Main OpenMS namespace. More...
Namespaces | |
Constants | |
Mathematical and physical constants namespace. | |
DIAHelpers | |
Exception | |
Exception namespace | |
ims | |
Interfaces | |
Internal | |
Namespace used to hide implementation details from users. | |
Logger | |
Log streams. | |
Math | |
Math namespace. | |
NNLS | |
OpenMSBoost | |
OptimizationFunctions | |
SimTypes | |
StringConversions | |
TargetedExperimentHelper | |
This class stores helper structures that are used in multiple classes of the TargetedExperiment (e.g. ReactionMonitoringTransition and IncludeExcludeTarget). | |
Classes | |
class | FeatureDeconvolution |
An algorithm to decharge features (i.e. as found by FeatureFinder). More... | |
class | ILPDCWrapper |
class | CompNovoIdentification |
run with CompNovoIdentification More... | |
class | CompNovoIdentificationBase |
run with CompNovoIdentificationBase More... | |
class | CompNovoIdentificationCID |
run with CompNovoIdentificationCID More... | |
class | CompNovoIonScoring |
run with CompNovoIonScoring More... | |
class | CompNovoIonScoringBase |
run with CompNovoIonScoringBase More... | |
class | CompNovoIonScoringCID |
run with CompNovoIonScoringCID More... | |
class | DeNovoAlgorithm |
Base class for ion scoring implementation for de novo algorithms. More... | |
class | DeNovoIdentification |
Base class for de novo identification. More... | |
class | DeNovoIonScoring |
Base class for ion scoring implementation for de novo algorithms. More... | |
class | DeNovoPostScoring |
Base class for ion scoring implementation for de novo algorithms. More... | |
class | AdductInfo |
class | AccurateMassSearchResult |
class | AccurateMassSearchEngine |
An algorithm to search for exact mass matches from a spectrum against a database (e.g. HMDB). More... | |
struct | ProbablePhosphoSites |
class | AScore |
Implementation of the Ascore For a given peptide sequence and its MS/MS spectrum it identifies the most probable phosphorylation-site(s). For each phosphorylation site a probability score is calculated. The algorithm is implemented according to Beausoleil et al. More... | |
class | ConsensusID |
Calculates a consensus ID from several ID runs. More... | |
class | FalseDiscoveryRate |
Calculates an FDR from identifications. More... | |
class | HMMState |
Hidden Markov Model State class for the Hidden Markov Model. More... | |
class | HiddenMarkovModel |
Hidden Markov Model implementation of PILIS. More... | |
class | IDDecoyProbability |
IDDecoyProbability calculates probabilities using decoy approach. More... | |
class | IDMapper |
Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications. More... | |
class | IDRipper |
Ripping protein/peptide identification according their file origin. More... | |
struct | PrecursorMassComparator |
class | SpectralMatch |
struct | SpectralMatchScoreComparator |
class | MetaboliteSpectralMatching |
class | PILISCrossValidation |
Implementation of a cross validation training for the PILIS model. More... | |
class | PILISIdentification |
This class actually implements a complete ProteinIdentification run with PILIS. More... | |
class | PILISModel |
This class implements the simulation of the spectra from PILIS. More... | |
class | PILISModelGenerator |
This class implements the simulation of the spectra from PILIS. More... | |
class | PILISNeutralLossModel |
This class implements the simulation of the spectra from PILIS. More... | |
class | PILISScoring |
This class actually implements the E-value based scoring of PILIS. More... | |
class | ProtonDistributionModel |
A proton distribution model to calculate the proton distribution over charged peptides. More... | |
class | BaseGroupFinder |
The base class of all element group finding algorithms. More... | |
class | BaseSuperimposer |
The base class of all superimposer algorithms. More... | |
class | ConsensusMapNormalizerAlgorithmMedian |
Algorithms of ConsensusMapNormalizer. More... | |
class | ConsensusMapNormalizerAlgorithmQuantile |
Algorithms of ConsensusMapNormalizer. More... | |
class | ConsensusMapNormalizerAlgorithmThreshold |
Algorithms of ConsensusMapNormalizer. More... | |
class | FeatureDistance |
A functor class for the calculation of distances between features or consensus features. More... | |
class | FeatureGroupingAlgorithm |
Base class for all feature grouping algorithms. More... | |
class | FeatureGroupingAlgorithmIdentification |
A map feature grouping algorithm for identified features. More... | |
class | FeatureGroupingAlgorithmLabeled |
A map feature grouping algorithm for labeling techniques with two labels. More... | |
class | FeatureGroupingAlgorithmQT |
A feature grouping algorithm for unlabeled data. More... | |
class | FeatureGroupingAlgorithmUnlabeled |
A map feature grouping algorithm for unlabeled data. More... | |
class | LabeledPairFinder |
The LabeledPairFinder allows the matching of labeled features (features with a fixed distance). More... | |
class | MapAlignmentAlgorithm |
Base class for all map-alignment algorithms. More... | |
class | MapAlignmentAlgorithmIdentification |
A map alignment algorithm based on peptide identifications from MS2 spectra. More... | |
class | MapAlignmentAlgorithmPoseClustering |
A map alignment algorithm based on pose clustering. More... | |
class | MapAlignmentAlgorithmSpectrumAlignment |
A map alignment algorithm based on spectrum similarity (dynamic programming). More... | |
class | MapAlignmentEvaluationAlgorithm |
Base class for all Caap evaluation algorithms. More... | |
class | MapAlignmentEvaluationAlgorithmPrecision |
Caap evaluation algorithm to obtain a precision value. More... | |
class | MapAlignmentEvaluationAlgorithmRecall |
Caap evaluation algorithm to obtain a recall value. More... | |
class | MapAlignmentTransformer |
The MapAlignmentTransformer class. More... | |
class | PoseClusteringAffineSuperimposer |
A superimposer that uses a voting scheme, also known as pose clustering, to find a good affine transformation. More... | |
class | PoseClusteringShiftSuperimposer |
A superimposer that uses a voting scheme, also known as pose clustering, to find a good shift transformation. More... | |
class | QTClusterFinder |
A variant of QT clustering for the detection of feature groups. More... | |
class | SimplePairFinder |
This class implements a simple point pair finding algorithm. More... | |
class | StablePairFinder |
This class implements a pair finding algorithm for consensus features. More... | |
class | TransformationDescription |
Generic description of a coordinate transformation. More... | |
class | TransformationModel |
Base class for transformation models. More... | |
class | TransformationModelBSpline |
B-spline (non-linear) model for transformations. More... | |
class | TransformationModelInterpolated |
Interpolation model for transformations. More... | |
class | TransformationModelLinear |
Linear model for transformations. More... | |
class | MRMFragmentSelection |
This class can select appropriate fragment ions of an MS/MS spectrum of a peptide. More... | |
class | ReactionMonitoringTransition |
This class stores a SRM/MRM transition. More... | |
class | ChromatogramExtractor |
The ChromatogramExtractor extracts chromatograms from a spectra file. More... | |
class | ChromatogramExtractorAlgorithm |
The ChromatogramExtractorAlgorithm extracts chromatograms from a MS data. More... | |
class | ConfidenceScoring |
class | OpenSwathDataAccessHelper |
Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interfaces. More... | |
class | FeatureOpenMS |
An implementation of the OpenSWATH Feature Access interface using OpenMS. More... | |
class | MRMFeatureOpenMS |
An implementation of the OpenSWATH MRM Feature Access interface using OpenMS. More... | |
class | TransitionGroupOpenMS |
An implementation of the OpenSWATH Transition Group Access interface using OpenMS. More... | |
class | SignalToNoiseOpenMS |
An implementation of the OpenSWATH SignalToNoise Access interface using OpenMS. More... | |
class | SimpleOpenMSSpectraFactory |
A factory method that returns two ISpectrumAccess implementations. More... | |
class | SpectrumAccessOpenMS |
An implementation of the OpenSWATH Spectrum Access interface using OpenMS. More... | |
class | SpectrumAccessOpenMSCached |
An implementation of the Spectrum Access interface using on-disk caching. More... | |
class | DiaPrescore |
Scoring of an spectrum given library intensities of a transition group. More... | |
class | DIAScoring |
Scoring of an spectrum at the peak apex of an chromatographic elution peak. More... | |
class | MRMDecoy |
This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object. More... | |
class | MRMFeatureFinderScoring |
The MRMFeatureFinder finds and scores peaks of transitions that co-elute. More... | |
class | MRMRTNormalizer |
The MRMRTNormalizer will find retention time peptides in data. More... | |
class | MRMTransitionGroupPicker |
The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors. More... | |
class | OpenSwathHelper |
A helper class that is used by several OpenSWATH tools. More... | |
struct | OpenSwath_Scores_Usage |
A structure to store which scores should be used by the Algorithm. More... | |
struct | OpenSwath_Scores |
A structure to hold the different scores computed by OpenSWATH. More... | |
class | OpenSwathScoring |
A class that calls the scoring routines. More... | |
class | PeakPickerMRM |
The PeakPickerMRM finds peaks a single chromatogram. More... | |
class | SpectrumAddition |
The SpectrumAddition is used to add up individual spectra. More... | |
class | SwathWindowLoader |
Class to read a file describing the Swath Windows. More... | |
class | TransitionTSVReader |
This class can convert TraML and TSV files into each other. More... | |
class | LocalLinearMap |
Trained Local Linear Map (LLM) model for peak intensity prediction. More... | |
class | PeakIntensityPredictor |
Predict peak heights of peptides based on Local Linear Map model. More... | |
class | IsobaricChannelExtractor |
Extracts individual channels from MS/MS spectra for isobaric labeling experiments. More... | |
class | IsobaricIsotopeCorrector |
Performs isotope impurity correction on the intensities extracted from an isobaric labeling experiment. More... | |
class | IsobaricNormalizer |
Performs median normalization on the extracted ratios of isobaric labeling experiment. More... | |
class | IsobaricQuantifier |
Given the extracted channel intensities the IsobaricQuantifier corrects and normalizes the intensities for further processing. More... | |
struct | IsobaricQuantifierStatistics |
Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion) More... | |
class | Matrix |
A two-dimensional matrix. Similar to std::vector, but uses a binary operator(,) for element access. More... | |
class | IsobaricQuantitationMethod |
Abstract base class describing an isobaric quantitation method in terms of the used channels and an isotope correction matrix. More... | |
class | ItraqChannelExtractor |
[experimental class] extracts the iTRAQ channels from tandem MS data and stores intensity values in a consensus map More... | |
class | ItraqConstants |
Some constants used throughout iTRAQ classes. More... | |
class | ItraqEightPlexQuantitationMethod |
iTRAQ 8 plex quantitation to be used with the IsobaricQuantitation. More... | |
class | ItraqFourPlexQuantitationMethod |
iTRAQ 4 plex quantitation to be used with the IsobaricQuantitation. More... | |
class | ItraqQuantifier |
Does post-processing on raw iTRAQ channel quantitation. More... | |
class | PeptideAndProteinQuant |
Helper class for peptide and protein quantification based on feature data annotated with IDs. More... | |
class | ProteinInference |
