diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 0d7f17d338946513268fb8a27d193797458e8e81..aa0c782d8aec5ccbd1e5f032b66c7e591ad329e5 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -23,6 +23,7 @@ set(CPP_FILES
pappsomspp/processing/combiners/traceminuscombiner.cpp
pappsomspp/processing/combiners/tracepluscombiner.cpp
+ pappsomspp/processing/filters/filterchargedeconvolution.cpp
pappsomspp/processing/filters/filtercomplementionenhancer.cpp
pappsomspp/processing/filters/filterlocalmaximum.cpp
pappsomspp/processing/filters/filtermorpho.cpp
@@ -32,7 +33,6 @@ set(CPP_FILES
pappsomspp/processing/filters/filterresample.cpp
pappsomspp/processing/filters/filtersuite.cpp
pappsomspp/processing/filters/filtertandemremovec13.cpp
- pappsomspp/processing/filters/filtertdfcorrectpeak.cpp
pappsomspp/processing/filters/filtertriangle.cpp
pappsomspp/processing/filters/savgolfilter.cpp
diff --git a/src/pappsomspp/processing/filters/filtertdfcorrectpeak.cpp b/src/pappsomspp/processing/filters/filterchargedeconvolution.cpp
similarity index 75%
rename from src/pappsomspp/processing/filters/filtertdfcorrectpeak.cpp
rename to src/pappsomspp/processing/filters/filterchargedeconvolution.cpp
index cf21b037082f754dbb3ed2128103fdcf51411b34..0bb4c720c2bbd50ad8292626ff7e0275b0c609fc 100644
--- a/src/pappsomspp/processing/filters/filtertdfcorrectpeak.cpp
+++ b/src/pappsomspp/processing/filters/filterchargedeconvolution.cpp
@@ -24,33 +24,34 @@
* along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
-#include "filtertdfcorrectpeak.h"
+#include "filterchargedeconvolution.h"
#include <QDebug>
using namespace pappso;
-FilterCorrectTdfPeaks::FilterCorrectTdfPeaks(PrecisionPtr precision_ptr)
+FilterChargeDeconvolution::FilterChargeDeconvolution(PrecisionPtr precision_ptr)
: m_precisionPtr(precision_ptr)
{
m_diffC12C13_z1 = DIFFC12C13;
m_diffC12C13_z2 = DIFFC12C13 / 2;
}
-FilterCorrectTdfPeaks::FilterCorrectTdfPeaks(const FilterCorrectTdfPeaks &other)
+FilterChargeDeconvolution::FilterChargeDeconvolution(
+ const FilterChargeDeconvolution &other)
: m_precisionPtr(other.m_precisionPtr)
{
m_diffC12C13_z1 = DIFFC12C13;
m_diffC12C13_z2 = DIFFC12C13 / 2;
}
-FilterCorrectTdfPeaks::~FilterCorrectTdfPeaks()
+FilterChargeDeconvolution::~FilterChargeDeconvolution()
{
}
Trace &
-FilterCorrectTdfPeaks::filter(Trace &data_points) const
+FilterChargeDeconvolution::filter(Trace &data_points) const
{
- std::vector<FilterCorrectTdfPeaks::DataPointInfoSp> data_points_info;
+ std::vector<FilterChargeDeconvolution::DataPointInfoSp> data_points_info;
data_points.sortY();
Trace new_trace;
@@ -68,11 +69,11 @@ FilterCorrectTdfPeaks::filter(Trace &data_points) const
qDebug() << data_points_info.size();
computeIsotopeDeconvolution(data_points_info);
qDebug() << data_points_info.size();
- transformToZ1ForAllDataPoint(data_points_info);
+ transformToMonoChargedForAllDataPoint(data_points_info);
for(DataPointInfoSp &dpi : data_points_info)
{
- qDebug() << dpi->C12_point.x << dpi->z_charge;
- new_trace.push_back(dpi->C12_point);
+ qDebug() << dpi->new_mono_charge_data_point.x << dpi->z_charge;
+ new_trace.push_back(dpi->new_mono_charge_data_point);
}
new_trace.sortX();
@@ -82,8 +83,8 @@ FilterCorrectTdfPeaks::filter(Trace &data_points) const
}
void
-pappso::FilterCorrectTdfPeaks::addDataPointToList(
- std::vector<FilterCorrectTdfPeaks::DataPointInfoSp> &points,
+pappso::FilterChargeDeconvolution::addDataPointToList(
+ std::vector<FilterChargeDeconvolution::DataPointInfoSp> &points,
pappso::DataPoint &data_point) const
{
DataPointInfoSp new_dpi(std::make_shared<DataPointInfo>());
@@ -98,9 +99,9 @@ pappso::FilterCorrectTdfPeaks::addDataPointToList(
}
void
-pappso::FilterCorrectTdfPeaks::addDataPointRefByExclusion(
- std::vector<FilterCorrectTdfPeaks::DataPointInfoSp> &points,
- FilterCorrectTdfPeaks::DataPointInfoSp &new_dpi) const
+pappso::FilterChargeDeconvolution::addDataPointRefByExclusion(
