diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index f9c95f1af5e9400c3989724227e10ab3785027e9..5d4ff25e22a1481189bbd82b1ef3a4e4dbfb7238 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -84,6 +84,10 @@ SET(CPP_FILES
pappsomspp/processing/filters/filtertriangle.cpp
pappsomspp/processing/filters/savgolfilter.cpp
+# pappsomspp/processing/filters/pwiz/ms/peakpickerqtof.hpp
+# pappsomspp/processing/filters/pwiz/ms/simplepicker.hpp
+# pappsomspp/processing/filters/pwiz/resample/convert2dense.hpp
+
pappsomspp/massspectrum/massspectrumid.cpp
pappsomspp/massspectrum/massspectrum.cpp
pappsomspp/massspectrum/qualifiedmassspectrum.cpp
diff --git a/src/pappsomspp/msrun/private/timsmsrunreaderms2.cpp b/src/pappsomspp/msrun/private/timsmsrunreaderms2.cpp
index f6b95f4880a78db71366f8640279ec514d195c0e..1fe9c37535c550cdd57c7ff635ed28e21c576b36 100644
--- a/src/pappsomspp/msrun/private/timsmsrunreaderms2.cpp
+++ b/src/pappsomspp/msrun/private/timsmsrunreaderms2.cpp
@@ -224,9 +224,9 @@ TimsMsRunReaderMs2::readSpectrumCollection(
qDebug() << item_list.size();
for(auto &item : item_list)
{
- qDebug() << item.qualified_mass_spectrum.getMassSpectrumSPtr()
- .get()
- ->toString();
+// qDebug() << item.qualified_mass_spectrum.getMassSpectrumSPtr()
+// .get()
+// ->toString();
handler.setQualifiedMassSpectrum(item.qualified_mass_spectrum);
qDebug();
}
diff --git a/src/pappsomspp/processing/filters/filterpseudocentroid.cpp b/src/pappsomspp/processing/filters/filterpseudocentroid.cpp
index a740dc766ac5148ca74a89ca07083d8052e396b6..0bf8dd8472908df0566b490d09feeee0217a984a 100644
--- a/src/pappsomspp/processing/filters/filterpseudocentroid.cpp
+++ b/src/pappsomspp/processing/filters/filterpseudocentroid.cpp
@@ -27,7 +27,7 @@
#include <QDebug>
#include "filterpseudocentroid.h"
-#include <pwiz/utility/findmf/base/ms/peakpickerqtof.hpp>
+#include "pwiz/ms/peakpickerqtof.hpp"
using namespace pappso;
@@ -114,3 +114,4 @@ uint32_t maxnumberofpeaks = 0 //!< max number of peaks returned by picker
qDebug();
return data_points;
}
+
diff --git a/src/pappsomspp/processing/filters/pwiz/ms/peakpickerqtof.hpp b/src/pappsomspp/processing/filters/pwiz/ms/peakpickerqtof.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..9cf1e101233d734157bd174acdb722d0d97495aa
--- /dev/null
+++ b/src/pappsomspp/processing/filters/pwiz/ms/peakpickerqtof.hpp
@@ -0,0 +1,290 @@
+//
+// $Id$
+//
+//
+// Original author: Witold Wolski <wewolski@gmail.com>
+//
+// Copyright : ETH Zurich
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+//
+
+# pragma once
+
+#include <boost/math/special_functions.hpp>
+#include "../resample/convert2dense.hpp"
+#include "pwiz/utility/findmf/base/filter/filter.hpp"
+#include "simplepicker.hpp"
+#include "pwiz/utility/findmf/base/filter/gaussfilter.hpp"
+#include "pwiz/utility/findmf/base/base/interpolate.hpp"
+#include "pwiz/utility/findmf/base/resample/determinebinwidth.hpp"
+#include "pwiz/utility/findmf/base/base/copyif.hpp"
+
+namespace ralab {
+namespace base {
+namespace ms {
+
+
+/// resamples spectrum, apply smoothing,
+/// determines zero crossings,
+/// integrates peaks.
+
+template<typename TReal>
+struct SimplePeakArea {
+ TReal integwith_;
+
+ SimplePeakArea(TReal integwith):integwith_(integwith) {}
+
+ /// intagrates the peak intesnities
+ template<typename Tzerocross, typename Tintensity, typename Tout>
+ void operator()( Tzerocross beginZ,
+ Tzerocross endZ,
+ Tintensity intensity,
+ Tintensity resmpled,
+ Tout area)const
+ {
+ typedef typename std::iterator_traits<Tout>::value_type AreaType;
+ for( ; beginZ != endZ ; ++beginZ, ++area )
+ {
+ size_t idx = static_cast<size_t>( *beginZ );
+ size_t start = static_cast<size_t>( boost::math::round( idx - integwith_ ) );
+ size_t end = static_cast<size_t>( boost::math::round( idx + integwith_ + 2.) );
+ AreaType aread = 0.;
+ for( ; start != end ; ++start )
+ {
+ aread += *(resmpled + start);
+ }
+ *area = aread;
+ }
+ }
+};
+
+/// extends peak to the left and to the right to the next local minimum or a predefined threshol
+/// or a maximum allowed extension.
+template<typename TReal>
+struct LocalMinPeakArea {
+ typedef TReal value_type;
+ TReal integwith_;
+ TReal threshold_;
+
+ LocalMinPeakArea(TReal integwith,//!<maximal allowed peak width +- in pixel
+ TReal threshold = .1// minimum intensity
+ ):integwith_(integwith),threshold_(threshold) {}
+
+
+
+ /// intagrates the peak intesnities
+ template< typename Tzerocross, typename Tintensity, typename Tout >
+ void operator()( Tzerocross beginZ,
+ Tzerocross endZ,
+ Tintensity intensity,
+ Tintensity resampled,
+ Tout area) const
+ {
+ typedef typename std::iterator_traits<Tout>::value_type AreaType;
+ for( ; beginZ != endZ ; ++beginZ, ++area )
+ {
+ size_t idx = static_cast<size_t>( *beginZ );
+ size_t start = static_cast<size_t>( boost::math::round( idx - integwith_ ) );
+ size_t end = static_cast<size_t>( boost::math::round( idx + integwith_ + 2) );
+
+ Tintensity st = intensity + start;
+ Tintensity en = intensity + end;
+ Tintensity center = intensity + idx;
+ std::ptrdiff_t x1 = std::distance(st, center);
+ std::ptrdiff_t y1 = std::distance(center,en);
+ mextend(st, en, center);
+ std::ptrdiff_t x2 = std::distance(intensity,st);
+ std::ptrdiff_t y2 = std::distance(intensity,en);
+ std::ptrdiff_t pp = std::distance(st,en);
+ AreaType areav = std::accumulate(resampled+x2,resampled+y2,0.);
+ *area = areav;
+ }
+ }
+
+private:
+ ///exend peak to left and rigth
+ template<typename TInt >
+ void mextend( TInt &start, TInt &end, TInt idx) const
+ {
+ typedef typename std::iterator_traits<TInt>::value_type Intensitytype;
+ //
+ for(TInt intens = idx ; intens >= start; --intens) {
+ Intensitytype val1 = *intens;
+ Intensitytype val2 = *(intens-1);
+ if(val1 > threshold_) {
+ if(val1 < val2 ) {
+ start = intens;
+ break;
+ }
+ }
+ else {
+ start = intens;
+ break;
+ }
+ }
+
+ for(TInt intens = idx ; intens <= end; ++intens) {
+ Intensitytype val1 = *intens;
+ Intensitytype val2 = *(intens+1);
+ if(val1 > threshold_) {
+ if(val1 < val2 ) {
+ end = intens;
+ break;
+ }
+ }
+ else {
+ end = intens;
+ break;
+ }
+ }
+ }
+};
+
+/// resamples spectrum, apply smoothing,
+/// determines zero crossings,
+/// integrates peaks.
