#include <Alignment/CSCOverlapsAlignmentAlgorithm/interface/CSCOverlapsAlignmentAlgorithm.h>
Public Member Functions | |
CSCOverlapsAlignmentAlgorithm (const edm::ParameterSet &iConfig) | |
void | initialize (const edm::EventSetup &iSetup, AlignableTracker *alignableTracker, AlignableMuon *alignableMuon, AlignableExtras *alignableExtras, AlignmentParameterStore *alignmentParameterStore) |
Call at beginning of job (must be implemented in derived class) More... | |
void | run (const edm::EventSetup &iSetup, const EventInfo &eventInfo) |
Run the algorithm (must be implemented in derived class) More... | |
void | terminate (const edm::EventSetup &iSetup) |
Call at end of each loop (must be implemented in derived class) More... | |
~CSCOverlapsAlignmentAlgorithm () | |
Public Member Functions inherited from AlignmentAlgorithmBase | |
virtual bool | addCalibrations (const Calibrations &) |
AlignmentAlgorithmBase (const edm::ParameterSet &) | |
Constructor. More... | |
virtual void | beginLuminosityBlock (const edm::EventSetup &setup) |
called at begin of luminosity block (no lumi block info passed yet) More... | |
virtual void | beginRun (const edm::EventSetup &setup) |
called at begin of run More... | |
virtual void | endLuminosityBlock (const edm::EventSetup &setup) |
called at end of luminosity block (no lumi block info passed yet) More... | |
virtual void | endRun (const EndRunInfo &runInfo, const edm::EventSetup &setup) |
called at end of run - order of arguments like in EDProducer etc. More... | |
virtual bool | processesEvents () |
Returns whether algorithm proccesses events in current configuration. More... | |
virtual bool | setParametersForRunRange (const RunRange &rr) |
virtual void | startNewLoop () |
virtual bool | supportsCalibrations () |
virtual void | terminate () |
Called at end of job (must be implemented in derived class) More... | |
virtual | ~AlignmentAlgorithmBase () |
Destructor. More... | |
Private Attributes | |
AlignableNavigator * | m_alignableNavigator |
std::vector< Alignable * > | m_alignables |
AlignmentParameterStore * | m_alignmentParameterStore |
bool | m_doAlignment |
std::vector< CSCChamberFitter > | m_fitters |
TH1F * | m_histP10 |
TH1F * | m_histP100 |
TH1F * | m_histP1000 |
double | m_maxRedChi2 |
double | m_minP |
std::string | m_mode_string |
std::string | m_propagatorName |
const Propagator * | m_propagatorPointer |
std::map< std::pair< CSCDetId, CSCDetId > , CSCPairResidualsConstraint * > | m_quickChamberLookup |
std::vector< std::string > | m_readTemporaryFiles |
std::string | m_reportFileName |
std::vector < CSCPairResidualsConstraint * > | m_residualsConstraints |
TrackTransformer * | m_trackTransformer |
std::string | m_writeTemporaryFile |
Additional Inherited Members | |
Public Types inherited from AlignmentAlgorithmBase | |
typedef std::pair< const Trajectory *, const reco::Track * > | ConstTrajTrackPair |
typedef std::vector < ConstTrajTrackPair > | ConstTrajTrackPairCollection |
typedef cond::RealTimeType < cond::runnumber >::type | RunNumber |
typedef std::pair< RunNumber, RunNumber > | RunRange |
Description: <one line="" class="" summary>="">
Implementation: <Notes on="" implementation>="">
Definition at line 61 of file CSCOverlapsAlignmentAlgorithm.h.
CSCOverlapsAlignmentAlgorithm::CSCOverlapsAlignmentAlgorithm | ( | const edm::ParameterSet & | iConfig | ) |
Definition at line 3 of file CSCOverlapsAlignmentAlgorithm.cc.
