Uses of Class
data.complexes.Complex

Packages that use Complex
data.complexes   
evaluation.comparison   
evaluation.complexquality   
methods.scores   
 

Uses of Complex in data.complexes
 

Methods in data.complexes that return Complex
 Complex Complex.copy()
          Creates a copy of this complex
 Complex ComplexSet.getComplex(int index)
          Returns the complex at a given index in the complex set list.
 Complex Complex.intersection(Complex other)
          Returns the intersection of both complexes.
 

Methods in data.complexes that return types with arguments of type Complex
 List<Complex> ComplexSet.getComplexes()
          Returns the list of complexes backing this complex set.
 Iterator<Complex> ComplexSet.iterator()
          Returns an iterator over the Complex objects in this set
 

Methods in data.complexes with parameters of type Complex
 void ComplexSet.addComplex(Complex toAdd)
          Adds a complex to the complex set.
 boolean ComplexSet.contains(Complex complex)
          Checks if a specified complex is contained in this set.
 Complex Complex.intersection(Complex other)
          Returns the intersection of both complexes.
 boolean ComplexSet.removeComplex(Complex toRemove)
          Removes a given complex from the complex set.
 

Method parameters in data.complexes with type arguments of type Complex
 void ComplexSet.addComplexes(Collection<Complex> toadd)
          Adds a list of complexes to the set
 

Uses of Complex in evaluation.comparison
 

Methods in evaluation.comparison with parameters of type Complex
static int ComplexSetComparison.complexesOverlap(Complex complex1, Complex complex2)
          Calculate the number of proteins which overlap between two given complexes.
 

Uses of Complex in evaluation.complexquality
 

Methods in evaluation.complexquality with parameters of type Complex
 float Colocalization.getColocalizationScore(Complex complex)
          Calculates the colocalization score of a given complex.
 float Colocalization.getPPV(Complex complex)
          Calculates the PPV according to TODO: [b] et al, 200x
 

Uses of Complex in methods.scores
 

Methods in methods.scores with parameters of type Complex
static float ComplexScoreCalculator.averageComplexScore(ProteinNetwork scoreNetwork, Complex complex)
          Calculates the score of a complex using a given scores network.
static float ComplexScoreCalculator.averageComplexScore(ProteinNetwork scoreNetwork, Complex complex, boolean ignoreMissingScores)
          Calculates the score of a complex using a given scores network.
static float ComplexScoreCalculator.averageComplexScore(ScoresCalculator scoreCalc, Complex complex)
          Calculates the score of a complex using a given scores calculator.
static float ComplexScoreCalculator.averageComplexScore(ScoresCalculator scoreCalc, Complex complex, boolean ignoreMissingScores)
          Calculates the score of a complex using a given scores calculator.