+template<typename TReal, template <typename B> class TIntegrator >
+struct PeakPicker {
+ typedef TReal value_type;
+ typedef TIntegrator<value_type> PeakIntegrator;
+
+ TReal resolution_;
+ ralab::base::resample::Convert2Dense c2d_; // resamples spectrum
+ std::vector<TReal> resampledmz_, resampledintensity_; // keeps result of convert to dense
+ std::vector<TReal> filter_, zerocross_, smoothedintensity_; // working variables
+ std::vector<TReal> peakmass_, peakarea_; //results
+ TReal smoothwith_;
+ TReal integrationWidth_;
+ ralab::base::ms::SimplePicker<TReal> simplepicker_;
+ ralab::base::resample::SamplingWith sw_;
+ PeakIntegrator integrator_;
+ TReal intensitythreshold_;
+ bool area_;
+ uint32_t maxnumbersofpeaks_;
+
+ PeakPicker(TReal resolution, //!< instrument resolution
+ std::pair<TReal, TReal> & massrange, //!< mass range of spectrum
+ TReal width = 2., //!< smooth width
+ TReal intwidth = 2., //!< integration width used for area compuation
+ TReal intensitythreshold = 10., // intensity threshold
+ bool area = true,//!< compute area or height? default - height.
+ uint32_t maxnumberofpeaks = 0, //!< maximum of peaks returned by picker
+ double c2d = 1e-5 //!< instrument resampling with small default dissables automatic determination
+ ): resolution_(resolution),c2d_( c2d ),smoothwith_(width),
+ integrationWidth_(intwidth),sw_(),integrator_(integrationWidth_),
+ intensitythreshold_(intensitythreshold),area_(area),maxnumbersofpeaks_(maxnumberofpeaks)
+ {
+ c2d_.defBreak(massrange,ralab::base::resample::resolution2ppm(resolution));
+ c2d_.getMids(resampledmz_);
+ ralab::base::filter::getGaussianFilterQuantile(filter_,width);
+ }
+
+
+ template<typename Tmass, typename Tintensity>
+ void operator()(Tmass begmz, Tmass endmz, Tintensity begint )
+ {
+ typename std::iterator_traits<Tintensity>::value_type minint = *std::upper_bound(begint,begint+std::distance(begmz,endmz),0.1);
+
+ //determine sampling with
+ double a = sw_(begmz,endmz);
+ //resmpale the spectrum
+ c2d_.am_ = a;
+ c2d_.convert2dense(begmz,endmz, begint, resampledintensity_);
+
+ //smooth the resampled spectrum
+ ralab::base::filter::filter(resampledintensity_, filter_, smoothedintensity_, true);
+ //determine zero crossings
+ zerocross_.resize( smoothedintensity_.size()/2 );
+ size_t nrzerocross = simplepicker_( smoothedintensity_.begin( ), smoothedintensity_.end(), zerocross_.begin(), zerocross_.size());
+
+ peakmass_.resize(nrzerocross);
+ //determine mass of zerocrossing
+ ralab::base::base::interpolate_linear( resampledmz_.begin(), resampledmz_.end(),
+ zerocross_.begin(), zerocross_.begin()+nrzerocross,
+ peakmass_.begin());
+
+ //determine peak area
+ if(area_) {
+ peakarea_.resize(nrzerocross);
+ integrator_( zerocross_.begin(), zerocross_.begin() + nrzerocross,
+ smoothedintensity_.begin(),resampledintensity_.begin(), peakarea_.begin() );
+ } else {
+ //determine intensity
+ peakarea_.resize(nrzerocross);
+ ralab::base::base::interpolate_cubic( smoothedintensity_.begin(), smoothedintensity_.end(),
+ zerocross_.begin(), zerocross_.begin()+nrzerocross,
+ peakarea_.begin());
+ }
+
+ TReal threshold = static_cast<TReal>(minint) * intensitythreshold_;
+
+ if(maxnumbersofpeaks_ > 0) {
+ double threshmax = getNToppeaks();
+ if(threshmax > threshold)
+ threshold = threshmax;
+ }
+
+
+ if(threshold > 0.01) {
+ filter(threshold);
+ }
+ }
+
+ /// get min instensity of peak to qualify for max-intensity;
+ TReal getNToppeaks() {
+ TReal intthres = 0.;
+ if(maxnumbersofpeaks_ < peakarea_.size())
+ {
+ std::vector<TReal> tmparea( peakarea_.begin(), peakarea_.end() );
+ std::nth_element(tmparea.begin(),tmparea.end() - maxnumbersofpeaks_, tmparea.end());
+ intthres = *(tmparea.end() - maxnumbersofpeaks_);
+ }
+ return intthres;
+ }
+
+
+ /// clean the masses using the threshold
+ void filter(TReal threshold) {
+ typename std::vector<TReal>::iterator a = ralab::base::utils::copy_if(peakarea_.begin(),peakarea_.end(),peakmass_.begin(),
+ peakmass_.begin(),boost::bind(std::greater<TReal>(),_1,threshold));
+ peakmass_.resize(std::distance(peakmass_.begin(),a));
+ typename std::vector<TReal>::iterator b = ralab::base::utils::copy_if(peakarea_.begin(),peakarea_.end(),
+ peakarea_.begin(),boost::bind(std::greater<TReal>(),_1,threshold));
+ peakarea_.resize(std::distance(peakarea_.begin(),b));
+ //int x = 1;
+ }
+
+ const std::vector<TReal> & getPeakMass() {
+ return peakmass_;
+ }
+
+ const std::vector<TReal> & getPeakArea() {
+ return peakarea_;
+ }
+
+ const std::vector<TReal> & getResampledMZ() {
+ return resampledmz_;
+ }
+
+ const std::vector<TReal> & getResampledIntensity() {
+ return resampledintensity_;
+ }
+
+ const std::vector<TReal> & getSmoothedIntensity() {
+ return smoothedintensity_;
+ }
+};
+}//ms
+}//base
+}//ralab
diff --git a/src/pappsomspp/processing/filters/pwiz/ms/simplepicker.hpp b/src/pappsomspp/processing/filters/pwiz/ms/simplepicker.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..0557cc666a7053135efca7f0ca63a0373500db46
--- /dev/null
+++ b/src/pappsomspp/processing/filters/pwiz/ms/simplepicker.hpp
@@ -0,0 +1,123 @@
+//
+// $Id$
+//
+//
+// Original author: Witold Wolski <wewolski@gmail.com>
+//
+// Copyright : ETH Zurich
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+//
+
+#ifndef SIMPLEPICKER_H
+#define SIMPLEPICKER_H
+
+#include <iterator>
+#include <vector>
+#include <stdexcept>
+#include <boost/lexical_cast.hpp>
+
+namespace ralab
+{
+ namespace base
+ {
+ namespace ms
+ {
+ /*! computes first derivative of a sequence, looks for zero crossings
+ */
+ template<class TReal>
+ struct SimplePicker{
+ std::vector<TReal> worker_;
+ double epsilon_;
+ bool problem_; //indicates if not the whole signal was picked.