[experimental class] given a peptide quantitation, infer corresponding protein quantities More... | |
class | ProteinResolver |
Helper class for peptide and protein quantification based on feature data annotated with IDs. More... | |
class | QuantitativeExperimentalDesign |
Merge files according to experimental design. More... | |
class | TMTSixPlexQuantitationMethod |
TMT 6plex quantitation to be used with the IsobaricQuantitation. More... | |
class | TMTTenPlexQuantitationMethod |
TMT 10plex quantitation to be used with the IsobaricQuantitation. More... | |
class | ModifiedPeptideGenerator |
struct | RNPxlModificationMassesResult |
class | RNPxlModificationsGenerator |
struct | SVMData |
Data structure used in SVMWrapper. More... | |
class | SVMWrapper |
Serves as a wrapper for the libsvm. More... | |
class | IncludeExcludeTarget |
This class stores a SRM/MRM transition. More... | |
class | InclusionExclusionList |
Provides functionality for writing inclusion or exclusion lists. More... | |
class | OfflinePrecursorIonSelection |
Implements different algorithms for precursor ion selection. More... | |
class | PrecursorIonSelection |
This class implements different precursor ion selection strategies. More... | |
class | PrecursorIonSelectionPreprocessing |
This class implements the database preprocessing needing for precursor ion selection. More... | |
class | PSLPFormulation |
Implements ILP formulation of precursor selection problems. More... | |
class | PSProteinInference |
This class implements protein inference for the precursor ion selection strategies. More... | |
class | TargetedExperiment |
This class stores an prediction of an SRM/MRM transition. More... | |
class | ConsoleUtils |
class | INIUpdater |
struct | ParameterInformation |
Struct that captures all information of a command line parameter. More... | |
class | ToolHandler |
class | TOPPBase |
Base class for TOPP applications. More... | |
class | AAIndex |
Representation of selected AAIndex properties. More... | |
class | AASequence |
Representation of a peptide/protein sequence. More... | |
class | EdwardsLippertIterator |
finds all Peptide Candidates with given masses and given fasta file More... | |
class | EdwardsLippertIteratorTryptic |
EdwardsLippertIterator that only retrieves tryptic sequences. More... | |
class | Element |
Representation of an element. More... | |
class | ElementDB |
Stores elements. More... | |
class | EmpiricalFormula |
Representation of an empirical formula. More... | |
class | EnzymaticDigestion |
Class for the enzymatic digestion of proteins. More... | |
class | IsotopeDistribution |
Isotope distribution class. More... | |
class | MassDecomposition |
Class represents a decomposition of a mass into amino acids. More... | |
class | MassDecompositionAlgorithm |
Mass decomposition algorithm, given a mass it suggests possible compositions. More... | |
class | ModificationDefinition |
Representation of modification definition. More... | |
class | ModificationDefinitionsSet |
Representation of a set of modification definitions. More... | |
class | ModificationsDB |
database which holds all residue modifications from UniMod More... | |
class | ModifierRep |
Implements modification for suffix arrays. More... | |
class | PepIterator |
Abstract base class for different peptide iterators. More... | |
class | Residue |
Representation of a residue. More... | |
class | ResidueDB |
residue data base which holds residues More... | |
class | ResidueModification |
Representation of a modification. More... | |
class | SvmTheoreticalSpectrumGenerator |
Simulates MS2 spectra with support vector machines. More... | |
class | SvmTheoreticalSpectrumGeneratorSet |
Loads SvmTheoreticalSpectrumGenerator instances for different charges. More... | |
class | SvmTheoreticalSpectrumGeneratorTrainer |
Train SVM models that are used by SvmTheoreticalSpectrumGenerator. More... | |
class | TheoreticalSpectrumGenerator |
Generates theoretical spectra with various options. More... | |
class | TrypticIterator |
finds all tryptic Peptides with every missed cleavage More... | |
class | WeightWrapper |
Encapsulated weight queries to simplify mono vs average weight computation. More... | |
class | AverageLinkage |
AverageLinkage ClusterMethod. More... | |
class | ClusterAnalyzer |
Bundles analyzing tools for a clustering (given as sequence of BinaryTreeNode's) More... | |
class | ClusterFunctor |
Base class for cluster functors. More... | |
class | ClusterHierarchical |
Hierarchical clustering with generic clustering functions. More... | |
class | UnnormalizedComparator |
Exception thrown if clustering is attempted without a normalized compare functor. More... | |
class | ClusteringGrid |
data structure to store 2D data to be clustered e.g. (m/z, retention time) coordinates from multiplex filtering More... | |
class | CompleteLinkage |
CompleteLinkage ClusterMethod. More... | |
class | EuclideanSimilarity |
CompareFunctor for 2Dpoints. More... | |
class | GridBasedCluster |
basic data structure for clustering More... | |
class | MinimumDistance |
basic data structure for distances between clusters More... | |
class | GridBasedClustering |
2D hierarchical clustering implementation optimized for large data sets containing many small clusters i.e. dimensions of clusters << dimension of entire dataset More... | |
class | HashGrid |
Container for (2-dimensional coordinate, value) pairs. More... | |
class | SingleLinkage |
SingleLinkage ClusterMethod. More... | |
class | BinnedSharedPeakCount |
Compare functor scoring the shared peaks for similarity measurement. More... | |
class | BinnedSpectralContrastAngle |
Compare functor scoring the spectral contrast angle for similarity measurement. More... | |
class | BinnedSpectrum |
This is a binned representation of a PeakSpectrum. More... | |
class | BinnedSpectrumCompareFunctor |
Base class for compare functors of BinnedSpectra. More... | |
class | BinnedSumAgreeingIntensities |
Compare functor scoring the sum of agreeing intensities for similarity measurement. More... | |
class | PeakAlignment |
make a PeakAlignment of two PeakSpectra More... | |
class | PeakSpectrumCompareFunctor |
Base class for compare functors of spectra, that return a similarity value for two spectra. More... | |
class | SpectraSTSimilarityScore |
Similarity score of SpectraST. More... | |
class | SpectrumAlignment |
Aligns the peaks of two spectra. More... | |
class | SpectrumAlignmentScore |
Similarity score via spectra alignment. More... | |
class | SpectrumCheapDPCorr |
SpectrumCheapDPCorr calculates an optimal alignment on stick spectra. More... | |
class | SpectrumPrecursorComparator |
SpectrumPrecursorComparator compares just the parent mass of two spectra. More... | |
class | SteinScottImproveScore |
Similarity score based of Stein & Scott. More... | |
class | ZhangSimilarityScore |
Similarity score of Zhang. More... | |
class | BinaryComposeFunctionAdapter |
Represents the binary compose function object adapter. More... | |
class | Factory |
Returns FactoryProduct* based on the name of the desired concrete FactoryProduct. More... | |
class | FactoryBase |
Base class for Factory<T> More... | |
class | FuzzyStringComparator |
Fuzzy comparison of strings, tolerates numeric differences. More... | |
class | LogConfigHandler |
The LogConfigHandler provides the functionality to configure the internal logging of OpenMS algorithms that use the global instances of LogStream. More... | |
struct | PrecisionWrapper |
Wrapper class to implement output with appropriate precision. See precisionWrapper(). More... | |
class | ProgressLogger |
Base class for all classes that want to report their progress. More... | |
class | SingletonRegistry |
Holds pointers to unique instance of a singleton factory. More... | |
class | StreamHandler |
Provides a central class to register globally used output streams. Currently supported streams are. More... | |
class | UnaryComposeFunctionAdapter |
Represents the function object unary adapter. More... | |
class | UniqueIdGenerator |
A generator for unique ids. More... | |
class | UniqueIdIndexer |
A base class for random access containers for classes derived from UniqueIdInterface that adds functionality to convert a unique id into an index into the container. More... | |
class | UniqueIdInterface |
A base class defining a common interface for all classes having a unique id. More... | |
class | VersionInfo |
Version information class. More... | |
class | Adduct |
class | BigString |
concatenates Proteins given as FASTAEntry to one big string separated by a unique character (by default $) More... | |
class | BinaryTreeNode |
Elements of a binary tree used to represent a hierarchical clustering process. More... | |
class | ChargePair |
Representation of a (putative) link between two Features, which stem from the same compound but have different charge (including different adduct ions (H+, Na+, ..) More... | |
class | Compomer |
Holds information on an edge connecting two features from a (putative) charge ladder. More... | |
class | ConstRefVector |
This vector holds pointer to the elements of another container. More... | |
class | ConvexHull2D |
A 2-dimensional hull representation in [counter]clockwise direction - depending on axis labelling. More... | |
class | CVMappingRule |
Representation of a CV Mapping rule used by CVMappings. More... | |
class | CVMappings |
Representation of controlled vocabulary mapping rules (for PSI formats) More... | |
class | CVMappingTerm |
Representation of controlled vocabulary term. More... | |
class | CVReference |
Controlled Vocabulary Reference. More... | |
class | DataValue |
Class to hold strings, numeric values, lists of strings and lists of numeric values. More... | |
class | Date |
Date Class. More... | |
class | DateTime |
DateTime Class. More... | |
class | DBoundingBox |
A D-dimensional bounding box. More... | |
class | DefaultParamHandler |
A base class for all classes handling default parameters. More... | |
class | DistanceMatrix |
A two-dimensional distance matrix, similar to OpenMS::Matrix. More... | |
class | DPosition |
Representation of a coordinate in D-dimensional space. More... | |
class | DRange |
A D-dimensional half-open interval. More... | |
class | GridFeature |
Representation of a feature in a hash grid. More... | |
struct | IsotopeCluster |
Stores information about an isotopic cluster (i.e. potential peptide charge variants) More... | |
class | ListUtils |
Collection of utility functions for management of vectors. More... | |
class | LPWrapper |
class | Map |
Map class based on the STL map (containing several convenience functions) More... | |
class | MassExplainer |
computes empirical formulas for given mass differences using a set of allowed elements More... | |
class | Param |
Management and storage of parameters / INI files. More... | |
class | QTCluster |
A representation of a QT cluster used for feature grouping. More... | |
class | SparseVector |
SparseVector implementation. The container will not actually store a specified type of element - the sparse element, e.g. zero (by default) More... | |
class | String |
A more convenient string class. More... | |
class | StringListUtils |
Utilities operating on lists of Strings. More... | |
class | StringUtils |
class | SuffixArray |
abstract class for suffix array More... | |
class | SuffixArrayPeptideFinder |
wrapper for easy use of sufArray More... | |
struct | FloatsWithTolLess |
comparator for two doubles with a tolerance value More... | |
struct | IntsInRangeLess |
comparator for two doubles with a tolerance value More... | |
class | SuffixArraySeqan |
Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum. More... | |
