AASequence | Representation of a peptide/protein sequence |
Acquisition | Information about one raw data spectrum that was combined with several other raw data spectra |
AcquisitionInfo | Description of the combination of raw data to a single spectrum |
AcquisitionInfoVisualizer | Class that displays all meta information for AcquisitionInfo objects |
AcquisitionVisualizer | Class that displays all meta information for Acquisition objects |
ANDIFile | File adapter for ANDI/MS files |
ANDIHandler | Read-only File handler for ANDIFile (Version 1.0) |
AreaIterator | Forward iterator for an area of peaks in an experiment |
AsymmetricStatistics | Internal class for asymmetric distributions |
AveragePosition | Maintain an average position by summing up positions with weights |
AxisTickCalculator | Calculates ticks for a given value range |
AxisWidget | Widget that represents an axis of a graph |
Base | Exception base class |
Base64 | Class to encode and decode Base64 |
BaseAlignment | Base alignment class |
BaseMapMatcher | The base class of the map matching algorithm |
BaseModel | Abstract base class for all D-dimensional models |
BasePairFinder | The base class of all element pair finding algorithms |
BasePairwiseMapMatcher | The base class of all pairwise point matching algorithms |
BaseSuperimposer | The base class of all superimposer algorithms |
BaseVisualizer | A base class for all visualizer classes |
BasicStatistics | Calculates some basic statistical parameters of a distribution: sum, mean, variance, and provides the normal approximation |
BernNorm | BernNorm scales the peaks by ranking them and then scaling them according to rank |
BiGaussFitter1D | Bigaussian distribution fitter (1-dim.) approximated using linear interpolation |
BiGaussModel | Bigaussian distribution approximated using linear interpolation |
BigString | Concatenates Proteins given as FASTAEntry to one big string separated by a unique character (by default $) |
BilinearInterpolation | Provides access to bilinearly interpolated values (and derivatives) from discrete data points. Values beyond the given range of data points are implicitly taken as zero |
binary_function | |
BinnedRep | Binned Representation of a PeakSpectrum (stick spectrum) |
BinnedRepCompareFunctor | Base class for compare functors of binned spectra which report the spectra similarity |
BinnedRepMutualInformation | Mutual Information content which is calculated from binned stick spectra |
BinnedRepSharedPeakCount | Calculates the Shared Peak Count for two binned spectra |
BinnedRepSpectrumContrastAngle | Calculates the spectral contrast angle between two spectra in bin representation |
BinnedRepSumAgreeingIntensities | Calculates the sum of agreeing intensities for two spectra in binned representation |
BufferOverflow | Buffer overflow exception |
CGAL::Cartesian | |
CGAL::Point_2 | |
ColorSelector | A widget for selecting a color |
ComplementFilter | Total intensity of peak pairs that could result from complementing fragments of charge state 1 |
ComplementMarker | ComplementMarker marks peak pairs which could represent y - b ion pairs |
ConsensusFeature | A 2-dimensional consensus feature |
ConsensusID | Calculates a consensus ID from several ID runs |
ConsensusMap | A container for consensus elements |
ConsensusPeak | A 2-dimensional consensus peak |
ConsensusXMLFile | This class provides Input functionality for ConsensusMaps and Output functionality for StarAlignments |
ConsensusXMLHandler | XML Handler for a consensusXML |
ContactPerson | Contact person information |
ContactPersonVisualizer | Class that displays all meta information for ContactPerson objects |
ContinuousWaveletTransform | This class is the base class of the continuous wavelet transformation |
ContinuousWaveletTransformNumIntegration | This class computes the continuous wavelet transformation using a marr wavelet |
ConversionError | Invalid conversion exception |
ConvexHull2D | A 2-dimensional convex hull representation (conterclockwise) |
DataFilterDialog | Dialog for creating and changing a DataFilter |
DataFilters | DataFilter array providing some convenience functions |
DataFilters::DataFilter | Representation of a peak/feature filter combining FilterType, FilterOperation and a value |
DataTable | A class that provides some functions for displaying data |
