org.geworkbench.util.pathwaydecoder.mutualinformation
Class AdjacencyMatrixDataSet

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
                              extended by 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)