LogStream.h File Reference

#include <OpenMS/DATASTRUCTURES/String.h>
#include <sstream>
#include <iostream>
#include <list>
#include <vector>
#include <ctime>
#include <map>

Go to the source code of this file.

Classes
class	LogStreamBuf
	Stream buffer used by LogStream. More...
struct	LogStreamBuf::StreamStruct
	Holds a stream that is connected to the LogStream. It also includes the minimum and maximum level at which the LogStream redirects messages to this stream. More...
struct	LogStreamBuf::LogCacheStruct
	Holds a counter of occurrences and an index for the occurrence sequence of the corresponding log message. More...
class	LogStreamNotifier
class	LogStream
	Log Stream Class. More...

Namespaces
	OpenMS
	Main OpenMS namespace.
	OpenMS::Logger
	Log streams.

Macros
#define	LOG_FATAL_ERROR   Log_fatal << __FILE__ << "(" << __LINE__ << "): "
	Macro to be used if fatal error are reported (processing stops) More...
#define	LOG_ERROR   Log_error
	Macro to be used if non-fatal error are reported (processing continues) More...
#define	LOG_WARN   Log_warn
	Macro if a warning, a piece of information which should be read by the user, should be logged. More...
#define	LOG_INFO   Log_info
	Macro if a information, e.g. a status should be reported. More...
#define	LOG_DEBUG   Log_debug << __FILE__ << "(" << __LINE__ << "): "
	Macro for general debugging information. More...

Variables
Logger::LogStream	Log_fatal
	Global static instance of a LogStream to capture messages classified as fatal errors. By default it is bound to cerr. More...
Logger::LogStream	Log_error
	Global static instance of a LogStream to capture messages classified as errors. By default it is bound to cerr. More...
Logger::LogStream	Log_warn
	Global static instance of a LogStream to capture messages classified as warnings. By default it is bound to cout. More...
Logger::LogStream	Log_info
	Global static instance of a LogStream to capture messages classified as information. By default it is bound to cout. More...
Logger::LogStream	Log_debug
	Global static instance of a LogStream to capture messages classified as debug output. By default it is not bound to any output stream. TOPP(AS)Base will connect cout, iff 0 < debug-level. More...

Macro Definition Documentation

LOG_DEBUG

#define LOG_DEBUG   Log_debug << __FILE__ << "(" << __LINE__ << "): "

Macro for general debugging information.

Referenced by UTILProteomicsLFQ::align_(), MRMTransitionGroupPicker::computeQuality_(), FullSwathFileConsumer::consumeSpectrum(), MRMTransitionGroupPicker::createMRMFeature(), PeptideIndexing::findDecoyString_(), RNPxlSearch::RNPxlParameterParsing::getAllFeasibleFragmentAdducts(), RNPxlSearch::RNPxlParameterParsing::getFeasibleFragmentAdducts(), MetaProSIPInterpolation::getHighPoints(), TOPPOpenSwathBase::loadSwathFiles(), TOPPGNPSExport::main_(), TOPPOpenSwathWorkflow::main_(), RNPxlSearch::main_(), TOPPMetaProSIP::main_(), TOPPMetaProSIP::normalizeToMax(), PeakPickerIterative::pick(), RNPxlSearch::postScoreHits_(), UTILProteomicsLFQ::quantifyFraction_(), MRMTransitionGroupPicker::recalculatePeakBorders_(), ConfidenceScoring::scoreMap(), RNPxlSearch::scorePartialLossFragments_(), and TOPPASBase::TOPPASreadyRead().

LOG_ERROR

#define LOG_ERROR   Log_error

Macro to be used if non-fatal error are reported (processing continues)

Referenced by TOPPASBase::addTOPPASFile(), RIntegration::checkRDependencies(), extractCachedMetaFilename(), GaussFilter::filter(), TOPPMetaProSIP::filterIsotopicIntensities(), PeptideIndexing::findDecoyString_(), TOPPOpenSwathBase::loadSwathFiles(), TOPPOpenSwathBase::loadTransitionList(), main(), TOPPMetaProSIP::main_(), QApplicationTOPP::notify(), INIFileEditorWindow::openFile(), DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >::parseEnzyme_(), and PeptideIndexing::run().

LOG_FATAL_ERROR

#define LOG_FATAL_ERROR   Log_fatal << __FILE__ << "(" << __LINE__ << "): "

Macro to be used if fatal error are reported (processing stops)

Referenced by UTILProteomicsLFQ::main_(), and UTILProteomicsLFQ::quantifyFraction_().

LOG_INFO

#define LOG_INFO   Log_info

Macro if a information, e.g. a status should be reported.

Referenced by TOPPViewBase::addDataFile(), UTILProteomicsLFQ::align_(), IDMapper::annotate(), UTILProteomicsLFQ::calculateSeeds_(), RIntegration::checkRDependencies(), MetaProSIPReporting::createPeptideCentricCSVReport(), MetaProSIPReporting::createQualityReport(), UTILProteomicsLFQ::estimateMedianChromatographicFWHM_(), TargetedSpectraExtractor::BinnedSpectrumComparator::init(), UTILProteomicsLFQ::link_(), main(), TOPPBayesianProteinInference::main_(), TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), TOPPOpenSwathWorkflow::main_(), UTILProteomicsLFQ::main_(), RNPxlSearch::main_(), TOPPMetaProSIP::main_(), SpectraMerger::mergeSpectra_(), AccurateMassSearchEngine::resolveAutoMode_(), PeptideIndexing::run(), and UTILProteomicsLFQ::transferIDsBetweenSameFraction_().

LOG_WARN

#define LOG_WARN   Log_warn

Macro if a warning, a piece of information which should be read by the user, should be logged.

Referenced by UTILProteomicsLFQ::centroidAndCorrectPrecursors_(), SignalToNoiseEstimatorMedian< ContainerT >::computeSTN_(), ChromatogramTools::convertSpectraToChromatograms(), TOPPMetaProSIP::extractIncorporationsAtCorrelationMaxima(), MetaProSIPXICExtraction::extractXICs(), PeptideIndexing::findDecoyString_(), RNPxlSearch::RNPxlParameterParsing::getTargetNucleotideToFragmentAdducts(), PeakIntegrator::integratePeak_(), TOPPOpenSwathBase::loadSwathFiles(), TOPPBayesianProteinInference::main_(), UTILProteomicsLFQ::main_(), RNPxlSearch::main_(), TOPPMetaProSIP::main_(), OpenMS::makePeakPositionUnique(), SpectraMerger::mergeSpectra_(), SpectraMerger::mergeSpectraPrecursors(), IDFilter::DigestionFilter::operator()(), IsInIsolationWindow< SpectrumType >::operator()(), UTILProteomicsLFQ::quantifyFraction_(), SpectrumLookup::readSpectra(), UTILProteomicsLFQ::recalibrateMasses_(), PeptideIndexing::run(), ConfidenceScoring::scoreMap(), and UTILProteomicsLFQ::transform_().