH 6/6] Better document the LOCAL_CMAKE_MODULE_PATH and use it.
---
CMakeLists.txt | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index c69c962bd..12c1c5721 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -38,14 +38,19 @@ message(STATUS "CMAKE_INSTALL_FULL_INCLUDEDIR: ${CMAKE_INSTALL_FULL_INCLUDEDIR}"
# Add folder where are supportive functions
set(CMAKE_UTILS_PATH ${CMAKE_SOURCE_DIR}/CMakeStuff)
set(CMAKE_TOOLCHAINS_PATH ${CMAKE_UTILS_PATH}/toolchains)
+
+# We need a variable that is not modified by CMake because we'll need to access
+# that specific directory later
set(LOCAL_CMAKE_MODULE_PATH ${CMAKE_UTILS_PATH}/modules)
message("CMakeLists.txt - LOCAL_CMAKE_MODULE_PATH:" ${LOCAL_CMAKE_MODULE_PATH})
-set(CMAKE_MODULE_PATH ${CMAKE_UTILS_PATH}/modules ${CMAKE_MODULE_PATH})
+
+# Now add our local path to the general path list.
+set(CMAKE_MODULE_PATH ${LOCAL_CMAKE_MODULE_PATH} ${CMAKE_MODULE_PATH})
# This include must come before all the others
# It must include the config-generated config.h file
# before the others.
-#include_directories(${CMAKE_BINARY_DIR})
+include_directories(${CMAKE_BINARY_DIR})
# Include the system's uname that fills in SYSTEM_UNAME_S.
# Sets WIN64 if SYSTEM_UNAME_S is "^.*MING64.*"
--
GitLab