DataValue | Class to hold a string or numeric value (UInt, Int, Real, DoubleReal) |
Date | Date Class |
DateTime | DateTime Class |
DBAdapter | A class for accessing and storing data in a SQL database |
DBConnection | A class for connecting to a SQL database |
DBConnection::InvalidQuery | Exception in case of an invalid Query |
DBConnection::NotConnected | Exception in case of trying to execute a query without having established a database connection |
DBoundingBox | A D-dimensional bounding box |
DBSpectrumSelectorDialog | Dialog that allow selecting a spectrum from a DB |
DefaultParamHandler | A base class for all classes handling default parameters |
DelaunayPairFinder | This class implements an element pair finding algorithm |
DelaunayPairFinder::GeometricTraits | |
DelaunayPairFinder::GeometricTraits::Construct_center_2 | |
DelaunayPairFinder::Point | |
Digestion | Meta information about digestion of a sample |
DigestionVisualizer | Class that displays all meta information of digestion objects |
DIntervalBase | A base class for D-dimensional interval |
DivisionByZero | Division by zero error exception |
DPeak | A D-dimensional peak |
DPeakArray | Peak container implemented as an array |
DPeakConstReferenceArray | This container holds pointer to the elements of another container |
DPeakConstReferenceArray::DPeakConstReferenceArrayConstIterator | ConstIterator for the DPeakConstReferenceArray |
DPeakConstReferenceArray::DPeakConstReferenceArrayIterator | Mutable iterator for the DPeakConstReferenceArray |
DPosition | Representation of a coordinate in D-dimensional space |
DRange | A D-dimensional half-open interval |
DRawDataPoint | D-dimensional raw data point |
DRawDataPoint::IntensityLess | Compare by getIntensity() |
DRawDataPoint::NthPositionLess | Comparator for the i-th coordinate of the position |
DRawDataPoint::PositionLess | Comparator for the position |
DSpectrum | Representation of a D-dimensional spectrum |
DTA2DFile | DTA2D File adapter |
DTAFile | File adapter for DTA files |
EdwardsLippertIterator | Finds all Peptide Candidates with given masses and given fasta file |
EdwardsLippertIteratorTryptic | EdwardsLippertIterator that only retrieves tryptic seqences |
Element | Representation of an element |
ElementDB | Stores elements |
ElementNotFound | Element could not be found exception |
ElementPair | A pair of element in two different maps |
EmgFitter1D | Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization |
EmgFitter1D::Data | Helper struct (contains the size of an area and a raw data container) |
EmgModel | Exponentially modified gaussian distribution model for elution profiles |
EmpiricalFormula | Representation of an empirical formula |
EnhancedTabBar | Tab bar which is aware of double clicking and has a context menu to close it |
EnzymaticDigestion | Class for the enzymatic digestion of proteins |
ExperimentalSettings | Description of the experimental settings |
ExperimentalSettingsVisualizer | Class that displays all meta information for ExperimentalSettings objects |
ExtendedIsotopeFitter1D | Extended isotope distribution fitter (1-dim.) approximated using linear interpolation |
ExtendedIsotopeModel | Extended isotope distribution approximated using linear interpolation |
ExternalAllocator | External allocator used in MSExperiment's std::vector to handle virtual memory, mapped to a swap file |
ExternalAllocator::rebind | Rebind allocator to type U |
ExternalAllocatorUnique | Unique settings for an ExternalAllocator |
Factory | Returns FactoryProduct* based on the name of the desired concrete FactoryProduct |
FactoryBase | Base class for Factory<T> |
FactoryProduct | Base class for all classes T whose objects need to be constructed by Factory<T> |
FASTAFile | This class serves for reading in FASTA files |
FastaIterator | Iterator over FASTA file |
FastaIteratorIntern | Iterator for a FASTA file |
FeaFiModule | Implements a module of the FeatureFinder algorithm |
Feature | A feature |
Feature::OverallQualityLess | Compare by getOverallQuality() |
FeatureDecharger | An algorithm to decharge features (i.e. as found by FeatureFinder) |
FeatureFinder | The main feature finder class |
FeatureFinderAlgorithm | Abstract base class for FeatureFinder algorithms |
FeatureFinderAlgorithmPicked | FeatureFinderAlgorithm for picked peaks |
