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

G

generateChart(List<ROCCurve>, List<String>) - Static method in class procope.evaluation.networkperformance.ROCCurveHandler

Creates a line diagram as a JFreeChart from a given list of ROC curves.

generateChart(List<ROCCurve>, List<String>, float) - Static method in class procope.evaluation.networkperformance.ROCCurveHandler

Creates a line diagram as a JFreeChart from a given list of ROC curves.

generateClusterer(Object...) - Method in class procope.tools.userclasses.UserClusterer

Generates the actual Clusterer object from this user clusterer.

generateHistogram(String, double[], boolean, int) - Static method in class procope.tools.ChartTools

Generates a histogram chart from a given dataset.

generateNetwork(ScoresCalculator) - Static method in class procope.data.networks.NetworkGenerator

Generate a network from a given scores calculator.

generateNetwork(ScoresCalculator, float) - Static method in class procope.data.networks.NetworkGenerator

Generate a network from a given scores calculator.

generateRandomNetwork(int, int) - Static method in class procope.data.networks.NetworkGenerator

Generates a random network with the given number of nodes and edges.

generateRandomNetwork(int, int, Random) - Static method in class procope.data.networks.NetworkGenerator

Generates a random network with the given number of nodes and edges.

generateScoresCalculator(PurificationData[], Object...) - Method in class procope.tools.userclasses.UserScoresCalculator

Generates the actual ScoresCalculator object for this user scores calculator.

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

Retrieves a value from the matrix.

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

Return the accuracy of the candidate set regarding the reference complex set.

getAlignment(int, int) - Method in class procope.tools.SequenceAligner

Returns the local sequence alignment for two given proteins.

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

Returns the length of the alignment

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

Returns the map which backs this object.

getAllHitIDs() - Method in class procope.methods.interologs.blast.BlastHits

Returns al ist of all proteins which were hit at least once in the database.

getAllQueryIDs() - Method in class procope.methods.interologs.blast.BlastHits

Returns a list of all proteins used as query in this BLAST result

getAllTerms() - Method in class procope.evaluation.complexquality.go.GONetwork

Get set of all term objects in the current network.

getAncestors(String) - Method in class procope.evaluation.complexquality.go.CommonAncestors

Returns all ancestors of a given GO term.

getAnnotatedProteinCount() - Static method in class procope.tools.namemapping.ProteinManager

Returns the number of proteins which have an annotation.

getAnnotation(String) - Method in class procope.data.networks.NetworkEdge

Retrieves a single annotation from the annotation list

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

Retrieves an annotation for a given protein.

getAnnotationCount(String) - Method in class procope.evaluation.complexquality.go.GOAnnotations

Returns the number of gene products annotated to a given GO term

getAnnotationKeys() - Method in class procope.data.networks.ProteinNetwork

Returns a set of all distinct annotation keys used in the network.

getAnnotations() - Method in class procope.data.networks.NetworkEdge

Returns all annotations associated with this edge

getAnnotations(int) - Static method in class procope.tools.namemapping.ProteinManager

Retrieves all annotations for a given protein.

getAttributes() - Method in class procope.data.petrinets.Arc

Returns the attributes of this arc

getAttributes() - Method in class procope.data.petrinets.Place

Returns the attributes of this place

getAttributes() - Method in class procope.data.petrinets.Transition

Returns the attributes associated with this transition.

getAverageColocalizationScore(ComplexSet, boolean, boolean) - Method in class procope.evaluation.complexquality.Colocalization

Calculates the average colocalization score for a given complex set.

getAveragePPV(ComplexSet, boolean, boolean) - Method in class procope.evaluation.complexquality.Colocalization

Calculates the average PPV for a given complex set.

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

Returns the bait of this purification experiment

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

Calculates a directed network containing all bait-prey interactions.

getBestHits(Integer) - Method in class procope.methods.interologs.blast.BlastHits

Returns all best hits for a given query.

getBidirectionalBestHits(BlastHits, BlastBBHConstraints) - Method in class procope.methods.interologs.blast.BlastHits

Calculate bidirectional best hits (BBHs).

