#include "SpectrumList_Filter.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/utility/misc/IntegerSet.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include "pwiz/data/msdata/examples.hpp"
#include "pwiz/data/msdata/Serializer_mzML.hpp"
#include <cstring>

Classes
struct	EvenPredicate

struct	EvenMS2Predicate

struct	SelectedIndexPredicate

struct	HasBinaryDataPredicate

Functions
void	printSpectrumList (const SpectrumList &sl, ostream &os)

SpectrumListPtr	createSpectrumList ()

void	testEven (SpectrumListPtr sl)

void	testEvenMS2 (SpectrumListPtr sl)

void	testSelectedIndices (SpectrumListPtr sl)

void	testHasBinaryData (SpectrumListPtr sl)

void	testIndexSet (SpectrumListPtr sl)

void	testScanNumberSet (SpectrumListPtr sl)

void	testScanEventSet (SpectrumListPtr sl)

void	testScanTimeRange (SpectrumListPtr sl)

void	testMSLevelSet (SpectrumListPtr sl)

void	testMS2Activation (SpectrumListPtr sl)

void	testMassAnalyzerFilter (SpectrumListPtr sl)

void	testMZPresentFilter (SpectrumListPtr sl)

void	testThermoFilterFilter (SpectrumListPtr sl)

void	test ()

int	main (int argc, char *argv[])

Variables
ostream *	os_ = 0

Function Documentation

◆ printSpectrumList()

void printSpectrumList	(	const SpectrumList &	sl,
		ostream &	os
	)

Definition at line 43 of file SpectrumList_FilterTest.cpp.

References MS_filter_string, MS_ms_level, MS_preset_scan_configuration, MS_scan_start_time, pwiz::msdata::SpectrumList::size(), and pwiz::msdata::SpectrumList::spectrum().

Referenced by createSpectrumList(), testEven(), testEvenMS2(), testHasBinaryData(), testIndexSet(), testMassAnalyzerFilter(), testMS2Activation(), testMSLevelSet(), testMZPresentFilter(), testScanEventSet(), testScanNumberSet(), testScanTimeRange(), testSelectedIndices(), and testThermoFilterFilter().

 {
     os << "size: " << sl.size() << endl;
 
     for (size_t i=0, end=sl.size(); i<end; i++)
     {
         SpectrumPtr spectrum = sl.spectrum(i, false);
         os << spectrum->index << " " 
            << spectrum->id << " "
            << "ms" << spectrum->cvParam(MS_ms_level).value << " "
            << "scanEvent:" << spectrum->scanList.scans[0].cvParam(MS_preset_scan_configuration).value << " "
            << "scanTime:" << spectrum->scanList.scans[0].cvParam(MS_scan_start_time).timeInSeconds() << " "
            << "scanFilter:" << spectrum->scanList.scans[0].cvParam(MS_filter_string).value << " "
            << endl;
     }
 }

◆ createSpectrumList()

SpectrumListPtr createSpectrumList ( )

Definition at line 61 of file SpectrumList_FilterTest.cpp.

References boost::lexical_cast(), MS_collision_induced_dissociation, MS_electron_transfer_dissociation, MS_emission_spectrum, MS_filter_string, MS_HCD, MS_IRMPD, MS_MS1_spectrum, MS_ms_level, MS_MSn_spectrum, MS_number_of_detector_counts, MS_orbitrap, MS_preset_scan_configuration, MS_quadrupole, MS_radial_ejection_linear_ion_trap, MS_scan_start_time, os_, printSpectrumList(), and UO_second.

Referenced by test().

