org.geworkbench.util.pathwaydecoder.mutualinformation
Class AdjacencyMatrixDataSet

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.util.pathwaydecoder.mutualinformation.AdjacencyMatrixDataSet

All Implemented Interfaces:

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

public class AdjacencyMatrixDataSet
extends CSAncillaryDataSet
implements DSAncillaryDataSet

Author:

John Watkinson

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

AdjacencyMatrixDataSet(AdjacencyMatrix matrix, int geneId, double threshold, int depth, java.lang.String name, java.lang.String networkName, DSMicroarraySet parent)

Method Summary

java.io.File	getDataSetFile() Gets the data set file.
int	getDepth()
int	getGeneId()
AdjacencyMatrix	getMatrix()
java.lang.String	getNetworkName()
double	getThreshold()
void	readFromFile(java.lang.String fileName, DSMicroarraySet<DSMicroarray> maSet)
void	setDataSetFile(java.io.File file) Sets the data set file.
void	setDepth(int depth)
void	setGeneId(int geneId)
void	setMatrix(AdjacencyMatrix matrix)
void	setNetworkName(java.lang.String networkName)
void	setThreshold(double threshold)
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

AdjacencyMatrixDataSet

public AdjacencyMatrixDataSet(AdjacencyMatrix matrix,
                              int geneId,
                              double threshold,
                              int depth,
                              java.lang.String name,
                              java.lang.String networkName,
                              DSMicroarraySet parent)

Method Detail

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

Overrides:

writeToFile in class CSDataSet

Parameters:

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

readFromFile

public void readFromFile(java.lang.String fileName,
                         DSMicroarraySet<DSMicroarray> maSet)

getMatrix

public AdjacencyMatrix getMatrix()

setMatrix

public void setMatrix(AdjacencyMatrix matrix)

getGeneId

public int getGeneId()

setGeneId

public void setGeneId(int geneId)

getThreshold

public double getThreshold()

setThreshold

public void setThreshold(double threshold)

getDepth

public int getDepth()

setDepth

public void setDepth(int depth)

getDataSetFile

public java.io.File getDataSetFile()

Description copied from interface: DSAncillaryDataSet

Gets the data set file.

Specified by:

getDataSetFile in interface DSAncillaryDataSet

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

Parameters:

file - the file to associate with this data set.

getNetworkName

public java.lang.String getNetworkName()

setNetworkName

public void setNetworkName(java.lang.String networkName)