Uses of Class
org.expasy.mzjava.core.ms.Tolerance

Packages that use Tolerance

Package	Description
org.expasy.mzjava.core.ms
org.expasy.mzjava.core.ms.cluster
org.expasy.mzjava.core.ms.library
org.expasy.mzjava.core.ms.spectrasim
org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor
org.expasy.mzjava.proteomics.mol.modification.unimod
org.expasy.mzjava.proteomics.ms.consensus
org.expasy.mzjava.proteomics.ms.dbsearch
org.expasy.mzjava.proteomics.ms.fragment
org.expasy.mzjava.proteomics.ms.ident
org.expasy.mzjava.spark
org.expasy.mzjava.utils.function

Uses of Tolerance in org.expasy.mzjava.core.ms

Subclasses of Tolerance in org.expasy.mzjava.core.ms

Modifier and Type	Class and Description
class	AbsoluteTolerance Implementation of Tolerance where the + and - is an absolute value Scaling to get around issues with representing some numbers as doubles.
class	PpmTolerance

Uses of Tolerance in org.expasy.mzjava.core.ms.cluster

Methods in org.expasy.mzjava.core.ms.cluster with parameters of type Tolerance

Modifier and Type	Method and Description
static <A extends PeakAnnotation,S extends PeakList<A>> SimilarityGraph<S>	PeakListSimGraphFactory.build(List<S> spectra, SimFunc<A,A> simFunc, Tolerance precursorTolerance, double scoreThreshold) Build a new DenseSimilarityGraph
static <A extends PeakAnnotation,S extends PeakList<A>,G extends SimilarityGraph<S>> G	PeakListSimGraphFactory.build(List<S> spectra, SimilarityGraphBuilder<S,G> builder, SimFunc<A,A> simFunc, Tolerance precursorTolerance, double scoreThreshold) Build a new SimilarityGraph

Constructors in org.expasy.mzjava.core.ms.cluster with parameters of type Tolerance

Constructor and Description
SpectrumClusterEvaluator(Tolerance tolerance, SimFunc<A,A> simFunc, ClusterBuilder<S> clusterBuilder)

Uses of Tolerance in org.expasy.mzjava.core.ms.library

Constructors in org.expasy.mzjava.core.ms.library with parameters of type Tolerance

Constructor and Description
DefaultSpectrumLibrary(Tolerance tolerance, Collection<S> spectra)
DiscreteSpectrumLibrary(double[] mzOffsets, Tolerance tolerance, Collection<S> spectra)

Uses of Tolerance in org.expasy.mzjava.core.ms.spectrasim

Constructors in org.expasy.mzjava.core.ms.spectrasim with parameters of type Tolerance

Constructor and Description
AbstractSimFunc(Tolerance tolerance) Creates a AbstractSimFunc that uses a DefaultPeakListAligner and clear processor chain.
DpSimFunc(int minPeakCount, Tolerance tolerance) Construct a NdpSimFunc that uses the default peak list aligner.
McNdpSimFunc(int minPeakCount, Tolerance tolerance) Construct a McNdpSimFunc that uses the default peak list aligner.
NdpSimFunc(int minPeakCount, Tolerance tolerance) Construct a NdpSimFunc that uses the default peak list aligner.
PearsonsSimFunc(int minPeakCount, Tolerance tolerance) Construct a PearsonsSimFunc that uses the default peak list aligner.
PspcSimFunc(int minPeakCount, Tolerance tolerance)
SharedPeakSimFunc(int minPeakCount, Tolerance tolerance) Construct a SharedPeakSimFunc that uses the default peak list aligner.
WeightedPearsonsSimFunc(Tolerance tolerance)

Uses of Tolerance in org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor

Constructors in org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor with parameters of type Tolerance

Constructor and Description
DefaultPeakListAligner(Tolerance error)
DefaultPeakListAligner(Tolerance tolerance, PeakPairSink<X,Y> sink)

Uses of Tolerance in org.expasy.mzjava.proteomics.mol.modification.unimod

Methods in org.expasy.mzjava.proteomics.mol.modification.unimod with parameters of type Tolerance

Modifier and Type	Method and Description
static List<Modification>	UnimodManager.getModifications(double mass, Tolerance tolerance)
static List<Modification>	UnimodManager.getModifications(double mass, Tolerance tolerance, Set<String> aminoAcids)