 {
     SpectrumListSimplePtr sl(new SpectrumListSimple);
 
     for (size_t i=0; i<11; ++i)
     {
         SpectrumPtr spectrum(new Spectrum);
         spectrum->index = i;
         spectrum->id = "scan=" + lexical_cast<string>(100+i);
         spectrum->setMZIntensityPairs(vector<MZIntensityPair>(i), MS_number_of_detector_counts);
 
         // add mz/intensity to the spectra for mzPresent filter
         vector<MZIntensityPair> mzint(i*2);
         for (size_t j=1.0; j<i*2; ++j)
         {
             mzint.insert(mzint.end(), MZIntensityPair(j*100, j*j));
         }
         spectrum->setMZIntensityPairs(mzint, MS_number_of_detector_counts);
 
         if (i == 10)
         {
             spectrum->set(MS_emission_spectrum);
             sl->spectra.push_back(spectrum);
             continue;
         }
 
         bool isMS1 = i%3==0;
         spectrum->set(MS_ms_level, isMS1 ? 1 : 2);
         spectrum->set(isMS1 ? MS_MS1_spectrum : MS_MSn_spectrum);
 
         // outfit the spectra with mass analyzer definitions to test the massAnalyzer filter
         spectrum->scanList.scans.push_back(Scan());
 
         spectrum->scanList.scans[0].instrumentConfigurationPtr = InstrumentConfigurationPtr(new InstrumentConfiguration());
         InstrumentConfigurationPtr p = spectrum->scanList.scans[0].instrumentConfigurationPtr;
         if (i%3 == 0)
         {
             p->componentList.push_back(Component(MS_orbitrap, 0/*order*/));
         }
         else
         {
             if (i % 2)
             {
                 p->componentList.push_back(Component(MS_quadrupole, 0/*order*/));
                 p->componentList.push_back(Component(MS_orbitrap, 1/*order*/));
             }
             else
                 p->componentList.push_back(Component(MS_radial_ejection_linear_ion_trap, 0/*order*/));
         }
 
         // add thermo scan filter lines to the MS1 spectra
         // MS1
         if (i == 0 || i == 6) // narrow window MS1
         {
             spectrum->scanList.scans[0].set(MS_filter_string, "FTMS + p NSI SIM ms [595.0000-655.0000]");
         }
         else if (i == 3 || i == 9) // wide window MS1
         {
             spectrum->scanList.scans[0].set(MS_filter_string, "FTMS + p NSI SIM ms [395.0000-1005.0000]");
         }
 
         if (i%3 != 0)
             spectrum->precursors.push_back(Precursor((i+4)*100, 3));
 
         // add precursors, activation types, and thermo scan filter lines to the MS2 spectra
         ostringstream filterLine;
         if (i==1 || i ==5) // ETD
         {
             spectrum->precursors[0].activation.set(MS_electron_transfer_dissociation);
             filterLine << "FTMS + c NSI Full ms2 " << (i + 4) * 100 << ".0000@etd30.00 [100.0000-2000.0000]";
         }
         else if (i==2) // CID
         {
             spectrum->precursors[0].activation.set(MS_collision_induced_dissociation);
             filterLine << "ITMS + c NSI Full ms2 " << (i + 4) * 100 << ".0000@cid30.00 [100.0000-2000.0000]";
         }
         else if (i==4) // HCD
         {
             spectrum->precursors[0].activation.set(MS_HCD);
             filterLine << "ITMS + c NSI Full ms2 " << (i + 4) * 100 << ".0000@hcd30.00 [100.0000-2000.0000]";
         }
         else if (i==8) // IRMPD
         {
             spectrum->precursors[0].activation.set(MS_IRMPD);
             filterLine << "ITMS + c NSI Full ms2 " << (i + 4) * 100 << ".0000@irmpd30.00 [100.0000-2000.0000]";
         }
         else if (i==7) // ETD + SA
         {
             spectrum->precursors[0].activation.set(MS_electron_transfer_dissociation);
             spectrum->precursors[0].activation.set(MS_collision_induced_dissociation);
             filterLine << "FTMS + c NSI Full ms2 " << (i + 4) * 100 << ".0000@irmpd30.00 [100.0000-2000.0000]";
         }
 
