org.geworkbench.bison.datastructure.bioobjects.microarray
Class CSSignificanceResultSet<T extends DSGeneMarker>

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<DSMicroarray>
                              extended by org.geworkbench.bison.datastructure.bioobjects.microarray.CSSignificanceResultSet<T>
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<DSMicroarray>, java.util.Collection<DSMicroarray>, java.util.List<DSMicroarray>, java.util.RandomAccess, DSAncillaryDataSet<DSMicroarray>, DSDataSet<DSMicroarray>, DSSignificanceResultSet<T>, DSItemList<DSMicroarray>, DSDescribable, DSExtendable, DSIdentifiable, DSNamed
Direct Known Subclasses:
CSAnovaResultSet, CSTTestResultSet

public class CSSignificanceResultSet<T extends DSGeneMarker>
extends CSAncillaryDataSet<DSMicroarray>
implements DSSignificanceResultSet<T>

Version:
$Id: CSSignificanceResultSet.java 8818 2012-01-31 22:07:39Z maz $
Author:
John Watkinson
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
 
Fields inherited from interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSSignificanceResultSet
CASE, CONTROL
 
Constructor Summary
CSSignificanceResultSet(DSMicroarraySet parent, java.lang.String label, java.lang.String[] caseLabels, java.lang.String[] controlLabels, double alpha)
           
 
Method Summary
 void addSigGenToPanel(T marker)
           
 double getCriticalPValue()
           
 java.lang.Double getFoldChange(T marker)
           
 boolean getIsLogNormalized()
           
 java.lang.String[] getLabels(int index)
           
 DSMicroarraySet getParentDataSet()
          Gets the parent data set for this ancillary data set.
 java.lang.Double getSignificance(T marker)
          Gets the significance value for the marker.
 DSPanel<T> getSignificantMarkers()
           
 java.lang.Double getTValue(T marker)
           
 void saveDataToCSVFile()
           
 void setFoldChange(T marker, double value)
           
 void setMarker(T marker, double value)
           
 void setSignificance(T marker, double value)
           
 void setTValue(T marker, double value)
           
 void sortMarkersBySignificance()
           
 
Methods inherited from class org.geworkbench.bison.datastructure.biocollections.CSAncillaryDataSet
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, writeToFile
 
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.DSDataSet
addObject, getColumnOrder, getCompatibilityLabel, getDataSetName, getExperimentInformation, getFile, getObject, isActive, setColumnOrder, setExperimentInformation, setFile, writeToFile
 
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

CSSignificanceResultSet

public CSSignificanceResultSet(DSMicroarraySet parent,
                               java.lang.String label,
                               java.lang.String[] caseLabels,
                               java.lang.String[] controlLabels,
                               double alpha)
Method Detail

getSignificance

public java.lang.Double getSignificance(T marker)
Description copied from interface: DSSignificanceResultSet
Gets the significance value for the marker.

Specified by:
getSignificance in interface DSSignificanceResultSet<T extends DSGeneMarker>

getTValue

public java.lang.Double getTValue(T marker)
Specified by:
getTValue in interface DSSignificanceResultSet<T extends DSGeneMarker>

setSignificance

public void setSignificance(T marker,
                            double value)
Specified by:
setSignificance in interface DSSignificanceResultSet<T extends DSGeneMarker>

setTValue

public void setTValue(T marker,
                      double value)
Specified by:
setTValue in interface DSSignificanceResultSet<T extends DSGeneMarker>

setFoldChange

public void setFoldChange(T marker,
                          double value)
Specified by:
setFoldChange in interface DSSignificanceResultSet<T extends DSGeneMarker>

getFoldChange

public java.lang.Double getFoldChange(T marker)
Specified by:
getFoldChange in interface DSSignificanceResultSet<T extends DSGeneMarker>

setMarker

public void setMarker(T marker,
                      double value)
Specified by:
setMarker in interface DSSignificanceResultSet<T extends DSGeneMarker>

addSigGenToPanel

public void addSigGenToPanel(T marker)
Specified by:
addSigGenToPanel in interface DSSignificanceResultSet<T extends DSGeneMarker>

getSignificantMarkers

public DSPanel<T> getSignificantMarkers()
Specified by:
getSignificantMarkers in interface DSSignificanceResultSet<T extends DSGeneMarker>

getCriticalPValue

public double getCriticalPValue()
Specified by:
getCriticalPValue in interface DSSignificanceResultSet<T extends DSGeneMarker>

getLabels

public java.lang.String[] getLabels(int index)
Specified by:
getLabels in interface DSSignificanceResultSet<T extends DSGeneMarker>

sortMarkersBySignificance

public void sortMarkersBySignificance()
Specified by:
sortMarkersBySignificance in interface DSSignificanceResultSet<T extends DSGeneMarker>

getParentDataSet

public DSMicroarraySet getParentDataSet()
Description copied from interface: DSAncillaryDataSet
Gets the parent data set for this ancillary data set.

Specified by:
getParentDataSet in interface DSAncillaryDataSet<DSMicroarray>
Specified by:
getParentDataSet in interface DSSignificanceResultSet<T extends DSGeneMarker>
Overrides:
getParentDataSet in class CSAncillaryDataSet<DSMicroarray>
Returns:

saveDataToCSVFile

public void saveDataToCSVFile()
Specified by:
saveDataToCSVFile in interface DSSignificanceResultSet<T extends DSGeneMarker>

getIsLogNormalized

public boolean getIsLogNormalized()
Specified by:
getIsLogNormalized in interface DSSignificanceResultSet<T extends DSGeneMarker>