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

Returns the bit score of the hit

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

Returns the list of child terms for this GO term.

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

Returns the clustering.

getClustering(int) - Method in class procope.methods.scores.bootstrap.BootstrapClusterings

Returns the clustering at a specific index

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

Returns the list of clusterings contained in this collection.

getColocalizationScore(Complex) - Method in class procope.evaluation.complexquality.Colocalization

Calculates the colocalization score of a given complex.

getCombinationType() - Method in class procope.data.networks.CombinationRules

Returns the combination type of this rules set.

getCommandLineParameters() - Method in class procope.methods.clustering.MCLParameters

Assemble command line parameters, directly used in command call

getCommonAncestors(String, String) - Method in class procope.evaluation.complexquality.go.CommonAncestors

Returns the set of common ancestors of two given GO terms.

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

Returns the list backing this complex.

getComplex(int) - Method in class procope.data.complexes.ComplexSet

Returns the complex at a given index in the complex set list.

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

Convenience and debugging method which translates this complex into a list of protein labels

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

Returns the number of complexes in this set

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

Returns the list of complexes backing this complex set.

getComplexInA() - Method in class procope.evaluation.comparison.ComplexMapping

Returns the complex in complex set A of this mapping.

getComplexInB() - Method in class procope.evaluation.comparison.ComplexMapping

Returns the complex in complex set B of this mapping.

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

Creates a network which contains a fully connected subgraph for each complex.

getCorrelationCoefficient() - Method in interface procope.tools.math.CorrelationCoefficient

Calculates the correlation coefficient for the current list of data points.

getCorrelationCoefficient() - Method in class procope.tools.math.PearsonCoefficient

Calculates the Pearson correlation coefficient for the current dataset.

getCorrelationCoefficient() - Method in class procope.tools.math.SpearmanCoefficient

Calculates Scorrelation coefficient for the current dataset.

getCutOffNetwork(float) - Method in class procope.data.networks.ProteinNetwork

Returns a network containing only edges with a weight greater or equal than a given cutoff value.

getCutOffNetwork(float, boolean) - Method in class procope.data.networks.ProteinNetwork

Returns a network containing only edges with a weight above or below a given cutoff value.

getData() - Method in class procope.evaluation.networkperformance.ROCCurve

Returns the list of ROCPoint objects in this curve.

getDataClass() - Method in class procope.tools.userclasses.UserParameter

Returns the data class of this parameter

getDataType() - Method in class procope.tools.userclasses.UserParameter

Returns the data type of this parameter

getDefaultValue() - Method in class procope.tools.userclasses.UserParameter

Returns the default value (string representation) of this parameter

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

Returns all incident edges of a given direction from a directed network.

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

Returns the weight of an edge between two given proteins.

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

Retrieves an annotation from a given edge.

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

Returns all annotations associated with a given edge.

getEdgeCount() - Method in class procope.data.networks.ProteinNetwork

Returns the number of edges in this network.

getEdgesArray() - Method in class procope.data.networks.ProteinNetwork

Returns an array containing all edges of the network.

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

Returns the MCL efficiency of the clustering with respect to the clustered network.

getElementCount() - Method in class procope.tools.SparseMatrixInt

Returns the number of elements set in this matrix

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

Returns the e-value of the hit

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

Returns the list of PurificationExperiment objects backing this dataset.

getFilteredNetwork(BooleanExpression) - Method in class procope.data.networks.ProteinNetwork

Filters the network using a given boolean expression.

getFilteredProteins(BooleanExpression) - Static method in class procope.tools.namemapping.ProteinManager

Return the subset of proteins which match a given expression.

getFirstIndices() - Method in class procope.tools.SparseMatrixInt

Get the list of indices which are set as a first index

getFP() - Method in class procope.evaluation.networkperformance.ROCPoint

Returns the false positive rate value of that point of the curve

getFromSAX(Attributes) - Static method in class procope.tools.userclasses.UserParameter

Get a user parameter from a SAX parses Attributes object

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

Returns the gap openings in the alignment

getGOTerms(int) - Method in class procope.evaluation.complexquality.go.GOAnnotations

Returns a set of identifiers of GO terms which are annotated to a given protein.

getHit(int, int) - Method in class procope.methods.interologs.blast.BlastHits

Retrieves a specific BLAST hit from the result.