FeatureFinderAlgorithmPicked::IsotopePattern | Helper structure for a found isotope pattern used in FeatureFinderAlgorithmPicked |
FeatureFinderAlgorithmPicked::MassTrace | Helper struct for mass traces used in FeatureFinderAlgorithmPicked |
FeatureFinderAlgorithmPicked::MassTraces | Helper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked |
FeatureFinderAlgorithmPicked::PeakInfo | Helper structure that stores precalculated information for each peak used in FeatureFinderAlgorithmPicked |
FeatureFinderAlgorithmPicked::Seed | Helper structure for seeds used in FeatureFinderAlgorithmPicked |
FeatureFinderAlgorithmPicked::TheoreticalIsotopePattern | Helper structure for a theoretical isotope pattern used in FeatureFinderAlgorithmPicked |
FeatureFinderAlgorithmSimple | FeatureFinderAlgorithm implementation using the Simple* modules |
FeatureFinderAlgorithmSimplest | FeatureFinderAlgorithm implementation using the Simple* modules |
FeatureFinderDefs | The purpose of this struct is to provide definitions of classes and typedefs which are used throughout all FeatureFinder classes |
FeatureFinderDefs::NoSuccessor | Exception that is thrown if a method a invalid IndexPair is given |
FeatureFinderDefs::UnableToFit | Exception used if a ModelFitter cannot fit a model i.e. data set with standard deviation of zero |
FeatureMap | A container for (composite) features |
FeaturePairsHandler | XML Handler for a DFeaturePairVector |
FeaturePairsXMLFile | This class provides Input/Output functionality for the class DFeaturePairVector |
FeatureXMLFile | This class provides Input/Output functionality for feature maps |
FeatureXMLHandler | XML Handler for a FeatureMap |
File | Basic file handling operations |
FileEmpty | File is empty |
FileHandler | Facilitates file handling by file type recognition |
FileNotFound | File not found exception |
FileNotReadable | File not readable exception |
FilterFunctor | A FilterFunctor extracts some spectrum characteristics for quality assessment |
Fitter1D | Abstract base class for all 1D-dimensional model fitter |
FuzzyStringComparator | Fuzzy comparison of strings, tolerates numeric differences |
FuzzyStringComparator::AbortComparison | Internal exeption class |
GaussFilter | This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform raw data |
GaussFitter1D | Gaussian distribution fitter (1-dim.) approximated using linear interpolation |
GaussModel | Normal distribution approximated using linear interpolation |
GlobalExceptionHandler | OpenMS global exception handler |
GoodDiffFilter | GoodDiffFilter counts the number ob peak pairs whose m/z difference can be explained by a amino acid loss |
Gradient | Representation of a HPLC gradient |
GradientVisualizer | GradientVisualizer is a visualizer class for objects of type gradient |
Grid | This class represents a D-dimensional grid over a LC/MS map |
GridCell | 2-dimensional grid cell over a map |
GridFile | Provides Input/Output functionality for instances of class DGrid |
GridHandler | XML Handler for a vector of grid cells including their transformations |
Group | A group of IndexTuple |
HashFunction | General Hash Function Template |
HashMap | Generic Hash Map Class |
HashMap::ConstIterator | HashMap const_iterator class |
HashMap::IllegalKey | HashMap illegal key exception |
HashMap::Iterator | HashMap iterator class |
HashMap::Node | HashMap node (internal use only) |
HasScanMode | Predicate that determines if a spectrum has a certain scan mode |
HierarchicalClustering | Complete or single linkage clustering based on DPosition<> |
Histogram | Representation of a histogram |
HistogramDialog | Dialog that show a HistogramWidget |
HistogramWidget | Widget which can visualize a histogram |
HPLC | Representation of a HPLC experiment |
HPLCVisualizer | Class that displays all meta information for HPLC objects |
IDFeatureMapper | Annotates a FeatureMap instance with PeptideIdentification instances |
IDFilter | Used to filter identifications by different criteria |
IDSpectrumMapper | Annotate a MSExperiment instances with ProteinIdentification instances |
IdXMLFile | Used to load and store IdXML files |
IllegalArgument | Some Argument contains illegal values |
IllegalPosition | Invalid 3-dimensional position exception |
IllegalSelfOperation | Illegal self operation exception |
IllegalTreeOperation | Illegal tree operation exception |
IncompatibleIterators | Incompatible iterator exception |