+
+ SimplePicker(TReal epsilon = 1e-3):epsilon_(epsilon),problem_(false){}
+ /*!
+ *returns number of zero crossings found
+ */
+ template<typename Tit, typename Outit>
+ size_t operator()(Tit beg, Tit end ,
+ Outit zerocrossings, //! picked peaks
+ size_t nzercross,
+ std::ptrdiff_t lag = 2 //must be even (leave odd out)
+ )
+ {
+ if((lag % 2 ) == 1){
+ return -1;
+ }
+ worker_.resize(std::distance(beg,end) - lag);
+ TReal * pworkerBeg = &worker_[0];
+ TReal * pworkerEnd = &worker_[0] + worker_.size();
+
+ Tit tbegin = beg;
+ Tit tbeginm1 = tbegin + ( lag);
+ for(;tbeginm1 != end ; ++tbeginm1, ++tbegin, ++pworkerBeg )
+ {
+ *pworkerBeg = (*tbeginm1 - *tbegin);
+ }
+
+ //reset worker
+ pworkerBeg = &worker_[0];
+ std::size_t crosscount = 0;
+ for( int i = 0 ; (pworkerBeg != pworkerEnd-1) ; ++pworkerBeg , ++i )
+ {
+ if(crosscount >= nzercross){
+ problem_ = true;
+ return crosscount; // protect against memmory violations
+ std::string x = "nzerocross:";
+ x+=boost::lexical_cast<std::string>(nzercross);
+ x+=" crosscount:";
+ x+=boost::lexical_cast<std::string>(crosscount);
+ x+=" i: ";
+ x+= boost::lexical_cast<std::string>(i);
+ x+=" worker size ";
+ x+= boost::lexical_cast<std::string>( worker_.size() );
+ x+=" : ";
+ x+=boost::lexical_cast<std::string>(__LINE__);
+ x+=" : ";
+ x+= __FILE__;
+ throw std::length_error(x.c_str());
+ }
+ TReal v1 = (*pworkerBeg);
+ TReal v2 = *(pworkerBeg + 1);
+ //peak detected ... detect a zero crossing
+ if((v1 > 0 && v2 < 0) && ((v1 - v2) > epsilon_))
+ {
+ //determine zero crossing....
+ double frac = v1 / ( v1 - v2 );
+ double idx = static_cast<float>(i + lag/2) + frac;
+ *zerocrossings = ( idx );
+ ++zerocrossings;
+ ++crosscount;
+ }else if( v1 > 0 && v2 == 0 ){
+ TReal v3 = *(pworkerBeg + 2);
+ if((v3 < 0) && ((v1 - v3) > epsilon_)){
+ *zerocrossings = (i + lag/2 + 1.);
+ }
+ }else{
+ //just continue, nothing to handle...
+ }
+ }
+ return crosscount;
+ }
+
+ bool getProblem() const{
+ return problem_;
+ }
+
+ };
+ }//ms
+ }//base
+}//ralab
+
+#endif // SIMPLEPICKER_H
diff --git a/src/pappsomspp/processing/filters/pwiz/resample/convert2dense.hpp b/src/pappsomspp/processing/filters/pwiz/resample/convert2dense.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..3ea0e09d81887553c21875897ce7a888148a83b0
--- /dev/null
+++ b/src/pappsomspp/processing/filters/pwiz/resample/convert2dense.hpp
@@ -0,0 +1,122 @@
+//
+// $Id$
+//
+//
+// Original author: Witold Wolski <wewolski@gmail.com>
+//
+// Copyright : ETH Zurich
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+//
+
+#ifndef CONVERT2DENSE_H
+#define CONVERT2DENSE_H
+
+#include <vector>
+#include <iostream>
+#include <numeric>
+#include <boost/assert.hpp>
+#include <boost/cstdint.hpp>
+#include "pwiz/utility/findmf/base/resample/masscomparefunctors.hpp"
+#include "pwiz/utility/findmf/base/resample/breakspec.hpp"
+#include "pwiz/utility/findmf/base/resample/bin1d.hpp"
+#include <QFile>
+
+
+namespace ralab
+{
+namespace base
+{
+namespace resample
+{
+typedef boost::int32_t int32_t;
+struct Convert2Dense
+{
+ ralab::base::resample::Bin1D bin_;
+ std::vector<int32_t> idx_;//small workder vecs
+ std::vector<double> weight_;
+ double am_; //parameter describing the sampling width
+ Convert2Dense(double am = 0.1):bin_(),idx_(),weight_(),am_() {
+ }
+
+ /// computes split points of an map.
+ std::size_t defBreak(std::pair<double, double> & mzrange, double ppm ) {
+ ralab::base::resample::PPMCompFunctor<double> ppmf(ppm);
+ ralab::base::resample::breaks( mzrange.first - 1., mzrange.second + 1., ppmf, bin_.breaks_ );
+ bin_.reset();
+ return bin_.breaks_.size();
+ }
+
+ /// Converts a sparse spec to a dense spec
+ template<typename Tmass, typename Tintens, typename Tout >
+ void convert2dense(Tmass beginMass, Tmass endMass, Tintens intens,
+ Tout ass
+ )
+ {
+ for( ; beginMass != (endMass -1) ; ++beginMass, ++intens ) {
+ double mass1 = *beginMass;
+ double mass2 = *(beginMass+1);
+ double predmass2 = mass1 + (am_* sqrt(mass1))*1.01;
+ if(mass2 > predmass2) {
+ mass2 = predmass2;
+ }
+
+ double deltamass = mass2-mass1;
+ double deltamasshalf;
+ if(true) {
+ deltamasshalf= deltamass/2.;
+ }
+ else {
+ deltamasshalf = deltamass;
+ }
+
+ bin_(mass1-deltamasshalf,mass2-deltamasshalf,idx_,weight_);
+
+ double intensd = static_cast<double>(*intens);
+ double sum = std::accumulate(weight_.begin(),weight_.end(),0.);
+ BOOST_ASSERT(fabs(deltamass- sum) < 1e-11);
+
+ double check = 0.;
+ for(std::size_t i = 0 ; i < idx_.size(); ++i) {
+ if((idx_[i]>=0) &(idx_[i] < static_cast<int32_t>(bin_.breaks_.size() - 1)))
+ {
+ double bb= intensd * weight_[i]/deltamass;
+ *(ass + idx_[i]) += bb;
+ check += bb;
+ }
+ }
+ //BOOST_ASSERT( fabs(check - intensd) < 1e-3 );
+
+ }
+ }//convert2dense
+
+ void getMids(std::vector<double> & mids)
+ {
+ ralab::base::resample::getMids(bin_.breaks_, mids );
+ }
+
+ /// Converts a sparse spec to a dense spec
+ template<typename Tmass, typename Tintens >
+ void convert2dense(Tmass beginMass, Tmass endMass, Tintens intens,
+ std::vector<typename std::iterator_traits<Tintens>::value_type > & gg
+ ) {
+ gg.resize(bin_.breaks_.size() - 1);
+ convert2dense(beginMass,endMass, intens, gg.begin());
+ }
+};
+
+
+}
+}
+}
+#endif // CONVERT2DENSE_H
diff --git a/src/pappsomspp/processing/tandem/tandemwrapper.cpp b/src/pappsomspp/processing/tandem/tandemwrapper.cpp
deleted file mode 100644
index 5a7e71da611232102f787ab81fed8021bcfd3353..0000000000000000000000000000000000000000
--- a/src/pappsomspp/processing/tandem/tandemwrapper.cpp
+++ /dev/null
@@ -1,200 +0,0 @@
-/**
- * \file tandemwrapper.cpp
- * \date 25/01/2020
- * \author Olivier Langella
- * \brief run tandem directly on Bruker's data
- */
-
-/*******************************************************************************
- * Copyright (c) 2020 Olivier Langella <Olivier.Langella@u-psud.fr>.
