Uses of Class
procope.data.purifications.PurificationData

Packages that use PurificationData
procope.data.networks   
procope.data.petrinets   
procope.data.purifications   
procope.examples   
procope.methods.scores   
procope.methods.scores.bootstrap   
procope.tools.userclasses   
 

Uses of PurificationData in procope.data.networks
 

Methods in procope.data.networks that return PurificationData
 PurificationData ProteinNetwork.derivePurificationData(boolean poolBaits)
          Creates a purification data object from a directed network.
 

Uses of PurificationData in procope.data.petrinets
 

Methods in procope.data.petrinets with parameters of type PurificationData
 void PetriNetCreator.addPurificationData(PurificationData data, String name)
          Adds a purification data set which will be integrated into the Petri net.
 

Uses of PurificationData in procope.data.purifications
 

Methods in procope.data.purifications that return PurificationData
 PurificationData PurificationData.merge(PurificationData mergeWith)
          Merges two purification datasets.
static PurificationData PurificationDataReader.readPurifications(File file)
          Read purification data from a given file.
static PurificationData PurificationDataReader.readPurifications(File file, boolean multiplyPreys)
          Read purification data from a given file.
static PurificationData PurificationDataReader.readPurifications(InputStream input)
          Read purification data from a given input stream.
static PurificationData PurificationDataReader.readPurifications(InputStream input, boolean multiplePreys)
          Read purification data from a given input stream.
static PurificationData PurificationDataReader.readPurifications(String file)
          Read purification data from a given file.
static PurificationData PurificationDataReader.readPurifications(String file, boolean multiplyPreys)
          Read purification data from a given file.
 

Methods in procope.data.purifications with parameters of type PurificationData
 PurificationData PurificationData.merge(PurificationData mergeWith)
          Merges two purification datasets.
static void PurificationDataWriter.writePurificationData(PurificationData data, File outfile)
          Writes a purification data set to a given file.
static void PurificationDataWriter.writePurificationData(PurificationData data, OutputStream stream)
          Writes a purification data set to a given output stream
static void PurificationDataWriter.writePurificationData(PurificationData data, String outfile)
          Writes a purification data set to a given file.
static void PurificationDataWriter.writeXGMML(PurificationData data, File outfile)
          Creates a Cytoscape-compatible XGMML file.
static void PurificationDataWriter.writeXGMML(PurificationData data, OutputStream outstream)
          Creates a Cytoscape-compatible XGMML file, but writes to an output stream.
static void PurificationDataWriter.writeXGMML(PurificationData data, String outfile)
          Creates a Cytoscape-compatible XGMML file.
 

Uses of PurificationData in procope.examples
 

Constructors in procope.examples with parameters of type PurificationData
DummyScores(PurificationData data)
           
 

Uses of PurificationData in procope.methods.scores
 

Constructors in procope.methods.scores with parameters of type PurificationData
DiceCoefficients(PurificationData data)
          Creates a new Dice coefficients calculator
HartCalculator(PurificationData dataset)
          Creates a new scores calculator from a given purification data set.
HartCalculator(PurificationData[] datasets)
          Creates a new scores calculator from an array of purification data sets.
PECalculator(PurificationData data, float r, float pseudocount)
          Creates a new Purification Enrichment calculator.
SocioAffinityCalculator(PurificationData data)
          Creates a new socio affinity scores calculator based on a given purification data set.
 

Constructor parameters in procope.methods.scores with type arguments of type PurificationData
HartCalculator(Collection<PurificationData> datasets)
          Creates a new scores calculator from a list of purification data sets.
 

Uses of PurificationData in procope.methods.scores.bootstrap
 

Methods in procope.methods.scores.bootstrap that return PurificationData
 PurificationData PurificationBootstrapSamples.getSample(int sample)
          Returns a given sample from the set.
 

Constructors in procope.methods.scores.bootstrap with parameters of type PurificationData
PurificationBootstrapSamples(PurificationData data, int numberOfSamples)
          Creates a new set of bootstrap samples.
 

Uses of PurificationData in procope.tools.userclasses
 

Methods in procope.tools.userclasses with parameters of type PurificationData
 ScoresCalculator UserScoresCalculator.generateScoresCalculator(PurificationData[] data, Object... additionalParameters)
          Generates the actual ScoresCalculator object for this user scores calculator.