IndexOverflow | Int overflow exception |
IndexTuple | This class stores some needful information of an element |
IndexTuple::IndexLess | Compare by getOverallQuality() |
IndexUnderflow | Int underflow exception |
INIFileEditorWindow | Shows the ParamEditor widget in a QMainWindow with a toolbar |
InIntensityRange | Predicate that determines if a peak lies inside/outside a specific intensity range |
InMSLevelRange | Predicate that determines if a spectrum lies inside/outside a specific MS level set |
InMzRange | Predicate that determines if a peak lies inside/outside a specific m/z range |
InRTRange | Predicate that determines if a spectrum lies inside/outside a specific retention time range |
InspectInfile | Inspect input file adapter |
InspectOutfile | Representation of an Inspect outfile |
Instrument | Description of a MS instrument |
InstrumentSettings | Description of the settings a MS Instrument was run with |
InstrumentSettingsVisualizer | Class that displays all meta information for InstrumentSettings objects |
InstrumentVisualizer | Class that displays all meta information for HPLC objects |
IntensityBalanceFilter | IntensityBalanceFilter divides the m/z-range into ten regions and sums the intensity in these regions |
IntensityIterator | Intensity iterator for a FeatureFinderDefs::IndexSet |
IntensityLess | Comparator that allows to compare the indices of two peaks by their intensity |
InternalCalibration | A simple calibration method using linear interpolation of given reference masses |
InterpolationModel | Abstract class for 1D-models that are approximated using linear interpolation |
InvalidIterator | Invalid iterator exception |
InvalidParameter | Exception indicating that an invalid parameter was handed over to an algorithm |
InvalidRange | Invalid range exception |
InvalidSize | Invalid UInt exception |
InvalidValue | Invalid value exception |
IonDetector | Description of a ion detector ( part of a MS Instrument ) |
IonDetectorVisualizer | Class that displays all meta information for IonDetector objects |
IonSource | Description of a ion source ( Part of a MS Instrument ) |
IonSourceVisualizer | Class that displays all meta information for IonSource objects |
IsEmptySpectrum | Predicate that determines if a spectrum is empty |
IsotopeCluster | Stores information about an isotopic cluster (i.e. potential peptide charge variants) |
IsotopeCluster::ChargedIndexSet | Index set with associated charge estimate |
IsotopeDiffFilter | IsotopeDiffFilter returns total intensity of peak pairs that could result from isotope peaks |
IsotopeDistribution | Isotope distribution class |
IsotopeFitter1D | Isotope distribution fitter (1-dim.) approximated using linear interpolation |
IsotopeMarker | IsotopeMarker marks peak pairs which could represent an ion and its isotope |
IsotopeModel | Isotope distribution approximated using linear interpolation |
IsotopeWavelet | Implements the isotope wavelet function |
IsotopeWavelet::fi_ | Internal union for fast computation of the power function |
IsotopeWaveletTransform | A class implementing the isotope wavelet transform. If you just want to find features using the isotope wavelet, take a look at the IsotopeWaveletFF class. Usually, you only have to consider the class at hand if you plan to change the basic implementation of the transform |
IsotopeWaveletTransform::BoxElement_ | Internally used data structure |
iterator | |
LayerData | Struct that stores the data for one layer |
LayerStatisticsDialog | Dialog showing statistics about the data of the current layer |
LayerStatisticsDialog::MetaStatsValue_ | Struct representing the statistics about one meta information |
LevMarqFitter1D | Abstract class for 1D-model fitter using Levenberg-Marquardt algorithm for parameter optimization |
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 |
LibSVMEncoder | Serves for encoding sequences into feature vectors |
LinearInterpolation | Provides access to linearly interpolated values (and derivatives) from discrete data points. Values beyond the given range of data points are implicitly taken as zero |
LinearMapping | This class represents a linear coordinate transformation |
LinearRegression | This class offers functions to perform least-squares fits to a straight line model, |
LinearResampler | Linear Resampling of raw data |