         spectrum->scanList.scans.push_back(Scan());
         spectrum->scanList.scans[0].set(MS_preset_scan_configuration, i%4);
         spectrum->scanList.scans[0].set(MS_scan_start_time, 420+i, UO_second);
         if (i % 3 != 0)
             spectrum->scanList.scans[0].set(MS_filter_string, filterLine.str());
         sl->spectra.push_back(spectrum);
     }
 
     if (os_)
     {
         *os_ << "original spectrum list:\n";
         printSpectrumList(*sl, *os_); 
         *os_ << endl;
     }
 
     return sl;
 }

◆ testEven()

void testEven ( SpectrumListPtr sl )

Definition at line 184 of file SpectrumList_FilterTest.cpp.

References ralab::base::filter::filter(), os_, printSpectrumList(), pwiz::analysis::SpectrumList_Filter::size(), pwiz::analysis::SpectrumList_Filter::spectrum(), pwiz::analysis::SpectrumList_Filter::spectrumIdentity(), and unit_assert.

Referenced by test().

 {
     if (os_) *os_ << "testEven:\n";
 
     SpectrumList_Filter filter(sl, EvenPredicate());
 
     if (os_) 
     {
         printSpectrumList(filter, *os_);
         *os_ << endl;
     }
 
     unit_assert(filter.size() == 6);
 
     for (size_t i=0, end=filter.size(); i<end; i++)
     {
         const SpectrumIdentity& id = filter.spectrumIdentity(i); 
         unit_assert(id.index == i);
         unit_assert(id.id == "scan=" + lexical_cast<string>(100+i*2));
 
         SpectrumPtr spectrum = filter.spectrum(i);
         unit_assert(spectrum->index == i);
         unit_assert(spectrum->id == "scan=" + lexical_cast<string>(100+i*2));
     }
 }

◆ testEvenMS2()

void testEvenMS2 ( SpectrumListPtr sl )

Definition at line 236 of file SpectrumList_FilterTest.cpp.

References ralab::base::filter::filter(), pwiz::msdata::SpectrumIdentity::id, os_, printSpectrumList(), pwiz::analysis::SpectrumList_Filter::size(), pwiz::analysis::SpectrumList_Filter::spectrumIdentity(), and unit_assert.

Referenced by test().

 {
     if (os_) *os_ << "testEvenMS2:\n";
 
     SpectrumList_Filter filter(sl, EvenMS2Predicate());
     
     if (os_) 
     {
         printSpectrumList(filter, *os_);
         *os_ << endl;
     }
 
     unit_assert(filter.size() == 3);
     unit_assert(filter.spectrumIdentity(0).id == "scan=102");
     unit_assert(filter.spectrumIdentity(1).id == "scan=104");
     unit_assert(filter.spectrumIdentity(2).id == "scan=108");
 }

◆ testSelectedIndices()

void testSelectedIndices ( SpectrumListPtr sl )

Definition at line 279 of file SpectrumList_FilterTest.cpp.

References ralab::base::filter::filter(), pwiz::msdata::SpectrumIdentity::id, os_, printSpectrumList(), pwiz::analysis::SpectrumList_Filter::size(), pwiz::analysis::SpectrumList_Filter::spectrumIdentity(), and unit_assert.

Referenced by test().

 {
     if (os_) *os_ << "testSelectedIndices:\n";
 
     SpectrumList_Filter filter(sl, SelectedIndexPredicate());
     
     if (os_) 
     {
         printSpectrumList(filter, *os_);
         *os_ << endl;
     }
 
     unit_assert(filter.size() == 3);
     unit_assert(filter.spectrumIdentity(0).id == "scan=101");
     unit_assert(filter.spectrumIdentity(1).id == "scan=103");
     unit_assert(filter.spectrumIdentity(2).id == "scan=105");
 }

◆ testHasBinaryData()

void testHasBinaryData ( SpectrumListPtr sl )

Definition at line 321 of file SpectrumList_FilterTest.cpp.