class | SuffixArrayTrypticCompressed |
Class that implements a suffix array for a String. It can be used to find peptide Candidates for a MS spectrum. More... | |
class | SuffixArrayTrypticSeqan |
Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum. More... | |
class | MorphologicalFilter |
This class implements baseline filtering operations using methods from mathematical morphology. More... | |
class | InternalCalibration |
A simple calibration method using linear interpolation of given reference masses. More... | |
class | TOFCalibration |
This class implements an external calibration for TOF data using external calibrant spectra. More... | |
class | DataFilters |
DataFilter array providing some convenience functions. More... | |
class | ElutionPeakDetection |
Extracts chromatographic peaks from a mass trace. More... | |
class | CmpMassTraceByMZ |
Method for the assembly of mass traces belonging to the same isotope pattern, i.e., that are compatible in retention times, mass-to-charge ratios, and isotope abundances. More... | |
class | FeatureHypothesis |
class | CmpHypothesesByScore |
class | FeatureFindingMetabo |
class | IsotopeDistributionCache |
Pre-calculate isotope distributions for interesting mass ranges. More... | |
class | MassTraceDetection |
A mass trace extraction method that gathers peaks similar in m/z and moving along retention time. More... | |
class | SplinePackage |
fundamental data structure for SplineSpectrum More... | |
class | SplineSpectrum |
Data structure for spline interpolation of MS1 spectra. More... | |
class | IDFilter |
Used to filter identifications by different criteria. More... | |
class | SignalToNoiseEstimator |
This class represents the abstract base class of a signal to noise estimator. More... | |
class | SignalToNoiseEstimatorMeanIterative |
Estimates the signal/noise (S/N) ratio of each data point in a scan based on an iterative scheme which discards high intensities. More... | |
class | SignalToNoiseEstimatorMedian |
Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram based) More... | |
class | SignalToNoiseEstimatorMedianRapid |
Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (window based) More... | |
class | GaussFilter |
This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data. More... | |
class | GaussFilterAlgorithm |
This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data. More... | |
class | LowessSmoothing |
LOWESS (locally weighted scatterplot smoothing). More... | |
class | SavitzkyGolayFilter |
Computes the Savitzky-Golay filter coefficients using QR decomposition. More... | |
class | BernNorm |
BernNorm scales the peaks by ranking them and then scaling them according to rank. More... | |
class | ComplementFilter |
total intensity of peak pairs that could result from complementing fragments of charge state 1 More... | |
class | ComplementMarker |
ComplementMarker marks peak pairs which could represent y - b ion pairs. More... | |
class | FilterFunctor |
A FilterFunctor extracts some spectrum characteristics for quality assessment. More... | |
class | GoodDiffFilter |
GoodDiffFilter counts the number ob peak pairs whose m/z difference can be explained by a amino acid loss. More... | |
class | IntensityBalanceFilter |
IntensityBalanceFilter divides the m/z-range into ten regions and sums the intensity in these regions. More... | |
class | IsotopeDiffFilter |
IsotopeDiffFilter returns total intensity of peak pairs that could result from isotope peaks. More... | |
class | IsotopeMarker |
IsotopeMarker marks peak pairs which could represent an ion and its isotope. More... | |
class | LinearResampler |
Linear Resampling of raw data. More... | |
class | LinearResamplerAlign |
Linear Resampling of raw data with alignment. More... | |
class | MarkerMower |
MarkerMower uses PeakMarker to find peaks, those that are not marked get removed. More... | |
class | NeutralLossDiffFilter |
NeutralLossDiffFilter returns the total intensity ob peak pairs whose m/z difference can be explained by a neutral loss. More... | |
class | NeutralLossMarker |
NeutralLossMarker marks peak pairs which could represent an ion an its neutral loss (water, ammonia) More... | |
class | NLargest |
NLargest removes all but the n largest peaks. More... | |
class | Normalizer |
Normalizer normalizes the peak intensities. More... | |
class | ParentPeakMower |
ParentPeakMower gets rid of high peaks that could stem from unfragmented precursor ions. More... | |
class | PeakMarker |
PeakMarker marks peaks that seem to fulfill some criterion. More... | |
class | Scaler |
Scaler scales the peak by ranking the peaks and assigning intensity according to rank. More... | |
class | SpectraMerger |
Merges blocks of MS or MS2 spectra. More... | |
class | SqrtMower |
Scales the intensity of peaks to the sqrt. More... | |
class | ThresholdMower |
ThresholdMower removes all peaks below a threshold. More... | |
class | TICFilter |
TICFilter calculates TIC. More... | |
class | WindowMower |
WindowMower augments the highest peaks in a sliding or jumping window. More... | |
class | Base64 |
Class to encode and decode Base64. More... | |
class | Bzip2Ifstream |
Decompresses files which are compressed in the bzip2 format (*.bz2) More... | |
class | Bzip2InputStream |
Implements the BinInputStream class of the xerces-c library in order to read bzip2 compressed XML files. More... | |
class | CachedmzML |
An class that uses on-disk caching to read and write spectra and chromatograms. More... | |
class | CompressedInputSource |
This class is based on xercesc::LocalFileInputSource. More... | |
class | ConsensusXMLFile |
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation. More... | |
class | ControlledVocabulary |
Representation of a controlled vocabulary. More... | |
class | CsvFile |
This class handles csv files. Currently only loading is implemented. More... | |
class | CVMappingFile |
Used to load CvMapping files. More... | |
class | MSDataCachedConsumer |
Transforming and cached writing consumer of MS data. More... | |
class | MSDataChainingConsumer |
Consumer class that passes all operations on to a set of consumers. More... | |
class | MSDataTransformingConsumer |
Transforming consumer of MS data. More... | |
class | MSDataWritingConsumer |
Consumer class that writes MS data to disk using the mzML format. More... | |
class | PlainMSDataWritingConsumer |
Consumer class that writes MS data to disk using the mzML format. More... | |
class | NoopMSDataWritingConsumer |
Consumer class that perform no operation. More... | |
class | NoopMSDataConsumer |
Consumer class that perform no operation. More... | |
class | FullSwathFileConsumer |
Abstract base class which can consume spectra coming from SWATH experiment stored in a single file. More... | |
class | RegularSwathFileConsumer |
In-memory implementation of FullSwathFileConsumer. More... | |
class | CachedSwathFileConsumer |
On-disk cached implementation of FullSwathFileConsumer. More... | |
class | DTA2DFile |
DTA2D File adapter. More... | |
class | DTAFile |
File adapter for DTA files. More... | |
class | EDTAFile |
File adapter for Enhanced DTA files. More... | |
class | FASTAFile |
This class serves for reading in FASTA files. More... | |
class | FastaIterator |
Iterator over FASTA file. More... | |
class | FastaIteratorIntern |
Iterator for a FASTA file. More... | |
class | FeatureXMLFile |
This class provides Input/Output functionality for feature maps. More... | |
class | FileHandler |
Facilitates file handling by file type recognition. More... | |
struct | FileTypes |
Centralizes the file types recognized by FileHandler. More... | |
class | GzipIfstream |
Decompresses files which are compressed in the gzip format (*.gzip) More... | |
class | GzipInputStream |
Implements the BinInputStream class of the xerces-c library in order to read gzip compressed XML files. More... | |
class | IndexedMzMLDecoder |
A class to analyze indexedmzML files and extract the offsets of individual tags. More... | |
class | MzMLSpectrumDecoder |
A class to decode input strings that contain an mzML chromatogram or spectrum tag. More... | |
class | IBSpectraFile |
Implements the export of consensusmaps into the IBSpectra format used by isobar to load quantification results. More... | |
class | IdXMLFile |
Used to load and store idXML files. More... | |
class | IndexedMzMLFile |
A class to read an indexedmzML file. More... | |
class | IndexedMzMLFileLoader |
A class to load an indexedmzML file. More... | |
class | InspectInfile |
Inspect input file adapter. More... | |
class | InspectOutfile |
Representation of an Inspect outfile. More... | |
class | KroenikFile |
File adapter for Kroenik (HardKloer sibling) files. More... | |
class | LibSVMEncoder |
Serves for encoding sequences into feature vectors. More... | |
class | MascotGenericFile |
Mascot input file adapter. More... | |
class | MascotInfile |
Mascot input file adapter. More... | |
class | MascotRemoteQuery |
Class which handles the communication between OpenMS and the Mascot server. More... | |
class | MascotXMLFile |
Used to load MascotXML files. More... | |
class | MS2File |
MS2 input file adapter. More... | |
class | MsInspectFile |
File adapter for MsInspect files. More... | |
class | MSNumpressCoder |
Class to encode and decode data encoded with MSNumpress. More... | |
class | MSPFile |
File adapter for MSP files (NIST spectra library) More... | |
class | MzDataFile |
File adapter for MzData files. More... | |
class | MzIdentMLFile |
File adapter for MzIdentML files. More... | |
class | MzMLFile |
File adapter for MzML files. More... | |
class | MzQuantMLFile |
File adapter for MzQuantML files. More... | |
class | MzTabNullAbleInterface |
class | MzTabNullNaNAndInfAbleInterface |
class | MzTabNullAbleBase |
class | MzTabNullNaNAndInfAbleBase |
class | MzTabDouble |
class | MzTabDoubleList |
class | MzTabInteger |
class | MzTabIntegerList |
class | MzTabBoolean |
class | MzTabString |
class | MzTabParameter |
class | MzTabParameterList |
class | MzTabStringList |
class | MzTabModification |
class | MzTabModificationList |
class | MzTabSpectraRef |
struct | MzTabSampleMetaData |
struct | MzTabSoftwareMetaData |
struct | MzTabModificationMetaData |
struct | MzTabAssayMetaData |
struct | MzTabCVMetaData |
struct | MzTabInstrumentMetaData |
struct | MzTabContactMetaData |
struct | MzTabMSRunMetaData |
struct | MzTabStudyVariableMetaData |
class | MzTabMetaData |
struct | MzTabProteinSectionRow |
struct | MzTabPeptideSectionRow |
struct | MzTabPSMSectionRow |
struct | MzTabSmallMoleculeSectionRow |
class | MzTab |
Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/. More... | |
class | MzTabFile |
File adapter for MzTab files. More... | |
class | MzXMLFile |
File adapter for MzXML 2.1 files. More... | |
class | OMSSACSVFile |
File adapter for OMSSACSV files. More... | |
class | OMSSAXMLFile |
Used to load OMSSAXML files. More... | |
class | FeatureFileOptions |
Options for loading files containing features. More... | |
class | PeakFileOptions |
Options for loading files containing peak data. More... | |
class | ParamXMLFile |
The file pendant of the Param class used to load and store the param datastructure as paramXML. More... | |
class | PeakTypeEstimator |
Estimates if the data of a spectrum is raw data or peak data. More... | |
class | PepNovoInfile |
PepNovo input file adapter. More... | |
class | PepNovoOutfile |
Representation of a PepNovo output file. More... | |
class | PepXMLFile |
Used to load and store PepXML files. More... | |
class | PepXMLFileMascot |
Used to load Mascot PepXML files. More... | |
class | ProtXMLFile |
Used to load (storing not supported, yet) ProtXML files. More... | |
