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Packages that use ExperimentObject | |
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com.compomics.util.experiment | This package contains MSExperiment main class and all sub-classes useful for the modeling of an experiment. |
com.compomics.util.experiment.biology | This package contains experiement classes related to biological entities. |
com.compomics.util.experiment.biology.atoms | |
com.compomics.util.experiment.biology.ions | This package contains experiment classes related to ions. |
com.compomics.util.experiment.biology.neutrallosses | |
com.compomics.util.experiment.identification | This package contains experiment classes related to identifications. |
com.compomics.util.experiment.identification.advocates | This package contains experiment classes related to modeling identifications. |
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. |
com.compomics.util.experiment.io.identifications.idfilereaders | This package contains experiment classes related to reading search engine files. |
com.compomics.util.experiment.io.massspectrometry | |
com.compomics.util.experiment.massspectrometry | This package contains experiment classes related to spectra. |
com.compomics.util.experiment.quantification | This package contains experiment classes related to quantification. |
com.compomics.util.experiment.quantification.reporterion | This package contains experiment classes related to reporter ions. |
com.compomics.util.experiment.quantification.reporterion.quantification | This package contains experiment classes related to quantification by reporter ions. |
Uses of ExperimentObject in com.compomics.util.experiment |
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Subclasses of ExperimentObject in com.compomics.util.experiment | |
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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. |
Uses of ExperimentObject in com.compomics.util.experiment.biology |
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Subclasses of ExperimentObject in com.compomics.util.experiment.biology | |
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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. |
Uses of ExperimentObject in com.compomics.util.experiment.biology.atoms |
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Subclasses of ExperimentObject in com.compomics.util.experiment.biology.atoms | |
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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 |
Uses of ExperimentObject in com.compomics.util.experiment.biology.ions |
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Subclasses of ExperimentObject in com.compomics.util.experiment.biology.ions | |
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class |
Glycon
This class will models a glycon fragment. |
class |
PeptideFragmentIon
This class models a peptide fragment ion. |
class |
Proton
This class represents a proton |
class |
ReporterIon
This class models a reporter ion. |
Uses of ExperimentObject in com.compomics.util.experiment.biology.neutrallosses |
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Subclasses of ExperimentObject in com.compomics.util.experiment.biology.neutrallosses | |
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class |
CH4OS
Neutral loss CH4OS, likely to be encountered on fragment from peptides containing an oxidized methionine. |
class |
H2O
A water loss, likely to be found on fragments from peptides containing the amino-acid D, E, S or T |
class |
H3PO4
A phosphorylation loss, likely to be found on fragments from phosphorylated peptides on Y. |
class |
HPO3
A phosphorylation loss, likely to be found on fragments from phosphorylated peptides on S or T. |
class |
NH3
A nitrium loss, likely to be found on fragments from peptides containing the amino-acid K, N, Q or R. |
Uses of ExperimentObject in com.compomics.util.experiment.identification |
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Subclasses of ExperimentObject in com.compomics.util.experiment.identification | |
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class |
FastaIndex
This class contains the index of a fasta file |
class |
Identification
This class contains identification results. |
class |
IdentificationMethod
This class will contain all methods used to obtain identifications. |
class |
Match
This is an abstract class for an identification match |
class |
PeptideAssumption
This object will models the assumption made by an advocate. |
Uses of ExperimentObject in com.compomics.util.experiment.identification.advocates |
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Subclasses of ExperimentObject in com.compomics.util.experiment.identification.advocates | |
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class |
PostProcessor
This object models a tool which post-processed identifications. |
class |
SearchEngine
This class models a search engine. |
Uses of ExperimentObject in com.compomics.util.experiment.identification.identifications |
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Subclasses of ExperimentObject in com.compomics.util.experiment.identification.identifications | |
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class |
Ms2Identification
This class models an Ms2 Identification. |
Uses of ExperimentObject in com.compomics.util.experiment.identification.matches |
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Subclasses of ExperimentObject in com.compomics.util.experiment.identification.matches | |
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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. |
Uses of ExperimentObject in com.compomics.util.experiment.io.identifications.idfilereaders |
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Subclasses of ExperimentObject in com.compomics.util.experiment.io.identifications.idfilereaders | |
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class |
MascotIdfileReader
This reader will import identifications from a Mascot dat file. |
class |
OMSSAIdfileReader
This reader will import identifications from an OMSSA omx file. |
class |
XTandemIdfileReader
This reader will import identifications from an X!Tandem xml result file. |
Uses of ExperimentObject in com.compomics.util.experiment.io.massspectrometry |
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Subclasses of ExperimentObject in com.compomics.util.experiment.io.massspectrometry | |
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class |
MgfIndex
This class contains the indexes of an mgf file after indexing mapped with the title of the spectrum |
Uses of ExperimentObject in com.compomics.util.experiment.massspectrometry |
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Subclasses of ExperimentObject in com.compomics.util.experiment.massspectrometry | |
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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 modilizes the precursor. |
class |
Spectrum
This class models a spectrum |
Uses of ExperimentObject in com.compomics.util.experiment.quantification |
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Subclasses of ExperimentObject in com.compomics.util.experiment.quantification | |
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class |
Quantification
This class contains quantification results. |
class |
QuantificationMethod
This class will models a quantification method. |
class |
Ratio
This class models an object. |
Uses of ExperimentObject in com.compomics.util.experiment.quantification.reporterion |
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Subclasses of ExperimentObject in com.compomics.util.experiment.quantification.reporterion | |
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class |
ReporterIonQuantification
This class will contain quantification results. |
class |
ReporterMethod
This class models a reporter quantification method. |
class |
ReporterMethodFactory
This factory imports reporter methods details from an xml file. |
Uses of ExperimentObject in com.compomics.util.experiment.quantification.reporterion.quantification |
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Subclasses of ExperimentObject in com.compomics.util.experiment.quantification.reporterion.quantification | |
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class |
PeptideQuantification
This class models quantification at the peptide level. |
class |
ProteinQuantification
This class models the quantification results for a protein match. |
class |
PsmQuantification
This class models the quantification at the MS2 spectrum level. |
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