From 26e29c7785c85357b2e801227b1789045806e761 Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Thu, 11 Feb 2021 12:25:14 +0100
Subject: [PATCH 1/4] Add mzExclusion filter
---
src/CMakeLists.txt | 1 +
.../filters/filterchargedeconvolution.cpp | 11 ++++---
.../filters/filterchargedeconvolution.h | 2 +-
.../processing/filters/filtersuitestring.cpp | 30 ++++++++++---------
.../tandemwrapper/xtandempresetsaxhandler.cpp | 12 ++++++--
tests/test_timsframe.cpp | 8 ++---
tests/test_timsxicextractor.cpp | 7 ++---
7 files changed, 38 insertions(+), 33 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 4832eca50..59820fda0 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -26,6 +26,7 @@ set(CPP_FILES
pappsomspp/processing/filters/filterchargedeconvolution.cpp
pappsomspp/processing/filters/filtercomplementionenhancer.cpp
+ pappsomspp/processing/filters/filterexclusionmz.cpp
pappsomspp/processing/filters/filterlocalmaximum.cpp
pappsomspp/processing/filters/filtermorpho.cpp
pappsomspp/processing/filters/filternameinterface.cpp
diff --git a/src/pappsomspp/processing/filters/filterchargedeconvolution.cpp b/src/pappsomspp/processing/filters/filterchargedeconvolution.cpp
index 06029816c..8d1c7a17c 100644
--- a/src/pappsomspp/processing/filters/filterchargedeconvolution.cpp
+++ b/src/pappsomspp/processing/filters/filterchargedeconvolution.cpp
@@ -81,7 +81,6 @@ pappso::FilterChargeDeconvolution::buildFilterFromString(
PrecisionFactory::fromString(precision.replace("dalton", " dalton")
.replace("ppm", " ppm")
.replace("res", " res"));
-
qDebug();
m_precisionPtrZ2 =
pappso::PrecisionFactory::getPrecisionPtrFractionInstance(
@@ -117,7 +116,7 @@ FilterChargeDeconvolution::filter(Trace &data_points) const
qDebug();
std::vector<FilterChargeDeconvolution::DataPointInfoSp> data_points_info;
data_points.sortY();
-
+ qDebug() << data_points.size();
Trace new_trace;
for(auto &data_point : data_points)
@@ -126,19 +125,19 @@ FilterChargeDeconvolution::filter(Trace &data_points) const
}
computeBestChargeOfDataPoint(data_points_info);
- qDebug() << data_points_info.size();
+// qDebug() << data_points_info.size();
computeIsotopeDeconvolution(data_points_info);
- qDebug() << data_points_info.size();
+// qDebug() << data_points_info.size();
transformToMonoChargedForAllDataPoint(data_points_info);
for(DataPointInfoSp &dpi : data_points_info)
{
- qDebug() << dpi->new_mono_charge_data_point.x << dpi->z_charge;
+// qDebug() << dpi->new_mono_charge_data_point.x << dpi->z_charge;
new_trace.push_back(dpi->new_mono_charge_data_point);
}
new_trace.sortX();
data_points = std::move(new_trace);
-
+ qDebug() << data_points.size();
qDebug();
return data_points;
}
diff --git a/src/pappsomspp/processing/filters/filterchargedeconvolution.h b/src/pappsomspp/processing/filters/filterchargedeconvolution.h
index 3ae2b9c40..83b1f619b 100644
--- a/src/pappsomspp/processing/filters/filterchargedeconvolution.h
+++ b/src/pappsomspp/processing/filters/filterchargedeconvolution.h
@@ -112,7 +112,7 @@ class PMSPP_LIB_DECL FilterChargeDeconvolution : public FilterNameInterface
std::vector<FilterChargeDeconvolution::DataPointInfoSp> &points,
DataPoint &data_point) const;
/**
- * @brief For eache datapointInfo add the datapoint to the lists by their