LmaGaussFitter1D | Gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization |
LmaGaussFitter1D::Data | Helper struct (contains the size of an area and a raw data container) |
LmaGaussModel | Normal distribution model for elution profiles |
LmaIsotopeFitter1D | Isotope distribution fitter (1-dim.) approximated using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization |
LmaIsotopeFitter1D::Data | Helper struct (contains the size of an area, a raw data container, the relative abundance of i-th isotopic peak and the distance between consecutive isotopic peaks) |
LmaIsotopeModel | Isotope distribution approximated using linear interpolation |
MapDewarper | This class applies a transformation as computed by class BaseMapMatcher to a set of features |
MapMatcherRegression | Map matching using linear regression |
MarkerMower | MarkerMower uses PeakMarker to find peaks, those that are not marked get removed |
MascotInfile | Mascot input file adapter |
MascotOutfile | Representation of a Mascot output file |
MascotXMLFile | Used to load MascotXML files |
MascotXMLHandler | Handler that is used for parsing MascotXML data |
MassAnalyzer | Descripton of a mass analyzer ( Part of a MS Instrument ) |
MassAnalyzerVisualizer | Class that displays all meta information for MassAnalyzer objects |
Matrix | A two-dimensional matrix. Similar to std::vector, but uses a binary operator(,) for element access |
MaxLikeliFitter1D | Abstract base class for all 1D-model fitters using maximum likelihood optimization |
MemoryMap | Cross platform memory mapping |
MetaInfo | A Type-Name-Value tuple class |
MetaInfoDescription | Description of the meta info added to each peak |
MetaInfoDescriptionVisualizer | Class that displays all meta information for MetaInfoDescription objects |
MetaInfoInterface | Interface for classes that can store arbitrary meta information (Type-Name-Value tupels) |
MetaInfoRegistry | Registry which assigns unique integer indices to strings |
MetaInfoVisualizer | MetaInfoVisualizer is a visualizer class for all classes that use one MetaInfo object as member |
MissingInformation | Not all required information provided |
ModelDescription | Stores the name and parameters of a model |
ModelFitter | Tests a group of data points in an LC-MS map for goodness-of-fit with a 2D averagine model |
Modification | Meta information about chemical modification of a sample |
ModificationVisualizer | Class that displays all meta information of modification objects |
ModifierRep | Implements modification for suffix arrays |
MorphFilter | This class is the baseclass of morphological filters |
MSExperiment | Representation of a mass spectrometry experiment |
MSMetaDataExplorer | A meta data visualization widget |
MSSpectrum | The representation of a 1D spectrum |
MSSpectrum::RTLess | Comparator for the retention time |
MultiGradient | A gradient of multiple colors and arbitrary distances between colors |
MultiGradientSelector | A widget witch allows constructing gradients of multiple colors |
MzDataExpSettHandler | XML handler for experimental settings of MzDataFile |
MzDataFile | File adapter for MzData files |
MzDataHandler | XML handler for MzDataFile |
MzIterator | M/z iterator for a FeatureFinderDefs::IndexSet |
MzXMLFile | File adapter for MzXML 2.1 files |
MzXMLHandler | XML handlers for MzXMLFile |
NeutralLossDiffFilter | NeutralLossDiffFilter returns the total intensity ob peak pairs whose m/z difference can be explained by a neutral loss |
NeutralLossMarker | NeutralLossMarker marks peak pairs which could represent an ion an its neutral loss (water, ammonia) |
NLargest | NLargest removes all but the n largest peaks |
Normalizer | Normalizer normalizes the peak intensities |
NotImplemented | Not implemented exception |
NullPointer | Null pointer argument is invalid exception |
OMSSAXMLFile | Used to load OMSSAXML files |
OMSSAXMLHandler | Handler that is used for parsing OMSSAXML data |
OpenDialog | Open spectrum dialog |
OptimizePeakDeconvolution | This class provides the deconvolution of peak regions using non-linear optimization |
OptimizePick | This class provides the non-linear optimization of the peak paramters |
OutOfGrid | Out of grid exception |
OutOfMemory | Out of memory exception |
OutOfRange | Out of range exception |
pair | |
PairMatcher | The PairMatcher allows the matching of labeled features (features with a fixed distance) |
