org.geworkbench.bison.datastructure.biocollections.pca
Class CSPCADataSet

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<T>
              org.geworkbench.bison.datastructure.complex.panels.CSItemList<T>
                  org.geworkbench.bison.datastructure.complex.panels.CSSequentialItemList<T>
                      org.geworkbench.bison.datastructure.biocollections.CSDataSet<T>
                          org.geworkbench.bison.datastructure.biocollections.CSAncillaryDataSet
                              org.geworkbench.bison.datastructure.biocollections.pca.CSPCADataSet

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess, DSAncillaryDataSet, DSDataSet, DSPCADataSet, DSItemList, DSDescribable, DSExtendable, DSIdentifiable, DSNamed

public class CSPCADataSet
extends CSAncillaryDataSet
implements DSPCADataSet

Version:

$Id: CSPCADataSet.java,v 1.1 2008-03-14 20:06:21 keshav Exp $

See Also:

Serialized Form

Field Summary

Fields inherited from class org.geworkbench.bison.datastructure.biocollections.CSDataSet

absPath, arraySetId, compatibilityLabel, dataSetProperties, descriptions, dirty, experimentInfo, extend, file, label, maResource

Fields inherited from class org.geworkbench.bison.datastructure.complex.panels.CSItemList

objectMap

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

CSPCADataSet(DSDataSet parent, java.lang.String label, java.lang.String variables, int numPCs, float[][] u_Matrix, java.util.HashMap eigenValues, java.util.HashMap eigenVectors, java.util.HashMap percentVariations)

Method Summary

java.io.File	getDataSetFile() Gets the data set file.
java.util.HashMap	getEigenValues()
java.util.HashMap	getEigenVectors()
int	getNumPCs()
java.util.HashMap	getPercentVars()
float[][]	getUMatrix()
java.lang.String	getVariables()
void	setDataSetFile(java.io.File file) Sets the data set file.
void	writeToFile(java.lang.String fileName) Writes the data set to the provided filename.

Methods inherited from class org.geworkbench.bison.datastructure.biocollections.CSAncillaryDataSet

getParentDataSet, setParent

Methods inherited from class org.geworkbench.bison.datastructure.biocollections.CSDataSet

addDescription, addNameValuePair, addObject, allowMultipleValues, clearName, forceUniqueValue, getCompatibilityLabel, getDataSetName, getDescriptions, getExperimentInformation, getFile, getID, getLabel, getObject, getPath, getValuesForName, isActive, isDirty, isUniqueValue, readFromResource, removeDescription, removeResource, setAbsPath, setDirty, setExperimentInformation, setFile, setID, setLabel, setResource, toString, writeToResource

Methods inherited from class org.geworkbench.bison.datastructure.complex.panels.CSSequentialItemList

add, add, remove

Methods inherited from class org.geworkbench.bison.datastructure.complex.panels.CSItemList

addAll, clear, equals, get, get, hashCode, rename

Methods inherited from class java.util.ArrayList

addAll, clone, contains, ensureCapacity, get, indexOf, isEmpty, lastIndexOf, remove, removeRange, set, size, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

iterator, listIterator, listIterator, subList

Methods inherited from class java.util.AbstractCollection

containsAll, removeAll, retainAll

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.geworkbench.bison.datastructure.biocollections.DSAncillaryDataSet

getParentDataSet

Methods inherited from interface org.geworkbench.bison.datastructure.biocollections.DSDataSet

addObject, getCompatibilityLabel, getDataSetName, getExperimentInformation, getFile, getObject, getPath, isActive, readFromResource, removeResource, setAbsPath, setExperimentInformation, setFile, setResource, writeToResource

Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSDescribable

addDescription, getDescriptions, removeDescription

Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSNamed

getLabel, setLabel

Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSExtendable

addNameValuePair, allowMultipleValues, clearName, forceUniqueValue, getValuesForName, isUniqueValue

Methods inherited from interface org.geworkbench.bison.datastructure.complex.panels.DSItemList

get, get, rename

Methods inherited from interface java.util.List

add, add, addAll, addAll, clear, contains, containsAll, equals, get, hashCode, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, retainAll, set, size, subList, toArray, toArray

Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSIdentifiable

getID, setID

Constructor Detail

CSPCADataSet

public CSPCADataSet(DSDataSet parent,
                    java.lang.String label,
                    java.lang.String variables,
                    int numPCs,
                    float[][] u_Matrix,
                    java.util.HashMap eigenValues,
                    java.util.HashMap eigenVectors,
                    java.util.HashMap percentVariations)

Method Detail

getDataSetFile

public java.io.File getDataSetFile()

Description copied from interface: DSAncillaryDataSet

Gets the data set file.

Specified by:

getDataSetFile in interface DSAncillaryDataSet

Specified by:

getDataSetFile in interface DSPCADataSet

Returns:

setDataSetFile

public void setDataSetFile(java.io.File file)

Description copied from interface: DSAncillaryDataSet

Sets the data set file.

Specified by:

setDataSetFile in interface DSAncillaryDataSet

Specified by:

setDataSetFile in interface DSPCADataSet

Parameters:

file - the file to associate with this data set.

getNumPCs

public int getNumPCs()

Specified by:

getNumPCs in interface DSPCADataSet

Returns:

getEigenValues

public java.util.HashMap getEigenValues()

Specified by:

getEigenValues in interface DSPCADataSet

Returns:

getPercentVars

public java.util.HashMap getPercentVars()

Specified by:

getPercentVars in interface DSPCADataSet

Returns:

getEigenVectors

public java.util.HashMap getEigenVectors()

Specified by:

getEigenVectors in interface DSPCADataSet

Returns:

getUMatrix

public float[][] getUMatrix()

Specified by:

getUMatrix in interface DSPCADataSet

Returns:

getVariables

public java.lang.String getVariables()

Specified by:

getVariables in interface DSPCADataSet

Returns:

writeToFile

public void writeToFile(java.lang.String fileName)

Description copied from interface: DSDataSet

Writes the data set to the provided filename.

Specified by:

writeToFile in interface DSDataSet

Specified by:

writeToFile in interface DSPCADataSet

Overrides:

writeToFile in class CSDataSet

Parameters:

fileName - the filename (path) to which to write this file.