- *
- * This file is part of PAPPSOms-tools.
- *
- * PAPPSOms-tools 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-tools 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-tools. If not, see <http://www.gnu.org/licenses/>.
- *
- ******************************************************************************/
-
-#include "tandemwrapper.h"
-#include <QCommandLineParser>
-#include <QDateTime>
-#include <QTimer>
-#include <QFile>
-#include <pappsomspp/pappsoexception.h>
-#include "tandemwrapperlib/tandemwrapperrun.h"
-
-
-TandemWrapper::TandemWrapper(QObject *parent) : QObject(parent)
-{
- // get the instance of the main application
- app = QCoreApplication::instance();
- // setup everything here
- // create any global objects
- // setup debug and warning mode
-}
-
-// 10ms after the application starts this method will run
-// all QT messaging is running at this point so threads, signals and slots
-// will all work as expected.
-void
-TandemWrapper::run()
-{
- qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
- /* ./src/pt-mzxmlconverter -i
- /gorgone/pappso/fichiers_fabricants/Bruker/tims_doc/tdf-sdk/example_data/200ngHeLaPASEF_2min_compressed.d/analysis.tdf
- -o
- /gorgone/pappso/versions_logiciels_pappso/xtpcpp/bruker/200ngHeLaPASEF_2min.mzXML
- */
-
- //./src/pt-mzxmlconverter -i
- /// gorgone/pappso/fichiers_fabricants/Bruker/tims_doc/tdf-sdk/example_data/200ngHeLaPASEF_2min_compressed.d/analysis.tdf
- //-o /tmp/test.xml
-
-
- QTextStream errorStream(stderr, QIODevice::WriteOnly);
- QTextStream outputStream(stdout, QIODevice::WriteOnly);
-
- try
- {
- qDebug();
- QCommandLineParser parser;
-
- // throw pappso::PappsoException("test");
- parser.setApplicationDescription(
- QString("%1 ")
- .arg(QCoreApplication::applicationName())
- .append(PAPPSOMSPP_NAME)
- .append(" ")
- .append(PAPPSOMSPP_VERSION)
- .append(" tandem run on Bruker's data"));
- parser.addHelpOption();
- parser.addVersionOption();
- QCommandLineOption tandemOption(
- QStringList() << "tandem",
- QCoreApplication::translate("tandem",
- "tandem executable binary file <tandem>."),
- QCoreApplication::translate("tandem", "tandem"));
-
-
- QCommandLineOption tmpDirOption(
- QStringList() << "t"
- << "tmp",
- QCoreApplication::translate("tmp", "temporary directory"));
-
- QCommandLineOption centroidOption(
- QStringList() << "centroid",
- QCoreApplication::translate("centroid",
- "centroid function parameters <centroid>."),
- QCoreApplication::translate("centroid", "centroid"));
-
-
- parser.addOption(tandemOption);
- parser.addOption(tmpDirOption);
- parser.addOption(centroidOption);
-
- qDebug();
-
- // Process the actual command line arguments given by the user
- parser.process(*app);
-
- // QCoreApplication * app(this);
- // Add your main code here
- qDebug();
- const QDateTime dt_begin = QDateTime::currentDateTime();
- const QStringList args = parser.positionalArguments();
-
-
- TandemWrapperRun tandem_run(parser.value(tandemOption),
- parser.value(tmpDirOption),
- parser.value(centroidOption));
-
- if(args.size() > 0)
- {
- tandem_run.run(args[0], outputStream, errorStream);
- }
-
- qDebug();
- }
- catch(pappso::PappsoException &error)
- {
- errorStream << "Oops! an error occurred in PAPPSO MS tools. Dont Panic :"
- << endl;
- errorStream << error.qwhat() << endl;
- exit(1);
- app->exit(1);
- }
-
- catch(std::exception &error)
- {
- errorStream << "Oops! an error occurred in PAPPSO MS tools. Dont Panic :"
- << endl;
- errorStream << error.what() << endl;
- exit(1);
- app->exit(1);
- }
-
-
- // you must call quit when complete or the program will stay in the
- // messaging loop
- quit();
-}
-
-// call this routine to quit the application
-void
-TandemWrapper::quit()
-{
- // you can do some cleanup here
- // then do emit finished to signal CoreApplication to quit
- emit finished();
-}
-
-// shortly after quit is called the CoreApplication will signal this routine
-// this is a good place to delete any objects that were created in the
-// constructor and/or to stop any threads
-void
-TandemWrapper::aboutToQuitApp()
-{
- // stop threads
- // sleep(1); // wait for threads to stop.
- // delete any objects
-}
-
-
-int
-main(int argc, char **argv)
-{
- // QTextStream consoleErr(stderr);
- // QTextStream consoleOut(stdout, QIODevice::WriteOnly);
- // ConsoleOut::setCout(new QTextStream(stdout, QIODevice::WriteOnly));
- // ConsoleOut::setCerr(new QTextStream(stderr, QIODevice::WriteOnly));
- qDebug();
- QCoreApplication app(argc, argv);
- qDebug();
- QCoreApplication::setApplicationName("tandemwrapper");
- QCoreApplication::setApplicationVersion(PAPPSOMSPP_VERSION);
- QLocale::setDefault(QLocale::system());
-
- // create the main class
- TandemWrapper myMain;
- // connect up the signals
- QObject::connect(&myMain, SIGNAL(finished()), &app, SLOT(quit()));
- QObject::connect(
- &app, SIGNAL(aboutToQuit()), &myMain, SLOT(aboutToQuitApp()));
- qDebug();
-
-
- // This code will start the messaging engine in QT and in
- // 10ms it will start the execution in the MainClass.run routine;
- QTimer::singleShot(10, &myMain, SLOT(run()));
- return app.exec();
-}
diff --git a/src/pappsomspp/processing/tandem/tandemwrapper.h b/src/pappsomspp/processing/tandem/tandemwrapper.h
deleted file mode 100644
index 36b6c472fd83fbff4c13a20353ec0de1c877ed7e..0000000000000000000000000000000000000000
--- a/src/pappsomspp/processing/tandem/tandemwrapper.h
+++ /dev/null
@@ -1,67 +0,0 @@
-/**
- * \file tandemwrapper.h
- * \date 25/01/2020
- * \author Olivier Langella
- * \brief run tandem directly on Bruker's data
- */
-
-/*******************************************************************************
- * Copyright (c) 2020 Olivier Langella <Olivier.Langella@u-psud.fr>.
- *
- * This file is part of PAPPSOms-tools.
- *
- * PAPPSOms-tools 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-tools 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-tools. If not, see <http://www.gnu.org/licenses/>.