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

Returns the hit end coordinate of the hit

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

Returns the internal ID of the hit protein

getHitsPerQuery(int) - Method in class procope.methods.interologs.blast.BlastHits

Returns all hits for a given query protein

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

Returns the hit start coordinate of the hit

getID() - Method in class procope.data.petrinets.Place

Returns the ID of this place

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

Returns the ID of this GO term.

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

Returns the identity of the alignment

getIn() - Method in class procope.data.petrinets.Transition

Returns the input arcs for this transition.

getInternalID(String) - Static method in class procope.tools.namemapping.ProteinManager

Returns the internal protein ID for a given String protein label

getInterologScore(int, int, int, int) - Method in class procope.methods.interologs.AlignmentInterologScorer

getInterologScore(int, int, int, int) - Method in class procope.methods.interologs.EvalueInterologScorer

getInterologScore(int, int, int, int) - Method in interface procope.methods.interologs.InterologScorer

Calculates the score of a new interolog based on the source proteins (the nodes of the original interaction) and the target proteins (the nodes of the transferred interaction).

getIntID(String) - Method in class procope.data.StringToIntMapper

Gets the integer ID for a given string

getItemCount() - Method in class procope.data.StringToIntMapper

Returns the number of registered strings in this mapper.

getLabel(int) - Static method in class procope.tools.namemapping.ProteinManager

Returns the protein label associated with a given internal id.

getLocalizationName(int) - Method in class procope.data.LocalizationData

Returns the name of a localization for a given internal integer ID

getLocalizations(int) - Method in class procope.data.LocalizationData

Get the set of localizations for a given protein.

getMapping() - Method in class procope.data.networks.CombinationRules

Returns the mapping network of this rules set.

getMatrixNames() - Static method in class procope.tools.SequenceAligner

Returns a list of possible substitution matrix names.

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

Returns the protein at a given index of in the complex.

getMinimalSpanningTree(ProteinNetwork) - Method in class procope.data.complexes.Complex

Returns the minimal spanning tree of this complex as a network object.

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

Returns the number of mismatches in the alignment

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

Returns the name of this GO term.

getName() - Method in class procope.tools.userclasses.UserClusterer

Returns the name of this clusterer

getName() - Method in class procope.tools.userclasses.UserParameter

Returns the name of this parameter

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

Returns the name of this scores calcuator

getNamespace() - Method in class procope.evaluation.complexquality.go.GONetwork

Returns the namespace used in this network.

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

Basically the same as ProteinNetwork.getNeighbors(int), but returns the IDs of all neighbors with descending weights.

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

Returns an array of proteins which contains all neighbors in the network of a given protein.

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

Returns all incident edges for a given protein in the network.

getNeighbors(int) - Method in class procope.tools.SparseMatrixInt

Return array of items which have a value associated with the given index

getNodeCount() - Method in class procope.data.networks.ProteinNetwork

Returns the number of nodes in this network.

getNodeMergeSeparator() - Method in class procope.data.networks.CombinationRules

Returns the node label merge separator

getNodes() - Method in class procope.data.networks.ProteinNetwork

Get list of proteins in this network.

getNonMappedComplexesA() - Method in class procope.evaluation.comparison.ComplexMappings

Returns the indices of all complexes of set A which are not mapped in this mapping set

getNonMappedComplexesB() - Method in class procope.evaluation.comparison.ComplexMappings

Returns the indices of all complexes of set B which are not mapped in this mapping set