class | PTMXMLFile |
Used to load and store PTMXML files. More... | |
class | QcMLFile |
File adapter for QcML files. More... | |
class | SequestInfile |
Sequest input file adapter. More... | |
class | SequestOutfile |
Representation of a Sequest output file. More... | |
class | SpecArrayFile |
File adapter for SpecArray (.pepList) files. More... | |
class | SVOutStream |
Stream class for writing to comma/tab/...-separated values files. More... | |
class | SwathFile |
File adapter for Swath files. More... | |
class | TextFile |
This class provides some basic file handling methods for text files. More... | |
class | ToolDescriptionFile |
File adapter for ToolDescriptor files. More... | |
class | TraMLFile |
File adapter for HUPO PSI TraML files. More... | |
class | TransformationXMLFile |
Used to load and store TransformationXML files. More... | |
class | UnimodXMLFile |
Used to load XML files from unimod.org files. More... | |
class | XMLValidator |
Validator for XML files. More... | |
class | XMassFile |
File adapter for 'XMass Analysis (fid)' files. More... | |
class | XTandemInfile |
XTandem input file. More... | |
class | XTandemXMLFile |
Used to load XTandemXML files. More... | |
class | BaseFeature |
A basic LC-MS feature. More... | |
class | ChromatogramPeak |
A 1-dimensional raw data point or peak for chromatograms. More... | |
class | ChromatogramTools |
Conversion class to convert chromatograms. More... | |
struct | PointerComparator |
Wrapper that takes a comparator for `something' and makes a comparator for pointers to `something' out of it. Normally you should use the make-function pointerComparator() because then you do not need to specify the template arguments. More... | |
struct | ReverseComparator |
Wrapper that reverses (exchanges) the two arguments of a comparator. Normally you should use the make-function reverseComparator() because then you do not need to specify the template arguments. More... | |
struct | LexicographicComparator |
A wrapper class that combines two comparators lexicographically. Normally you should use the make-function lexicographicComparator() because then you do not need to specify the template arguments. More... | |
struct | PairComparatorFirstElement |
Class for comparison of std::pair using first ONLY e.g. for use with std::sort. More... | |
struct | PairComparatorSecondElement |
Class for comparison of std::pair using second ONLY e.g. for use with std::sort. More... | |
struct | PairComparatorFirstElementMore |
Class for comparison of std::pair using first ONLY e.g. for use with std::sort. More... | |
struct | PairComparatorSecondElementMore |
Class for comparison of std::pair using second ONLY e.g. for use with std::sort. More... | |
struct | PairMatcherFirstElement |
Class for comparison of std::pair using first ONLY e.g. for use with std::sort. More... | |
struct | PairMatcherSecondElement |
Struct for comparison of std::pair using second ONLY e.g. for use with std::sort. More... | |
struct | EqualInTolerance |
Struct for binary predicate to consider equality with a certain tolerance. More... | |
class | ConsensusFeature |
A 2-dimensional consensus feature. More... | |
class | ConsensusMap |
A container for consensus elements. More... | |
class | MapConversion |
struct | DPeak |
Metafunction to choose among Peak1D respectively Peak2D through a template argument. More... | |
struct | DRichPeak |
Metafunction to choose among RichPeak1D respectively RichPeak2D through a template argument. More... | |
class | Feature |
An LC-MS feature. More... | |
class | FeatureHandle |
Representation of a Peak2D, RichPeak2D or Feature . More... | |
struct | AnnotationStatistics |
class | FeatureMap |
A container for features. More... | |
class | MassTrace |
A container type that gathers peaks similar in m/z and moving along retention time. More... | |
class | MRMFeature |
A multi-chromatogram MRM feature. More... | |
class | MRMTransitionGroup |
The representation of a transition group that has information about the individual chromatograms as well as the transitions it refers to. More... | |
class | MSChromatogram |
The representation of a chromatogram. More... | |
class | MSExperiment |
In-Memory representation of a mass spectrometry experiment. More... | |
class | MSSpectrum |
The representation of a 1D spectrum. More... | |
class | OnDiscMSExperiment |
Representation of a mass spectrometry experiment on disk. More... | |
class | Peak1D |
A 1-dimensional raw data point or peak. More... | |
class | Peak2D |
A 2-dimensional raw data point or peak. More... | |
struct | PeakIndex |
Index of a peak or feature. More... | |
class | RangeManager |
Handles the management of a position and intensity range. More... | |
class | HasMetaValue |
Predicate that determines if a class has a certain metavalue. More... | |
class | InRTRange |
Predicate that determines if a spectrum lies inside/outside a specific retention time range. More... | |
class | InMSLevelRange |
Predicate that determines if a spectrum lies inside/outside a specific MS level set. More... | |
class | HasScanMode |
Predicate that determines if a spectrum has a certain scan mode. More... | |
class | HasScanPolarity |
Predicate that determines if a spectrum has a certain scan polarity. More... | |
class | IsEmptySpectrum |
Predicate that determines if a spectrum is empty. More... | |
class | IsZoomSpectrum |
Predicate that determines if a spectrum is a zoom (enhanced resolution) spectrum. More... | |
class | HasActivationMethod |
Predicate that determines if a spectrum was generated using any activation method given in the constructor list. More... | |
class | InPrecursorMZRange |
Predicate that determines if a spectrum's precursor is within a certain m/z range. More... | |
class | HasPrecursorCharge |
Predicate that determines if a spectrum has a certain precursor charge as given in the constructor list. More... | |
class | InMzRange |
Predicate that determines if a peak lies inside/outside a specific m/z range. More... | |
class | InIntensityRange |
Predicate that determines if a peak lies inside/outside a specific intensity range. More... | |
class | IsInCollisionEnergyRange |
Predicate that determines if an MSn spectrum was generated with a collision energy in the given range. More... | |
class | IsInIsolationWindowSizeRange |
Predicate that determines if the width of the isolation window of an MSn spectrum is in the given range. More... | |
class | RichPeak1D |
A 1-dimensional raw data point or peak with meta information. More... | |
class | RichPeak2D |
A 2-dimensional raw data point or peak with meta information. More... | |
class | BSpline2d |
b spline interpolation More... | |
class | CubicSpline2d |
cubic spline interpolation as described in R.L. Burden, J.D. Faires, Numerical Analysis, 4th ed. PWS-Kent, 1989, ISBN 0-53491-585-X, pp. 126-131. More... | |
class | NonNegativeLeastSquaresSolver |
Wrapper for a non-negative least squares (NNLS) solver. More... | |
class | Spline2d |
Wrapper for Spline interpolation. More... | |
class | Acquisition |
Information about one raw data spectrum that was combined with several other raw data spectra. More... | |
class | AcquisitionInfo |
Description of the combination of raw data to a single spectrum. More... | |
class | ChromatogramSettings |
Representation of chromatogram settings, e.g. SRM/MRM chromatograms. More... | |
class | ContactPerson |
Contact person information. More... | |
class | CVTerm |
Representation of controlled vocabulary term. More... | |
class | CVTermList |
Representation of controlled vocabulary term list. More... | |
class | DataProcessing |
Description of the applied preprocessing steps. More... | |
class | Digestion |
Meta information about digestion of a sample. More... | |
class | DocumentIdentifier |
Manage source document information. More... | |
class | DocumentIDTagger |
Tags OpenMS file containers with a DocumentID. More... | |
class | ExperimentalSettings |
Description of the experimental settings. More... | |
class | Gradient |
Representation of a HPLC gradient. More... | |
class | HPLC |
Representation of a HPLC experiment. More... | |
class | Identification |
Represents a object which can store the information of an analysisXML instance. More... | |
class | IdentificationHit |
Represents a object which can store the information of an analysisXML instance. More... | |
class | Instrument |
Description of a MS instrument. More... | |
class | InstrumentSettings |
Description of the settings a MS Instrument was run with. More... | |
class | IonDetector |
Description of a ion detector (part of a MS Instrument) More... | |
class | IonSource |
Description of an ion source (part of a MS Instrument) More... | |
class | MassAnalyzer |
Description of a mass analyzer (part of a MS Instrument) More... | |
class | MetaInfo |
A Type-Name-Value tuple class. More... | |
class | MetaInfoDescription |
Description of the meta data arrays of MSSpectrum. More... | |
class | MetaInfoInterface |
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples). More... | |
class | MetaInfoRegistry |
Registry which assigns unique integer indices to strings. More... | |
class | Modification |
Meta information about chemical modification of a sample. More... | |
class | MSQuantifications |
class | PeptideEvidence |
Representation of a peptide evidence. More... | |
class | PeptideHit |
Representation of a peptide hit. More... | |
class | PeptideIdentification |
Represents the peptide hits for a spectrum. More... | |
class | Precursor |
Precursor meta information. More... | |
class | Product |
Product meta information. More... | |
class | ProteinHit |
Representation of a protein hit. More... | |
class | ProteinIdentification |
Representation of a protein identification run. More... | |
class | Sample |
Meta information about the sample. More... | |
class | SampleTreatment |
Base class for sample treatments (Digestion, Modification, Tagging, ...) More... | |
struct | ScanWindow |
Scan window description. More... | |
class | Software |
Description of the software used for processing. More... | |
class | SourceFile |
Description of a file location, used to store the origin of (meta) data. More... | |
class | SpectrumIdentification |
Represents a object which can store the information of an analysisXML instance. More... | |
class | SpectrumSettings |
Representation of 1D spectrum settings. More... | |
class | Tagging |
Meta information about tagging of a sample e.g. ICAT labeling. More... | |
class | DetectabilitySimulation |
Simulates peptide detectability. More... | |
class | DigestSimulation |
Simulates protein digestion. More... | |
class | EGHFitter1D |
Exponential-Gaussian hybrid distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen implementation) for parameter optimization. More... | |
class | EGHModel |
Exponential-Gaussian hybrid distribution model for elution profiles. More... | |
class | IonizationSimulation |
Simulates Protein ionization. More... | |
class | BaseLabeler |
Abstract base class for all kinds of labeling techniques. More... | |
class | ICPLLabeler |
Simulate ICPL experiments. More... | |
class | ITRAQLabeler |
Simulate iTRAQ experiments. More... | |
class | LabelFreeLabeler |
Abstract base class for all kinds of labeling techniques. More... | |
class | O18Labeler |
Simulate O-18 experiments. More... | |
class | SILACLabeler |
Simulate SILAC experiments. More... | |
class | MSSim |
Central class for simulation of mass spectrometry experiments. More... | |
class | RawMSSignalSimulation |
Simulates MS signals for a given set of peptides. More... | |
class | RawTandemMSSignalSimulation |
Simulates tandem MS signals for a given set of peptides. More... | |