References edm::hlt::Exception, CSCOverlapsAlignmentAlgorithm_diskfitters_cff::fitters, edm::ParameterSet::getParameter(), i, CSCPairResidualsConstraint::kModePhiPos, CSCPairResidualsConstraint::kModePhiy, CSCPairResidualsConstraint::kModePhiz, CSCPairResidualsConstraint::kModeRadius, m_combineME11, m_drdz, m_fiducial_ME11, m_fiducial_ME12, m_fiducial_MEx1, m_fiducial_MEx2, m_fitters, m_histP10, m_histP100, m_histP1000, m_hitsPerChamber, m_makeHistograms, m_mode, m_mode_string, m_occupancy, m_offsetResiduals, m_offsetResiduals_normalized, m_offsetResiduals_weighted, M_PI, m_propagatorName, m_propagatorPointer, m_quickChamberLookup, m_residualsConstraints, m_RPhipos_mem1, m_RPhipos_mem2, m_RPhipos_mem3, m_RPhipos_mem4, m_RPhipos_mep1, m_RPhipos_mep2, m_RPhipos_mep3, m_RPhipos_mep4, m_slope, m_slope_MEm1, m_slope_MEm2, m_slope_MEm3, m_slope_MEm4, m_slope_MEp1, m_slope_MEp2, m_slope_MEp3, m_slope_MEp4, m_slopeFromTrackRefit, m_slopeResiduals, m_slopeResiduals_normalized, m_slopeResiduals_weighted, m_trackTransformer, m_XYpos_mem1, m_XYpos_mem2, m_XYpos_mem3, m_XYpos_mem4, m_XYpos_mep1, m_XYpos_mep2, m_XYpos_mep3, m_XYpos_mep4, TFileService::make(), NULL, AlCaHLTBitMon_QueryRunRegistry::string, and HLT_25ns14e33_v1_cff::TrackTransformer.
CSCOverlapsAlignmentAlgorithm::~CSCOverlapsAlignmentAlgorithm | ( | ) |
Definition at line 184 of file CSCOverlapsAlignmentAlgorithm.cc.
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Call at beginning of job (must be implemented in derived class)
Implements AlignmentAlgorithmBase.
Definition at line 186 of file CSCOverlapsAlignmentAlgorithm.cc.
References AlignmentParameterStore::alignables(), MuonSubdetId::CSC, CSCDetId, edm::hlt::Exception, mergeVDriftHistosByStation::file, MillePedeFileConverter_cfg::fileName, edm::EventSetup::get(), i, input, m_alignableNavigator, m_alignables, m_alignmentParameterStore, m_readTemporaryFiles, m_residualsConstraints, DetId::Muon, and NULL.
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Run the algorithm (must be implemented in derived class)
Implements AlignmentAlgorithmBase.
Definition at line 228 of file CSCOverlapsAlignmentAlgorithm.cc.
References CSCDetId::chamber(), MuonSubdetId::CSC, CSCDetId, CSCDetId::endcap(), edm::EventSetup::get(), m_combineME11, m_histP10, m_histP100, m_histP1000, m_makeHistograms, m_minP, m_propagatorName, m_propagatorPointer, m_quickChamberLookup, m_residualsConstraints, m_RPhipos_mem1, m_RPhipos_mem2, m_RPhipos_mem3, m_RPhipos_mem4, m_RPhipos_mep1, m_RPhipos_mep2, m_RPhipos_mep3, m_RPhipos_mep4, m_slopeFromTrackRefit, m_trackTransformer, m_XYpos_mem1, m_XYpos_mem2, m_XYpos_mem3, m_XYpos_mem4, m_XYpos_mep1, m_XYpos_mep2, m_XYpos_mep3, m_XYpos_mep4, python.multivaluedict::map(), Trajectory::measurements(), DetId::Muon, NULL, reco::TrackBase::p(), PV3DBase< T, PVType, FrameType >::perp(), PV3DBase< T, PVType, FrameType >::phi(), HLT_25ns14e33_v1_cff::propagator, CSCDetId::ring(), TrackTransformer::setServices(), relativeConstraints::station, CSCDetId::station(), AlignmentAlgorithmBase::EventInfo::trajTrackPairs(), PV3DBase< T, PVType, FrameType >::x(), and PV3DBase< T, PVType, FrameType >::y().
Referenced by Types.EventID::cppID(), and Types.LuminosityBlockID::cppID().
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Call at end of each loop (must be implemented in derived class)
Implements AlignmentAlgorithmBase.
Definition at line 310 of file CSCOverlapsAlignmentAlgorithm.cc.
References CSCPairResidualsConstraint::kModeRadius, m_alignableNavigator, m_alignmentParameterStore, m_combineME11, m_doAlignment, m_fitters, m_makeHistograms, m_mode, m_reportFileName, m_residualsConstraints, m_writeTemporaryFile, convertSQLitetoXML_cfg::output, zeeHLT_cff::report, and AlCaHLTBitMon_QueryRunRegistry::string.