+ * @brief For each datapointInfo add the datapoint to the lists by their
* exclusion range
* @return the vecotr of datapointInfo with their lists of isotopics peaks
*/
diff --git a/src/pappsomspp/processing/filters/filtersuitestring.cpp b/src/pappsomspp/processing/filters/filtersuitestring.cpp
index 56adc81bb..963fd53cf 100644
--- a/src/pappsomspp/processing/filters/filtersuitestring.cpp
+++ b/src/pappsomspp/processing/filters/filtersuitestring.cpp
@@ -32,6 +32,7 @@
#include <QStringList>
#include <QDebug>
#include "../../exception/exceptionnotrecognized.h"
+#include "filterexclusionmz.h"
namespace pappso
{
FilterSuiteString::FilterSuiteString(const QString &strBuildParams)
@@ -75,30 +76,31 @@ FilterSuiteString::toString() const
void
FilterSuiteString::buildFilterFromString(const QString &strBuildParams)
{
- qDebug() << strBuildParams;
+ qInfo() << strBuildParams;
QStringList filters = strBuildParams.split(" ", QString::SkipEmptyParts);
for(QString filter_str : filters)
{
- qDebug() << filter_str;
if(filter_str.startsWith("complementIonEnhancer|"))
{
m_filterVector.push_back(
std::make_shared<FilterComplementIonEnhancer>(filter_str));
}
+ else if(filter_str.startsWith("chargeDeconvolution|"))
+ {
+ m_filterVector.push_back(
+ std::make_shared<FilterChargeDeconvolution>(filter_str));
+ }
+ else if(filter_str.startsWith("mzExclusion|"))
+ {
+ m_filterVector.push_back(
+ std::make_shared<FilterMzExclusion>(filter_str));
+ }
else
{
- if(filter_str.startsWith("chargeDeconvolution|"))
- {
- m_filterVector.push_back(
- std::make_shared<FilterChargeDeconvolution>(filter_str));
- }
- else
- {
- throw pappso::ExceptionNotRecognized(
- QString("building Filter from string %1 is "
- "not possible")
- .arg(filter_str));
- }
+ throw pappso::ExceptionNotRecognized(
+ QString("building Filter from string %1 is "
+ "not possible")
+ .arg(filter_str));
}
}
}
diff --git a/src/pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.cpp b/src/pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.cpp
index a052e706f..de622cb38 100644
--- a/src/pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.cpp
+++ b/src/pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.cpp
@@ -261,9 +261,17 @@ XtandemPresetSaxHandler::getNumberOfThreads() const
const QString
XtandemPresetSaxHandler::getMs2FiltersOptions() const
{
+ QString filter_suite;
PrecisionPtr precision = PrecisionFactory::getPrecisionPtrInstance(
m_ms2precisionUnit, m_ms2precisionValue);
- return QString("chargeDeconvolution|%1")
- .arg(precision->toString().replace(" ", ""));
+ QString charge_decon_filter = QString("chargeDeconvolution|%1")
+ .arg(precision->toString().replace(" ", ""));
+
+ PrecisionPtr precision_exclu = PrecisionFactory::getPrecisionPtrInstance(
+ m_ms2precisionUnit, m_ms2precisionValue / 2);
+ QString mz_exclusion_filter =
+ QString("mzExclusion|%1").arg(precision_exclu->toString().replace(" ", ""));
+ filter_suite = charge_decon_filter + " " + mz_exclusion_filter;
+ return filter_suite;
}
} // namespace pappso
diff --git a/tests/test_timsframe.cpp b/tests/test_timsframe.cpp
index b96f680ca..a483b527e 100644
--- a/tests/test_timsframe.cpp
+++ b/tests/test_timsframe.cpp
@@ -225,9 +225,7 @@ TEST_CASE("test tims frames", "[timsframe]")