class | RTSimulation |
Simulates/Predicts retention times for peptides or peptide separation. More... | |
class | File |
Basic file handling operations. More... | |
class | FileWatcher |
Watcher that monitors file changes. More... | |
class | JavaInfo |
Detect Java and retrieve information. More... | |
class | StopWatch |
StopWatch Class. More... | |
class | SysInfo |
Some static functions to get system information. More... | |
class | BaseModel |
Abstract base class for all D-dimensional models. More... | |
class | BiGaussFitter1D |
BiGaussian distribution fitter (1-dim.) approximated using linear interpolation. More... | |
class | BiGaussModel |
BiGaussian distribution approximated using linear interpolation. More... | |
class | EGHTraceFitter |
A RT Profile fitter using an Exponential Gaussian Hybrid background model. More... | |
class | EmgFitter1D |
Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen implementation) for parameter optimization. More... | |
class | EmgModel |
Exponentially modified gaussian distribution model for elution profiles. More... | |
class | EmgScoring |
Scoring of an elution peak using an exponentially modified gaussian distribution model. More... | |
class | ExtendedIsotopeFitter1D |
Extended isotope distribution fitter (1-dim.) approximated using linear interpolation. More... | |
class | ExtendedIsotopeModel |
Extended isotope distribution approximated using linear interpolation. More... | |
class | FeaFiModule |
Implements a module of the FeatureFinder algorithm. More... | |
class | FeatureFinder |
The main feature finder class. More... | |
struct | Summary |
Summary of fitting results. More... | |
class | FeatureFinderAlgorithm |
Abstract base class for FeatureFinder algorithms. More... | |
class | FeatureFinderAlgorithmIsotopeWavelet |
Implements the isotope wavelet feature finder. More... | |
class | FeatureFinderAlgorithmMRM |
FeatureFinderAlgorithm for MRM experiments. More... | |
class | FeatureFinderAlgorithmPicked |
FeatureFinderAlgorithm for picked peaks. More... | |
struct | FeatureFinderAlgorithmPickedHelperStructs |
Wrapper struct for all the classes needed by the FeatureFinderAlgorithmPicked and the associated classes. More... | |
struct | FeatureFinderDefs |
The purpose of this struct is to provide definitions of classes and typedefs which are used throughout all FeatureFinder classes. More... | |
class | Fitter1D |
Abstract base class for all 1D-dimensional model fitter. More... | |
class | GaussFitter1D |
Gaussian distribution fitter (1-dim.) approximated using linear interpolation. More... | |
class | GaussModel |
Normal distribution approximated using linear interpolation. More... | |
class | GaussTraceFitter |
Fitter for RT profiles using a Gaussian background model. More... | |
class | InterpolationModel |
Abstract class for 1D-models that are approximated using linear interpolation. More... | |
class | IsotopeFitter1D |
Isotope distribution fitter (1-dim.) approximated using linear interpolation. More... | |
class | IsotopeModel |
Isotope distribution approximated using linear interpolation. More... | |
class | IsotopeWavelet |
Implements the isotope wavelet function. More... | |
class | IsotopeWaveletTransform |
A class implementing the isotope wavelet transform. If you just want to find features using the isotope wavelet, take a look at the FeatureFinderAlgorithmIsotopeWavelet class. Usually, you only have to consider the class at hand if you plan to change the basic implementation of the transform. More... | |
class | LevMarqFitter1D |
Abstract class for 1D-model fitter using Levenberg-Marquardt algorithm for parameter optimization. More... | |
class | MaxLikeliFitter1D |
Abstract base class for all 1D-model fitters using maximum likelihood optimization. More... | |
class | ModelDescription |
Stores the name and parameters of a model. More... | |
class | MultiplexClustering |
clusters results from multiplex filtering More... | |
class | MultiplexFiltering |
base class for filtering centroided and profile data for peak patterns More... | |
class | MultiplexFilteringCentroided |
filters centroided data for peak patterns More... | |
class | MultiplexFilteringProfile |
filters centroided and profile data for peak patterns More... | |
class | MultiplexFilterResult |
data structure storing all peaks (and optionally their raw data points) corresponding to one specific peak pattern More... | |
class | MultiplexFilterResultPeak |
data structure storing a single peak that passed all filters More... | |
class | MultiplexFilterResultRaw |
data structure storing a single raw data point that passed all filters More... | |
class | MultiplexPeakPattern |
data structure for pattern of isotopic peaks More... | |
class | PeakWidthEstimator |
Rough estimation of the peak width at m/z. More... | |
class | ProductModel |
Class for product models i.e. models with D independent dimensions. More... | |
class | ProductModel< 2 > |
The class template is only implemented for D=2 because we use Peak2D here. More... | |
class | SeedListGenerator |
Generate seed lists for feature detection. More... | |
class | TraceFitter |
Abstract fitter for RT profile fitting. More... | |
class | ContinuousWaveletTransform |
This class is the base class of the continuous wavelet transformation. More... | |
class | ContinuousWaveletTransformNumIntegration |
This class computes the continuous wavelet transformation using a marr wavelet. More... | |
class | OptimizePeakDeconvolution |
This class provides the deconvolution of peak regions using non-linear optimization. More... | |
class | OptimizePick |
This class provides the non-linear optimization of the peak parameters. More... | |
class | PeakPickerCWT |
This class implements a peak picking algorithm using wavelet techniques. More... | |
class | PeakPickerHiRes |
This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width. More... | |
struct | PeakCandidate |
A small structure to hold peak candidates. More... | |
class | PeakPickerIterative |
This class implements a peak-picking algorithm for high-resolution MS data (specifically designed for TOF-MS data). More... | |
class | PeakPickerMaxima |
This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width. More... | |
class | PeakPickerSH |
class | PeakShape |
Internal representation of a peak shape (used by the PeakPickerCWT) More... | |
class | TwoDOptimization |
This class provides the two-dimensional optimization of the picked peak parameters. More... | |
class | FeatureFinderAlgorithmSH |
The Superhirn FeatureFinderAlgorithm. More... | |
class | FeatureFinderAlgorithmSHCtrl |
A facade for various Superhirn FeatureFinder classes. Use FeatureFinderAlgorithmSH instead. More... | |
class | BackgroundControl |
class | BackgroundIntensityBin |
class | CentroidData |
class | CentroidPeak |
class | DeconvPeak |
class | ClusteredMS2ConsensusSpectrum |
class | ConsensusIsotopePattern |
class | Deisotoper |
struct | MS1Signal |
class | FeatureLCProfile |
class | FTPeakDetectController |
class | IsotopicDist |
class | LCElutionPeak |
class | LCMS |
class | LCMSCData |
class | MS1FeatureMerger |
class | MS2ConsensusSpectrum |
class | MS2Feature |
class | MS2Fragment |
class | MS2Info |
class | MSPeak |
class | ProcessData |
class | RawData |
class | SHFeature |
class | SuperHirnParameters |
SuperHirn parameters singleton class containing all static configuration variables. More... | |
class | SuperHirnUtil |
class | Annotation1DCaret |
An annotation item which paints a set of carets on the canvas. More... | |
class | Annotation1DDistanceItem |
An annotation item which represents a measured distance between two peaks. More... | |
class | Annotation1DItem |
An abstract class acting as an interface for the different 1D annotation items. More... | |
class | Annotation1DPeakItem |
A peak annotation item. More... | |
class | Annotation1DTextItem |
An annotation item which represents an arbitrary text on the canvas. More... | |
class | Annotations1DContainer |
Container for annotations to content of Spectrum1DCanvas. More... | |
class | IDEvaluationBase |
Main window of the IDEvaluation tool. More... | |
class | INIFileEditorWindow |
shows the ParamEditor widget in a QMainWindow with a toolbar More... | |
class | QApplicationTOPP |
Extension to the QApplication for running TOPPs GUI tools. More... | |
class | TOPPASBase |
Main window of the TOPPAS tool. More... | |
class | TOPPViewBase |
Main window of TOPPView tool. More... | |
class | AxisPainter |
Draws a coordinate axis. It has only static methods, that's why the constructor is private. More... | |
class | AxisTickCalculator |
Calculates ticks for a given value range. More... | |
class | AxisWidget |
Widget that represents an axis of a graph. More... | |
class | ColorSelector |
A widget for selecting a color. More... | |
class | DataFilterDialog |
Dialog for creating and changing a DataFilter. More... | |
class | FeatureEditDialog |
Dialog for editing a feature. More... | |
class | HistogramDialog |
Dialog that show a HistogramWidget. More... | |
class | LayerStatisticsDialog |
Dialog showing statistics about the data of the current layer. More... | |
class | SaveImageDialog |
Dialog for saving an image. More... | |
class | Spectrum1DGoToDialog |
simple goto/set visible area dialog for exact placement of the viewing window More... | |
class | Spectrum2DGoToDialog |
GoTo dialog used to zoom to a m/z and retention time range or to a feature. More... | |
class | SpectrumAlignmentDialog |
Lets the user select two spectra and set the parameters for the spectrum alignment. More... | |
class | TheoreticalSpectrumGenerationDialog |
Dialog which allows to enter an AA sequence and generates a theoretical spectrum for it. More... | |
class | ToolsDialog |
TOPP tool selection dialog. More... | |
class | TOPPASInputFileDialog |
Dialog which allows to specify an input file. More... | |
class | TOPPASInputFilesDialog |
Dialog which allows to specify a list of input files. More... | |
class | TOPPASIOMappingDialog |
Dialog which allows to configure the input/output parameter mapping of an edge. More... | |
class | TOPPASOutputFilesDialog |
Dialog which allows to specify the directory for the output files. More... | |
class | TOPPASToolConfigDialog |
TOPP tool configuration dialog. More... | |
class | TOPPASVertexNameDialog |
Dialog which allows to change the name of an input vertex. More... | |
class | TOPPViewOpenDialog |
Dataset opening options for TOPPView. More... | |
class | EnhancedTabBar |
Convenience tab bar implementation. More... | |
class | EnhancedTabBarWidgetInterface |
Widgets that are placed into an EnhancedTabBar must implement this interface. More... | |
class | EnhancedWorkspace |
class | GUIProgressLoggerImpl |
Implements a GUI version of the ProgressLoggerImpl. More... | |
class | HistogramWidget |
Widget which can visualize a histogram. More... | |
class | LayerData |
Class that stores the data for one layer. More... | |
class | ListEditor |
Editor for editing int, double and string lists (including output and input file lists) More... | |
class | MetaDataBrowser |
A meta data visualization widget. More... | |
class | MultiGradient |
A gradient of multiple colors and arbitrary distances between colors. More... | |
class | MultiGradientSelector |
A widget witch allows constructing gradients of multiple colors. More... | |
class | ParamEditor |
A GUI for editing or viewing a Param object. More... | |
class | SpectraIdentificationViewWidget |
Tabular visualization / selection of identified spectra. More... | |
class | SpectraViewWidget |
Hierarchical visualization and selection of spectra. More... | |
class | Spectrum1DCanvas |