Uses of Tolerance in org.expasy.mzjava.proteomics.ms.consensus

Fields in org.expasy.mzjava.proteomics.ms.consensus declared as Tolerance

Modifier and Type	Field and Description
protected Tolerance	PeptideConsensusSpectrum.Builder.fragmentTolerance

Methods in org.expasy.mzjava.proteomics.ms.consensus with parameters of type Tolerance

Modifier and Type	Method and Description
PeptideConsensusSpectrum.FilterParametersSetter	PeptideConsensusSpectrum.AnnotationParametersSetter.setAnnotationParameters(Tolerance fragmentTolerance, PeptideFragmenter fragmenter)
PeptideConsensusSpectrum.FilterParametersSetter	PeptideConsensusSpectrum.Builder.setAnnotationParameters(Tolerance fragmentTolerance, PeptideFragmenter fragmenter)

Constructors in org.expasy.mzjava.proteomics.ms.consensus with parameters of type Tolerance

Constructor and Description
PeptideFragmentAnnotator(Tolerance tolerance, PeptideSpectrum theoreticalSpectrum)

Uses of Tolerance in org.expasy.mzjava.proteomics.ms.dbsearch

Methods in org.expasy.mzjava.proteomics.ms.dbsearch with parameters of type Tolerance

Modifier and Type	Method and Description
Set<Digest>	DigestDB.getPeptides(double targetMass, Tolerance tolerance) Retrieves all the peptides that have a mass that is within tolerance of targetMass
Set<Digest>	ArrayDigestDB.getPeptides(double targetMass, Tolerance tolerance)
void	DigestDB.getPeptides(double targetMass, Tolerance tolerance, Collection<Digest> collection) Add all the peptides that have a mass that is within tolerance of targetMass to the peptides collection
void	ArrayDigestDB.getPeptides(double targetMass, Tolerance tolerance, Collection<Digest> collection)
PeptideSpectrumDB.DigestSourceDSL	PeptideSpectrumDB.StartDSL.setPrecursorTolerance(Tolerance precursorTolerance) Set the precursor tolerance

Constructors in org.expasy.mzjava.proteomics.ms.dbsearch with parameters of type Tolerance

Constructor and Description
PeptideSpectrumDB(Tolerance precursorTolerance, PeptideFragmenter fragmenter, DigestDB digestDB, PeptideSpectrumCache peptideSpectrumCache, PeakProcessorChain<PepFragAnnotation> processorChain) Construct a PeptideSpectrumDB backed by the fragmenter, proteinDB and peptideSpectrumCache.

Uses of Tolerance in org.expasy.mzjava.proteomics.ms.fragment

Constructors in org.expasy.mzjava.proteomics.ms.fragment with parameters of type Tolerance

Constructor and Description
PeptideFragmentAnnotator(PeptideFragmenter fragmenter, Tolerance tolerance)

Uses of Tolerance in org.expasy.mzjava.proteomics.ms.ident

Methods in org.expasy.mzjava.proteomics.ms.ident with parameters of type Tolerance

Modifier and Type	Method and Description
boolean	ModificationMatch.isWithinTolerance(Tolerance tolerance) Checks whether all modification candidates are within tolerance of the massShift.

Constructors in org.expasy.mzjava.proteomics.ms.ident with parameters of type Tolerance

Constructor and Description
ModListModMatchResolver(Tolerance tolerance, Collection<Modification> mods)
ModListModMatchResolver(Tolerance tolerance, Modification... mods)

Uses of Tolerance in org.expasy.mzjava.spark

Methods in org.expasy.mzjava.spark that return Tolerance

Modifier and Type	Method and Description
protected Tolerance	CachedPpmTolerance.build()
protected Tolerance	CachedAbsoluteTolerance.build()

Uses of Tolerance in org.expasy.mzjava.utils.function

Fields in org.expasy.mzjava.utils.function declared as Tolerance

Modifier and Type	Field and Description
protected Tolerance	ChargeMzSplitter.tolerance

Constructors in org.expasy.mzjava.utils.function with parameters of type Tolerance

Constructor and Description
ChargeMzSplitter(Tolerance tolerance)
PrecursorSplitter(Tolerance tolerance)