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Packages that use Complex | |
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procope.data.complexes | |
procope.evaluation.comparison | |
procope.evaluation.complexquality | |
procope.methods.scores |
Uses of Complex in procope.data.complexes |
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Methods in procope.data.complexes that return Complex | |
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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 | |
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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 | |
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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 | |
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void |
ComplexSet.addComplexes(Collection<Complex> toadd)
Adds a list of complexes to the set |
Uses of Complex in procope.evaluation.comparison |
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Methods in procope.evaluation.comparison with parameters of type Complex | |
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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 |
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Methods in procope.evaluation.complexquality with parameters of type Complex | |
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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 |
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Methods in procope.methods.scores with parameters of type Complex | |
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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. |
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