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

java.lang.Object
  extended by java.util.AbstractCollection<E>
      extended by java.util.AbstractList<E>
          extended by java.util.ArrayList<T>
              extended by org.geworkbench.bison.datastructure.complex.panels.CSItemList<T>
                  extended by org.geworkbench.bison.datastructure.complex.panels.CSSequentialItemList<T>
                      extended by org.geworkbench.bison.datastructure.biocollections.CSDataSet<T>
                          extended by org.geworkbench.bison.datastructure.biocollections.CSAncillaryDataSet<DSBioObject>
                              extended by org.geworkbench.bison.datastructure.biocollections.pca.CSPCADataSet
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<DSBioObject>, java.util.Collection<DSBioObject>, java.util.List<DSBioObject>, java.util.RandomAccess, DSAncillaryDataSet<DSBioObject>, DSDataSet<DSBioObject>, DSPCADataSet, DSItemList<DSBioObject>, DSDescribable, DSExtendable, DSIdentifiable, DSNamed

public class CSPCADataSet
extends CSAncillaryDataSet<DSBioObject>
implements DSPCADataSet

Version:
$Id: CSPCADataSet.java 8481 2011-11-02 15:43:58Z zji $
See Also:
Serialized Form

Field Summary
 
Fields inherited from class org.geworkbench.bison.datastructure.biocollections.CSDataSet
columnOrder, compatibilityLabel, dataSetProperties, description, experimentInfo, extend, file, label
 
Fields inherited from class java.util.AbstractList
modCount
 
Constructor Summary
CSPCADataSet(DSDataSet<? extends DSMicroarray> parent, java.lang.String label, java.lang.String variables, int numPCs, float[][] u_Matrix, java.util.HashMap<java.lang.Integer,java.lang.Double> eigenValues, java.util.HashMap<java.lang.Integer,java.util.List<java.lang.String>> eigenVectors, java.util.HashMap<java.lang.Integer,java.lang.String> percentVariations)
           
 
Method Summary
 java.util.HashMap<java.lang.Integer,java.lang.Double> getEigenValues()
           
 java.util.HashMap<java.lang.Integer,java.util.List<java.lang.String>> getEigenVectors()
           
 int getNumPCs()
           
 java.util.HashMap<java.lang.Integer,java.lang.String> getPercentVars()
           
 float[][] getUMatrix()
           
 java.lang.String getVariables()
           
 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
addNameValuePair, addObject, allowMultipleValues, clearName, forceUniqueValue, getColumnOrder, getCompatibilityLabel, getDataSetName, getDescription, getExperimentInformation, getFile, getID, getLabel, getObject, getValuesForName, isActive, isUniqueValue, setColumnOrder, setDescription, setExperimentInformation, setFile, setID, setLabel, toString
 
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, hashCode, set, setLabel
 
Methods inherited from class java.util.ArrayList
addAll, clone, contains, ensureCapacity, get, indexOf, isEmpty, lastIndexOf, remove, removeRange, 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, getColumnOrder, getCompatibilityLabel, getDataSetName, getExperimentInformation, getFile, getObject, isActive, setColumnOrder, setExperimentInformation, setFile
 
Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSDescribable
getDescription, setDescription
 
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
 
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<? extends DSMicroarray> parent,
                    java.lang.String label,
                    java.lang.String variables,
                    int numPCs,
                    float[][] u_Matrix,
                    java.util.HashMap<java.lang.Integer,java.lang.Double> eigenValues,
                    java.util.HashMap<java.lang.Integer,java.util.List<java.lang.String>> eigenVectors,
                    java.util.HashMap<java.lang.Integer,java.lang.String> percentVariations)
Method Detail

getNumPCs

public int getNumPCs()
Specified by:
getNumPCs in interface DSPCADataSet
Returns:

getEigenValues

public java.util.HashMap<java.lang.Integer,java.lang.Double> getEigenValues()
Specified by:
getEigenValues in interface DSPCADataSet
Returns:

getPercentVars

public java.util.HashMap<java.lang.Integer,java.lang.String> getPercentVars()
Specified by:
getPercentVars in interface DSPCADataSet
Returns:

getEigenVectors

public java.util.HashMap<java.lang.Integer,java.util.List<java.lang.String>> 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<DSBioObject>
Overrides:
writeToFile in class CSDataSet<DSBioObject>
Parameters:
fileName - the filename (path) to which to write this file.