References pwiz::msdata::DetailLevel_FullData, pwiz::msdata::DetailLevel_FullMetadata, pwiz::msdata::SpectrumListWrapper::empty(), ralab::base::filter::filter(), pwiz::msdata::examples::initializeTiny(), os_, printSpectrumList(), pwiz::msdata::Serializer_mzML::read(), pwiz::msdata::MSData::run, pwiz::analysis::SpectrumList_Filter::size(), pwiz::msdata::Run::spectrumListPtr, unit_assert, unit_assert_operator_equal, and pwiz::msdata::Serializer_mzML::write().

Referenced by test().

 {
     if (os_) *os_ << "testHasBinaryData:\n";
 
     MSData msd;
     examples::initializeTiny(msd);
 
     shared_ptr<stringstream> ss(new stringstream);
     Serializer_mzML serializer;
     serializer.write(*ss, msd);
 
     MSData msd2;
     serializer.read(ss, msd2);
 
     sl = msd2.run.spectrumListPtr;
 
     {
         SpectrumList_Filter filter(sl, HasBinaryDataPredicate(DetailLevel_FullMetadata));
         unit_assert(filter.empty());
     }
 
     {
         SpectrumList_Filter filter(sl, HasBinaryDataPredicate(DetailLevel_FullData));
     
         if (os_) 
         {
             printSpectrumList(filter, *os_);
             *os_ << endl;
         }
 
         unit_assert_operator_equal(4, filter.size());
     }
 }

◆ testIndexSet()

void testIndexSet ( SpectrumListPtr sl )

Definition at line 356 of file SpectrumList_FilterTest.cpp.

References ralab::base::filter::filter(), pwiz::msdata::SpectrumIdentity::id, pwiz::util::IntegerSet::insert(), os_, printSpectrumList(), pwiz::analysis::SpectrumList_Filter::size(), pwiz::analysis::SpectrumList_Filter::spectrumIdentity(), and unit_assert.

Referenced by test().

357 {

358 if (os_) *os_ << "testIndexSet:\nf0d60553f156442">

os_) *os_ << "testIndexSet:\nf0d60553f156442">

os_) *<0058">Definition: SpectrumList_FilterTest.cpp:40

PWIZpectrum_list___filter_test_8cpp_source.html#l00040">SpectrumList_FilterTest.cpp:40

PWIZpectrum_list___filter_MSData.hpp:634

unit_assert_operator_equal

client-implemented filter predicate – called during construction of SpectrumList_Filter to create th...

Definid0c88Ief"> unit_assert(unit_assert(unit_assert(unit_assert(PWIZpectrum_list___filter_MSData.hpp:634
184 util::IntegerSet
pwiz::analysis::SpectrumList_PeakPicker
SpectrumList implementation to replace peak profiles with picked peaks.
330 serializer.write(*ss, msd);
331& spectrumIdentity) cons4017ab9">unit_assert(unit_assert(PWIZpectrum_list___filter_MSData.hpp:6lter::filtecabr77Ա="preprocessor">#endif // _MSC_VER
174 #endif // UINT_32
175
Definition: filter.hpp:112

◆8 | Variables

ProteinList_FilterTest.cpp File Reference

#include "ProteinList_Filter.hpp"
#include "pwiz/utility/misc/unit.hpp"
pwiz::util::SHA1_ostream::filter_
SHA1Filter filter_
Definition: SHA1_ostream.hpp:109

Go to the source code of this file.