*/
pappso::MsFileAccessor accessor(
- "/home/langella/developpement/git/bruker/"
- "200ngHeLaPASEF_2min_compressed.d/"
- "analysis.tdf",
+ "/data/test_tdf_quality/2-3-2021_1_HeLa10ng_871.d/analysis.tdf",
"a1");
@@ -253,14 +251,14 @@ TEST_CASE("test tims frames", "[timsframe]")
}
pappso::QualifiedMassSpectrum mass_spectrum =
- tims2_reader->qualifiedMassSpectrum(7);
+ tims2_reader->qualifiedMassSpectrum(33373);
INFO("mass_spectrum.getMsLevel()=" << mass_spectrum.getMsLevel());
INFO("mass_spectrum.getPrecursorMz()=" << mass_spectrum.getPrecursorMz());
INFO("mass_spectrum.getMassSpectrumId().getSpectrumIndex()="
<< mass_spectrum.getMassSpectrumId().getSpectrumIndex());
-
+ INFO(mass_spectrum.getMassSpectrumSPtr()->xValues().at(0));
REQUIRE_FALSE(mass_spectrum.getMassSpectrumCstSPtr().get()->back().x <
40.0);
diff --git a/tests/test_timsxicextractor.cpp b/tests/test_timsxicextractor.cpp
index 9804bc247..842766250 100644
--- a/tests/test_timsxicextractor.cpp
+++ b/tests/test_timsxicextractor.cpp
@@ -68,9 +68,7 @@ TEST_CASE("Extracting XIC from timsdata.", "[TimsXicExtractor]")
*/
pappso::MsFileAccessor accessor(
- "/home/langella/developpement/git/bruker/"
- "200ngHeLaPASEF_2min_compressed.d/"
- "analysis.tdf",
+ "/data/test_tdf_quality/2-3-2021_1_HeLa10ng_871.d/analysis.tdf",
"a1");
@@ -91,8 +89,7 @@ TEST_CASE("Extracting XIC from timsdata.", "[TimsXicExtractor]")
pappso::TimsDataSp tims_data = tims2_reader->getTimsDataSPtr();
-
-
+
std::vector<std::size_t> precursor_list = {3, 4, 5, 3000, 3001};
std::vector<pappso::TimsXicStructure> xic_list;
--
GitLab
From e39b62e2f83f1fd5b7d7ab95a550cde73dc5e2a0 Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Tue, 16 Feb 2021 13:27:23 +0100
Subject: [PATCH 2/4] correct the double make of the filterSuiteString pointer
---
.../filters/filterchargedeconvolution.cpp | 3 +++
.../processing/filters/filterchargedeconvolution.h | 1 +
.../processing/tandemwrapper/tandemwrapperrun.cpp | 13 +++++++++++--
.../processing/tandemwrapper/tandemwrapperrun.h | 4 +---
4 files changed, 16 insertions(+), 5 deletions(-)
diff --git a/src/pappsomspp/processing/filters/filterchargedeconvolution.cpp b/src/pappsomspp/processing/filters/filterchargedeconvolution.cpp
index 8d1c7a17c..175b7d6c7 100644
--- a/src/pappsomspp/processing/filters/filterchargedeconvolution.cpp
+++ b/src/pappsomspp/processing/filters/filterchargedeconvolution.cpp
@@ -34,6 +34,7 @@ pappso::FilterChargeDeconvolution::FilterChargeDeconvolution(
const QString &strBuildParams)
{
buildFilterFromString(strBuildParams);
+ qInfo() << "ChargeDeconvolution created";
}
@@ -62,6 +63,7 @@ FilterChargeDeconvolution::FilterChargeDeconvolution(
FilterChargeDeconvolution::~FilterChargeDeconvolution()
{
+ qInfo() << "ChargeDeconvolution destroyed";
}
@@ -316,3 +318,4 @@ pappso::FilterChargeDeconvolution::transformToMonoChargedForAllDataPoint(
}
}
}
+
diff --git a/src/pappsomspp/processing/filters/filterchargedeconvolution.h b/src/pappsomspp/processing/filters/filterchargedeconvolution.h
index 83b1f619b..85c99a039 100644
--- a/src/pappsomspp/processing/filters/filterchargedeconvolution.h
+++ b/src/pappsomspp/processing/filters/filterchargedeconvolution.h
