de.unihalle.informatik.Alida.demo
Class ALDClusterExperiment

java.lang.Object
  extended by de.unihalle.informatik.Alida.operator.ALDOperator
      extended by de.unihalle.informatik.Alida.demo.ALDClusterExperiment
All Implemented Interfaces:
ALDConfigurationValidator, ALDOperatorExecutionProgressEventListener, EventListener

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

Demo operator to cluster experimental data.

First, optionally the data are normalized. Second, again optionally, the data are subjected to a PCA. Finally clustered via k-means.

Author:
posch

Nested Class Summary
 
Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
ALDOperator.HidingMode
 
Field Summary
 
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider
 
Constructor Summary
ALDClusterExperiment()
          Default constructor.
ALDClusterExperiment(ExperimentalData _experiment)
          Constructor.
 
Method Summary
 List<Set<Integer>> getClusters()
          Get value of result.
 Boolean getDoNormalize()
           
 Boolean getDoPCA()
           
 ExperimentalData getExperiment()
          Get value of experiment.
 ExperimentalData getNormalizedExperiment()
           
protected  void operate()
          This method does the actual work and needs to be implemented by every subclass.
 void setDoNormalize(Boolean doNormalize)
           
 void setDoPCA(Boolean doPCA)
           
 void setExperiment(ExperimentalData value)
          Set value of data.
 
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
addOperatorExecutionProgressEventListener, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, getHidingMode, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterNames, getSupplementalNames, getVerbose, getVersion, handleOperatorExecutionProgressEvent, isConfigured, print, print, print, printInterface, printInterface, readHistory, readResolve, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, runOp, runOp, runOp, setConstructionMode, setHidingMode, setName, setParameter, setVerbose, toStringVerbose, unconfiguredItems, validate, validateCustom, validateGeneric, writeHistory, writeHistory, writeHistory
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ALDClusterExperiment

public ALDClusterExperiment()
                     throws ALDOperatorException
Default constructor.

Throws:
ALDOperatorException

ALDClusterExperiment

public ALDClusterExperiment(ExperimentalData _experiment)
                     throws ALDOperatorException
Constructor.

Parameters:
_experiment - Experimental data
Throws:
ALDOperatorException
Method Detail

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

getClusters

public List<Set<Integer>> getClusters()
Get value of result. Explanation: Normalized experiment.

Returns:
value of result

getExperiment

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

Returns:
value of data

setExperiment

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

Parameters:
value - New value of data

getDoNormalize

public Boolean getDoNormalize()
Returns:
the doNormalize

setDoNormalize

public void setDoNormalize(Boolean doNormalize)
Parameters:
doNormalize - the doNormalize to set

getDoPCA

public Boolean getDoPCA()
Returns:
the doPCA

setDoPCA

public void setDoPCA(Boolean doPCA)
Parameters:
doPCA - the doPCA to set

getNormalizedExperiment

public ExperimentalData getNormalizedExperiment()
Returns:
the normalizedExperiment


Copyright © 2010–2014 Martin Luther University Halle-Wittenberg, Institute of Computer Science, Pattern Recognition and Bioinformatics. All rights reserved.