Canvas for visualization of one or several spectra. More... | |
class | Spectrum1DWidget |
Widget for visualization of several spectra. More... | |
class | Spectrum2DCanvas |
Canvas for 2D-visualization of peak map, feature map and consensus map data. More... | |
class | Spectrum2DWidget |
Widget for 2D-visualization of peak map and feature map data. More... | |
class | Spectrum3DCanvas |
Canvas for 3D-visualization of peak map data. More... | |
class | Spectrum3DOpenGLCanvas |
OpenGL Canvas for 3D-visualization of map data. More... | |
class | Spectrum3DWidget |
Widget for 3D-visualization of map data. More... | |
class | SpectrumCanvas |
Base class for visualization canvas classes. More... | |
class | SpectrumWidget |
Base class for spectrum widgets. More... | |
class | TOPPASEdge |
An edge representing a data flow in TOPPAS. More... | |
class | TOPPASInputFileListVertex |
A vertex representing an input file list. More... | |
class | TOPPASLogWindow |
QTextEdit implementation with a "clear" button in the context menu. More... | |
class | TOPPASMergerVertex |
A special vertex that allows to merge several inputs. More... | |
class | TOPPASOutputFileListVertex |
A vertex representing an output file list. More... | |
class | TOPPASResource |
Represents a data resource for TOPPAS workflows. More... | |
class | TOPPASResources |
A dictionary mapping string keys to lists of TOPPASResource objects. More... | |
class | FakeProcess |
A FakeProcess class. More... | |
class | TOPPASScene |
A container for all visual items of a TOPPAS workflow. More... | |
class | TOPPASTabBar |
Convenience tab bar implementation. More... | |
class | TOPPASToolVertex |
A vertex representing a TOPP tool. More... | |
class | TOPPASTreeView |
Tree view implementation for the list of TOPP tools. More... | |
class | TOPPASVertex |
The base class of the different vertex classes. More... | |
class | TOPPASWidget |
Widget visualizing and allowing to edit TOPP pipelines. More... | |
class | TOPPViewBehaviorInterface |
Interface class to model different behaviors of TOPPView. More... | |
class | TOPPViewIdentificationViewBehavior |
Behavior of TOPPView in identification mode. More... | |
class | TOPPViewSpectraViewBehavior |
Behavior of TOPPView in spectra view mode. More... | |
class | AcquisitionInfoVisualizer |
Class that displays all meta information for AcquisitionInfo objects. More... | |
class | AcquisitionVisualizer |
Class that displays all meta information for Acquisition objects. More... | |
class | BaseVisualizer |
A base class for all visualizer classes. More... | |
class | BaseVisualizerGUI |
A base class for all visualizer classes. More... | |
class | ContactPersonVisualizer |
Class that displays all meta information for ContactPerson objects. More... | |
class | DataProcessingVisualizer |
Class that displays all meta information for DataProcessing objects. More... | |
class | DigestionVisualizer |
Class that displays all meta information of digestion objects. More... | |
class | DocumentIdentifierVisualizer |
Class that displays all meta information for DocumentIdentifier objects. More... | |
class | ExperimentalSettingsVisualizer |
Class that displays all meta information for ExperimentalSettings objects. More... | |
class | GradientVisualizer |
GradientVisualizer is a visualizer class for objects of type gradient. More... | |
class | HPLCVisualizer |
Class that displays all meta information for HPLC objects. More... | |
class | InstrumentSettingsVisualizer |
Class that displays all meta information for InstrumentSettings objects. More... | |
class | InstrumentVisualizer |
Class that displays all meta information for an MS instrument. More... | |
class | IonDetectorVisualizer |
Class that displays all meta information for IonDetector objects. More... | |
class | IonSourceVisualizer |
Class that displays all meta information for IonSource objects. More... | |
class | MassAnalyzerVisualizer |
Class that displays all meta information for MassAnalyzer objects. More... | |
class | MetaInfoDescriptionVisualizer |
Class that displays all meta information for MetaInfoDescription objects. More... | |
class | MetaInfoVisualizer |
MetaInfoVisualizer is a visualizer class for all classes that use one MetaInfo object as member. More... | |
class | ModificationVisualizer |
Class that displays all meta information of modification objects. More... | |
class | PeptideHitVisualizer |
Class that displays all meta information for PeptideHit objects. More... | |
class | PeptideIdentificationVisualizer |
Class that displays all meta information for PeptideIdentification objects. More... | |
class | PrecursorVisualizer |
Class that displays all meta information for Precursor objects. More... | |
class | ProductVisualizer |
Class that displays all meta information for Product objects. More... | |
class | ProteinHitVisualizer |
Class that displays all meta information for ProteinHit objects. More... | |
class | ProteinIdentificationVisualizer |
Class that displays all meta information for ProteinIdentification objects. More... | |
class | SampleVisualizer |
Class that displays all meta information of sample objects. More... | |
class | ScanWindowVisualizer |
Class that displays all meta information for ScanWindow objects. More... | |
class | SoftwareVisualizer |
Class that displays all meta information for Software objects. More... | |
class | SourceFileVisualizer |
Class that displays all meta information for SourceFile objects. More... | |
class | SpectrumSettingsVisualizer |
Class that displays all meta information for SpectrumSettings objects. More... | |
class | TaggingVisualizer |
Class that displays all meta information of tagging objects. More... | |
class | OpenSwathTSVWriter |
Class to write out an OpenSwath TSV output (mProphet input) More... | |
class | OpenSwathWorkflow |
Class to execute an OpenSwath Workflow. More... | |
Typedefs | |
typedef Map < Internal::ToolDescriptionInternal, Internal::ToolDescriptionInternal > | ToolMapping |
Updates an INI. More... | |
typedef Map< String, Internal::ToolDescription > | ToolListType |
Handles lists of TOPP and UTILS tools and their categories (for TOPPAS) More... | |
typedef OPENMS_INT32_TYPE | Int32 |
Signed integer type (32bit) More... | |
typedef OPENMS_INT64_TYPE | Int64 |
Signed integer type (64bit) More... | |
typedef OPENMS_UINT64_TYPE | UInt64 |
Unsigned integer type (64bit) More... | |
typedef time_t | Time |
Time type. More... | |
typedef unsigned int | UInt |
Unsigned integer type. More... | |
typedef int | Int |
Signed integer type. More... | |
typedef OPENMS_BYTE_TYPE | Byte |
Byte type. More... | |
typedef OPENMS_UINT64_TYPE | UID |
A unique object ID (as unsigned 64bit type). More... | |
typedef size_t | Size |
Size type e.g. used as variable which can hold result of size() More... | |
typedef ptrdiff_t | SignedSize |
Signed Size type e.g. used as pointer difference. More... | |
typedef std::vector< Int > | IntList |
Vector of signed integers. More... | |
typedef std::vector< double > | DoubleList |
Vector of double precision real types. More... | |
typedef std::vector< String > | StringList |
Vector of String. More... | |
typedef boost::shared_ptr < const Eigen::MatrixXd > | EigenMatrixXdPtr |
typedef boost::shared_ptr < Eigen::MatrixXd > | MutableEigenMatrixXdPtr |
typedef std::pair< String, MzTabString > | MzTabOptionalColumnEntry |
typedef std::vector < MzTabProteinSectionRow > | MzTabProteinSectionRows |
typedef std::vector < MzTabPeptideSectionRow > | MzTabPeptideSectionRows |
typedef std::vector < MzTabPSMSectionRow > | MzTabPSMSectionRows |
typedef std::vector < MzTabSmallMoleculeSectionRow > | MzTabSmallMoleculeSectionRows |
typedef Peak2D | PeakType |
typedef std::multimap< int, MSPeak > | elution_peak |
typedef std::vector< elution_peak > | MZ_series |
typedef std::vector < elution_peak >::iterator | MZ_series_ITERATOR |
typedef std::multimap< int, MSPeak >::iterator | SIGNAL_iterator |
typedef MSSpectrum< Peak1D > | PeakSpectrum |
Spectrum consisting of raw data points or peaks. More... | |
typedef MSExperiment< Peak1D > | PeakMap |
Two-dimensional map of raw data points or peaks. More... | |
typedef MSSpectrum< RichPeak1D > | RichPeakSpectrum |
Spectrum consisting of raw data points or peaks with meta information. More... | |
typedef MSExperiment< RichPeak1D > | RichPeakMap |
Two-dimensional map of raw data points or peaks with meta information. More... | |
typedef MSChromatogram < ChromatogramPeak > | Chromatogram |
Chromatogram consisting of raw data points or peaks. More... | |
Enumerations | |
enum | ASCII { ASCII__BACKSPACE = '\b', ASCII__BELL = '\a', ASCII__CARRIAGE_RETURN = '\r', ASCII__HORIZONTAL_TAB = '\t', ASCII__NEWLINE = '\n', ASCII__RETURN = ASCII__NEWLINE, ASCII__SPACE = ' ', ASCII__TAB = ASCII__HORIZONTAL_TAB, ASCII__VERTICAL_TAB = '\v', ASCII__COLON = ':', ASCII__COMMA = ',', ASCII__EXCLAMATION_MARK = '!', ASCII__POINT = '.', ASCII__QUESTION_MARK = '?', ASCII__SEMICOLON = ';' } |
enum | MzTabCellStateType { MZTAB_CELLSTATE_DEFAULT, MZTAB_CELLSTATE_NULL, MZTAB_CELLSTATE_NAN, MZTAB_CELLSTATE_INF, SIZE_OF_MZTAB_CELLTYPE } |
Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/. More... | |
enum | Newline { nl } |
custom newline indicator More... | |
Functions | |
std::ostream & | operator<< (std::ostream &os, const AccurateMassSearchResult &amsr) |
std::ostream & | operator<< (std::ostream &os, const ItraqQuantifier::ItraqQuantifierStats &stats) |
template<typename InputPeakType > | |
bool | enclosesBoundingBox (const Feature &f, typename MSExperiment< InputPeakType >::CoordinateType rt, typename MSExperiment< InputPeakType >::CoordinateType mz) |
std::ostream & | operator<< (std::ostream &os, const PSLPFormulation::IndexTriple &triple) |
std::ostream & | operator<< (std::ostream &os, const AASequence &peptide) |
std::istream & | operator>> (std::istream &os, const AASequence &peptide) |
std::ostream & | operator<< (std::ostream &, const Element &) |
std::ostream & | operator<< (std::ostream &os, const EmpiricalFormula &formula) |
std::ostream & | operator<< (std::ostream &os, const Residue &residue) |
bool | compareBinaryTreeNode (const BinaryTreeNode &x, const BinaryTreeNode &y) |
returns the value of (x.distance < y.distance) for use with sort More... | |
template<UInt N, typename T > | |
std::size_t | hash_value (const DPosition< N, T > &b) |
template<class OP1 , class OP2 , class OP3 > | |
BinaryComposeFunctionAdapter < OP1, OP2, OP3 > | binaryCompose (const OP1 &o1, const OP2 &o2, const OP3 &o3) |
Convenience function for the BinaryComposeFunctionAdapter adapter. More... | |
std::ostream & | operator<< (std::ostream &os, const Exception::BaseException &e) |
Output operator for exceptions. More... | |
std::ostream & | operator<< (std::ostream &os, LogConfigHandler const &lch) |
Overload for the insertion operator (operator<<) to have a formatted output of the LogConfigHandler. More... | |
template<typename FloatingPointType > | |
const PrecisionWrapper < FloatingPointType > | precisionWrapper (const FloatingPointType rhs) |
Wrapper function that sets the appropriate precision for output temporarily. The original precision is restored afterwards so that no side effects remain. This is a "make"-function that deduces the typename FloatingPointType from its argument and returns a PrecisionWrapper<FloatingPointType>. More... | |
template<typename FloatingPointType > | |
std::ostream & | operator<< (std::ostream &os, const PrecisionWrapper< FloatingPointType > &rhs) |
Output operator for a PrecisionWrapper. Specializations are defined for float, double, long double. More... | |
std::ostream & | operator<< (std::ostream &os, StreamHandler const &stream_handler) |
