de.unihalle.informatik.Alida.demo
Class SummarizeClusters

java.lang.Object
  extended by de.unihalle.informatik.Alida.operator.ALDOperator
      extended by de.unihalle.informatik.Alida.demo.SummarizeClusters
All Implemented Interfaces:
ALDConfigurationValidator

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION)
public class SummarizeClusters
extends ALDOperator

Demo operator to summarize the cluster detecteded within experimental data.

Author:
posch

Nested Class Summary
 
Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
ALDOperator.HidingMode
 
Field Summary
private  java.util.List<java.util.Set<java.lang.Integer>> clusters
          Clusters represented as a list of clusters, where each cluster is a set of experiment Ids, i.e. indices into to input experimental data.
private  ExperimentalData experiment
          Input data
private  ExperimentalData summaryOfExperiment
          Summary of experiment .
 
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
completeDAG, name, portHashAccess, verbose, versionProvider
 
Constructor Summary
SummarizeClusters()
          Default constructor.
SummarizeClusters(ExperimentalData _experiment)
          Constructor.
 
Method Summary
 java.util.List<java.util.Set<java.lang.Integer>> getClusters()
           
 ExperimentalData getExperiment()
          Get value of experiment.
 ExperimentalData getSummaryOfExperiment()
           
protected  void operate()
          This method does the actual work and needs to be implemented by every subclass.
 void setClusters(java.util.List<java.util.Set<java.lang.Integer>> clusters)
           
 void setExperiment(ExperimentalData value)
          Set value of data.
 
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
deserializeFromXmlFile, fieldContained, getALDPortHashAccessKey, getConstructionMode, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterNames, getSupplementalNames, getVerbose, getVersion, isConfigured, parametersToXmlObject, print, print, print, printInterface, printInterface, readHistory, readResolve, reinitializeParameterDescriptors, runOp, runOp, runOp, serializeToXmlFile, setConstructionMode, setName, setParameter, setParametersFromXml, setParametersFromXml, setVerbose, toStringVerbose, unconfiguredItems, validate, validateCustom, validateGeneric, writeHistory, writeHistory, writeHistory, writeParametersToXml
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

clusters

@Parameter(label="Clusters",
           direction=IN,
           description="Clusters")
private transient java.util.List<java.util.Set<java.lang.Integer>> clusters
Clusters represented as a list of clusters, where each cluster is a set of experiment Ids, i.e. indices into to input experimental data.


experiment

@Parameter(label="Experimental data",
           required=true,
           direction=IN,
           description="Experimental data to cluster")
private ExperimentalData experiment
Input data


summaryOfExperiment

@Parameter(label="Summary",
           direction=OUT,
           description="Summary of experimental data")
private transient ExperimentalData summaryOfExperiment
Summary of experiment .

Constructor Detail

SummarizeClusters

public SummarizeClusters()
                  throws ALDOperatorException
Default constructor.

Throws:
ALDOperatorException

SummarizeClusters

public SummarizeClusters(ExperimentalData _experiment)
                  throws ALDOperatorException
Constructor.

Parameters:
experiment - Experimental data
Throws:
ALDOperatorException
Method Detail

getClusters

public java.util.List<java.util.Set<java.lang.Integer>> getClusters()
Returns:
the clusters

getExperiment

public ExperimentalData getExperiment()
Get value of experiment. Explanation: Experimental data to be normalized.

Returns:
value of data

getSummaryOfExperiment

public ExperimentalData getSummaryOfExperiment()
Returns:
the summaryOfExperiment

operate

protected void operate()
                throws ALDOperatorException,
                       ALDProcessingDAGException
Description copied from class: ALDOperator
This method does the actual work and needs to be implemented by every subclass.

Specified by:
operate in class ALDOperator
Throws:
ALDOperatorException
ALDProcessingDAGException

setClusters

public void setClusters(java.util.List<java.util.Set<java.lang.Integer>> clusters)
Parameters:
clusters - the clusters to set

setExperiment

public void setExperiment(ExperimentalData value)
Set value of data. Explanation: Experimental data to be normalized.

Parameters:
value - New value of data