- *
- ******************************************************************************/
-
-#pragma once
-
-#include <QDebug>
-
-#include <QObject>
-#include <QCoreApplication>
-#include "../../config.h"
-
-class TandemWrapper : public QObject
-{
- Q_OBJECT
-
- private:
- QCoreApplication *app;
-
- public:
- explicit TandemWrapper(QObject *parent = 0);
- /////////////////////////////////////////////////////////////
- /// Call this to quit application
- /////////////////////////////////////////////////////////////
- void quit();
-
- signals:
- /////////////////////////////////////////////////////////////
- /// Signal to finish, this is connected to Application Quit
- /////////////////////////////////////////////////////////////
- void finished();
-
- public slots:
- /////////////////////////////////////////////////////////////
- /// This is the slot that gets called from main to start everything
- /// but, everthing is set up in the Constructor
- /////////////////////////////////////////////////////////////
- void run();
-
- /////////////////////////////////////////////////////////////
- /// slot that get signal when that application is about to quit
- /////////////////////////////////////////////////////////////
- void aboutToQuitApp();
-};
diff --git a/src/pappsomspp/processing/tandem/tandemwrapperlib/tandemwrapperrun.cpp b/src/pappsomspp/processing/tandem/tandemwrapperlib/tandemwrapperrun.cpp
deleted file mode 100644
index e88649fcd0a0e749fe851fc6f7a558358e081889..0000000000000000000000000000000000000000
--- a/src/pappsomspp/processing/tandem/tandemwrapperlib/tandemwrapperrun.cpp
+++ /dev/null
@@ -1,366 +0,0 @@
-/**
- * \file lib/tandemwrapperrun.cpp
- * \date 25/01/2020
- * \author Olivier Langella
- * \brief actually does really run tandem directly on Bruker's data
- */
-
-/*******************************************************************************
- * Copyright (c) 2020 Olivier Langella <Olivier.Langella@u-psud.fr>.
- *
- * This file is part of PAPPSOms-tools.
- *
- * PAPPSOms-tools 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-tools 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-tools. If not, see <http://www.gnu.org/licenses/>.
- *
- ******************************************************************************/
-
-#include "tandemwrapperrun.h"
-#include <QDebug>
-#include <QFileInfo>
-#include <QSettings>
-#include <pappsomspp/pappsoexception.h>
-#include <pappsomspp/msfile/msfileaccessor.h>
-#include <pappsomspp/msrun/private/timsmsrunreaderms2.h>
-#include <pappsomspp/processing/filters/filterpseudocentroid.h>
-#include <pappsomspp/msrun/mzxmloutput.h>
-#include "xtandeminputsaxhandler.h"
-
-TandemWrapperRun::TandemWrapperRun(const QString &tandem_binary,
- const QString &tmp_dir,
- const QString ¢roid_options)
-{
-
- setTandemBinaryPath(tandem_binary);
- m_centroidOptions = centroid_options;
-}
-
-TandemWrapperRun::~TandemWrapperRun()
-{
-}
-
-void
-TandemWrapperRun::setTandemBinaryPath(const QString &tandem_binary_path)
-{
-
- m_tandemBinary = tandem_binary_path;
- QSettings settings;
- if(m_tandemBinary.isEmpty())
- {
- m_tandemBinary =
- settings.value("path/tandem_binary", "/usr/bin/tandem").toString();
- }
- // check for tandem executable
- m_tandemVersion = checkXtandemVersion(m_tandemBinary);
-
- qDebug() << m_tandemVersion;
- settings.setValue("path/tandem_binary", m_tandemBinary);
-}
-
-
-const QString
-TandemWrapperRun::checkXtandemVersion(const QString &tandem_bin_path)
-{
- qDebug();
- // check tandem path
- QFileInfo tandem_exe(tandem_bin_path);
- if(!tandem_exe.exists())
- {
- // dir.path() returns the unique directory path
- throw pappso::PappsoException(
- QObject::tr(
- "X!Tandem software not found at %1.\nPlease check the X!Tandem "
- "installation on your computer and set tandem.exe path.")
- .arg(tandem_exe.absoluteFilePath()));
- }
- if(!tandem_exe.isReadable())
- {
- // dir.path() returns the unique directory path
- throw pappso::PappsoException(
- QObject::tr("Please check permissions on X!Tandem software found at %1 "
- "(file not readable).")
- .arg(tandem_exe.absoluteFilePath()));
- }
- if(!tandem_exe.isExecutable())
- {
- // dir.path() returns the unique directory path
- throw pappso::PappsoException(
- QObject::tr("Please check permissions on X!Tandem software found at %1 "
- "(file not executable).")
- .arg(tandem_exe.absoluteFilePath()));
- }
-
-
- QString version_return;
- QStringList arguments;
-
- arguments << "-v";
-
- QProcess *xt_process = new QProcess();
- // hk_process->setWorkingDirectory(QFileInfo(_hardklor_exe).absolutePath());
-
- xt_process->start(tandem_bin_path, arguments);
-
- if(!xt_process->waitForStarted())
- {
- throw pappso::PappsoException(
- QObject::tr("X!Tandem %1 process failed to start")
- .arg(m_tandemVersion));
- }
-
- while(xt_process->waitForReadyRead(1000))
- {
- }
- /*
- if (!xt_process->waitForFinished(_max_xt_time_ms)) {
- throw pappso::PappsoException(QObject::tr("can't wait for X!Tandem process
- to finish : timeout at %1").arg(_max_xt_time_ms));
- }
- */
- QByteArray result = xt_process->readAll();
-
-
- qDebug() << result.constData();
-
- // X! TANDEM Jackhammer TPP (2013.06.15.1 - LabKey, Insilicos, ISB)
-
- QRegExp parse_version("(.*) TANDEM ([A-Z,a-z, ]+) \\(([^ ,^\\)]*)(.*)");
- qDebug() << parse_version;
- // Pattern patt = Pattern.compile("X! TANDEM [A-Z]+ \\((.*)\\)",
- // Pattern.CASE_INSENSITIVE);
-
- if(parse_version.exactMatch(result.constData()))
- {
- version_return = QString("X!Tandem %1 %2")
- .arg(parse_version.capturedTexts()[2])
- .arg(parse_version.capturedTexts()[3]); //.join(" ");
- }
- else
- {
- throw pappso::PappsoException(
- QObject::tr("This executable %1 may not be a valid X!Tandem software. "
- "Please check your X!Tandem installation.")
