Uses of Class
com.compomics.util.experiment.biology.Protein

Packages that use Protein
com.compomics.util.experiment.biology This package contains experiement classes related to biological entities. 
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. 
 

Uses of Protein in com.compomics.util.experiment.biology
 

Methods in com.compomics.util.experiment.biology that return types with arguments of type Protein
 ArrayList<Protein> Peptide.getParentProteins()
          Getter for the parent proteins
 

Methods in com.compomics.util.experiment.biology with parameters of type Protein
 boolean Protein.isSameAs(Protein anotherProtein)
          A method to compare proteins.
 

Method parameters in com.compomics.util.experiment.biology with type arguments of type Protein
 void Peptide.setParentProteins(ArrayList<Protein> parentProteins)
          Sets the parent proteins
 

Constructor parameters in com.compomics.util.experiment.biology with type arguments of type Protein
Peptide(String aSequence, Double mass, ArrayList<Protein> parentProteins, ArrayList<ModificationMatch> modifications)
          Constructor for the peptide
 

Uses of Protein in com.compomics.util.experiment.identification
 

Methods in com.compomics.util.experiment.identification that return Protein
 Protein SequenceDataBase.getProtein(String proteinKey)
          Returns a protein indexed by its key.
 

Methods in com.compomics.util.experiment.identification with parameters of type Protein
 void SequenceDataBase.addProtein(Protein protein)
          Adds a protein to the map.
 

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

Methods in com.compomics.util.experiment.identification.matches that return Protein
 Protein ProteinMatch.getMainMatch()
          Returns the main match after protein inference
 Protein ProteinMatch.getTheoreticProtein(String accession)
          getter for the matching protein
 

Methods in com.compomics.util.experiment.identification.matches with parameters of type Protein
 void ProteinMatch.addTheoreticProtein(Protein protein)
          setter for the matching protein
 boolean ProteinMatch.contains(Protein aProtein)
          Returns a boolean indicating whether a protein was found in this protein match
 void ProteinMatch.setMainMatch(Protein mainMatch)
          Sets the main protein after protein inference
 

Constructors in com.compomics.util.experiment.identification.matches with parameters of type Protein
ProteinMatch(Protein protein)
          Constructor for the protein match
 



Copyright © 2011. All Rights Reserved.