Overload for the insertion operator (operator<<) to have a formatted output of the StreamHandler. More... | |
template<typename Type > | |
std::string | typeAsString (const Type &=Type()) |
Returns the Type as as std::string. More... | |
template<class OP1 , class OP2 > | |
UnaryComposeFunctionAdapter < OP1, OP2 > | unaryCompose (const OP1 &o1, const OP2 &o2) |
convenience function for the UnaryComposeFunctionAdapter adapter More... | |
std::ostream & | operator<< (std::ostream &os, const ChargePair &cons) |
Print the contents of a ChargePair to a stream. More... | |
template<UInt D> | |
std::ostream & | operator<< (std::ostream &os, const DBoundingBox< D > &bounding_box) |
Print the contents to a stream. More... | |
template<typename Value > | |
std::ostream & | operator<< (std::ostream &os, const DistanceMatrix< Value > &matrix) |
Print the contents to a stream. More... | |
template<UInt D, typename TCoordinateType > | |
DPosition< D, TCoordinateType > | operator* (DPosition< D, TCoordinateType > position, typename DPosition< D, TCoordinateType >::CoordinateType scalar) |
Scalar multiplication (a bit inefficient) More... | |
template<UInt D, typename TCoordinateType > | |
DPosition< D, TCoordinateType > | operator* (typename DPosition< D, TCoordinateType >::CoordinateType scalar, DPosition< D, TCoordinateType > position) |
Scalar multiplication (a bit inefficient) More... | |
template<UInt D, typename TCoordinateType > | |
DPosition< D, TCoordinateType > | operator/ (DPosition< D, TCoordinateType > position, typename DPosition< D, TCoordinateType >::CoordinateType scalar) |
Scalar multiplication (a bit inefficient) More... | |
template<UInt D, typename TCoordinateType > | |
std::ostream & | operator<< (std::ostream &os, const DPosition< D, TCoordinateType > &pos) |
Print the contents to a stream. More... | |
template<UInt D> | |
std::ostream & | operator<< (std::ostream &os, const DRange< D > &area) |
Print the contents to a stream. More... | |
template<typename T > | |
std::ostream & | operator<< (std::ostream &os, const std::vector< T > &v) |
Output stream operator for std::vectors. More... | |
template<typename TString > | |
std::vector< String > & | operator<< (std::vector< String > &sl, const TString &string) |
Operator for appending entries with less code. More... | |
template<typename Value > | |
std::ostream & | operator<< (std::ostream &os, const Matrix< Value > &matrix) |
Print the contents to a stream. More... | |
std::ostream & | operator<< (std::ostream &os, const Param ¶m) |
Output of Param to a stream. More... | |
static EigenMatrixXdPtr | convertOpenMSMatrix2EigenMatrixXd (const Matrix< double > &m) |
static bool | matrixIsIdentityMatrix (const Matrix< double > &channel_frequency) |
Int32 | endianize32 (Int32 &n) |
Endianizes a 32 bit type from big endian to little endian and vice versa. More... | |
Int64 | endianize64 (Int64 &n) |
Endianizes a 64 bit type from big endian to little endian and vice versa. More... | |
std::ostream & | operator<< (std::ostream &os, const ControlledVocabulary &cv) |
Print the contents to a stream. More... | |
void | FunctionSpectrumNOP (MSSpectrum< Peak1D > &) |
Empty (NOP) function. More... | |
void | FunctionChromatogramNOP (MSChromatogram< ChromatogramPeak > &) |
Empty (NOP) function. More... | |
std::ostream & | operator<< (std::ostream &os, const ChromatogramPeak &point) |
Print the contents to a stream. More... | |
template<class Cmp > | |
PointerComparator< Cmp > | pointerComparator (Cmp const &cmp) |
Make-function to create a PointerComparator from another comparator without the need to specify the template arguments. More... | |
template<class Cmp > | |
ReverseComparator< Cmp > | reverseComparator (Cmp const &cmp) |
Make-function to create a ReverseComparator from another comparator without the need to specify the template arguments. More... | |
template<typename Cmp1 , typename Cmp2 > | |
LexicographicComparator< Cmp1, Cmp2 > | lexicographicComparator (Cmp1 const &cmp1, Cmp2 const &cmp2) |
Make-function to create a LexicographicComparator from two other comparators without the need to specify the template arguments. More... | |
std::ostream & | operator<< (std::ostream &os, const ConsensusFeature &cons) |
Print the contents of a ConsensusFeature to a stream. More... | |
std::ostream & | operator<< (std::ostream &os, const ConsensusMap &cons_map) |
Print the contents of a ConsensusMap to a stream. More... | |
std::ostream & | operator<< (std::ostream &os, const FeatureHandle &cons) |
Print the contents of a FeatureHandle to a stream. More... | |
std::ostream & | operator<< (std::ostream &os, const AnnotationStatistics &ann) |
Print content of an AnnotationStatistics object to a stream. More... | |
std::ostream & | operator<< (std::ostream &os, const FeatureMap &map) |
template<typename PeakT > | |
std::ostream & | operator<< (std::ostream &os, const MSChromatogram< PeakT > &chrom) |
Print the contents to a stream. More... | |
template<typename PeakT , typename ChromatogramPeakT > | |
std::ostream & | operator<< (std::ostream &os, const MSExperiment< PeakT, ChromatogramPeakT > &exp) |
Print the contents to a stream. More... | |
template<typename PeakT > | |
std::ostream & | operator<< (std::ostream &os, const MSSpectrum< PeakT > &spec) |
Print the contents to a stream. More... | |
std::ostream & | operator<< (std::ostream &os, const Peak1D &point) |
Print the contents to a stream. More... | |
std::ostream & | operator<< (std::ostream &os, const Peak2D &point) |
Print the contents to a stream. More... | |
std::ostream & | operator<< (std::ostream &os, const ChromatogramSettings &spec) |
Print the contents to a stream. More... | |
std::ostream & | operator<< (std::ostream &os, const ExperimentalSettings &exp) |
Print the contents to a stream. More... | |
std::ostream & | operator<< (std::ostream &os, const SpectrumSettings &spec) |
Print the contents to a stream. More... | |
template<typename PeakType > | |
bool | intensityComparator (const PeakType &a, const PeakType &b) |
template<typename PeakType > | |
bool | intensityAscendingComparator (const PeakType &a, const PeakType &b) |
template<typename PeakType > | |
bool | intensityPointerComparator (PeakType *a, PeakType *b) |
template<typename PeakType > | |
bool | positionComparator (const PeakType &a, const PeakType &b) |
bool | sort_peaks_by_intensity (const PeakCandidate &a, const PeakCandidate &b) |
std::ostream & | operator<< (std::ostream &, CentroidData &) |
std::ostream & | operator<< (std::ostream &, CentroidPeak &) |
std::ostream & | operator<< (std::ostream &, DeconvPeak &) |
SUPERHIRN_DLLAPI std::ostream & | operator<< (std::ostream &, Deisotoper &) |
std::ostream & | operator<< (std::ostream &out, RawData &data) |
std::ostream & | operator<< (std::ostream &os, const LayerData &rhs) |
Print the contents to a stream. More... | |
Numbers of digits used for writing floating point numbers (a.k.a. precision). | |
These functions are provided to unify the handling of this issue throughout OpenMS. (So please don't use ad-hoc numbers ;-) ) If you want to avoid side effects you can use precisionWrapper() to write a floating point number with appropriate precision; in this case the original state of the stream is automatically restored afterwards. See precisionWrapper() for details. In practice, the number of decimal digits that the type can represent without loss of precision are 6 digits for single precision and 15 digits for double precision. We have Example: #define NUMBER 12345.67890123456789012345678901
std::cout << NUMBER << '\n'; // default precision, writes: 12345.7
double d = NUMBER;
std::cout.precision(writtenDigits<double>(0.0)); // explicit template instantiation
std::cout << writtenDigits<double>(0.0) << ": " << d << '\n'; // writes: 15: 12345.6789012346
float r = NUMBER;
std::cout.precision(writtenDigits(r)); // type deduced from argument
long double l = NUMBER;
std::cout.precision(writtenDigits(1L)); // argument is not used, but L suffix indicates a long double
double x = 88.99;
std::cout.precision(15);
std::cout << "15: " << x << '\n'; // writes: 15: 88.99
std::cout.precision(16);
std::cout << "16: " << x << '\n'; // writes: 16: 88.98999999999999
| |
template<typename FloatingPointType > | |
Int | writtenDigits (const FloatingPointType &=FloatingPointType()) |
Number of digits commonly used for writing a floating point type (a.k.a. precision). Specializations are defined for float, double, long double. More... | |
template<> | |
Int | writtenDigits< float > (const float &) |
Number of digits commonly used for writing a float (a.k.a. precision). More... | |
template<> | |
Int | writtenDigits< double > (const double &) |
Number of digits commonly used for writing a double (a.k.a. precision). More... | |
template<> | |
Int | writtenDigits< int > (const int &) |
We do not want to bother people who unintentionally provide an int argument to this. More... | |
template<> | |
Int | writtenDigits< unsigned int > (const unsigned int &) |
We do not want to bother people who unintentionally provide an unsigned int argument to this. More... | |
template<> | |
Int | writtenDigits< long int > (const long int &) |
We do not want to bother people who unintentionally provide a long int argument to this. More... | |
template<> | |
Int | writtenDigits< unsigned long int > (const unsigned long int &) |
We do not want to bother people who unintentionally provide an unsigned long int argument to this. More... | |
template<> | |
Int | writtenDigits< DataValue > (const DataValue &) |
DataValue will be printed like double. More... | |
template<> | |
Int | writtenDigits< long double > (const long double &) |
Number of digits commonly used for writing a long double (a.k.a. precision). ... More... | |
Variables | |
struct OpenMS::PrecursorMassComparator | PrecursorMZLess |
struct OpenMS::SpectralMatchScoreComparator | SpectralMatchScoreGreater |
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... | |
StreamHandler | STREAM_HANDLER |
Global StreamHandler instance. More... | |
const double | BinaryDataEncoder_default_numpressErrorTolerance = .0001 |
Main OpenMS namespace.
In this namespace all the main OpenMS classes are located.
typedef boost::shared_ptr< const Eigen::MatrixXd > EigenMatrixXdPtr |
Matrix utility functions.
typedef std::multimap<int, MSPeak> elution_peak |
typedef boost::shared_ptr< Eigen::MatrixXd > MutableEigenMatrixXdPtr |
typedef std::vector<elution_peak> MZ_series |
typedef std::vector<elution_peak>::iterator MZ_series_ITERATOR |
typedef std::pair<String, MzTabString> MzTabOptionalColumnEntry |
typedef std::vector<MzTabPeptideSectionRow> MzTabPeptideSectionRows |
typedef std::vector<MzTabProteinSectionRow> MzTabProteinSectionRows |
typedef std::vector<MzTabPSMSectionRow> MzTabPSMSectionRows |
typedef std::vector<MzTabSmallMoleculeSectionRow> MzTabSmallMoleculeSectionRows |
typedef std::multimap<int, MSPeak>::iterator SIGNAL_iterator |
typedef Map<String, Internal::ToolDescription> ToolListType |
Updates an INI.
map each old TOPP/UTIL to its new Name
enum ASCII |
enum Newline |
|
inline |
Convenience function for the BinaryComposeFunctionAdapter
adapter.
bool OpenMS::compareBinaryTreeNode | ( | const BinaryTreeNode & | x, |
const BinaryTreeNode & | y | ||
) |
returns the value of (x.distance < y.distance) for use with sort
|
static |
References Matrix< Value >::cols(), and Matrix< Value >::rows().
bool OpenMS::enclosesBoundingBox | ( | const Feature & | f, |
typename MSExperiment< InputPeakType >::CoordinateType | rt, | ||
typename MSExperiment< InputPeakType >::CoordinateType | mz | ||
) |
References Feature::getConvexHulls().
|
inline |
Endianizes a 32 bit type from big endian to little endian and vice versa.