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

Returns the number of experiments contained in this dataset

getNumberOfHits() - Method in class procope.methods.interologs.blast.BlastHits

Returns the number of hits in this BLAST result

getNumberOfLocalizations() - Method in class procope.data.LocalizationData

Returns the number of different localizations in the dataset

getNumberOfSamples() - Method in class procope.methods.scores.bootstrap.PurificationBootstrapSamples

Returns the number of bootstrap samples contained in this set.

getOut() - Method in class procope.data.petrinets.Transition

Returns the output arcs for this transition

getOverlap() - Method in class procope.evaluation.comparison.ComplexMapping

Gets the overlap between the two complexes in this mapping

getParamemeters() - Method in class procope.methods.clustering.MarkovClusterer

Returns the mcl parameters for this clusterer

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

getParameters() - Method in class procope.tools.userclasses.UserClusterer

Returns the parameters of this clusterer

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

Returns the parameters of this scores calculator.

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

Returns the list of parent terms for this GO term.

getPlaceID() - Method in class procope.data.petrinets.Arc

Returns the ID of the place associated with this arc

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

Returns the positive predictive value (PPV) of the candidate set regarding the reference complex set.

getPPV(Complex) - Method in class procope.evaluation.complexquality.Colocalization

Calculates the PPV according to Pu et al., 2007

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

Returns the total number of preys in this dataset.

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

Returns the list of prey proteins for this experiment.

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

Returns the number of proteins in this set as the sum of the single complex sizes.

getProteinCount() - Static method in class procope.tools.namemapping.ProteinManager

Returns the number of registered proteins.

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

Returns the set of internal IDs which are involved in this complex.

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

Returns the set of proteins involved in this complex set.

getProteins() - Method in class procope.data.networks.ProteinNetwork

Returns the set of proteins which are contained as nodes in this network

getProteins() - Method in interface procope.data.ProteinSet

Returns the set of proteins this object is working with or containing.

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

Returns the set of proteins which are contained in this purification data set

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

Returns the set of proteins involved in this purification experiment (the bait and all preys)

getProteins() - Method in class procope.evaluation.complexquality.go.FunctionalSimilaritiesSchlicker

Returns the set of proteins contained in the annotations used in this scores calculator.

getProteins() - Method in class procope.evaluation.complexquality.go.GOAnnotations

Returns the proteins which are used in this annotation set.

getProteins() - Method in class procope.examples.DummyScores

getProteins() - Method in class procope.methods.scores.DiceCoefficients

Returns the proteins involved in the purification data set for this Dice coefficients calculator

getProteins() - Method in class procope.methods.scores.HartCalculator

Returns all proteins of the purification data set used in this scores calculator

getProteins() - Method in class procope.methods.scores.PECalculator

Returns all proteins of the purification data set used in this scores calculator

getProteins() - Method in class procope.methods.scores.ScoresCalculator

Returns the set of proteins involved in this scores calculator.

getProteins() - Method in class procope.methods.scores.SocioAffinityCalculator

Returns all proteins of the purification data set used in this scores calculator

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

Returns the query end coordinate of the hit

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

Returns the internal ID of the query protein

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

Returns the query start coordinate of the hit

getRoot() - Method in class procope.evaluation.complexquality.go.GONetwork

Returns the root term of this ontology network (actually of the namespace which is used in this network).

getSample(int) - Method in class procope.methods.scores.bootstrap.PurificationBootstrapSamples

Returns a given sample from the set.

getScore(int, int) - Method in class procope.evaluation.complexquality.go.FunctionalSimilarities

Calculates the semantic similarity score of two given proteins.

getScore(int, int) - Method in class procope.evaluation.complexquality.go.FunctionalSimilaritiesSchlicker

Calculates the functional similarity of two given proteins.

getScore(int, int) - Method in class procope.examples.DummyScores

getScore(int, int) - Method in class procope.methods.scores.DiceCoefficients

Returns the Dice coefficient for two given proteins, returns 0 if the protein indices are out of range or if protein1==protein2

getScore(int, int) - Method in class procope.methods.scores.HartCalculator

Calculates the score of the given protein.

getScore(int, int) - Method in class procope.methods.scores.PECalculator

Calculates the Purification Enrichment score for two given proteins.

getScore(int, int) - Method in class procope.methods.scores.ScoresCalculator

Returns the interaction score for two given proteins.

getScore(String, String) - Method in class procope.methods.scores.ScoresCalculator

Returns the interaction score for two given proteins provided as String identifiers.

getScore(int, int) - Method in class procope.methods.scores.SocioAffinityCalculator

Calculates the socio affinity score for two given proteins based on the purification data set provided in the constructor.

