A B C D E F G H I L M N P R S T U V W X

M

main(String[]) - Static method in class procope.examples.ProtManager

main(String[]) - Static method in class procope.examples.UseCase1

main(String[]) - Static method in class procope.examples.UseCase2

main(String[]) - Static method in class procope.examples.UseCase3

main(String[]) - Static method in class procope.examples.UseCase4

main(String[]) - Static method in class procope.tools.namemapping.ProteinManager

mapComplexes(ComplexSet, ComplexSet, int) - Static method in class procope.evaluation.comparison.ComplexSetComparison

Calculates a mapping between two given complex sets by comparing the protein overlaps of their complexes.

mapComplexesConsistently(ComplexSet, ComplexSet, int) - Static method in class procope.evaluation.comparison.ComplexSetComparison

Calculates a mapping between two given complex sets by comparing the protein overlaps of their complexes.

mapComplexesExactly(ComplexSet, ComplexSet) - Static method in class procope.evaluation.comparison.ComplexSetComparison

Find complexes in two given complex sets which are identical

mapComplexesMultiple(ComplexSet, ComplexSet, int) - Static method in class procope.evaluation.comparison.ComplexSetComparison

Calculates a mapping between two given complex sets by comparing the protein overlaps of their complexes.

MarkovClusterer - Class in procope.methods.clustering

Performs clustering using the Markov Cluster Algorithm as proposed in the PhD thesis Graph Clustering by Flow Simulation by Stijn van Dongen.

MarkovClusterer() - Constructor for class procope.methods.clustering.MarkovClusterer

Creates an MCL cluster with default parameters.

MarkovClusterer(MCLParameters) - Constructor for class procope.methods.clustering.MarkovClusterer

Creates an MCL clusterer with a given set of parameters.

max(Comparable, Comparable) - Static method in class procope.tools.Tools

Returns the maximum of two Comparable objects

MCLEfficiencyCalculator - Class in procope.methods.clustering

Calculates the quality of a clustering using a given scores network according to the method proposed in the PhD of Stijn van Dongen (for a reference see: MarkovClusterer).

MCLEfficiencyCalculator() - Constructor for class procope.methods.clustering.MCLEfficiencyCalculator

MCLParameters - Class in procope.methods.clustering

Represents a set of parameters for MCL clustering.

MCLParameters() - Constructor for class procope.methods.clustering.MCLParameters

Creates a set of MCL parameters with default settings.

merge(PurificationData) - Method in class procope.data.purifications.PurificationData

Merges two purification datasets.

min(Comparable, Comparable) - Static method in class procope.tools.Tools

Returns the minimum of two Comparable objects

MINOVERLAP - Static variable in class procope.tools.Tools

Default minimum overlap required for two complexes to be mapped to each other

MTRandom - Class in procope.tools.math

MTRandom() - Constructor for class procope.tools.math.MTRandom

The default constructor for an instance of MTRandom.

MTRandom(boolean) - Constructor for class procope.tools.math.MTRandom

This version of the constructor can be used to implement identical behaviour to the original C code version of this algorithm including exactly replicating the case where the seed value had not been set prior to calling genrand_int32.

MTRandom(long) - Constructor for class procope.tools.math.MTRandom

This version of the constructor simply initialises the class with the given 64 bit seed value.

MTRandom(byte[]) - Constructor for class procope.tools.math.MTRandom

This version of the constructor initialises the class with the given byte array.

MTRandom(int[]) - Constructor for class procope.tools.math.MTRandom

This version of the constructor initialises the class with the given integer array.

multiplePreys() - Method in class procope.data.purifications.PurificationExperiment

Returns if multiple occurences of the same prey are allowed in the preys list.

multiplePurifications() - Method in class procope.tools.userclasses.UserScoresCalculator

Returns whether this scores calculator accepts multiple purification data sets.