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Definition at line 143 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by initialize(), and terminate().
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Definition at line 142 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by initialize().
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Definition at line 141 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by initialize(), and terminate().
bool CSCOverlapsAlignmentAlgorithm::m_combineME11 |
Definition at line 126 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), CSCOverlapsAlignmentAlgorithm(), CSCPairResidualsConstraint::dphidzFromTrack(), run(), and terminate().
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Definition at line 139 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by terminate().
TH1F* CSCOverlapsAlignmentAlgorithm::m_drdz |
Definition at line 97 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCOverlapsAlignmentAlgorithm().
bool CSCOverlapsAlignmentAlgorithm::m_errorFromRMS |
Definition at line 128 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::error().
bool CSCOverlapsAlignmentAlgorithm::m_fiducial |
Definition at line 120 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack().
TProfile* CSCOverlapsAlignmentAlgorithm::m_fiducial_ME11 |
Definition at line 75 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and CSCPairResidualsConstraint::isFiducial().
TProfile* CSCOverlapsAlignmentAlgorithm::m_fiducial_ME12 |
Definition at line 76 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and CSCPairResidualsConstraint::isFiducial().
TProfile* CSCOverlapsAlignmentAlgorithm::m_fiducial_MEx1 |
Definition at line 77 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and CSCPairResidualsConstraint::isFiducial().
TProfile* CSCOverlapsAlignmentAlgorithm::m_fiducial_MEx2 |
Definition at line 78 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and CSCPairResidualsConstraint::isFiducial().
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Definition at line 144 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and terminate().
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Definition at line 152 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
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Definition at line 153 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
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Definition at line 154 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
TH1F* CSCOverlapsAlignmentAlgorithm::m_hitsPerChamber |
Definition at line 73 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCOverlapsAlignmentAlgorithm().
bool CSCOverlapsAlignmentAlgorithm::m_makeHistograms |
Definition at line 130 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), CSCPairResidualsConstraint::configure(), CSCOverlapsAlignmentAlgorithm(), CSCPairResidualsConstraint::isFiducial(), run(), and terminate().
double CSCOverlapsAlignmentAlgorithm::m_maxdrdz |
Definition at line 119 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack().
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Definition at line 136 of file CSCOverlapsAlignmentAlgorithm.h.
int CSCOverlapsAlignmentAlgorithm::m_minHitsPerChamber |
Definition at line 118 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCPairResidualsConstraint::dphidzFromTrack().
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Definition at line 135 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by run().
int CSCOverlapsAlignmentAlgorithm::m_minStationsInTrackRefits |
Definition at line 123 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::dphidzFromTrack().
int CSCOverlapsAlignmentAlgorithm::m_minTracksPerOverlap |
Definition at line 129 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::valid().
int CSCOverlapsAlignmentAlgorithm::m_mode |
Definition at line 117 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), CSCOverlapsAlignmentAlgorithm(), CSCPairResidualsConstraint::error(), terminate(), and CSCPairResidualsConstraint::value().
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Definition at line 133 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm().
TH2F* CSCOverlapsAlignmentAlgorithm::m_occupancy |
Definition at line 99 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCOverlapsAlignmentAlgorithm().
TH1F* CSCOverlapsAlignmentAlgorithm::m_offsetResiduals |
Definition at line 93 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCOverlapsAlignmentAlgorithm().
TH1F* CSCOverlapsAlignmentAlgorithm::m_offsetResiduals_normalized |
Definition at line 95 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCOverlapsAlignmentAlgorithm().
TH1F* CSCOverlapsAlignmentAlgorithm::m_offsetResiduals_weighted |
Definition at line 94 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCOverlapsAlignmentAlgorithm().
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Definition at line 149 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
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Definition at line 150 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
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Definition at line 146 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
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Definition at line 138 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by initialize().
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Definition at line 134 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by terminate().
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Definition at line 145 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), initialize(), run(), and terminate().
