| Modifier and Type | Class and Description |
|---|---|
class |
MsExperiment
This class represents the experiment.
|
class |
ProteomicAnalysis
This class models a proteomic analysis.
|
class |
SampleAnalysisSet
A sample measurement set is a set of replicates from a common sample.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AminoAcidPattern
An amino acid pattern is a sequence of amino acids.
|
class |
AminoAcidSequence
This class represents a series of amino acids with associated modifications.
|
class |
Atom
This interface contains information about atoms.
|
class |
Enzyme
This class models an enzyme.
|
class |
Ion
This class models an ion.
|
class |
MassGap
An undefined mass gap.
|
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 |
Helium
The helium atom.
|
class |
Hydrogen
The hydrogen atom.
|
class |
Iodine
Iodine.
|
class |
Lithium
The Lithium atom.
|
class |
Nitrogen
The nitrogen atom.
|
class |
Oxygen
The oxygen atom.
|
class |
Phosphorus
The phosphorus atom.
|
class |
Selenium
Selenium.
|
class |
Sodium
The sodium atom.
|
class |
Sulfur
The sulfur atom.
|
| Modifier and Type | Class and Description |
|---|---|
class |
ElementaryIon
This class represents an elementary ion.
|
class |
Glycan
This class represents a glycan.
|
class |
ImmoniumIon
Represents an immonium ion.
|
class |
PeptideFragmentIon
This class models a peptide fragment ion.
|
class |
PrecursorIon
A precursor ion.
|
class |
RelatedIon
Represents a related ion, i.e., an ion that is related to a given amino acid,
and is its own factory.
|
class |
ReporterIon
This class models a reporter ion and is its own factory.
|
class |
TagFragmentIon
A fragment ion obtained from a tag.
|
| Modifier and Type | Class and Description |
|---|---|
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 |
SpectrumIdentificationAssumption
Spectrum identification assumption made by an identification algorithm.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Tag
This class represents a sequence mass tag.
|
| 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 |
FastaIndex
This class contains the index of a FASTA file.
|
| Modifier and Type | Class and Description |
|---|---|
class |
PeptideAssumption
This object will models the assumption made by an advocate.
|
class |
TagAssumption
This class represent a tag assumption made by an identification algorithm
based on a sequence tag.
|
| Modifier and Type | Class and Description |
|---|---|
class |
MzIdentMLIdfileSearchParametersConverter
Reads search parameters from a mzIdentML result files.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AndromedaIdfileReader
This IdfileReader reads identifications from an Andromeda result file.
|
class |
DirecTagIdfileReader
An identification file reader for Direct tag results.
|
class |
MsAmandaIdfileReader
This IdfileReader reads identifications from an MS Amanda csv result file.
|
class |
MzIdentMLIdfileReader
This IdfileReader reads identifications from an mzIdentML result file.
|
class |
NovorIdfileReader
This IdfileReader reads identifications from a Novor csv result file.
|
class |
PepNovoIdfileReader
This class can be used to parse PepNovo identification files.
|
class |
PNovoIdfileReader
This class can be used to parse pNovo identification files.
|
class |
TideIdfileReader
This IdfileReader reads identifications from an Tide tsv results 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
An abstract quantification class.
|
| Modifier and Type | Class and Description |
|---|---|
class |
ReporterIonQuantification
This class contains quantification parameters.
|
class |
ReporterMethodFactory
This factory imports reporter methods details from an XMl file.
|
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