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java.lang.Objectde.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.demo.ALDClusterExperiment
@ALDAOperator(genericExecutionMode=ALL, level=APPLICATION) public class ALDClusterExperiment
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.
Nested Class Summary |
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Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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ALDOperator.HidingMode |
Field Summary | |
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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 java.lang.Boolean |
doNormalize
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private java.lang.Boolean |
doPCA
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private ExperimentalData |
experiment
Input data |
private ExperimentalData |
normalizedExperiment
Normalization experiment in case normalization was requested. |
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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completeDAG, name, portHashAccess, verbose, versionProvider |
Constructor Summary | |
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ALDClusterExperiment()
Default constructor. |
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ALDClusterExperiment(ExperimentalData _experiment)
Constructor. |
Method Summary | |
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java.util.List<java.util.Set<java.lang.Integer>> |
getClusters()
Get value of result. |
java.lang.Boolean |
getDoNormalize()
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java.lang.Boolean |
getDoPCA()
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ExperimentalData |
getExperiment()
Get value of experiment. |
ExperimentalData |
getNormalizedExperiment()
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protected void |
operate()
This method does the actual work and needs to be implemented by every subclass. |
void |
setDoNormalize(java.lang.Boolean doNormalize)
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void |
setDoPCA(java.lang.Boolean doPCA)
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void |
setExperiment(ExperimentalData value)
Set value of data. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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@Parameter(label="Clusters", direction=OUT, description="Clusters") private transient java.util.List<java.util.Set<java.lang.Integer>> clusters
@Parameter(label="Normalize data", direction=IN, required=false, description="Initially normalize the experimental data") private java.lang.Boolean doNormalize
@Parameter(label="use PCA", direction=IN, required=false, description="apply PCA before clustering") private java.lang.Boolean doPCA
@Parameter(label="Experimental data", required=true, direction=IN, description="Experimental data to cluster") private ExperimentalData experiment
@Parameter(label="Normalized experimental data", direction=OUT, description="Normalized experimental data") private ExperimentalData normalizedExperiment
Constructor Detail |
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public ALDClusterExperiment() throws ALDOperatorException
ALDOperatorException
public ALDClusterExperiment(ExperimentalData _experiment) throws ALDOperatorException
experiment
- Experimental data
ALDOperatorException
Method Detail |
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public java.util.List<java.util.Set<java.lang.Integer>> getClusters()
public java.lang.Boolean getDoNormalize()
public java.lang.Boolean getDoPCA()
public ExperimentalData getExperiment()
public ExperimentalData getNormalizedExperiment()
protected void operate() throws ALDOperatorException, ALDProcessingDAGException
ALDOperator
operate
in class ALDOperator
ALDOperatorException
ALDProcessingDAGException
public void setDoNormalize(java.lang.Boolean doNormalize)
doNormalize
- the doNormalize to setpublic void setDoPCA(java.lang.Boolean doPCA)
doPCA
- the doPCA to setpublic void setExperiment(ExperimentalData value)
value
- New value of data
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