PairMatcher::Comparator | Compare to pairs by comparing their qualities |
Param | Management and storage of parameters / INI files |
Param::ParamEntry | Parameter entry used to store the actual information inside of a Param entry |
Param::ParamIterator | Forward const iterator for the Param class |
Param::ParamIterator::TraceInfo | Struct that captures information on entered / left nodes for ParamIterator |
Param::ParamNode | Node inside a Param object which is used to build the internal tree |
ParamEditor | A GUI for editing or viewing a Param object |
ParamEditorDelegate | Internal delegate class for QTreeWidget |
ParamTree | QTreeWidget that emits a signal whenever a new row is selected |
ParamXMLHandler | XML Handler for Param files |
ParentFilter | Parentfilter returns parent-ion charge and mass |
ParentPeakMower | ParentPeakMower gets rid of high peaks that could stem from unfragmented precursor ions |
ParseError | Parse Error exception |
Peak1D | A 1-dimensional peak |
Peak2D | A 2-dimensional peak |
PeakDensityFilter | PeakDensityfilter calculates peak density |
PeakFileOptions | Options for loading files containing peak data |
PeakIcon | Class for drawing icons with a QPainter |
PeakMarker | PeakMarker marks peaks that seem to fulfill some criterion |
PeakPicker | This class is the base class for every peak picker |
PeakPickerCWT | This class implements a peak picking algorithm using wavelet techniques (as described by Lange et al. (2006) Proc. PSB-06) |
PeakPickerCWT::PeakArea_ | Class for the internal peak representation |
PeakShape | This class is a internal representation (used by the PeakPickerCWT) of a peak shape |
PeakShape::PositionLess | Comparator for the width |
PeakShapeType | Peak shape type (asymmetric lorentzian or asymmetric hyperbolic secans squared) |
PeakSpectrumCompareFunctor | Base class for compare functors of spectra; compare functors returns a similiarity value of two spectra |
PeakTypeEstimator | Estimates if the data of a spectrum is raw data or peak data |
PenaltyFactors | Class for the penalty factors used during the optimization |
PenaltyFactorsIntensity | Class for the penalty factors used during the optimization |
PepIterator | Abstract base class for different peptide iterators |
PepNovoInfile | PepNovo input file adapter |
PepNovoOutfile | Representation of a PepNovo output file |
PeptideHit | Representation of a peptide hit |
PeptideHit::ScoreLess | Lesser predicate for scores of hits |
PeptideHit::ScoreMore | Greater predicate for scores of hits |
PeptideHitVisualizer | Class that displays all meta information for PeptideHit objects |
PeptideIdentification | Represents the peptide hits for a spectrum |
PeptideIdentificationVisualizer | Class that displays all meta information for PeptideIdentification objects |
PersistentObject | Base class for all persistent objects |
PickedPeak1D | 1-dimensional picked peak |
PickedPeak1D::WidthLess | Comparator for the width |
PILISScoring | This class actually implements the E-value based scoring of PILIS |
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 |
PoseClusteringAffineSuperimposer | Superimposer that uses a voting scheme to find a good affine transformation |
PoseClusteringPairwiseMapMatcher | This class represents a point matching algorithm |
PoseClusteringShiftSuperimposer | Superimposer that uses a voting scheme to find a good translation |
PoseClusteringShiftSuperimposer::Shift | Intensity bounding box |
Postcondition | Postcondition failed exception |
PreciseTime | Time class |
Precondition | Precondition failed exception |
Precursor | Precursor meta information |
PrecursorPeak | Internal class used to store some information about precursor ions |
PrecursorVisualizer | Class that displays all meta information for Precursor objects |
PreprocessingFunctor | Base class for Spectrum preprocessing classes |
ProcessingMethod | Descripton of the applied preprocessing steps |
ProcessingMethodVisualizer | Class that displays all meta information for ProcessingMethod objects |
ProcessResource | OS based process restrictions |
ProductModel | Class for product models i.e. models with D independent dimensions |
ProgressLogger | Base class for all classes that want to report their progess |
ProteinHit | Representation of a protein hit |
ProteinHitVisualizer | Class that displays all meta information for ProteinHit objects |