@@ -150,3 +150,4 @@ class PMSPP_LIB_DECL FilterChargeDeconvolution : public FilterNameInterface
PrecisionPtr m_precisionPtrZ2;
};
} // namespace pappso
+
diff --git a/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.cpp b/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.cpp
index b895b34c8..0dac8a026 100644
--- a/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.cpp
+++ b/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.cpp
@@ -289,8 +289,17 @@ TandemWrapperRun::readTandemPresetFile(const QString &tandem_preset_file)
}
QString ms2_filters_str = preset_handler.getMs2FiltersOptions();
- msp_ms2FilterSuiteString =
- std::make_shared<pappso::FilterSuiteString>(ms2_filters_str);
+ if(!ms2_filters_str.isEmpty())
+ {
+ msp_ms2FilterSuiteString =
+ std::make_shared<pappso::FilterSuiteString>(ms2_filters_str);
+ }
+ else
+ {
+ msp_ms2FilterSuiteString =
+ std::make_shared<pappso::FilterSuiteString>(
+ "chargeDeconvolution|0.02dalton mzExclusion|0.01dalton");
+ }
}
else
{
diff --git a/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.h b/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.h
index 7d66899d7..158eb7b3a 100644
--- a/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.h
+++ b/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.h
@@ -119,9 +119,7 @@ class PMSPP_LIB_DECL TandemWrapperRun : public QObject
int m_maxTandemRunTimeMs = (60000 * 60 * 24); // 1 day
QProcess *m_xtProcess = nullptr;
- std::shared_ptr<FilterSuiteString> msp_ms2FilterSuiteString =
- std::make_shared<pappso::FilterSuiteString>(
- "chargeDeconvolution|0.02dalton");
+ std::shared_ptr<FilterSuiteString> msp_ms2FilterSuiteString = nullptr;
QTextStream *mp_outputStream = nullptr;
QTextStream *mp_errorStream = nullptr;
--
GitLab
From 663d72945e04bdc6e9bbe28c35971f6304b9c71b Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Tue, 16 Feb 2021 13:40:41 +0100
Subject: [PATCH 3/4] memory leak corrected in chargeDeconvolution filter
shared_ptr --> weak_ptr
---
.../filters/filterchargedeconvolution.cpp | 37 +++++++++----------
.../filters/filterchargedeconvolution.h | 7 ++--
2 files changed, 21 insertions(+), 23 deletions(-)
diff --git a/src/pappsomspp/processing/filters/filterchargedeconvolution.cpp b/src/pappsomspp/processing/filters/filterchargedeconvolution.cpp
index 175b7d6c7..be799bf27 100644
--- a/src/pappsomspp/processing/filters/filterchargedeconvolution.cpp
+++ b/src/pappsomspp/processing/filters/filterchargedeconvolution.cpp
@@ -127,13 +127,13 @@ FilterChargeDeconvolution::filter(Trace &data_points) const
}
computeBestChargeOfDataPoint(data_points_info);
-// qDebug() << data_points_info.size();
+ // qDebug() << data_points_info.size();
computeIsotopeDeconvolution(data_points_info);
-// qDebug() << data_points_info.size();
+ // qDebug() << data_points_info.size();
transformToMonoChargedForAllDataPoint(data_points_info);
for(DataPointInfoSp &dpi : data_points_info)
{
-// qDebug() << dpi->new_mono_charge_data_point.x << dpi->z_charge;
+ // qDebug() << dpi->new_mono_charge_data_point.x << dpi->z_charge;
new_trace.push_back(dpi->new_mono_charge_data_point);
}
@@ -179,11 +179,11 @@ pappso::FilterChargeDeconvolution::addDataPointRefByExclusion(
// add the datapoint to the list and add the parent pointer
