Uses of Class
com.compomics.util.experiment.personalization.ExperimentObject

Packages that use ExperimentObject
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.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
 

Subclasses of ExperimentObject in com.compomics.util.experiment
 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
 

Subclasses of ExperimentObject in com.compomics.util.experiment.biology
 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
 

Subclasses of ExperimentObject in com.compomics.util.experiment.biology.atoms
 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
 

Subclasses of ExperimentObject in com.compomics.util.experiment.biology.ions
 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.identification
 

Subclasses of ExperimentObject in com.compomics.util.experiment.identification
 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.
 

Uses of ExperimentObject in com.compomics.util.experiment.identification.advocates
 

Subclasses of ExperimentObject in com.compomics.util.experiment.identification.advocates
 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
 

Subclasses of ExperimentObject in com.compomics.util.experiment.identification.identifications
 class Ms2Identification
          This class models an Ms2 Identification.
 

Uses of ExperimentObject in com.compomics.util.experiment.identification.matches
 

Subclasses of ExperimentObject in com.compomics.util.experiment.identification.matches
 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
 

Subclasses of ExperimentObject in com.compomics.util.experiment.io.identifications.idfilereaders
 class AndromedaIdfileReader
          This IdfileReader reads identifications out of an Andromeda result file
 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
 

Subclasses of ExperimentObject in com.compomics.util.experiment.io.massspectrometry
 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
 

Subclasses of ExperimentObject in com.compomics.util.experiment.massspectrometry
 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
 

Subclasses of ExperimentObject in com.compomics.util.experiment.quantification
 class Quantification
          This class contains quantification results.
 class Ratio
          This class models an object.
 

Uses of ExperimentObject in com.compomics.util.experiment.quantification.reporterion
 

Subclasses of ExperimentObject in com.compomics.util.experiment.quantification.reporterion
 class QuantificationMatch
          abstract class for a quantification match
 class ReporterIonQuantification
          This class will contain quantification results.
 class ReporterMethodFactory
          This factory imports reporter methods details from an xml file.
 

Uses of ExperimentObject in com.compomics.util.experiment.quantification.reporterion.quantification
 

Subclasses of ExperimentObject in com.compomics.util.experiment.quantification.reporterion.quantification
 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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