- .arg(tandem_bin_path));
- }
-
- QProcess::ExitStatus Status = xt_process->exitStatus();
- delete xt_process;
- if(Status != 0)
- {
- // != QProcess::NormalExit
- throw pappso::PappsoException(
- QObject::tr("error executing X!Tandem Status != 0 : %1 %2\n%3")
- .arg(tandem_bin_path)
- .arg(arguments.join(" ").arg(result.data())));
- }
- qDebug();
- return version_return;
-}
-
-
-bool
-TandemWrapperRun::shouldIstop()
-{
- return false;
-}
-
-
-void
-TandemWrapperRun::readyReadStandardOutput()
-{
- *mp_outputStream << m_xtProcess->readAllStandardOutput();
-}
-
-void
-TandemWrapperRun::readyReadStandardError()
-{
- *mp_errorStream << m_xtProcess->readAllStandardError();
-}
-
-void
-TandemWrapperRun::writeFinalTandemOutput(const QString &tmp_tandem_output,
- const QString &final_tandem_output)
-{
-}
-
-
-void
-TandemWrapperRun::wrapTandemInputFile(const QString &tandem_input_file)
-{
- // read original tandem input file
- // store original ms data file name
- // create new mzXML data file in temporary directory
- // create new tandem input file based on new mzXML file
- QString mzxml_data_file_name = "/tmp/msdata.mzxml";
- QString wrapped_tandem_input = "/tmp/input_tandem.xml";
- QString wrapped_tandem_output = "/tmp/output_tandem.xml";
-
- XtandemInputSaxHandler wrap_input(
- mzxml_data_file_name, wrapped_tandem_input, wrapped_tandem_output);
-
- QFile qfile(tandem_input_file);
- QXmlInputSource xmlInputSource(&qfile);
- QXmlSimpleReader simplereader;
- simplereader.setContentHandler(&wrap_input);
- simplereader.setErrorHandler(&wrap_input);
-
- if(simplereader.parse(xmlInputSource))
- {
- }
- else
- {
- throw pappso::PappsoException(
- QObject::tr("Error reading %1 X!Tandem input file :\n %2")
- .arg(tandem_input_file)
- .arg(wrap_input.errorString()));
- }
-
- // convert to mzXML
- QString original_msdata_file_name = wrap_input.getOriginalMsDataFileName();
- convertOrginalMsData2mzXmlData(original_msdata_file_name,
- mzxml_data_file_name);
-
- // launch tandem
- runTandem(wrapped_tandem_input);
-
- // rewrite tandem result file
- writeFinalTandemOutput(wrapped_tandem_output,
- wrap_input.getOriginalTandemOutputFileName());
-}
-
-void
-TandemWrapperRun::convertOrginalMsData2mzXmlData(const QString &origin,
- const QString &target) const
-{
- qDebug();
- pappso::MsFileAccessor origin_access(origin, "runa1");
- origin_access.setPreferedFileReaderType(pappso::MzFormat::brukerTims,
- pappso::FileReaderType::tims_ms2);
- origin_access.getMsRunIds();
-
- pappso::MsRunReaderSPtr p_reader;
- p_reader = origin_access.msRunReaderSp(origin_access.getMsRunIds().front());
- if(!m_centroidOptions.isEmpty())
- {
- pappso::TimsMsRunReaderMs2 *tims2_reader =
- dynamic_cast<pappso::TimsMsRunReaderMs2 *>(p_reader.get());
- if(tims2_reader != nullptr)
- {
- qDebug();
- QStringList option_list = m_centroidOptions.split(" ");
- std::shared_ptr<pappso::FilterPseudoCentroid> ms2filter =
- std::make_shared<pappso::FilterPseudoCentroid>(
- option_list.at(0).toDouble(),
- option_list.at(1).toDouble(),
- option_list.at(2).toDouble(),
- option_list.at(3).toDouble());
-
- tims2_reader->setMs2FilterCstSPtr(ms2filter);
- qDebug();
- }
- }
-
-
- pappso::MzxmlOutput *p_mzxml_output;
- QFile output_file(target);
- // qDebug() << " TsvDirectoryWriter::writeSheet " <<
- // QFileInfo(*_p_ofile).absoluteFilePath();
- if(output_file.open(QIODevice::WriteOnly))
- {
- p_mzxml_output =
- new pappso::MzxmlOutput(QTextStream(&output_file).device());
-
- p_mzxml_output->maskMs1(true);
-
- p_mzxml_output->setReadAhead(true);
-
- p_mzxml_output->write(p_reader.get());
-
- p_mzxml_output->close();
- }
- else
- {
- throw pappso::PappsoException(
- tr("unable to write into %1 mzXML output file").arg(target));
- }
-
- qDebug();
-}
-
-void
-TandemWrapperRun::run(const QString &tandem_input_file,
- QTextStream &output_stream,
- QTextStream &error_stream)
-{
- mp_outputStream = &output_stream;
- mp_errorStream = &error_stream;
-
- wrapTandemInputFile(tandem_input_file);
- mp_outputStream = nullptr;
- mp_errorStream = nullptr;
-}
-
-void
-TandemWrapperRun::runTandem(const QString &tandem_input_file)
-{
-
- m_xtProcess = new QProcess();
- QStringList arguments;
- arguments << tandem_input_file;
- // hk_process->setWorkingDirectory(QFileInfo(_hardklor_exe).absolutePath());
- m_xtProcess->start(m_tandemBinary, arguments);
-
- qDebug() << m_tandemBinary << " " << m_xtProcess->arguments();
-
- connect(m_xtProcess,
- &QProcess::readyReadStandardOutput,
- this,
- &TandemWrapperRun::readyReadStandardOutput);
- connect(m_xtProcess,
- &QProcess::readyReadStandardError,
- this,
- &TandemWrapperRun::readyReadStandardError);
-
-
- if(!m_xtProcess->waitForStarted())
- {
- throw pappso::PappsoException(
- QObject::tr("X!Tandem process failed to start"));
- }
-
- while(m_xtProcess->waitForFinished(m_maxTandemRunTimeMs))
- {
- //_p_monitor->appendText(xt_process->readAll().data());
- // data.append(xt_process->readAll());
- if(shouldIstop())
- {
- m_xtProcess->kill();
- delete m_xtProcess;
- throw pappso::PappsoException(
- QObject::tr("X!Tandem stopped by the user processing on file %1")
- .arg(tandem_input_file));
- }
- }
-
- QProcess::ExitStatus Status = m_xtProcess->exitStatus();
-
- delete m_xtProcess;
- if(Status != 0)
- {
- // != QProcess::NormalExit
- throw pappso::PappsoException(
- QObject::tr("error executing X!Tandem Status != 0 : %1")
- .arg(m_tandemBinary));
- }
- m_xtProcess = nullptr;
-}
diff --git a/src/pappsomspp/processing/tandem/tandemwrapperlib/tandemwrapperrun.h b/src/pappsomspp/processing/tandem/tandemwrapperlib/tandemwrapperrun.h
deleted file mode 100644
index 416bf87da97ec5fa06a39f70ee77622529c6da74..0000000000000000000000000000000000000000
--- a/src/pappsomspp/processing/tandem/tandemwrapperlib/tandemwrapperrun.h
+++ /dev/null
@@ -1,107 +0,0 @@
-/**
- * \file lib/tandemwrapperrun.h
- * \date 25/01/2020
- * \author Olivier Langella
- * \brief actually does really run tandem directly on Bruker's data
- */
-
-/*******************************************************************************
- * Copyright (c) 2020 Olivier Langella <Olivier.Langella@u-psud.fr>.
- *
- * This file is part of PAPPSOms-tools.
- *
- * PAPPSOms-tools 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-tools 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-tools. If not, see <http://www.gnu.org/licenses/>.