i_z1->get()->z1_vect.push_back(new_dpi);
new_dpi->parent = *i_z1;
- DataPointInfoSp parent_z1 = i_z1->get()->parent;
+ DataPointInfoSp parent_z1 = i_z1->get()->parent.lock();
while(parent_z1 != nullptr)
{
parent_z1.get()->z1_vect.push_back(new_dpi);
- parent_z1 = parent_z1->parent;
+ parent_z1 = parent_z1->parent.lock();
}
i_z1++;
}
@@ -203,11 +203,11 @@ pappso::FilterChargeDeconvolution::addDataPointRefByExclusion(
// add the datapoint to the list and add the parent pointer
i_z2->get()->z2_vect.push_back(new_dpi);
new_dpi->parent = *i_z2;
- DataPointInfoSp parent_z2 = i_z2->get()->parent;
+ DataPointInfoSp parent_z2 = i_z2->get()->parent.lock();
while(parent_z2 != nullptr)
{
parent_z2.get()->z2_vect.push_back(new_dpi);
- parent_z2 = parent_z2->parent;
+ parent_z2 = parent_z2->parent.lock();
}
i_z2++;
}
@@ -224,27 +224,27 @@ pappso::FilterChargeDeconvolution::computeBestChargeOfDataPoint(
if(data_point_info.get()->z1_vect.size() >= 1 &&
data_point_info.get()->z2_vect.size() == 0)
{
- for(DataPointInfoSp other : data_point_info.get()->z1_vect)
+ for(std::weak_ptr<DataPointInfo> other : data_point_info.get()->z1_vect)
{
- other->z_charge = 1;
+ other.lock()->z_charge = 1;
}
data_point_info.get()->z_charge = 1;
}
else if(data_point_info.get()->z1_vect.size() == 0 &&
data_point_info.get()->z2_vect.size() >= 1)
{
- for(DataPointInfoSp other : data_point_info.get()->z2_vect)
+ for(std::weak_ptr<DataPointInfo> other : data_point_info.get()->z2_vect)
{
- other->z_charge = 2;
+ other.lock()->z_charge = 2;
}
data_point_info.get()->z_charge = 2;
}
else if(data_point_info.get()->z1_vect.size() >= 1 &&
data_point_info.get()->z2_vect.size() >= 1)
{
- for(DataPointInfoSp other : data_point_info.get()->z2_vect)
+ for(std::weak_ptr<DataPointInfo> other : data_point_info.get()->z2_vect)
{
- other->z_charge = 2;
+ other.lock()->z_charge = 2;
}
data_point_info.get()->z_charge = 2;
}
@@ -268,7 +268,7 @@ pappso::FilterChargeDeconvolution::computeIsotopeDeconvolution(
for(DataPointInfoSp &data_point_info : data_points_info)
{
- if(data_point_info->parent == nullptr)
+ if(data_point_info->parent.lock() == nullptr)
{
DataPointInfoSp deconvoluted_point(std::make_shared<DataPointInfo>());
@@ -279,18 +279,18 @@ pappso::FilterChargeDeconvolution::computeIsotopeDeconvolution(
if(data_point_info->z_charge == 1)
{
- for(DataPointInfoSp data : data_point_info->z1_vect)
+ for(std::weak_ptr<DataPointInfo> data : data_point_info->z1_vect)
{
deconvoluted_point->new_mono_charge_data_point.y +=
- data->data_point.y;
+ data.lock()->data_point.y;
}
}
else if(data_point_info->z_charge == 2)
{
- for(DataPointInfoSp data : data_point_info->z2_vect)
+ for(std::weak_ptr<DataPointInfo> data : data_point_info->z2_vect)
{
deconvoluted_point->new_mono_charge_data_point.y +=
- data->data_point.y;
+ data.lock()->data_point.y;
}
}
else // if z.charge == 0
@@ -318,4 +318,3 @@ pappso::FilterChargeDeconvolution::transformToMonoChargedForAllDataPoint(
}
}
}
-
diff --git a/src/pappsomspp/processing/filters/filterchargedeconvolution.h b/src/pappsomspp/processing/filters/filterchargedeconvolution.h
index 85c99a039..144faa632 100644
--- a/src/pappsomspp/processing/filters/filterchargedeconvolution.h
