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. 
 

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 SequenceFactory.getProtein(String accession)
          Returns the desired protein
 

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
 



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