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

T

TermSimilarities - Interface in procope.evaluation.complexquality.go

This interface must be implemented by classes which calculate a semantic similarity of two GO terms.

TermSimilaritiesSchlicker - Class in procope.evaluation.complexquality.go

Implements the calculation of similarities between two GO terms as described in

TermSimilaritiesSchlicker(GONetwork, GOAnnotations, TermSimilaritiesSchlicker.TermSimilarityMeasure, boolean) - Constructor for class procope.evaluation.complexquality.go.TermSimilaritiesSchlicker

Creates a new term similarity calculator.

TermSimilaritiesSchlicker.TermSimilarityMeasure - Enum in procope.evaluation.complexquality.go

The similarity to be used.

Tools - Class in procope.tools

Contains helper methods used throughout the whole library.

ToPNetGenerator - Class in procope.data.petrinets

Converts a Petri net to a ToPNet .places and .interactions file pair.

ToPNetGenerator() - Constructor for class procope.data.petrinets.ToPNetGenerator

toString() - Method in class procope.data.complexes.Complex

Returns the string representation of this complex as the string representation of the backing list of internal IDs

toString() - Method in class procope.data.complexes.ComplexSet

Returns a string representation of this complex set constructed by a list of string representations of the contained Complex objects

toString() - Method in class procope.evaluation.comparison.BroheeSimilarity

Returns a string representation of the comparison results

toString() - Method in class procope.evaluation.complexquality.go.GOTerm

Returns a String representation of this GO term containing its id but no parent or child relationships.

toString() - Method in class procope.methods.interologs.blast.BlastHit

Returns a simple string representation of the hit.

Transition - Class in procope.data.petrinets

Represents one transition in a Petri net.

Transition(Arc[], Arc[]) - Constructor for class procope.data.petrinets.Transition

Create transition consisting of given sets of input and output arcs

Transition(Arc[], Arc[], Map<String, String>) - Constructor for class procope.data.petrinets.Transition

Create transition consisting of given sets of input and output arcs and a map of attributes