ProteinIdentification | Representation of a peptide/protein ProteinIdentification |
ProteinIdentification::SearchParameters | Search parameters of the DB search |
ProteinIdentificationVisualizer | Class that displays all meta information for ProteinIdentification objects |
ProtonDistributionModel | A proton distribution model to calculate the proton distribution over charged peptides |
PTMXMLFile | Used to load and store PTMXML files |
PTMXMLHandler | Handler that is used for parsing PTMXML data |
QDate | |
QDateTime | |
QDialog | |
QGLWidget | |
QItemDelegate | |
QMainWindow | |
QTabBar | |
QTreeWidget | |
QWidget | |
RangeManager | Handles the managment of a position and intensity range |
RawDataPoint1D | 1-dimensional raw data point |
RawDataPoint1D::IntensityLess | Compare by getIntensity() |
RawDataPoint1D::PositionLess | Comparator for the position |
RawDataPoint2D | 2-dimensional raw data point |
RawDataPoint2D::IntensityLess | Compare by getIntensity() |
RawDataPoint2D::NthPositionLess | Comparator for the n-th coordinate of the position |
RawDataPoint2D::PositionLess | Comparator for the position |
RequiredParameterNotGiven | A required parameter was not given |
Residue | Representation of a residue |
ResidueDB | Residue data base which holds residues |
ResidueModification | Representation of a modification |
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 |
ROCCurve | ROCCurves show the tradeoff in sensitivity and specitivity for binary classifiers using different cutoff values |
ROCCurve::simsortdec | Predicate for sort() |
RtIterator | Retention time iterator for a FeatureFinderDefs::IndexSet |
Sample | Meta information about the sample |
SampleTreatment | Base class for sample treatments (Digestion, Modification, Tagging, ...) |
SampleVisualizer | Class that displays all meta information of sample objects |
SaveImageDialog | Dialog for saving an image |
SavitzkyGolayFilter | Computes the Savitzky-Golay filter coefficients using QR decomposition |
Scaler | Scaler scales the peak by ranking the peaks and assigning intensity according to rank |
SequestInfile | Sequest input file adapter |
SequestOutfile | Representation of a Sequest output file |
SignalToNoiseEstimator | This class represents the abstract base class of a signal to noise estimator |
SignalToNoiseEstimator::GaussianEstimate | Protected struct to store parameters my, sigma for a gaussian distribution |
SignalToNoiseEstimatorMeanIterative | Estimates the signal/noise (S/N) ratio of each data point in a scan based on an iterative scheme which discards high intensities |
SignalToNoiseEstimatorMedian | Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram based) |
SimpleExtender | Implements the extension phase of the FeatureFinder as described by Groepl et al. (2005) |
SimpleExtender::IndexWithPriority | A helper structure to sort indizes by their priority |
SimpleExtender::IndexWithPriority::PriorityLess | Compares two indizes by priority |
SimplePairFinder | This class implements a simple point pair finding algorithm |
SimpleSeeder | Simple seeding class that uses the strongest peak as next seed |
SingletonRegistry | Holds pointers to unique instance of a singleton factory |
SizeUnderflow | UInt underflow exception |
SmoothFilter | Base class for all noise filter implementations |
Software | Description of the software used for processing |
SoftwareVisualizer | Class that displays all meta information for Software objects |
SourceFile | Description of a file location, used to store the origin of (meta) data |
SourceFileVisualizer | Class that displays all meta information for SourceFile objects |
SparseVector | Binned sparse vector implementation, which does not contain zero-elements |
SparseVector::DoubleProxy | Class DoubleProxy allows the SparseVector to differentiate between writing and reading, so zeros can be ignored |
SparseVector::SparseVectorConstIterator | Const_iterator for SparseVector |
SparseVector::SparseVectorIterator | Iterator for SparseVector |
Spectrum1DCanvas | Canvas for visualization of one or several spectra |
Spectrum1DGoToDialog | Simple goto/set visible area dialog for exact placement of the viewing window |
Spectrum1DPrefDialog | Preferences dialog for Spectrum1DWidget |
Spectrum1DWidget | Widget for visualization of several spectra |