+++ b/src/pappsomspp/processing/filters/filterchargedeconvolution.h
@@ -57,11 +57,11 @@ class PMSPP_LIB_DECL FilterChargeDeconvolution : public FilterNameInterface
// range of mass possible for z2 peak (~0.5mz)
std::pair<double, double> z2_range;
// datapointInfo where the mass is in the range
- FilterChargeDeconvolution::DataPointInfoSp parent = nullptr;
+ std::weak_ptr<DataPointInfo> parent;
// list of datapointinfo with 1mz diff multiple
- std::vector<FilterChargeDeconvolution::DataPointInfoSp> z1_vect;
+ std::vector<std::weak_ptr<DataPointInfo>> z1_vect;
// list of datapointinfo with 2mz diff multiple
- std::vector<FilterChargeDeconvolution::DataPointInfoSp> z2_vect;
+ std::vector<std::weak_ptr<DataPointInfo>> z2_vect;
};
public:
@@ -150,4 +150,3 @@ class PMSPP_LIB_DECL FilterChargeDeconvolution : public FilterNameInterface
PrecisionPtr m_precisionPtrZ2;
};
} // namespace pappso
-
--
GitLab
From c2ea3eb289a9bc23074e0b93ab6e37ec8bdfdd26 Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Tue, 16 Feb 2021 13:41:21 +0100
Subject: [PATCH 4/4] Add new filter mzExclusion
---
.../processing/filters/filterexclusionmz.cpp | 127 ++++++++++++++++++
.../processing/filters/filterexclusionmz.h | 79 +++++++++++
2 files changed, 206 insertions(+)
create mode 100644 src/pappsomspp/processing/filters/filterexclusionmz.cpp
create mode 100644 src/pappsomspp/processing/filters/filterexclusionmz.h
diff --git a/src/pappsomspp/processing/filters/filterexclusionmz.cpp b/src/pappsomspp/processing/filters/filterexclusionmz.cpp
new file mode 100644
index 000000000..48e73f00b
--- /dev/null
+++ b/src/pappsomspp/processing/filters/filterexclusionmz.cpp
@@ -0,0 +1,127 @@
+/**
+ * \file pappsomspp/processing/filters/filterexclusionmz.cpp
+ * \date 09/02/2021
+ * \author Thomas Renne
+ * \brief Delete small peaks in the exclusion range
+ */
+
+/*******************************************************************************
+ * Copyright (c) 2021 Thomas Renne <thomas.renne@e.email>.
+ *
+ * This file is part of the PAPPSOms++ library.
+ *
+ * PAPPSOms++ is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * PAPPSOms++ is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+
+#include "filterexclusionmz.h"
+#include <QDebug>
+#include "../../exception/exceptionnotrecognized.h"
+
+using namespace pappso;
+
+FilterMzExclusion::FilterMzExclusion(const QString &strBuildParams)
+{
+ buildFilterFromString(strBuildParams);
+}
+
+FilterMzExclusion::FilterMzExclusion(pappso::PrecisionPtr precision_ptr)
+ : m_exclusionPrecision(precision_ptr)
+{
+}
+
+FilterMzExclusion::FilterMzExclusion(const pappso::FilterMzExclusion &other)
+ : m_exclusionPrecision(other.m_exclusionPrecision)
+{
+}
+
+FilterMzExclusion::~FilterMzExclusion()
+{
+}
+
+void
+pappso::FilterMzExclusion::buildFilterFromString(const QString &strBuildParams)
+{
+ qDebug();
+ if(strBuildParams.startsWith("mzExclusion|"))
+ {
+ QStringList params =
+ strBuildParams.split("|").back().split(";", QString::SkipEmptyParts);
+
+ QString precision = params.at(0);
+ m_exclusionPrecision =
+ PrecisionFactory::fromString(precision.replace("dalton", " dalton")
+ .replace("ppm", " ppm")
+ .replace("res", " res"));
+ }
+ else
+ {
+ throw pappso::ExceptionNotRecognized(
