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[Fix] Remaining memory leaks in tests #5494

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merged 3 commits into from Sep 22, 2021
Merged

[Fix] Remaining memory leaks in tests #5494

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d005888
[Fix] FeatureFinderAlgorithmPicked memory leak
dvdvgt Aug 16, 2021
dde932e
[Fix] PeptideHit and TSG memory leak
dvdvgt Aug 20, 2021
26f34fe
Use RAIICleanup instead of shared_ptr
dvdvgt Sep 10, 2021
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8 changes: 4 additions & 4 deletions src/openms/include/OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmPicked.h
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Expand Up @@ -232,7 +232,7 @@ namespace OpenMS

@return A pointer to the trace fitter that should be used.
*/
TraceFitter* chooseTraceFitter_(double& tau);
std::unique_ptr<TraceFitter> chooseTraceFitter_(double& tau);

double intensityScore_(Size rt_bin, Size mz_bin, double intensity) const;

Expand All @@ -251,7 +251,7 @@ namespace OpenMS
@param traces Original mass traces found in the experiment.
@param new_traces Mass traces created by cropping the original mass traces.
*/
void cropFeature_(TraceFitter* fitter,
void cropFeature_(std::shared_ptr<TraceFitter> fitter,
const MassTraces& traces,
MassTraces& new_traces);

Expand All @@ -278,7 +278,7 @@ namespace OpenMS

@return true if the feature is valid
*/
bool checkFeatureQuality_(TraceFitter* fitter,
bool checkFeatureQuality_(std::shared_ptr<TraceFitter> fitter,
MassTraces& feature_traces,
const double& seed_mz, const double& min_feature_score,
String& error_msg, double& fit_score, double& correlation, double& final_score);
Expand All @@ -296,7 +296,7 @@ namespace OpenMS
@param peak The Seed Peak
@param path The path where to put the debug files (default is debug/features)
*/
void writeFeatureDebugInfo_(TraceFitter* fitter,
void writeFeatureDebugInfo_(std::shared_ptr<TraceFitter> fitter,
const MassTraces& traces,
const MassTraces& new_traces,
bool feature_ok, const String error_msg, const double final_score, const Int plot_nr, const PeakType& peak,
Expand Down
16 changes: 12 additions & 4 deletions src/openms/source/CHEMISTRY/TheoreticalSpectrumGenerator.cpp
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Expand Up @@ -41,6 +41,7 @@
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/CHEMISTRY/ResidueDB.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/CONCEPT/RAIICleanup.h>

#include <unordered_set>

Expand Down Expand Up @@ -144,7 +145,17 @@ namespace OpenMS
PeakSpectrum::StringDataArray* ion_names;
PeakSpectrum::IntegerDataArray* charges;

bool charges_dynamic = false, ion_names_dynamic = false;
bool charges_dynamic = false;
bool ion_names_dynamic = false;

// Assure memory is freed even if an exception occurs.
RAIICleanup _(
[&]
{
if (charges_dynamic) delete charges;
if (ion_names_dynamic) delete ion_names;
}
);

if (spectrum.getIntegerDataArrays().empty())
{
Expand Down Expand Up @@ -212,9 +223,6 @@ namespace OpenMS
}
}

if (charges_dynamic) delete charges;
if (ion_names_dynamic) delete ion_names;

if (sort_by_position_) spectrum.sortByPositionPresorted(chunks.getChunks());

// set MS Level
Expand Down
4 changes: 1 addition & 3 deletions src/openms/source/METADATA/PeptideHit.cpp
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Expand Up @@ -126,11 +126,9 @@ namespace OpenMS
MetaInfoInterface::operator=(source);
sequence_ = source.sequence_;
score_ = source.score_;
analysis_results_ = nullptr;
delete analysis_results_;
if (source.analysis_results_ != nullptr)
{
// free memory first
delete analysis_results_;
analysis_results_ = new std::vector<PepXMLAnalysisResult>(*source.analysis_results_);
}
rank_ = source.rank_;
Expand Down
23 changes: 10 additions & 13 deletions src/openms/source/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmPicked.cpp
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Expand Up @@ -678,7 +678,7 @@ namespace OpenMS

