Package | Description |
---|---|
com.compomics.util.experiment |
This package contains MSExperiment main class and all sub-classes useful for the modeling of an experiment.
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com.compomics.util.experiment.biology |
This package contains experiement classes related to biological entities.
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com.compomics.util.experiment.biology.atoms | |
com.compomics.util.experiment.biology.ions |
This package contains experiment classes related to ions.
|
com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
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com.compomics.util.experiment.identification.advocates |
This package contains experiment classes related to modeling identifications.
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com.compomics.util.experiment.identification.identifications |
This package contains experiment classes related to MS/MS identifications.
|
com.compomics.util.experiment.identification.matches |
This package contains experiment classes releated to matches.
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com.compomics.util.experiment.io.identifications.idfilereaders |
This package contains experiment classes related to reading search engine files.
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com.compomics.util.experiment.io.massspectrometry | |
com.compomics.util.experiment.massspectrometry |
This package contains experiment classes related to spectra.
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com.compomics.util.experiment.quantification |
This package contains experiment classes related to quantification.
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com.compomics.util.experiment.quantification.matches | |
com.compomics.util.experiment.quantification.reporterion |
This package contains experiment classes related to reporter ions.
|
Modifier and Type | Class and Description |
---|---|
class |
MsExperiment
This class represents the experiment.
|
class |
ProteomicAnalysis
This class models a proteomic analysis.
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class |
SampleAnalysisSet
A sample measurement set is a set of replicates from a common sample.
|
Modifier and Type | Class and Description |
---|---|
class |
Atom
This interface contains information about atoms
|
class |
Enzyme
This class models an enzyme.
|
class |
Ion
This class models an ion.
|
class |
NeutralLoss
This class represents a neutral loss.
|
class |
Peptide
This class models a peptide.
|
class |
Protein
This class models a protein.
|
class |
PTM
This class models a post-translational modification.
|
class |
Sample
This class models a proteomic sample.
|
Modifier and Type | Class and Description |
---|---|
class |
Carbon
Carbon.
|
class |
Hydrogen
An hydrogen atom.
|
class |
Nitrogen
A nitrogen atom.
|
class |
Oxygen
An oxygen atom.
|
class |
Phosphorus
A phosphorus atom.
|
class |
Sulfur
A sulfur atom.
|
Modifier and Type | Class and Description |
---|---|
class |
ElementaryIon
This class represents an elementary ion.
|
class |
Glycon
This class will models a glycon fragment.
|
class |
ImmoniumIon
Represents an immonium ion.
|
class |
PeptideFragmentIon
This class models a peptide fragment ion.
|
class |
PrecursorIon
A precursor ion.
|
class |
ReporterIon
This class models a reporter ion and is its own factory.
|
Modifier and Type | Class and Description |
---|---|
class |
FastaIndex
This class contains the index of a FASTA file.
|
class |
Identification
This class contains identification results.
|
class |
IdentificationMatch
This is an abstract class for an identification match.
|
class |
IdentificationMethod
This class will contain all methods used to obtain identifications.
|
class |
PeptideAssumption
This object will models the assumption made by an advocate.
|
Modifier and Type | Class and Description |
---|---|
class |
PostProcessor
This object models a tool which post-processed identifications.
|
class |
SearchEngine
This class models a search engine.
|
Modifier and Type | Class and Description |
---|---|
class |
Ms2Identification
This class models an Ms2 Identification.
|
Modifier and Type | Class and Description |
---|---|
class |
IonMatch
This class will model the assignment of a peak to a theoretical ion.
|
class |
ModificationMatch
This class models the match between theoretic ptm and identification results.
|
class |
PeptideMatch
This class models a peptide match.
|
class |
ProteinMatch
This class models a protein match.
|
class |
SpectrumMatch
This class models a spectrum match.
|
Modifier and Type | Class and Description |
---|---|
class |
AndromedaIdfileReader
This IdfileReader reads identifications from an Andromeda result file.
|
Modifier and Type | Class and Description |
---|---|
class |
MgfIndex
This class contains the indexes of an mgf file after indexing mapped with the
title of the spectrum.
|
Modifier and Type | Class and Description |
---|---|
class |
Charge
This class models a charge.
|
class |
MS1Spectrum
This class models an MS1 spectrum.
|
class |
MSnSpectrum
This class models an MSn spectrum.
|
class |
Peak
This class represents a peak.
|
class |
Precursor
This class models a precursor.
|
class |
Spectrum
This class models a spectrum.
|
Modifier and Type | Class and Description |
---|---|
class |
Quantification
This class contains quantification results.
|
class |
QuantificationMatch
Abstract class for a quantification match.
|
class |
Ratio
This class models an object.
|
Modifier and Type | Class and Description |
---|---|
class |
PeptideQuantification
This class models quantification of a peptide.
|
class |
ProteinQuantification
This class models the quantification of a protein.
|
class |
PsmQuantification
This class models the quantification of a spectrum.
|
Modifier and Type | Class and Description |
---|---|
class |
ReporterIonQuantification
This class will contain quantification results.
|
class |
ReporterMethodFactory
This factory imports reporter methods details from an XMl file.
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