Referenced by Base64::decodeCompressed_(), Base64::decodeIntegersCompressed_(), Base64::encode(), and Base64::encodeIntegers().
|
inline |
Endianizes a 64 bit type from big endian to little endian and vice versa.
Referenced by Base64::decodeCompressed_(), Base64::decodeIntegersCompressed_(), Base64::encode(), and Base64::encodeIntegers().
void OpenMS::FunctionChromatogramNOP | ( | MSChromatogram< ChromatogramPeak > & | ) |
Empty (NOP) function.
Referenced by MSDataTransformingConsumer::MSDataTransformingConsumer().
void OpenMS::FunctionSpectrumNOP | ( | MSSpectrum< Peak1D > & | ) |
Empty (NOP) function.
Referenced by MSDataTransformingConsumer::MSDataTransformingConsumer().
std::size_t OpenMS::hash_value | ( | const DPosition< N, T > & | b | ) |
Hash value for OpenMS::DPosition.
References DPosition< D, TCoordinateType >::begin(), and DPosition< D, TCoordinateType >::end().
bool OpenMS::intensityAscendingComparator | ( | const PeakType & | a, |
const PeakType & | b | ||
) |
References Peak2D::getIntensity().
bool OpenMS::intensityComparator | ( | const PeakType & | a, |
const PeakType & | b | ||
) |
References Peak2D::getIntensity().
bool OpenMS::intensityPointerComparator | ( | PeakType * | a, |
PeakType * | b | ||
) |
References Peak2D::getIntensity().
LexicographicComparator< Cmp1, Cmp2 > lexicographicComparator | ( | Cmp1 const & | cmp1, |
Cmp2 const & | cmp2 | ||
) |
Make-function to create a LexicographicComparator from two other comparators without the need to specify the template arguments.
The usage is similar to pointerComparator() or reverseComparator(), which see.
References Matrix< Value >::rows().
DPosition<D, TCoordinateType> OpenMS::operator* | ( | DPosition< D, TCoordinateType > | position, |
typename DPosition< D, TCoordinateType >::CoordinateType | scalar | ||
) |
Scalar multiplication (a bit inefficient)
DPosition<D, TCoordinateType> OpenMS::operator* | ( | typename DPosition< D, TCoordinateType >::CoordinateType | scalar, |
DPosition< D, TCoordinateType > | position | ||
) |
Scalar multiplication (a bit inefficient)
DPosition<D, TCoordinateType> OpenMS::operator/ | ( | DPosition< D, TCoordinateType > | position, |
typename DPosition< D, TCoordinateType >::CoordinateType | scalar | ||
) |
Scalar multiplication (a bit inefficient)
|
inline |
Output stream operator for std::vectors.
os | The target stream. |
v | The vector to write to stream. |
References writtenDigits().
|
inline |
Operator for appending entries with less code.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const AnnotationStatistics & | ann | ||
) |
Print content of an AnnotationStatistics object to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | out, |
RawData & | data | ||
) |
SUPERHIRN_DLLAPI std::ostream& OpenMS::operator<< | ( | std::ostream & | , |
Deisotoper & | |||
) |
|
inline |
Output operator for a PrecisionWrapper. Specializations are defined for float, double, long double.
References PrecisionWrapper< FloatingPointType >::ref_, and writtenDigits().
std::ostream& OpenMS::operator<< | ( | std::ostream & | , |
CentroidData & | |||
) |
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const ExperimentalSettings & | exp | ||
) |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const ChargePair & | cons | ||
) |
Print the contents of a ChargePair to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | , |
CentroidPeak & | |||
) |
std::ostream& OpenMS::operator<< | ( | std::ostream & | , |
DeconvPeak & | |||
) |
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const ItraqQuantifier::ItraqQuantifierStats & | stats | ||
) |
std::ostream& OpenMS::operator<< | ( | std::ostream & | , |
const Element & | |||
) |
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
StreamHandler const & | stream_handler | ||
) |
Overload for the insertion operator (operator<<) to have a formatted output of the StreamHandler.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const ChromatogramSettings & | spec | ||
) |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const SpectrumSettings & | spec | ||
) |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const ControlledVocabulary & | cv | ||
) |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
LogConfigHandler const & | lch | ||
) |
Overload for the insertion operator (operator<<) to have a formatted output of the LogConfigHandler.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const FeatureHandle & | cons | ||
) |
Print the contents of a FeatureHandle to a stream.
std::ostream & operator<< | ( | std::ostream & | os, |
const DBoundingBox< D > & | bounding_box | ||
) |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const AccurateMassSearchResult & | amsr | ||
) |
Referenced by SVOutStream::writeValueOrNan().
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const EmpiricalFormula & | formula | ||
) |
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const Peak1D & | point | ||
) |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const ChromatogramPeak & | point | ||
) |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const FeatureMap & | map | ||
) |
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const DRange< D > & | area | ||
) |
Print the contents to a stream.
|
inline |
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const LayerData & | rhs | ||
) |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const ConsensusMap & | cons_map | ||
) |
Print the contents of a ConsensusMap to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const ConsensusFeature & | cons | ||
) |
Print the contents of a ConsensusFeature to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const Peak2D & | point | ||
) |
Print the contents to a stream.
std::ostream & operator<< | ( | std::ostream & | os, |
const Matrix< Value > & | matrix | ||
) |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const DPosition< D, TCoordinateType > & | pos | ||
) |
Print the contents to a stream.
References precisionWrapper().
std::ostream & operator<< | ( | std::ostream & | os, |
const DistanceMatrix< Value > & | matrix | ||
) |
Print the contents to a stream.
References writtenDigits< double >().
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const AASequence & | peptide | ||
) |
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const Param & | param | ||
) |
Output of Param to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const MSChromatogram< PeakT > & | chrom | ||
) |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const Residue & | residue | ||
) |
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const MSSpectrum< PeakT > & | spec | ||
) |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, |
const MSExperiment< PeakT, ChromatogramPeakT > & | exp | ||
) |
Print the contents to a stream.
std::istream& OpenMS::operator>> | ( | std::istream & | os, |
const AASequence & | peptide | ||
) |
PointerComparator< Cmp > pointerComparator | ( | Cmp const & | cmp | ) |
Make-function to create a PointerComparator from another comparator without the need to specify the template arguments.
For example,
int i = 88, j = 99; if ( pointerComparator(std::less<int>())(&i,&j) ) { // yes, 88 < 99. }
Referenced by ConstRefVector< ContainerT >::sortByComparator(), ConstRefVector< ContainerT >::sortByIntensity(), and ConstRefVector< ContainerT >::sortByPosition().
bool OpenMS::positionComparator | ( | const PeakType & | a, |
const PeakType & | b | ||
) |
References Peak2D::getMZ().
|
inline |
Wrapper function that sets the appropriate precision for output temporarily. The original precision is restored afterwards so that no side effects remain. This is a "make"-function that deduces the typename FloatingPointType from its argument and returns a PrecisionWrapper<FloatingPointType>.
Example:
Result:
Note: Unfortunately we cannot return a const& - this will change when rvalue references become part of the new C++ standard. In the meantime, we need a copy constructor for PrecisionWrapper.
Referenced by operator<<(), DTA2DFile::store(), and DTA2DFile::storeTIC().
ReverseComparator< Cmp > reverseComparator | ( | Cmp const & | cmp | ) |
Make-function to create a ReverseComparator from another comparator without the need to specify the template arguments.
For example,
int i = 88, j = 99; if ( reverseComparator(std::less<int>())(j,i) ) { // yes, 99 > 88. }
Referenced by WindowMower::filterPeakSpectrumForTopNInJumpingWindow(), MSChromatogram< ChromatogramPeakType >::sortByIntensity(), MSSpectrum< RichPeak1D >::sortByIntensity(), and ConstRefVector< ContainerT >::sortByIntensity().
bool sort_peaks_by_intensity | ( | const PeakCandidate & | a, |
const PeakCandidate & | b | ||
) |
References PeakCandidate::peak_apex_intensity.
Referenced by PeakPickerIterative::pick().
std::string OpenMS::typeAsString | ( | const Type & | = Type() | ) |
Returns the Type
as as std::string.
Have you ever spent a long time trying to find out what a typedef
actually "points" to? Then this can help.
typeAsString is implemented as a function template. There are two ways to us this:
The typeAsString< SomeType >() version seems to go a bit deeper. Sometimes the results depend on how the typeAsString() is instantiated in the first place. The argument given to the function is never used, it only serves to infer the type. You can even supply function pointers, etc.
Example (Tutorial_typeAsString.cpp):
|
inline |
convenience function for the UnaryComposeFunctionAdapter
adapter
|
inline |
Number of digits commonly used for writing a floating point type (a.k.a. precision). Specializations are defined for float, double, long double.
The general template definition will return the default precision of 6 according to 27.4.4.1 basic_iosconstructors (C++ Standard).
Referenced by OpenMS::StringConversions::floatToString(), MSDataWritingConsumer::MSDataWritingConsumer(), StringUtils::numberLength(), and operator<<().
|
inline |
DataValue will be printed like double.
|
inline |
Number of digits commonly used for writing a double
(a.k.a. precision).
Referenced by InternalCalibration::calibrateMapSpectrumwise(), operator<<(), and DTAFile::store().
|
inline |
Number of digits commonly used for writing a float
(a.k.a. precision).
|
inline |
We do not want to bother people who unintentionally provide an int argument to this.
|
inline |
Number of digits commonly used for writing a long
double
(a.k.a. precision). ...
Note: On Microsoft platforms, the I/O system seems to treat long
double
just like double
. We observed that std::numeric_limits<long double>::digits10 == 18
with GCC 3.4 on MinGW, but this promise is not kept by the Microsoft I/O system libraries. Therefore we use the value of digits10
for double
also for long
double
. See http://msdn.microsoft.com/ + search: "long double".
|
inline |
We do not want to bother people who unintentionally provide a long int argument to this.
|
inline |
We do not want to bother people who unintentionally provide an unsigned int argument to this.
|
inline |
We do not want to bother people who unintentionally provide an unsigned long int argument to this.
const double BinaryDataEncoder_default_numpressErrorTolerance = .0001 |
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.
Referenced by main().
Logger::LogStream Log_error |
Global static instance of a LogStream to capture messages classified as errors. By default it is bound to cerr.
Referenced by main().
Logger::LogStream Log_fatal |
Global static instance of a LogStream to capture messages classified as fatal errors. By default it is bound to cerr.
Logger::LogStream Log_info |
Global static instance of a LogStream to capture messages classified as information. By default it is bound to cout.
Logger::LogStream Log_warn |
Global static instance of a LogStream to capture messages classified as warnings. By default it is bound to cout.
struct OpenMS::PrecursorMassComparator PrecursorMZLess |
struct OpenMS::SpectralMatchScoreComparator SpectralMatchScoreGreater |
StreamHandler STREAM_HANDLER |
Global StreamHandler instance.
OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 16:18:43 using doxygen 1.8.5 |