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

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.bioobjects.microarray.CSMasterRegulatorResultSet<T>

All Implemented Interfaces:

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

public class CSMasterRegulatorResultSet<T extends DSGeneMarker>
extends CSAncillaryDataSet
implements DSMasterRagulatorResultSet<T>

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

Fields inherited from interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRagulatorResultSet

CASE, CONTROL

Constructor Summary

CSMasterRegulatorResultSet(DSMicroarraySet parent, java.lang.String label, int markerCount)

Method Summary

java.io.File	getDataSetFile() Gets the data set file.
int	getGeneNumInRegulon(DSGeneMarker TF)
int	getGeneNumInTargetList(DSGeneMarker TF)
DSItemList<DSGeneMarker>	getGenesInRegulon(DSGeneMarker TF)
DSItemList<DSGeneMarker>	getGenesInTargetList(DSGeneMarker TF)
int	getMarkerCount()
DSMicroarraySet	getMicroarraySet() Gets information for the marker.
double	getPValue(DSGeneMarker TF)
double	getPValueOf(DSGeneMarker TF, DSGeneMarker targetGene)
DSSignificanceResultSet<DSGeneMarker>	getSignificanceResultSet()
DSItemList<DSGeneMarker>	getTFs()
double	getTTestValueOf(DSGeneMarker TF, DSGeneMarker targetGene)
void	setDataSetFile(java.io.File file) Sets the data set file.
void	setGenesInRegulon(DSGeneMarker TF, DSItemList<DSGeneMarker> markers)
void	setGenesInTargetList(DSGeneMarker TF, DSItemList<DSGeneMarker> markers)
void	setPValue(DSGeneMarker TF, double pValue)
void	setPValueOf(DSGeneMarker TF, DSGeneMarker targetGene, double pValue)
void	setSignificanceResultSet(DSSignificanceResultSet<DSGeneMarker> sigSet)
void	setTTestValueOf(DSGeneMarker TF, DSGeneMarker targetGene, double tTestValue)

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, writeToFile, 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, writeToFile, 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

CSMasterRegulatorResultSet

public CSMasterRegulatorResultSet(DSMicroarraySet parent,
                                  java.lang.String label,
                                  int markerCount)

Method Detail

getMicroarraySet

public DSMicroarraySet getMicroarraySet()

Description copied from interface: DSMasterRagulatorResultSet

Gets information for the marker.

Specified by:

getMicroarraySet in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

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.

setGenesInRegulon

public void setGenesInRegulon(DSGeneMarker TF,
                              DSItemList<DSGeneMarker> markers)

Specified by:

setGenesInRegulon in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

setGenesInTargetList

public void setGenesInTargetList(DSGeneMarker TF,
                                 DSItemList<DSGeneMarker> markers)

Specified by:

setGenesInTargetList in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getGenesInRegulon

public DSItemList<DSGeneMarker> getGenesInRegulon(DSGeneMarker TF)

Specified by:

getGenesInRegulon in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getGenesInTargetList

public DSItemList<DSGeneMarker> getGenesInTargetList(DSGeneMarker TF)

Specified by:

getGenesInTargetList in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getPValueOf

public double getPValueOf(DSGeneMarker TF,
                          DSGeneMarker targetGene)

Specified by:

getPValueOf in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getTTestValueOf

public double getTTestValueOf(DSGeneMarker TF,
                              DSGeneMarker targetGene)

Specified by:

getTTestValueOf in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

setPValueOf

public void setPValueOf(DSGeneMarker TF,
                        DSGeneMarker targetGene,
                        double pValue)

Specified by:

setPValueOf in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

setTTestValueOf

public void setTTestValueOf(DSGeneMarker TF,
                            DSGeneMarker targetGene,
                            double tTestValue)

Specified by:

setTTestValueOf in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getGeneNumInRegulon

public int getGeneNumInRegulon(DSGeneMarker TF)

Specified by:

getGeneNumInRegulon in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getGeneNumInTargetList

public int getGeneNumInTargetList(DSGeneMarker TF)

Specified by:

getGeneNumInTargetList in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

setPValue

public void setPValue(DSGeneMarker TF,
                      double pValue)

Specified by:

setPValue in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getPValue

public double getPValue(DSGeneMarker TF)

Specified by:

getPValue in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getTFs

public DSItemList<DSGeneMarker> getTFs()

Specified by:

getTFs in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

setSignificanceResultSet

public void setSignificanceResultSet(DSSignificanceResultSet<DSGeneMarker> sigSet)

Specified by:

setSignificanceResultSet in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getSignificanceResultSet

public DSSignificanceResultSet<DSGeneMarker> getSignificanceResultSet()

Specified by:

getSignificanceResultSet in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getMarkerCount

public int getMarkerCount()

Specified by:

getMarkerCount in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>