Uses of Class
procope.data.complexes.Complex

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

Uses of Complex in procope.data.complexes
 

Methods in procope.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 procope.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 procope.data.complexes with parameters of type Complex
 void ComplexSet.addComplex(Complex toAdd)
          Adds a complex to the complex set.
 float Complex.calculateJaccardIndex(Complex other)
          Calculates the Jaccard index as a measure of similarity between two complexes.
 int Complex.calculateOverlap(Complex other)
          Calculates the number of overlapping proteins with another complex.
 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 procope.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 procope.evaluation.comparison
 

Methods in procope.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 procope.evaluation.complexquality
 

Methods in procope.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 Pu et al., 2007
 

Uses of Complex in procope.methods.scores
 

Methods in procope.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.