- *
- ******************************************************************************/
-
-#pragma once
-
-#include <QDebug>
-#include <QObject>
-#include <QProcess>
-
-/**
- * @todo write docs
- */
-class TandemWrapperRun : public QObject
-{
- Q_OBJECT
- public:
- /** @brief prepare a tandem run
- * @param tandem_binary file path to tandem.exe if not set, a default value is
- * given in QSettings
- * @param tmp_dir temporary directory, where to write mzXML file conversion if
- * not set, a default value is given in QSettings
- * @param centroid_options controls the way MS2 spectrum are centroided from
- * raw bruker's data if not set, a default value is given in QSettings
- */
- TandemWrapperRun(const QString &tandem_binary,
- const QString &tmp_dir,
- const QString ¢roid_options);
-
- /** @brief run a tandem job
- * @param tandem_input_file tandem xml input file
- * @param output_stream standard output where to write tandem stdout
- * @param error_stream standard error where to write tandem stderr
- */
- void run(const QString &tandem_input_file,
- QTextStream &output_stream,
- QTextStream &error_stream);
-
- /**
- * Destructor
- */
- ~TandemWrapperRun();
-
- private:
- void setTandemBinaryPath(const QString &tandem_binary_path);
- bool shouldIstop();
- const QString checkXtandemVersion(const QString &tandem_bin_path);
- void wrapTandemInputFile(const QString &tandem_input_file);
-
- void convertOrginalMsData2mzXmlData(const QString &origin,
- const QString &target) const;
-
-
- /** @brief run a tandem job
- * @param tandem_input_file tandem xml input file
- */
- void runTandem(const QString &tandem_input_file);
-
- /** @brief tandem output modification
- * tandem output is modified to contain the Bruker's file as input and
- * centroidization parameters
- * @param tmp_tandem_output raw tandem output filename
- * @param final_tandem_output final destination file for modified tandem
- * output
- */
- void writeFinalTandemOutput(const QString &tmp_tandem_output,
- const QString &final_tandem_output);
-
-
- private slots:
- void readyReadStandardOutput();
- void readyReadStandardError();
-
- private:
- QString m_tandemBinary;
- QString m_tandemVersion;
- QString m_tmpDir;
- QString m_centroidOptions;
- int m_maxTandemRunTimeMs = (60000 * 60 * 24); // 1 day
- QProcess *m_xtProcess = nullptr;
-
- QTextStream *mp_outputStream = nullptr;
- QTextStream *mp_errorStream = nullptr;
-};
diff --git a/src/pappsomspp/processing/tandem/tandemwrapperlib/xtandeminputsaxhandler.cpp b/src/pappsomspp/processing/tandem/tandemwrapperlib/xtandeminputsaxhandler.cpp
deleted file mode 100644
index d46f082250aa813da1506250818f2a2f910cfcb8..0000000000000000000000000000000000000000
--- a/src/pappsomspp/processing/tandem/tandemwrapperlib/xtandeminputsaxhandler.cpp
+++ /dev/null
@@ -1,306 +0,0 @@
-/**
- * \file lib/xtandeminputsaxhandler.cpp
- * \date 25/01/2020
- * \author Olivier Langella
- * \brief rewrites tandem xml input file with temporary files
- */
-
-/*******************************************************************************
- * Copyright (c) 2020 Olivier Langella <Olivier.Langella@u-psud.fr>.
- *
- * This file is part of PAPPSOms-tools.
- *
- * PAPPSOms-tools 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-tools 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-tools. If not, see <http://www.gnu.org/licenses/>.
- *
- ******************************************************************************/
-
-
-#include "xtandeminputsaxhandler.h"
-#include <pappsomspp/pappsoexception.h>
-#include <QFileInfo>
-
-XtandemInputSaxHandler::XtandemInputSaxHandler(
- const QString &destinationMzXmlFile,
- const QString &destinationTandemInputFile,
- const QString &destinationTandemOutputFile)
- : m_destinationTandemInputFile(destinationTandemInputFile)
-{
- m_destinationMzXmlFileName = destinationMzXmlFile;
- m_destinationTandemOutputFileName = destinationTandemOutputFile;
- m_destinationTandemInputFileName =
- QFileInfo(destinationTandemInputFile).absoluteFilePath();
-
- m_destinationTandemInputFile.open(QIODevice::WriteOnly);
- p_writeXmlTandemInput = new QXmlStreamWriter();
- p_writeXmlTandemInput->setDevice(&m_destinationTandemInputFile);
-}
-
-XtandemInputSaxHandler::~XtandemInputSaxHandler()
-{
- m_destinationTandemInputFile.close();
- delete p_writeXmlTandemInput;
-}
-
-void
-XtandemInputSaxHandler::writeOpenTag(const QString &qName,
- const QXmlAttributes &attributes)
-{
- p_writeXmlTandemInput->writeStartElement(qName);
- for(std::size_t i = 0; i < attributes.length(); i++)
- {
- p_writeXmlTandemInput->writeAttribute(attributes.qName(i),
- attributes.value(i));
- }
-}
-
-bool
-XtandemInputSaxHandler::startElement(const QString &namespaceURI,
- const QString &localName,
- const QString &qName,
- const QXmlAttributes &attributes)
-{
- /*
-<?xml version="1.0" encoding="UTF-8"?>
-<bioml label="20191222_18_EF1_test_condor_22janv_third_step.xml">
-<note type="heading">Paths</note>
-<note type="input" label="list path, default
-parameters">/gorgone/pappso/jouy/presets/metapappso/Lumos_04112019_PROTEOCARDIS_THIRD_STEP_AB.xml</note>
-<note type="input" label="list path, taxonomy
-information">/gorgone/pappso/jouy/users/Celine/2019_Lumos/20191222_107_Juste_APD/metapappso_condor/params/xtandem_database_third_step_test_condor_22janv.database</note>
-<note type="input" label="spectrum,
-path">/gorgone/pappso/jouy/raw/2019_Lumos/20191222_107_Juste/20191222_18_EF1.mzXML</note>
-<note type="heading">Protein general</note>
-<note type="input" label="protein, taxon">usedefined</note>
-<note type="heading">Output</note>
-<note type="input" label="output,
-path">/gorgone/pappso/jouy/users/Celine/2019_Lumos/20191222_107_Juste_APD/metapappso_condor/test_run/20191222_18_EF1_third_step_test_condor_22janv.xml</note>
-</bioml>
-*/
- m_tagStack.push_back(qName);
- bool is_ok = true;
-
- try
- {
- m_currentText.clear();
- //<bioml label="example api document">
- if(m_tagStack.size() == 1)
- {
- if(qName != "bioml")
- {
- m_errorString = QObject::tr(
- "ERROR in XtandemInputSaxHandler::startElement "
- "root tag %1 is not <bioml>")
- .arg(qName);
- m_isTandemParameter = false;
- return false;
- }
- else
- {
-
- m_isTandemParameter = true;
- // label="20191222_18_EF1_test_condor_22janv_third_step.xml"
- m_labelName = attributes.value("label");
-
- writeOpenTag(qName, attributes);
- }
- }
- // startElement_group
-
- if(qName == "note")
- {
- is_ok = startElement_note(attributes);
- }
- }
- catch(pappso::PappsoException exception_pappso)
- {
- m_errorString = QObject::tr(
- "ERROR in XtandemInputSaxHandler::startElement "
- "tag %1, PAPPSO exception:\n%2")
- .arg(qName)
- .arg(exception_pappso.qwhat());