+ QString("building mzExclusion from string %1 is not possible")
+ .arg(strBuildParams));
+ }
+ qDebug();
+}
+
+pappso::Trace &
+pappso::FilterMzExclusion::filter(pappso::Trace &data_points) const
+{
+ qDebug();
+ qDebug() << "before" << data_points.size();
+ data_points.sortY();
+
+ Trace new_trace = removeTraceInExclusionMargin(data_points);
+ new_trace.sortX();
+ data_points = std::move(new_trace);
+ qDebug() << "after" << data_points.size();
+ qDebug();
+ return data_points;
+}
+
+QString
+pappso::FilterMzExclusion::toString() const
+{
+ QString strCode =
+ QString("mzExclusion|%1").arg(m_exclusionPrecision->toString());
+ strCode.replace(" ", "");
+
+ return strCode;
+}
+
+pappso::Trace
+pappso::FilterMzExclusion::removeTraceInExclusionMargin(
+ pappso::Trace &points) const
+{
+ Trace new_trace;
+ std::vector<MzRange> excluded_ranges;
+
+ for(auto &data_point : points)
+ {
+ auto exclude_index = excluded_ranges.begin(), end = excluded_ranges.end();
+
+ exclude_index =
+ std::find_if(exclude_index, end, [&data_point](MzRange range) {
+ return (data_point.x >= range.lower() &&
+ data_point.x <= range.upper());
+ });
+ if(exclude_index == end)
+ {
+ new_trace.push_back(data_point);
+ MzRange new_range(data_point.x, m_exclusionPrecision);
+ excluded_ranges.push_back(new_range);
+ }
+ }
+
+ return new_trace;
+}
diff --git a/src/pappsomspp/processing/filters/filterexclusionmz.h b/src/pappsomspp/processing/filters/filterexclusionmz.h
new file mode 100644
index 000000000..bbc117d3b
--- /dev/null
+++ b/src/pappsomspp/processing/filters/filterexclusionmz.h
@@ -0,0 +1,79 @@
+/**
+ * \file pappsomspp/processing/filters/filterexclusionmz.h
+ * \date 09/02/2021
+ * \author Thomas Renne
+ * \brief Delete small peaks in the exclusion range
+ */
+
+/*******************************************************************************
+ * Copyright (c) 2021 Thomas Renne <thomas.renne@e.email>.
+ *
+ * This file is part of the PAPPSOms++ library.
+ *
+ * PAPPSOms++ is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * PAPPSOms++ is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+
+#pragma once
+
+#include "filternameinterface.h"
+#include "../../trace/trace.h"
+
+namespace pappso
+{
+
+class PMSPP_LIB_DECL FilterMzExclusion : public FilterNameInterface
+{
+ public:
+ /**
+ * Default constructor
+ */
+ FilterMzExclusion(PrecisionPtr precision_ptr);
+
+
+ /**
+ * @param strBuildParams string to build the filter
+ * "mzExclusion|0.02dalton"
+ */
+ FilterMzExclusion(const QString &strBuildParams);
+
+ /**
+ * Copy constructor
+ *
+ * @param other TODO
+ */
+ FilterMzExclusion(const FilterMzExclusion &other);
+
+ /**
+ * Destructor
+ */
+ virtual ~FilterMzExclusion();
+
+ /**
+ * @brief get all the datapoints and remove different isotope and add their
+ * intensity and change to charge = 1 when the charge is known
+ * @return a list of datapoint
+ */
+ Trace &filter(Trace &data_points) const override;
+ QString toString() const override;
+
+ private:
+ void buildFilterFromString(const QString &strBuildParams) override;
+ Trace removeTraceInExclusionMargin(Trace &points) const;
+
+
+ private:
+ PrecisionPtr m_exclusionPrecision;
+};
+} // namespace pappso
--
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