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

Returns the sensitivity of the candidate complex set regarding the reference complex set.

getSequence(int) - Method in class procope.methods.interologs.Sequences

Returns the sequence for a given internal protein ID.

getSequencePool() - Method in class procope.tools.SequenceAligner

getSetA() - Method in class procope.evaluation.comparison.ComplexMappings

Returns the first complex set involved in this mapping set.

getSetB() - Method in class procope.evaluation.comparison.ComplexMappings

Returns the second complex set involved in this mapping set.

getSource() - Method in class procope.data.networks.NetworkEdge

Returns the protein from which this edge is originating.

getStringID(int) - Method in class procope.data.StringToIntMapper

Returns the string associated with an integer ID.

getSynonyms() - Static method in class procope.tools.namemapping.ProteinManager

Return the Synonyms object currently used

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

Returns all synonyms associated with a given identifier.

getTarget() - Method in class procope.data.networks.NetworkEdge

Returns the protein to which this edge is leading.

getTempFilename() - Static method in class procope.tools.Tools

Returns an unused temporary file name.

getTerm(String) - Method in class procope.evaluation.complexquality.go.GONetwork

Returns the term object with a given GO identifier.

getTP() - Method in class procope.evaluation.networkperformance.ROCPoint

Returns the true positive rate value of that point of the curve

getValues(int) - Method in class procope.tools.SparseMatrixInt

Return array of values associated with a given index.

getWeight() - Method in class procope.data.networks.NetworkEdge

Returns the weight of this edge

getWeightMergeKey1() - Method in class procope.data.networks.CombinationRules

Returns the first weight merge key.

getWeightMergeKey2() - Method in class procope.data.networks.CombinationRules

Returns the second weight merge key.

getWeightMergePolicy() - Method in class procope.data.networks.CombinationRules

Returns the weight merge policy of this rules set.

getX() - Method in class procope.evaluation.comparison.Point

Returns the x coordinate

getY() - Method in class procope.evaluation.comparison.Point

Returns the y coordinate

GOAnnotationReader - Class in procope.evaluation.complexquality.go

Contains static methods to read annotations from a GO annotations file.

GOAnnotations - Class in procope.evaluation.complexquality.go

Represents a set of gene-product to GO-term annotations which are normally read from a file.

GOAnnotations() - Constructor for class procope.evaluation.complexquality.go.GOAnnotations

Create new empty GO annotations object.

GONetwork - Class in procope.evaluation.complexquality.go

Represents the ontology network of one GO namespace.

GONetwork(String, GONetwork.Namespace, GONetwork.Relationships) - Constructor for class procope.evaluation.complexquality.go.GONetwork

Creates a GO network from a given file in OBO format, using a given namespaces and the specified relationships

GONetwork(File, GONetwork.Namespace, GONetwork.Relationships) - Constructor for class procope.evaluation.complexquality.go.GONetwork

Creates a GO network from a given file in OBO format, using a given namespaces and the specified relationships

GONetwork.Namespace - Enum in procope.evaluation.complexquality.go

The GO namespaces.

GONetwork.Relationships - Enum in procope.evaluation.complexquality.go

GO ontology relationships which can be followed while constructing the ontology network.

GOTerm - Class in procope.evaluation.complexquality.go

Represents a single GO term in an ontology network.

GOTerm(String) - Constructor for class procope.evaluation.complexquality.go.GOTerm

Creates a term object with the given GO term ID and name

GZIP_MAGIC - Static variable in class procope.tools.Tools