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.biology.neutrallosses   
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. e.g., pepties, proteins, modifications and spectra. 
com.compomics.util.experiment.identification.ptm   
com.compomics.util.experiment.io.identifications   
com.compomics.util.experiment.quantification.reporterion This package contains experiment classes related to reporter ions. 
com.compomics.util.gui.spectrum This package contains GUI classes related to Spectrum and Chromatogram visualization. 
com.compomics.util.protein The classes in this package concern useful Objects and their operations for modelling and handling proteins. 
 

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
Atom
          This interface contains information about atoms
Enzyme
          This class models an enzyme.
EnzymeFactory
          This factory will provide the implemented enzymes.
FragmentFactory
          This factory generates the expected fragment ions from a peptide sequence.
GlyconFactory
          This factory will provide theoretic glycons.
Ion
          This class models an ion.
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.
 

Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.biology.neutrallosses
NeutralLoss
          This class represents a neutral loss.
 

Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.identification
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
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.ptm
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.io.identifications
PTMFactory
          This factory will load PTM from an XML file and provide them on demand as standard class.
 

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.spectrum
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.protein
Enzyme
          This class models an enzyme.
 



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