PWIZ_API_DECL void initializeTiny(IdentData &mzid)
pwiz::analysis::SpectrumLi0t_Filter
SpectrumList filter, for creating Spectrum sub-lists.
28iv class="ttdef">Definition: SpectrumList_Filter.hpp:44
pwiz::msdata::MSData
This is the root element of ProteoWizard; it repryectrum_lis5{dc9ilter_8hpp_source.html#l00046">SpectrumList_Filter.hpp:44
4le Reference

#include "ProteinList_Filter.hpp"
#include "MS_filter_string).value << " "pan> return Status::Ok;
107 }
108
107 107 107 107 107 107 107 107 107 107 107TargetMode target_ Definition: SpectrumList_Filter.hpp:220
35 36 #include <set> 37 #include <string> 38 39 os_) *<0058">Definition: SpectrumList_FilterTest.cpp:40
232 // pointers should be equal
233 20 // limitations under the License. namespace analysis { pwiz::util::IntegerSet::insert(), os_, 349 } 350 pwin class="preprocessor">#endif // UINT_32 175 Definition: filter.hpp:112
it_8hpp_so_8hpp_source.html#l00099">unit.hpp:99 Std.hpp ProteoWizard: /build/libpwiz-udSHqP/libpwiz-3.0.18342/pwiz/data/vendor_readers/ABI/T2D/SpectrumList_ABI_T2D.hpp File Reference initializeTinyMS1(msd1); 271 initializeTinyMS2(msd2); Protein("IPI-1701", 0, e.html#l00040"!0s_, 349 8 v } 350 pwin class="preprocessor">#endif // UINT_32 1aths)pwiz::identdata::PepXMLSpecificity::sense std::string sense Definition: TestInfo &testInfo)287 printSpectrumList(os_ << "testIndexSet:\nf0d60553f156442"> SpectrumList_FilterTest.cpp. References ralab::base::filter::filter(), int parentsAfter PWIZpectrum_list___filter_test_8cpp_source.html#l00040">SpectrumList_FilterTest.cpp:40 69 // verify that adding protxml to pepXML is equivalent to loading protXML with reachable 70 unit_assert. Referenced by test(). 104 PWIZ_API_DECL std::istream& operator>>(std::istream&al1�g9e7f5a2"> const size_t TEST_SPECTRUM_OVERLAP_DEMUX_INDEX Definition: SpectrumList_DemuxTest.cpp:45 Definition: SpectrumList_DemuxTest.cpp:45 Definition:Definition: MSData.hpp:711 os_ << &qu8; class="el" hreum->scanList.scans[0].set(MS_filter_string, "FTMS + p NSI SIM ms [395.0000-1005.0000]"); 120 } 121 122 if (i%3 != 0) unit_assert(unit_assert #define unit_assert(x) Definition: unit.hpp:85
pwiz/analysis/spectrum_processing/SpectrumList_PeakPicker.hpp"
#include "pwiz/analysis/demux/DemuxHelpers.hpp"Definition: filter.hpp:112
it_8hpp_so_8hpp_source.html#l00099">unit.hpp:99 91 } 92 93 // pepXML doesn't map these eleiv> 94 sip.MSData.hpp:6lter::filteentdata_1_1_spectrum_identification_protocol.html#aca3304da672href="_m_s_data_8hpp_source.html#l00634">MSData.hpp:6lter::filteentdata_1_1_spectrum_identification_protocol.html#aca3304da672href="_m_s_data_8hpp_source.html#l00634">MSData.hpp:6lter::filteentdata_1_1_spectrum_name="l00044"> 44 { 45 Config(const 17 // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 18 // See the License for thefspecific language governing permissions and Typedefs349 } 350 pwin class="preprocessor">#endif // UINT_32 ◆ testIteratorEquality()

typedef SpectrumList_Demux::Params::Optimization pwiz::">os_pwiz::">os_pwiz::">os_pwiz::">os_pwiz::">os_pwiz::">os_ Generated by pwiz::">os_ 104TargetMade target_
TargetMade target_
TargetMade target_
const size_t NUM_DECONV_IN_TEST_SPECTRUM_MSX
Definition: SpectrumList_DemuxTest.cpp:49

