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

P

pack(byte[]) - Static method in class procope.tools.math.MTRandom

This simply utility method can be used in cases where a byte array of seed data is to be used to repeatedly re-seed the random number sequence.

parseAnnotations(String) - Static method in class procope.tools.Tools

Parse annotations from a string coming from a network or annotations file.

parseBlastHits(String) - Static method in class procope.methods.interologs.blast.BlastHitFileParser

Parse BLAST hits from a given BLAST hit file in tabular format.

parseBlastHits(File) - Static method in class procope.methods.interologs.blast.BlastHitFileParser

Parse BLAST hits from a given BLAST hit file in tabular format.

parseBlastHits(InputStream) - Static method in class procope.methods.interologs.blast.BlastHitFileParser

Parse BLAST hits from a given input stream.

parseCalculators(InputStream) - Static method in class procope.tools.userclasses.UserScoresCalculator

Parse user scores calculators from a given XML input stream.

parseClusterers(InputStream) - Static method in class procope.tools.userclasses.UserClusterer

Parses user clusterers from a given XML input stream

parsePlace(String) - Static method in class procope.data.petrinets.PetriNetCreator

Parses a place from a given Petri net input line

parseTransition(String) - Static method in class procope.data.petrinets.PetriNetCreator

Parses a transition from a given Petri net input line

PearsonCoefficient - Class in procope.tools.math

Implements the Pearson product-moment correlation coefficient which calculates the correlation between two given lists of data points.

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

PECalculator - Class in procope.methods.scores

Calculates Purification Enrichment scores according to

PECalculator(PurificationData, float, float) - Constructor for class procope.methods.scores.PECalculator

Creates a new Purification Enrichment calculator.

PetriNetCreator - Class in procope.data.petrinets

Generates a Petri net which integrates data from an arbitrary number of networks, complex sets and purification data sets.

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

Creates a new Petri net creator which writes its output to a given file.

PetriNetCreator(File) - Constructor for class procope.data.petrinets.PetriNetCreator

Creates a new Petri net creator which writes its output to a given file.

PetriNetCreator(OutputStream) - Constructor for class procope.data.petrinets.PetriNetCreator

Creates a new Petri net creator which writes its output to a given output stream.

Place - Class in procope.data.petrinets

Represents one place in a Petri net.

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

Create place having the given string identifier

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

Create places having the given string identifier and a set of attributes.

Point - Class in procope.evaluation.comparison

Represents a pair of two values.

Point(float, float) - Constructor for class procope.evaluation.comparison.Point

Creates a new point of two given values

procope.data - package procope.data

procope.data.complexes - package procope.data.complexes

procope.data.networks - package procope.data.networks

procope.data.petrinets - package procope.data.petrinets

procope.data.purifications - package procope.data.purifications

procope.evaluation.comparison - package procope.evaluation.comparison

procope.evaluation.complexquality - package procope.evaluation.complexquality

procope.evaluation.complexquality.go - package procope.evaluation.complexquality.go

procope.evaluation.networkperformance - package procope.evaluation.networkperformance

procope.examples - package procope.examples

procope.methods.clustering - package procope.methods.clustering

procope.methods.interologs - package procope.methods.interologs

procope.methods.interologs.blast - package procope.methods.interologs.blast

procope.methods.scores - package procope.methods.scores

procope.methods.scores.bootstrap - package procope.methods.scores.bootstrap

procope.tools - package procope.tools

procope.tools.math - package procope.tools.math

procope.tools.namemapping - package procope.tools.namemapping

procope.tools.userclasses - package procope.tools.userclasses

ProCopeException - Exception in procope.tools

This exception is thrown by various methods of this library.

ProCopeException(String) - Constructor for exception procope.tools.ProCopeException

Constructs an LibraryNameException with the specified detail message.

ProteinManager - Class in procope.tools.namemapping

This class contains static methods which perform the mapping of string identifiers for proteins to internal integer IDs.

ProteinNetwork - Class in procope.data.networks

Represents a network of binary protein interactions.

ProteinNetwork() - Constructor for class procope.data.networks.ProteinNetwork

Creates an empty undirected network.

ProteinNetwork(boolean) - Constructor for class procope.data.networks.ProteinNetwork

Creates an empty network.

ProteinSet - Interface in procope.data

This interface is implemented by classes which work on or contain a distinct set of proteins which are represented by internal IDs (see also: ProteinManager).

ProtManager - Class in procope.examples

ProtManager() - Constructor for class procope.examples.ProtManager

PurificationBootstrapSamples - Class in procope.methods.scores.bootstrap

Represents a set of bootstrap samples of a purification data set.

PurificationBootstrapSamples(String) - Constructor for class procope.methods.scores.bootstrap.PurificationBootstrapSamples

Reads bootstrap samples from a file.

PurificationBootstrapSamples(InputStream) - Constructor for class procope.methods.scores.bootstrap.PurificationBootstrapSamples

Reads bootstrap samples from an input stream.

PurificationBootstrapSamples(PurificationData, int) - Constructor for class procope.methods.scores.bootstrap.PurificationBootstrapSamples

Creates a new set of bootstrap samples.

PurificationData - Class in procope.data.purifications

A set of protein purification experiments where each experiment constists of a bait protein along with a list of prey proteins it purified.

PurificationData() - Constructor for class procope.data.purifications.PurificationData

Creates an empty purification dataset

PurificationDataReader - Class in procope.data.purifications

Contains static methods to read purification data from a file.

PurificationDataReader() - Constructor for class procope.data.purifications.PurificationDataReader

PurificationDataWriter - Class in procope.data.purifications

Writes purification data to a given file or stream.

PurificationExperiment - Class in procope.data.purifications

Represents a single purification experiment having a bait protein and a list of prey proteins which were purified by that bait.

PurificationExperiment(int) - Constructor for class procope.data.purifications.PurificationExperiment

Creates a new purification experiment having a given bait.

PurificationExperiment(int, boolean) - Constructor for class procope.data.purifications.PurificationExperiment

Creates a new purification experiment having a given bait.