org.geworkbench.bison.datastructure.bioobjects.microarray
Class CSMasterRegulatorResultSet<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.CSMasterRegulatorResultSet<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>, DSMasterRagulatorResultSet<T>, DSItemList<DSMicroarray>, DSDescribable, DSExtendable, DSIdentifiable, DSNamed

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

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.DSMasterRagulatorResultSet
ACTIVATOR, REPRESSOR
 
Constructor Summary
CSMasterRegulatorResultSet(DSMicroarraySet parent, java.lang.String label, int markerCount)
           
 
Method Summary
 DSItemList<DSGeneMarker> getActivators()
           
 DSItemList<DSGeneMarker> getGenesInRegulon(DSGeneMarker TF)
           
 DSItemList<DSGeneMarker> getGenesInTargetList(DSGeneMarker TF)
           
 int getMarkerCount()
           
 double getMaxValue()
           
 DSMicroarraySet getMicroarraySet()
           
 double getMinValue()
           
 char getMode(DSGeneMarker TF)
           
 java.lang.Object getNES(DSGeneMarker TF)
           
 java.lang.Object getOddRatio(DSGeneMarker TF)
           
 double getPValue(DSGeneMarker TF)
           
 int getRank(DSGeneMarker marker)
           
 DSItemList<DSGeneMarker> getRepressors()
           
 DSItemList<DSGeneMarker> getTFs()
           
 double getValue(DSGeneMarker key)
           
 void setGenesInRegulon(DSGeneMarker TF, DSItemList<DSGeneMarker> markers)
           
 void setGenesInTargetList(DSGeneMarker TF, DSItemList<DSGeneMarker> markers)
           
 void setMaxValue(double val)
           
 void setMinValue(double val)
           
 void setMode(DSGeneMarker TF, char mode)
           
 void setNES(DSGeneMarker TF, java.lang.Object nes)
           
 void setOddRatio(DSGeneMarker TF, java.lang.Object odd)
           
 void setPValue(DSGeneMarker TF, double pValue)
           
 void setRanks(java.util.Map<DSGeneMarker,java.lang.Integer> ranks)
           
 void setValues(java.util.Map<DSGeneMarker,java.lang.Double> values)
           
 
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, 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.DSAncillaryDataSet
getParentDataSet
 
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

CSMasterRegulatorResultSet

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

getMicroarraySet

public DSMicroarraySet getMicroarraySet()
Specified by:
getMicroarraySet in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

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>

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>

setMode

public void setMode(DSGeneMarker TF,
                    char mode)
Specified by:
setMode in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getMode

public char getMode(DSGeneMarker TF)
Specified by:
getMode in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getActivators

public DSItemList<DSGeneMarker> getActivators()
Specified by:
getActivators in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getRepressors

public DSItemList<DSGeneMarker> getRepressors()
Specified by:
getRepressors in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getTFs

public DSItemList<DSGeneMarker> getTFs()
Specified by:
getTFs in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getMarkerCount

public int getMarkerCount()
Specified by:
getMarkerCount in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

setValues

public void setValues(java.util.Map<DSGeneMarker,java.lang.Double> values)
Specified by:
setValues in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getValue

public double getValue(DSGeneMarker key)
Specified by:
getValue in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

setMinValue

public void setMinValue(double val)
Specified by:
setMinValue in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

setMaxValue

public void setMaxValue(double val)
Specified by:
setMaxValue in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getMinValue

public double getMinValue()
Specified by:
getMinValue in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getMaxValue

public double getMaxValue()
Specified by:
getMaxValue in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getRank

public int getRank(DSGeneMarker marker)
Specified by:
getRank in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

setRanks

public void setRanks(java.util.Map<DSGeneMarker,java.lang.Integer> ranks)
Specified by:
setRanks in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

setOddRatio

public void setOddRatio(DSGeneMarker TF,
                        java.lang.Object odd)
Specified by:
setOddRatio in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getOddRatio

public java.lang.Object getOddRatio(DSGeneMarker TF)
Specified by:
getOddRatio in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

setNES

public void setNES(DSGeneMarker TF,
                   java.lang.Object nes)
Specified by:
setNES in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>

getNES

public java.lang.Object getNES(DSGeneMarker TF)
Specified by:
getNES in interface DSMasterRagulatorResultSet<T extends DSGeneMarker>