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

D

decompose(ProteinNetwork, float) - Method in class procope.data.complexes.ComplexSet

Decomposes a complex set with respect to a given scores network.

DEFAULT_BINARY - Static variable in class procope.methods.clustering.MarkovClusterer

Default MCL binary: mcl, requires this binary in the current PATH

DEFAULT_DELIMITER - Static variable in class procope.data.complexes.ComplexSetWriter

Default delimiter which seperates the proteins of a complex: TAB

DEFAULT_SEPARATOR - Static variable in class procope.data.complexes.ComplexSetReader

Default separator which seperates the proteins of a complex: TAB

DEFAULT_SEPARATOR - Static variable in class procope.data.networks.NetworkWriter

Default separator for the fields of each edge: TAB

deleteEdge(int, int) - Method in class procope.data.networks.ProteinNetwork

Deletes an edge from the network along with all of its annotations.

depthFirstSearch(int, NetworkSearchCallback) - Method in class procope.data.networks.ProteinNetwork

Performs a depth-first search one the network.

derivePurificationData(boolean) - Method in class procope.data.networks.ProteinNetwork

Creates a purification data object from a directed network.

DiceCoefficients - Class in procope.methods.scores

Provides an efficient implementation of "Dice coefficients", a protein protein affinity measure derived from purification datasets according to

DiceCoefficients(PurificationData) - Constructor for class procope.methods.scores.DiceCoefficients

Creates a new Dice coefficients calculator

DummyClusterer - Class in procope.examples

DummyClusterer(int, int) - Constructor for class procope.examples.DummyClusterer

DummyClusterer - Class in procope.tools.userclasses

A simple user-defined clusterer.

DummyClusterer(int, int) - Constructor for class procope.tools.userclasses.DummyClusterer

Create new test clusterer

DummyScores - Class in procope.examples

DummyScores(PurificationData) - Constructor for class procope.examples.DummyScores