// choose fitter
double egh_tau = 0.0;
TraceFitter* fitter = chooseTraceFitter_(egh_tau);
std::shared_ptr<TraceFitter> fitter = chooseTraceFitter_(egh_tau);

fitter->setParameters(trace_fitter_params);
fitter->fit(traces);
Expand Down Expand Up @@ -756,10 +756,10 @@ namespace OpenMS
// Extract some of the model parameters.
if (egh_tau != 0.0)
{
egh_tau = (static_cast<EGHTraceFitter*>(fitter))->getTau();
egh_tau = (std::dynamic_pointer_cast<EGHTraceFitter>(fitter))->getTau();
f.setMetaValue("EGH_tau", egh_tau);
f.setMetaValue("EGH_height", (static_cast<EGHTraceFitter*>(fitter))->getHeight());
f.setMetaValue("EGH_sigma", (static_cast<EGHTraceFitter*>(fitter))->getSigma());
f.setMetaValue("EGH_height", (std::dynamic_pointer_cast<EGHTraceFitter>(fitter))->getHeight());
f.setMetaValue("EGH_sigma", (std::dynamic_pointer_cast<EGHTraceFitter>(fitter))->getSigma());
}

// Calculate the mass of the feature: maximum, average, monoisotopic
Expand Down Expand Up @@ -794,9 +794,6 @@ namespace OpenMS
// - as we scaled the isotope distribution to
f.setIntensity(fitter->getArea() / getIsotopeDistribution_(f.getMZ()).max);

// we do not need the fitter anymore
delete fitter;

//add convex hulls of mass traces
for (Size j = 0; j < traces.size(); ++j)
{
Expand Down Expand Up @@ -1696,19 +1693,19 @@ namespace OpenMS
return final;
}

TraceFitter* FeatureFinderAlgorithmPicked::chooseTraceFitter_(double& tau)
std::unique_ptr<TraceFitter> FeatureFinderAlgorithmPicked::chooseTraceFitter_(double& tau)
{
// choose fitter
if (param_.getValue("feature:rt_shape") == "asymmetric")
{
OPENMS_LOG_DEBUG << "use asymmetric rt peak shape" << std::endl;
tau = -1.0;
return new EGHTraceFitter();
return std::make_unique<EGHTraceFitter>();
}
else // if (param_.getValue("feature:rt_shape") == "symmetric")
{
OPENMS_LOG_DEBUG << "use symmetric rt peak shape" << std::endl;
return new GaussTraceFitter();
return std::make_unique<GaussTraceFitter>();
}
}

Expand Down Expand Up @@ -1746,7 +1743,7 @@ namespace OpenMS
return final;
}

void FeatureFinderAlgorithmPicked::cropFeature_(TraceFitter* fitter,
void FeatureFinderAlgorithmPicked::cropFeature_(std::shared_ptr<TraceFitter> fitter,
const MassTraces& traces,
MassTraces& new_traces)
{
Expand Down Expand Up @@ -1825,7 +1822,7 @@ namespace OpenMS
new_traces.baseline = traces.baseline;
}

bool FeatureFinderAlgorithmPicked::checkFeatureQuality_(TraceFitter* fitter,
bool FeatureFinderAlgorithmPicked::checkFeatureQuality_(std::shared_ptr<TraceFitter> fitter,
MassTraces& feature_traces,
const double& seed_mz, const double& min_feature_score,
String& error_msg, double& fit_score, double& correlation, double& final_score)
Expand Down Expand Up @@ -1907,7 +1904,7 @@ namespace OpenMS
return true;
}

void FeatureFinderAlgorithmPicked::writeFeatureDebugInfo_(TraceFitter* fitter,
void FeatureFinderAlgorithmPicked::writeFeatureDebugInfo_(std::shared_ptr<TraceFitter> fitter,
const MassTraces& traces,
const MassTraces& new_traces,
bool feature_ok, const String error_msg, const double final_score, const Int plot_nr, const PeakType& peak,
Expand Down