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

A

acceptBBH(int, int, BlastHit, BlastHit) - Method in class procope.methods.interologs.blast.BlastBBHAlignmentLengthConstraint

Accepts a BBH if the give minimum fraction of both protein sequences is covered by the BLAST alignment.

acceptBBH(int, int, BlastHit, BlastHit) - Method in interface procope.methods.interologs.blast.BlastBBHConstraints

Function which is called by the BBH calculator to ask whether a given BBH is accepted or not.

add(int, String) - Method in class procope.methods.interologs.Sequences

Adds a single sequence to this set.

add(int, int, int) - Method in class procope.tools.SparseMatrixInt

Increase the value of a given cell.

addAll(Sequences) - Method in class procope.methods.interologs.Sequences

Adds all sequences of another Sequences object to this set.

addAnnotation(int, String) - Method in class procope.evaluation.complexquality.go.GOAnnotations

Adds the annotation of a given protein to a GO term.

addAnnotation(int, String, Object) - Static method in class procope.tools.namemapping.ProteinManager

Adds an annotation to the protein with a given internal ID.

addAnnotations(int, Map<String, Object>) - Static method in class procope.tools.namemapping.ProteinManager

Adds set of annotations to a protein with a given internal ID.

addChild(HierarchicalTreeNode) - Method in class procope.methods.clustering.HierarchicalTreeNode

add a child to this node

addClustering(BootstrapClustering) - Method in class procope.methods.scores.bootstrap.BootstrapClusterings

Adds a clustering to this clusterings list.

addComplex(Complex) - Method in class procope.data.complexes.ComplexSet

Adds a complex to the complex set.

addComplexes(Collection<Complex>) - Method in class procope.data.complexes.ComplexSet

Adds a list of complexes to the set

addComplexSet(ComplexSet, String) - Method in class procope.data.petrinets.PetriNetCreator

Adds a ComplexSet which will be integrated into the Petri net.

addExperiment(PurificationExperiment) - Method in class procope.data.purifications.PurificationData

Adds a specified experiment to the dataset.

addExperiments(Collection<PurificationExperiment>) - Method in class procope.data.purifications.PurificationData

Adds a list of purification experiments to the dataset

addInteractionNetwork(ProteinNetwork, String, boolean) - Method in class procope.data.petrinets.PetriNetCreator

Adds a ProteinNetwork which will be integrated into the Petri net.

addLocalization(int, String) - Method in class procope.data.LocalizationData

Annotate a protein with a given localization.

addMappingNetwork(ProteinNetwork, boolean) - Method in class procope.tools.namemapping.Synonyms

Adds all mappings induced by the edges of a given directed network to the synonyms list.

addNameMappings(ProteinNetwork, boolean) - Static method in class procope.tools.namemapping.ProteinManager

Add a list of name mappings to the protein manager.

addPrey(int) - Method in class procope.data.purifications.PurificationExperiment

Add a prey to the list of preys for this experiment

addPreys(Collection<Integer>) - Method in class procope.data.purifications.PurificationExperiment

Add a list of preys to this experiment.

addProtein(int) - Method in class procope.data.complexes.Complex

Adds a protein to the complex.

addProteins(Collection<Integer>) - Method in class procope.data.complexes.Complex

Adds a list of proteins to the complex.

addPurificationData(PurificationData, String) - Method in class procope.data.petrinets.PetriNetCreator

Adds a purification data set which will be integrated into the Petri net.

addSynonym(String, String) - Method in class procope.tools.namemapping.Synonyms

Adds a new synonym.

addToSequencePool(Sequences) - Method in class procope.tools.SequenceAligner

Add a set of sequences to the sequence pool of this aligner.

AlignmentInterologScorer - Class in procope.methods.interologs

Implements interolog scoring using similarity or identity from pairwise sequence alignments of the homologs.

AlignmentInterologScorer(SequenceAligner, AlignmentInterologScorer.AlignmentScoring) - Constructor for class procope.methods.interologs.AlignmentInterologScorer

Creates a new alignment length interolog scorer.

AlignmentInterologScorer.AlignmentScoring - Enum in procope.methods.interologs

Defines the alignment measure which will be used

Arc - Class in procope.data.petrinets

Represents one arc in a Petri net (the connection between a place and a transition).

Arc(String) - Constructor for class procope.data.petrinets.Arc

Creates an arc to a given place

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

Creates an arc to a given places having a specified set of attributes

areColocalized(int, int) - Method in class procope.data.LocalizationData

Determines whether two proteins are colocalized.

arrCopyOf(T[], int) - Static method in class procope.tools.Tools

Exact copy of the Arrays#copyOf method from the Sun JRE 6.0 Copied into this project to assure Java 5.0 compatibility

arrCopyOf(U[], int, Class<? extends T[]>) - Static method in class procope.tools.Tools

Exact copy of the Arrays#copyOf method from the Sun JRE 6.0 Copied into this project to assure Java 5.0 compatibility

arrCopyOf(int[], int) - Static method in class procope.tools.Tools

Exact copy of the Arrays#copyOf method from the Sun JRE 6.0 Copied into this project to assure Java 5.0 compatibility

arrCopyOf(float[], int) - Static method in class procope.tools.Tools

Exact copy of the Arrays#copyOf method from the Sun JRE 6.0 Copied into this project to assure Java 5.0 compatibility

arrCopyOf(double[], int) - Static method in class procope.tools.Tools

Exact copy of the Arrays#copyOf method from the Sun JRE 6.0 Copied into this project to assure Java 5.0 compatibility

averageComplexScore(ProteinNetwork, Complex) - Static method in class procope.methods.scores.ComplexScoreCalculator

Calculates the score of a complex using a given scores network.

averageComplexScore(ScoresCalculator, Complex) - Static method in class procope.methods.scores.ComplexScoreCalculator

Calculates the score of a complex using a given scores calculator.

averageComplexScore(ProteinNetwork, Complex, boolean) - Static method in class procope.methods.scores.ComplexScoreCalculator

Calculates the score of a complex using a given scores network.

averageComplexScore(ScoresCalculator, Complex, boolean) - Static method in class procope.methods.scores.ComplexScoreCalculator

Calculates the score of a complex using a given scores calculator.

averageComplexSetScore(ProteinNetwork, ComplexSet, boolean) - Static method in class procope.methods.scores.ComplexScoreCalculator

Calculates the average complex score of a given complex set.

averageComplexSetScore(ScoresCalculator, ComplexSet, boolean) - Static method in class procope.methods.scores.ComplexScoreCalculator

Calculates the average complex score of a given complex set.

averageComplexSetScore(ProteinNetwork, ComplexSet, boolean, boolean) - Static method in class procope.methods.scores.ComplexScoreCalculator

Calculates the average complex score of a given complex set.

averageComplexSetScore(ScoresCalculator, ComplexSet, boolean, boolean) - Static method in class procope.methods.scores.ComplexScoreCalculator

Calculates the average complex score of a given complex set.