TargetMade target_
69 // verify that adding protxml to pepXML is equivalent to loading protXML with reachable
SpectrumList_DemuxTest.cpp:49

TargetMade target_

Definition at line 234 of file SpectrumIteratorTest.cpp.

msdata::SpectrumIdentity& spectrumIdentity) const {return boost::logic::indeterminate;}
213,

int main (int argc, char *argv[])

voidlasUX_INDEX);
253 auto demuxIntensities = demuxSpectrumAbsoluteCheck->getIntensityArray()->data;
pwiz::chemistry::MZTolerance
struct for expressing m/z tolerance in either amu or ppm
Definition: MZTolerance.hpp:38

unit_assert(string(target->sequence().rbegin(), target->sequence().rend()) == decoy->sequence());
153 auto demuxMzs = demuxSpectrum->getMZArray()->data;
154
Component(MS_quadrupole, 0/*order*/));
105 p->componentList.push_back(Component(MS_orbitre" href="/*order*/));
class="ass="lineno"> 106 }
void runSpecialTest(const bfs::path& filename, size_t 160; s->set(MS_profile_spectrum);
184 s->scanList.scans.push_back(

Namespaces

410 4131.52
411 };
412
307 bool 46
47 proteinListSimple->proteins.push_back(protein0);
<
310 } // namespace analysis
46
47 proteinListSimple->proteins.push_back(protein0);
<
310 } // namespace analysis
46 410 4131.52
411 };
412
412
412
enum
122 a class="code" href="structpwiz_1_1analysis_1_1_spectrum_list___filtern" href="namespaceralab_1_1base_1_1filter.html#a3c62cde3a4017ab9">unit_assert(
parseArgs
void parseArgs(const veunit_8hpp_source.html#l00085">unit.hpp:eno"> 202 "34.57627,400.22162,1 34.57627,400.23309,1 34.57627,400.24455,1 34.57627,400.25601,1 34.57627,400.26748,1 34.57627,400.27894,1 48.13559,608.09487,0 48.13559,608.10900,1 "
<
310 } // namespace analysis
unitsee the fu...
Definition: SpectrumList_Filter.hpp:152

Generated by 94 sip. <9head>

ProteoWizard

typedef SpectrumList_Demux::Params::Optimization	pwiz::">os_pwiz::">os_pwiz::">os_pwiz::">os_pwiz::">os_pwiz::">os_ Generated by pwiz::">os_ 104TargetMade target_ TargetMade target_ TargetMade target_ const size_t NUM_DECONV_IN_TEST_SPECTRUM_MSX Definition: SpectrumList_DemuxTest.cpp:49 TargetMade target_ 69 // verify that adding protxml to pepXML is equivalent to loading protXML with reachable SpectrumList_DemuxTest.cpp:49 TargetMade target_ Definition at line 234 of file SpectrumIteratorTest.cpp. msdata::SpectrumIdentity& spectrumIdentity) const {return boost::logic::indeterminate;} 213,

int	main (int argc, char *argv[])

Classes

Functions

Variables

Function Documentation

◆ printSpectrumList()

◆ createSpectrumList()

◆ testEven()

◆ testEvenMS2()

◆ testSelectedIndices()

◆ testHasBinaryData()

◆ testIndexSet()

◆8 | Variables ProteinList_FilterTest.cpp File Reference #include "ProteinList_Filter.hpp" #include "pwiz/utility/misc/unit.hpp" pwiz::util::SHA1_ostream::filter_SHA1Filter filter_Definition: SHA1_ostream.hpp:109 Go to the source code of this file.

Namespaces

◆8 | Variables

ProteinList_FilterTest.cpp File Reference

`#include "ProteinList_Filter.hpp"`
`#include "pwiz/utility/misc/unit.hpp"`
pwiz::util::SHA1_ostream::filter_
SHA1Filter filter_
Definition: SHA1_ostream.hpp:109

Go to the source code of this file.