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Packages that use Protein | |
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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 |
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Methods in com.compomics.util.experiment.biology that return types with arguments of type Protein | |
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ArrayList<Protein> |
Peptide.getParentProteins()
Getter for the parent proteins |
Methods in com.compomics.util.experiment.biology with parameters of type Protein | |
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boolean |
Protein.isSameAs(Protein anotherProtein)
A method to compare proteins. |
Method parameters in com.compomics.util.experiment.biology with type arguments of type Protein | |
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void |
Peptide.setParentProteins(ArrayList<Protein> parentProteins)
Sets the parent proteins |
Constructor parameters in com.compomics.util.experiment.biology with type arguments of type Protein | |
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Peptide(String aSequence,
Double mass,
ArrayList<Protein> parentProteins,
ArrayList<ModificationMatch> modifications)
Constructor for the peptide |
Uses of Protein in com.compomics.util.experiment.identification |
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Methods in com.compomics.util.experiment.identification that return Protein | |
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Protein |
SequenceDataBase.getProtein(String proteinKey)
Returns a protein indexed by its key. |
Methods in com.compomics.util.experiment.identification with parameters of type Protein | |
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void |
SequenceDataBase.addProtein(Protein protein)
Adds a protein to the map. |
Uses of Protein in com.compomics.util.experiment.identification.matches |
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Methods in com.compomics.util.experiment.identification.matches that return Protein | |
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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 | |
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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 | |
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ProteinMatch(Protein protein)
Constructor for the protein match |
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