- return false;
- }
- catch(std::exception exception_std)
- {
- m_errorString = QObject::tr(
- "ERROR in XtandemInputSaxHandler::startElement "
- "tag %1, std exception:\n%2")
- .arg(qName)
- .arg(exception_std.what());
- return false;
- }
- return is_ok;
-}
-
-bool
-XtandemInputSaxHandler::endElement(const QString &namespaceURI,
- const QString &localName,
- const QString &qName)
-{
-
- bool is_ok = true;
- // endElement_peptide_list
- try
- {
-
- if(qName == "note")
- {
- is_ok = endElement_note();
- }
- else
- {
- p_writeXmlTandemInput->writeCharacters(m_currentText);
- p_writeXmlTandemInput->writeEndElement();
- }
- }
- catch(pappso::PappsoException exception_pappso)
- {
- m_errorString = QObject::tr(
- "ERROR in XtandemInputSaxHandler::endElement tag "
- "%1, PAPPSO exception:\n%2")
- .arg(qName)
- .arg(exception_pappso.qwhat());
- return false;
- }
- catch(std::exception exception_std)
- {
- m_errorString = QObject::tr(
- "ERROR in XtandemInputSaxHandler::endElement tag "
- "%1, std exception:\n%2")
- .arg(qName)
- .arg(exception_std.what());
- return false;
- }
-
- m_currentText.clear();
- m_tagStack.pop_back();
-
- return is_ok;
-}
-
-bool
-XtandemInputSaxHandler::startDocument()
-{
-
- p_writeXmlTandemInput->setAutoFormatting(true);
- p_writeXmlTandemInput->writeStartDocument("1.0");
- return true;
-}
-
-bool
-XtandemInputSaxHandler::endDocument()
-{
- p_writeXmlTandemInput->writeEndDocument();
- return true;
-}
-
-bool
-XtandemInputSaxHandler::characters(const QString &str)
-{
- m_currentText += str;
- return true;
-}
-
-
-bool
-XtandemInputSaxHandler::error(const QXmlParseException &exception)
-{
- m_errorString = QObject::tr(
- "Parse error at line %1, column %2 :\n"
- "%3")
- .arg(exception.lineNumber())
- .arg(exception.columnNumber())
- .arg(exception.message());
- qDebug() << m_errorString;
- return false;
-}
-
-
-bool
-XtandemInputSaxHandler::fatalError(const QXmlParseException &exception)
-{
- m_errorString = QObject::tr(
- "Parse error at line %1, column %2 :\n"
- "%3")
- .arg(exception.lineNumber())
- .arg(exception.columnNumber())
- .arg(exception.message());
- qDebug() << m_errorString;
- return false;
-}
-
-QString
-XtandemInputSaxHandler::errorString() const
-{
- return m_errorString;
-}
-
-
-bool
-XtandemInputSaxHandler::startElement_note(QXmlAttributes attributes)
-{
- // qDebug() << "XtandemParamSaxHandler::startElement_note begin " <<
- // <note type="input"
- // label="output,path">/gorgone/pappso/jouy/users/Celine/2019_Lumos/20191222_107_Juste_APD/metapappso_condor/test_run/20191222_18_EF1_third_step_test_condor_22janv.xml</note>
-
- writeOpenTag("note", attributes);
- m_currentLabel = "";
-
- if(attributes.value("type") == "input")
- {
- m_currentLabel = attributes.value("label");
- }
-
- // qDebug() << "XtandemParamSaxHandler::startElement_note _current_label " <<
- // _current_label;
- return true;
-}
-
-bool
-XtandemInputSaxHandler::endElement_note()
-{
- // qDebug() << "XtandemParamSaxHandler::endElement_note begin " <<
- // _current_label << " " << _current_text.simplified();
- if(m_currentLabel == "output, path")
- {
- m_originTandemOutpuFileName = m_currentText;
- p_writeXmlTandemInput->writeCharacters(m_destinationTandemOutputFileName);
- }
- else if(m_currentLabel == "spectrum, path")
- {
- //<note type="input"
- // label="spectrum,path">/gorgone/pappso/jouy/raw/2019_Lumos/20191222_107_Juste/20191222_18_EF1.mzXML</note>
- m_originMzDataFileName = m_currentText;
- p_writeXmlTandemInput->writeCharacters(m_destinationMzXmlFileName);
- }
- else
- {
- p_writeXmlTandemInput->writeCharacters(m_currentText);
- }
- p_writeXmlTandemInput->writeEndElement();
- return true;
-}
-
-
-const QString &
-XtandemInputSaxHandler::getOriginalMsDataFileName() const
-{
- return m_originMzDataFileName;
-}
-
-const QString &
-XtandemInputSaxHandler::getOriginalTandemOutputFileName() const
-{
- return m_originTandemOutpuFileName;
-}
diff --git a/src/pappsomspp/processing/tandem/tandemwrapperlib/xtandeminputsaxhandler.h b/src/pappsomspp/processing/tandem/tandemwrapperlib/xtandeminputsaxhandler.h
deleted file mode 100644
index 697f3296f31f9d7942016dda28a947dee252fd52..0000000000000000000000000000000000000000
--- a/src/pappsomspp/processing/tandem/tandemwrapperlib/xtandeminputsaxhandler.h
+++ /dev/null
@@ -1,95 +0,0 @@
-/**
- * \file lib/xtandeminputsaxhandler.h
- * \date 25/01/2020
- * \author Olivier Langella
- * \brief rewrites tandem xml input file with temporary files
- */
-
-/*******************************************************************************
- * Copyright (c) 2020 Olivier Langella <Olivier.Langella@u-psud.fr>.
- *
- * This file is part of PAPPSOms-tools.
- *
- * PAPPSOms-tools 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-tools 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-tools. If not, see <http://www.gnu.org/licenses/>.
- *
- ******************************************************************************/
-
-#pragma once
-
-#include <QDebug>
-#include <QXmlDefaultHandler>
-#include <QXmlStreamWriter>
-/**
- * @todo write docs
- */
-class XtandemInputSaxHandler : public QXmlDefaultHandler
-{
- public:
- /**
- * Default constructor
- */
- XtandemInputSaxHandler(const QString &destinationMzXmlFile,
- const QString &destinationTandemInputFile,
- const QString &destinationTandemOutputFile);
-
- /**
- * Destructor
- */
- ~XtandemInputSaxHandler();
-
-
- bool startElement(const QString &namespaceURI,
- const QString &localName,
- const QString &qName,
- const QXmlAttributes &attributes) override;
-
- bool endElement(const QString &namespaceURI,
- const QString &localName,
- const QString &qName) override;
-
- bool startDocument() override;
-
- bool endDocument() override;
-
- bool characters(const QString &str) override;
-
- bool fatalError(const QXmlParseException &exception) override;
- bool error(const QXmlParseException &exception) override;
-
- QString errorString() const;
-
- const QString &getOriginalMsDataFileName() const;
- const QString &getOriginalTandemOutputFileName() const;
-
- private:
- bool startElement_note(QXmlAttributes attributes);
- bool endElement_note();
- void writeOpenTag(const QString &qName, const QXmlAttributes &attributes);
-
-
- private:
- QString m_destinationMzXmlFileName;
- QString m_originMzDataFileName;
- QString m_destinationTandemInputFileName;
- QString m_originTandemOutpuFileName;
- QString m_destinationTandemOutputFileName;
- QFile m_destinationTandemInputFile;
- QXmlStreamWriter *p_writeXmlTandemInput;
- std::vector<QString> m_tagStack;
- bool m_isTandemParameter = false;
- QString m_errorString;
- QString m_currentText;
- QString m_currentLabel;
- QString m_labelName;
-};