Spectrum2DCanvas | Canvas for 2D-visualization of peak map and feature map data |
Spectrum2DGoToDialog | GoTo dialog used to zoom to a m/z and retention time range or to a feature |
Spectrum2DPrefDialog | Preferences dialog for Spectrum2DWidget |
Spectrum2DWidget | Widget for 2D-visualization of peak map and feature map data |
Spectrum3DCanvas | Canvas for 3D-visualization of peak map data |
Spectrum3DOpenGLCanvas | OpenGL Canvas for 3D-visualization of map data |
Spectrum3DPrefDialog | Preferences dialog for Spectrum3DWidget |
Spectrum3DWidget | Widget for 3D-visualization of map data |
SpectrumAlignment | Aligns the peaks of two spectra |
SpectrumAlignmentScore | Similarity score via spectra alignment |
SpectrumCanvas | Base class for visualization canvas classes |
SpectrumCheapDPCorr | SpectrumCheapDPCorr calculates an optimal alignment on stick spectra |
SpectrumPrecursorComparator | SpectrumPrecursorComparator compares just the parent mass of two spectra |
SpectrumSettings | Representation of 1D spectrum settings |
SpectrumSettingsVisualizer | Class that displays all meta information for SpectrumSettings objects |
SpectrumWidget | Base class for spectrum widgets |
SqrtMower | Scales the intensity of peaks to the sqrt |
StarAlignment | A star alignment class |
StopWatch | StopWatch Class |
String | A more convenient string class |
StringList | String list |
StringManager | Helper class for XML parsing that handles the memory management for conversions of Xerces strings |
SuffixArray | Abstract class for suffix array |
SuffixArrayPeptideFinder | Wrapper for easy use of sufArray |
SuffixArraySeqan | Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum |
SuffixArrayTrypticCompressed | Class that implements a suffix array for a String. It can be used to find peptide Candidates for a MS spectrum |
SuffixArrayTrypticSeqan | Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum |
SVMWrapper | Serves as a wrapper for the libsvm |
Tagging | Meta information about tagging of a sample e.g. ICAT labeling |
TaggingVisualizer | Class that displays all meta information of tagging objects |
TextFile | This class provides some basic file handling methods and facilitates reading, writing and handling text files |
TheoreticalSpectrumGenerator | Generates theoretical spectra with various options |
ThresholdMower | ThresholdMower removes all peaks below a Threshold |
TICFilter | TICFilter calculates TIC |
TimeStamp | Time stamp class |
TOFCalibration | This class implements an external calibration for TOF data using external calibrant spectra |
TOFCalibration::UnableToCalibrate | Inner Classes for Exception handling |
ToolsDialog | Dialog for executing a TOPP Tool |
TopHatFilter | This class represents a Top Hat baseline filter |
TOPPBase | Base class for TOPP applications |
TOPPBase::ParameterInformation | Stuct that captures all information of a parameter |
TOPPViewBase | Main window of TOPPView tool |
TOPPViewPrefDialog | Preferences dialog for TOPPView |
TrypticIterator | Finds all tryptic Peptides with every missed cleavage |
TwoDOptimization | This class provides the two-dimensional optimization of the picked peak parameters |
TwoDOptimization::IndexLess | Comparator for the retention time |
Ui::DataFilterDialogTemplate | |
Ui::LayerStatisticsDialogTemplate | |
Ui::OpenDialogTemplate | |
Ui::ParamEditorTemplate | |
Ui::Spectrum1DGoToDialogTemplate | |
Ui::Spectrum1DPrefDialogTemplate | |
Ui::Spectrum2DGoToDialogTemplate | |
Ui::Spectrum2DPrefDialogTemplate | |
Ui::Spectrum3DPrefDialogTemplate | |
Ui::TOPPViewPrefDialogTemplate | |
UnableToCreateFile | Unable to create file exception |
unary_function | |
UniqueIdGenerator | Generator for unique IDs |
UnregisteredParameter | An unregistered parameter was accessed |
VersionInfo | Version information class |
WindowMower | WindowMower augments the highest peaks in a sliding window |
WrongParameterType | A parameter was accessed with the wrong type |
xercesc::DefaultHandler | |
xercesc::ErrorHandler | |
XMLFile | Base class for loading/storing XML files that have a handler derived from XMLHandler |
XMLHandler | Base class for XML handlers |
XMLHandler::EndParsingSoftly | Exception that is thrown if the parsing is ended by some event (e.g. if only a prefix of the XML file is needed) |
XMLValidator | Validator for XML files |
ZhangSimilarityScore | Similarity score of Zhang |