TH2F* CSCOverlapsAlignmentAlgorithm::m_RPhipos_mem1 |
Definition at line 112 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
TH2F* CSCOverlapsAlignmentAlgorithm::m_RPhipos_mem2 |
Definition at line 113 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
TH2F* CSCOverlapsAlignmentAlgorithm::m_RPhipos_mem3 |
Definition at line 114 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
TH2F* CSCOverlapsAlignmentAlgorithm::m_RPhipos_mem4 |
Definition at line 115 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
TH2F* CSCOverlapsAlignmentAlgorithm::m_RPhipos_mep1 |
Definition at line 108 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
TH2F* CSCOverlapsAlignmentAlgorithm::m_RPhipos_mep2 |
Definition at line 109 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
TH2F* CSCOverlapsAlignmentAlgorithm::m_RPhipos_mep3 |
Definition at line 110 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
TH2F* CSCOverlapsAlignmentAlgorithm::m_RPhipos_mep4 |
Definition at line 111 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
TH1F* CSCOverlapsAlignmentAlgorithm::m_slope |
Definition at line 80 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCOverlapsAlignmentAlgorithm().
TH1F* CSCOverlapsAlignmentAlgorithm::m_slope_MEm1 |
Definition at line 85 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCOverlapsAlignmentAlgorithm().
TH1F* CSCOverlapsAlignmentAlgorithm::m_slope_MEm2 |
Definition at line 86 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCOverlapsAlignmentAlgorithm().
TH1F* CSCOverlapsAlignmentAlgorithm::m_slope_MEm3 |
Definition at line 87 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCOverlapsAlignmentAlgorithm().
TH1F* CSCOverlapsAlignmentAlgorithm::m_slope_MEm4 |
Definition at line 88 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCOverlapsAlignmentAlgorithm().
TH1F* CSCOverlapsAlignmentAlgorithm::m_slope_MEp1 |
Definition at line 84 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCOverlapsAlignmentAlgorithm().
TH1F* CSCOverlapsAlignmentAlgorithm::m_slope_MEp2 |
Definition at line 83 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCOverlapsAlignmentAlgorithm().
TH1F* CSCOverlapsAlignmentAlgorithm::m_slope_MEp3 |
Definition at line 82 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCOverlapsAlignmentAlgorithm().
TH1F* CSCOverlapsAlignmentAlgorithm::m_slope_MEp4 |
Definition at line 81 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCOverlapsAlignmentAlgorithm().
bool CSCOverlapsAlignmentAlgorithm::m_slopeFromTrackRefit |
Definition at line 122 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), CSCOverlapsAlignmentAlgorithm(), and run().
TH1F* CSCOverlapsAlignmentAlgorithm::m_slopeResiduals |
Definition at line 90 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCOverlapsAlignmentAlgorithm().
TH1F* CSCOverlapsAlignmentAlgorithm::m_slopeResiduals_normalized |
Definition at line 92 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCOverlapsAlignmentAlgorithm().
TH1F* CSCOverlapsAlignmentAlgorithm::m_slopeResiduals_weighted |
Definition at line 91 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCOverlapsAlignmentAlgorithm().
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Definition at line 148 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
double CSCOverlapsAlignmentAlgorithm::m_truncateOffsetResid |
Definition at line 125 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack().
double CSCOverlapsAlignmentAlgorithm::m_truncateSlopeResid |
Definition at line 124 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack().
bool CSCOverlapsAlignmentAlgorithm::m_useHitWeights |
Definition at line 121 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack(), and CSCPairResidualsConstraint::isFiducial().
bool CSCOverlapsAlignmentAlgorithm::m_useTrackWeights |
Definition at line 127 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCPairResidualsConstraint::addTrack().
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Definition at line 137 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by terminate().
TH2F* CSCOverlapsAlignmentAlgorithm::m_XYpos_mem1 |
Definition at line 104 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
TH2F* CSCOverlapsAlignmentAlgorithm::m_XYpos_mem2 |
Definition at line 105 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
TH2F* CSCOverlapsAlignmentAlgorithm::m_XYpos_mem3 |
Definition at line 106 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
TH2F* CSCOverlapsAlignmentAlgorithm::m_XYpos_mem4 |
Definition at line 107 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
TH2F* CSCOverlapsAlignmentAlgorithm::m_XYpos_mep1 |
Definition at line 100 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
TH2F* CSCOverlapsAlignmentAlgorithm::m_XYpos_mep2 |
Definition at line 101 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
TH2F* CSCOverlapsAlignmentAlgorithm::m_XYpos_mep3 |
Definition at line 102 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().
TH2F* CSCOverlapsAlignmentAlgorithm::m_XYpos_mep4 |
Definition at line 103 of file CSCOverlapsAlignmentAlgorithm.h.
Referenced by CSCOverlapsAlignmentAlgorithm(), and run().