+ std::vector<FilterChargeDeconvolution::DataPointInfoSp> &points,
+ FilterChargeDeconvolution::DataPointInfoSp &new_dpi) const
{
auto i_z1 = points.begin(), end = points.end();
while(i_z1 != end)
@@ -146,8 +147,9 @@ pappso::FilterCorrectTdfPeaks::addDataPointRefByExclusion(
}
void
-pappso::FilterCorrectTdfPeaks::computeBestChargeOfDataPoint(
- std::vector<FilterCorrectTdfPeaks::DataPointInfoSp> &data_points_info) const
+pappso::FilterChargeDeconvolution::computeBestChargeOfDataPoint(
+ std::vector<FilterChargeDeconvolution::DataPointInfoSp> &data_points_info)
+ const
{
for(DataPointInfoSp &data_point_info : data_points_info)
{
@@ -189,10 +191,12 @@ pappso::FilterCorrectTdfPeaks::computeBestChargeOfDataPoint(
}
void
-pappso::FilterCorrectTdfPeaks::computeIsotopeDeconvolution(
- std::vector<FilterCorrectTdfPeaks::DataPointInfoSp> &data_points_info) const
+pappso::FilterChargeDeconvolution::computeIsotopeDeconvolution(
+ std::vector<FilterChargeDeconvolution::DataPointInfoSp> &data_points_info)
+ const
{
- std::vector<FilterCorrectTdfPeaks::DataPointInfoSp> deconvoluted_points_info;
+ std::vector<FilterChargeDeconvolution::DataPointInfoSp>
+ deconvoluted_points_info;
for(DataPointInfoSp &data_point_info : data_points_info)
{
@@ -201,29 +205,27 @@ pappso::FilterCorrectTdfPeaks::computeIsotopeDeconvolution(
DataPointInfoSp deconvoluted_point(std::make_shared<DataPointInfo>());
deconvoluted_point->z_charge = data_point_info->z_charge;
+ deconvoluted_point->new_mono_charge_data_point =
+ data_point_info->data_point;
if(data_point_info->z_charge == 1)
{
- deconvoluted_point->C12_point = data_point_info->data_point;
for(DataPointInfoSp data : data_point_info->z1_vect)
{
- deconvoluted_point->C12_point.incrementY(data->data_point.y);
+ deconvoluted_point->data_point.y += data->data_point.y;
}
}
else if(data_point_info->z_charge == 2)
{
- deconvoluted_point->C12_point = data_point_info->data_point;
for(DataPointInfoSp data : data_point_info->z2_vect)
{
- deconvoluted_point->C12_point.incrementY(data->data_point.y);
- // qInfo() << data->data_point.y << "++ "
- // <<
- // deconvoluted_point->C12_point.y;
+ deconvoluted_point->data_point.y += data->data_point.y;
}
}
else // if z.charge == 0
{
- deconvoluted_point->C12_point = data_point_info->data_point;
+ deconvoluted_point->new_mono_charge_data_point =
+ data_point_info->data_point;
}
deconvoluted_points_info.push_back(deconvoluted_point);
}
@@ -232,14 +234,16 @@ pappso::FilterCorrectTdfPeaks::computeIsotopeDeconvolution(
}
void
-pappso::FilterCorrectTdfPeaks::transformToZ1ForAllDataPoint(
- std::vector<FilterCorrectTdfPeaks::DataPointInfoSp> &data_points_info) const
+pappso::FilterChargeDeconvolution::transformToMonoChargedForAllDataPoint(
+ std::vector<FilterChargeDeconvolution::DataPointInfoSp> &data_points_info)
+ const
{
for(DataPointInfoSp &dpi : data_points_info)
{
if(dpi->z_charge == 2)
{
- dpi->C12_point.incrementX(dpi->C12_point.x - 1);
+ dpi->new_mono_charge_data_point.x +=
+ dpi->new_mono_charge_data_point.x - MHPLUS;
}
}
}
diff --git a/src/pappsomspp/processing/filters/filtertdfcorrectpeak.h b/src/pappsomspp/processing/filters/filterchargedeconvolution.h
similarity index 66%
rename from src/pappsomspp/processing/filters/filtertdfcorrectpeak.h
rename to src/pappsomspp/processing/filters/filterchargedeconvolution.h
index c7122d663f71031985ab4c068bdd36c467572005..4003736d9e5e95c8566efa0231ac0bd49214541a 100644
--- a/src/pappsomspp/processing/filters/filtertdfcorrectpeak.h
+++ b/src/pappsomspp/processing/filters/filterchargedeconvolution.h
@@ -1,5 +1,5 @@
/**
- * \file pappsomspp/processing/filters/filtertdfcorrectpeak.h
+ * \file pappsomspp/processing/filters/filterchargedeconvolution.h
* \date 30/09/2020
* \author Thomas Renne
* \brief Sum peaks and transform mz to fit charge = 1
@@ -33,7 +33,7 @@
/**
* @brief tries to keep as much as possible monoisotopes, removing any possible
