Uses of Package
com.compomics.util.experiment.biology

Packages that use com.compomics.util.experiment.biology
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.aminoacids   
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.matches This package contains experiment classes releated to matches. 
com.compomics.util.experiment.identification.protein_inference.proteintree   
com.compomics.util.experiment.identification.ptm   
com.compomics.util.experiment.identification.ptm.ptmscores   
com.compomics.util.experiment.identification.scoring   
com.compomics.util.experiment.quantification.reporterion This package contains experiment classes related to reporter ions. 
com.compomics.util.gui This package contains basic GUI classes. 
com.compomics.util.gui.ptm   
com.compomics.util.gui.searchsettings   
com.compomics.util.gui.spectrum This package contains GUI classes related to Spectrum and Chromatogram visualization. 
com.compomics.util.preferences   
 

Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment
Sample
          This class models a proteomic sample.
 

Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.biology
AminoAcid
          Class representing amino acids.
AminoAcidPattern
          An amino acid pattern is a sequence of amino-acids.
Atom
          This interface contains information about atoms
ElementaryElement
          This class can be used to retrieve elementary elements like a neutron.
Enzyme
          This class models an enzyme.
EnzymeFactory
          This factory will provide the implemented enzymes.
GlyconFactory
          This factory will provide theoretic glycons.
Ion
          This class models an ion.
Ion.IonType
          An enumerator of the supported ion types.
IonFactory
          This factory generates the expected ions from a peptide.
Mutation
          This class represents a mutation of one amino acid to another from the 20-letter amino acid alphabet.
NeutralLoss
          This class represents a neutral loss.
Peptide
          This class models a peptide.
Protein
          This class models a protein.
PTM
          This class models a post-translational modification.
PTMFactory
          This factory will load PTM from an XML file and provide them on demand as standard class.
Sample
          This class models a proteomic sample.
 

Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.biology.aminoacids
AminoAcid
          Class representing amino acids.
 

Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.biology.atoms
Atom
          This interface contains information about atoms
 

Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.biology.ions
Ion
          This class models an ion.
NeutralLoss
          This class represents a neutral loss.
Peptide
          This class models a peptide.
 

Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.identification
Enzyme
          This class models an enzyme.
Ion
          This class models an ion.
Ion.IonType
          An enumerator of the supported ion types.
NeutralLoss
          This class represents a neutral loss.
Peptide
          This class models a peptide.
Protein
          This class models a protein.
 

Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.identification.matches
Enzyme
          This class models an enzyme.
Ion
          This class models an ion.
Peptide
          This class models a peptide.
 

Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.identification.protein_inference.proteintree
Enzyme
          This class models an enzyme.
 

Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.identification.ptm
Ion.IonType
          An enumerator of the supported ion types.
Peptide
          This class models a peptide.
PTM
          This class models a post-translational modification.
 

Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.identification.ptm.ptmscores
Ion.IonType
          An enumerator of the supported ion types.
Peptide
          This class models a peptide.
PTM
          This class models a post-translational modification.
 

Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.identification.scoring
Ion.IonType
          An enumerator of the supported ion types.
Peptide
          This class models a peptide.
 

Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.quantification.reporterion
Sample
          This class models a proteomic sample.
 

Classes in com.compomics.util.experiment.biology used by com.compomics.util.gui
AminoAcidPattern
          An amino acid pattern is a sequence of amino-acids.
 

Classes in com.compomics.util.experiment.biology used by com.compomics.util.gui.ptm
PTM
          This class models a post-translational modification.
 

Classes in com.compomics.util.experiment.biology used by com.compomics.util.gui.searchsettings
Enzyme
          This class models an enzyme.
 

Classes in com.compomics.util.experiment.biology used by com.compomics.util.gui.spectrum
Ion
          This class models an ion.
Ion.IonType
          An enumerator of the supported ion types.
NeutralLoss
          This class represents a neutral loss.
Peptide
          This class models a peptide.
 

Classes in com.compomics.util.experiment.biology used by com.compomics.util.preferences
Ion.IonType
          An enumerator of the supported ion types.
NeutralLoss
          This class represents a neutral loss.
Peptide
          This class models a peptide.
PTM
          This class models a post-translational modification.
 



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