- * C13 peaks
+ * C13 peaks and monocharges each z=2 peaks
*
* first sort peaks by decreasing intensities, then keep most intense ones and
* avoid any peaks in possible C13 windows after
@@ -42,7 +42,7 @@
namespace pappso
{
-class PMSPP_LIB_DECL FilterCorrectTdfPeaks : public FilterInterface
+class PMSPP_LIB_DECL FilterChargeDeconvolution : public FilterInterface
{
private:
struct DataPointInfo;
@@ -51,50 +51,50 @@ class PMSPP_LIB_DECL FilterCorrectTdfPeaks : public FilterInterface
{
int z_charge = -1;
DataPoint data_point;
- DataPoint C12_point;
+ DataPoint new_mono_charge_data_point;
std::pair<double, double> z1_range;
std::pair<double, double> z2_range;
- FilterCorrectTdfPeaks::DataPointInfoSp parent = nullptr;
- std::vector<FilterCorrectTdfPeaks::DataPointInfoSp> z1_vect;
- std::vector<FilterCorrectTdfPeaks::DataPointInfoSp> z2_vect;
+ FilterChargeDeconvolution::DataPointInfoSp parent = nullptr;
+ std::vector<FilterChargeDeconvolution::DataPointInfoSp> z1_vect;
+ std::vector<FilterChargeDeconvolution::DataPointInfoSp> z2_vect;
};
public:
/**
* Default constructor
*/
- FilterCorrectTdfPeaks(PrecisionPtr precision_ptr);
+ FilterChargeDeconvolution(PrecisionPtr precision_ptr);
/**
* Copy constructor
*
* @param other TODO
*/
- FilterCorrectTdfPeaks(const FilterCorrectTdfPeaks &other);
+ FilterChargeDeconvolution(const FilterChargeDeconvolution &other);
/**
* Destructor
*/
- virtual ~FilterCorrectTdfPeaks();
+ virtual ~FilterChargeDeconvolution();
Trace &filter(Trace &data_points) const override;
private:
void addDataPointToList(
- std::vector<FilterCorrectTdfPeaks::DataPointInfoSp> &points,
+ std::vector<FilterChargeDeconvolution::DataPointInfoSp> &points,
DataPoint &data_point) const;
void addDataPointRefByExclusion(
- std::vector<FilterCorrectTdfPeaks::DataPointInfoSp> &points,
- FilterCorrectTdfPeaks::DataPointInfoSp &new_dpi) const;
+ std::vector<FilterChargeDeconvolution::DataPointInfoSp> &points,
+ FilterChargeDeconvolution::DataPointInfoSp &new_dpi) const;
void computeBestChargeOfDataPoint(
- std::vector<FilterCorrectTdfPeaks::DataPointInfoSp> &data_points_info)
+ std::vector<FilterChargeDeconvolution::DataPointInfoSp> &data_points_info)
const;
void computeIsotopeDeconvolution(
- std::vector<FilterCorrectTdfPeaks::DataPointInfoSp> &data_points_info)
+ std::vector<FilterChargeDeconvolution::DataPointInfoSp> &data_points_info)
const;
- void transformToZ1ForAllDataPoint(
- std::vector<FilterCorrectTdfPeaks::DataPointInfoSp> &data_points_info)
+ void transformToMonoChargedForAllDataPoint(
+ std::vector<FilterChargeDeconvolution::DataPointInfoSp> &data_points_info)
const;
private:
diff --git a/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.cpp b/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.cpp
index b189592211b384c52949340611f7b74642952d96..73239df3d0fea46b3a4c4ce92b18eacda2a350f5 100644
--- a/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.cpp
+++ b/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.cpp
@@ -36,7 +36,7 @@
#include "../../msrun/private/timsmsrunreaderms2.h"
#include "../../processing/filters/filterpseudocentroid.h"
#include "../../processing/filters/filtertriangle.h"
-#include "../../processing/filters/filtertdfcorrectpeak.h"
+#include "../../processing/filters/filterchargedeconvolution.h"
#include "../../msrun/output/mzxmloutput.h"
#include "xtandeminputsaxhandler.h"
#include "xtandemoutputsaxhandler.h"
@@ -365,8 +365,9 @@ TandemWrapperRun::convertOrginalMsData2mzXmlData(const QString &origin,
std::shared_ptr<FilterSuite> ms2filter =
std::make_shared<FilterSuite>();
- ms2filter.get()->push_back(std::make_shared<FilterCorrectTdfPeaks>(
- pappso::PrecisionFactory::getDaltonInstance(0.01)));
+ ms2filter.get()->push_back(
+ std::make_shared<FilterChargeDeconvolution>(
+ pappso::PrecisionFactory::getDaltonInstance(0.01)));
tims2_reader->setMs2FilterCstSPtr(ms2filter);
}