org.geworkbench.util.pathwaydecoder.mutualinformation
Class MindyData

java.lang.Object
  extended by org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData
All Implemented Interfaces:
java.io.Serializable

public class MindyData
extends java.lang.Object
implements java.io.Serializable

Class containing MINDY run results.

Version:
$Id: MindyData.java 8424 2011-10-19 16:34:53Z zji $
Author:
mhall, oshteynb
See Also:
Serialized Form

Constructor Summary
MindyData(CSMicroarraySet arraySet, java.util.ArrayList<DSMicroarray> arrayForMindyRun, float setFraction, DSGeneMarker transFac)
           
MindyData(CSMicroarraySet arraySet, java.util.List<MindyResultRow> data, float setFraction)
          Constructor.
 
Method Summary
 void addToSortkeyMap(java.text.Collator myCollator, DSGeneMarker target)
          used for sorting
 void addToTargetInfoMap(double correlation, DSGeneMarker target)
          used for sorting
 double calcPearsonCorrelation(DSGeneMarker target)
          Pearson correlation between target and TF
 java.util.ArrayList<DSGeneMarker> convertToDSGeneMarker(java.util.List<MindyGeneMarker> list)
           
 java.util.ArrayList<MindyGeneMarker> convertToMindyGeneMarker(java.util.List<DSGeneMarker> list)
           
static java.util.ArrayList<DSMicroarray> createArrayForMindyRun(DSMicroarraySet inSet, DSPanel<DSMicroarray> arraySet)
           
 java.util.ArrayList<DSMicroarray> getArrayForMindyRun()
           
 CSMicroarraySet getArraySet()
           
 double getCorrelation(DSGeneMarker target)
          Pearson correlation between the transcription factor and the target gene.
 int getDataSize()
           
 int getFilteredDataSize()
           
 ModulatorStatistics getFilteredStatistics(DSGeneMarker modulator)
           
 java.text.CollationKey getGeneNameSortKey(DSGeneMarker target)
          Gene name CollationKey that is used for sorting
 java.util.HashMap<DSGeneMarker,ModulatorInfo> getModulatorInfoMap()
           
 java.util.List<DSGeneMarker> getModulators()
          Get the list of mondulators.
 java.util.List<MindyResultRow> getRows(DSGeneMarker modulator)
          Get the list of MINDY result rows
 java.util.List<MindyResultRow> getRows(DSGeneMarker modulator, java.util.List<DSGeneMarker> limitTargets)
          Get the list of MINDY result rows
 float getScore(DSGeneMarker modulator, DSGeneMarker target)
          Get the score
 float getSetFraction()
          Get the fraction of the sample to display on the heat map.
 ModulatorStatistics getStatistics(DSGeneMarker modulator)
          Get the statics for the specified modulator.
 java.util.List<DSGeneMarker> getTargets(DSGeneMarker modulator)
          Get a list of targets for one modulator
 java.util.List<DSGeneMarker> getTargets(java.util.List<DSGeneMarker> modulatorsList)
          Get a list of targets for all modulator in the list
 DSGeneMarker getTranscriptionFactor()
          Get the transcription factor specified for MINDY data.
 void initFilteredModulatorInfoMap()
           
 boolean isAnnotated()
           
 boolean isEmpty()
           
 void setAnnotated(boolean annotated)
           
 void setFilteredModulatorInfoMap(java.util.HashMap<DSGeneMarker,ModulatorInfo> filteredModulatorInfoMap)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

MindyData

public MindyData(CSMicroarraySet arraySet,
                 java.util.ArrayList<DSMicroarray> arrayForMindyRun,
                 float setFraction,
                 DSGeneMarker transFac)

MindyData

public MindyData(CSMicroarraySet arraySet,
                 java.util.List<MindyResultRow> data,
                 float setFraction)
Constructor.

Parameters:
arraySet - - microarray set
data - - list of MINDY result rows
setFraction - - Sample per Condition in fraction
Method Detail

setFilteredModulatorInfoMap

public void setFilteredModulatorInfoMap(java.util.HashMap<DSGeneMarker,ModulatorInfo> filteredModulatorInfoMap)

initFilteredModulatorInfoMap

public void initFilteredModulatorInfoMap()

getModulatorInfoMap

public java.util.HashMap<DSGeneMarker,ModulatorInfo> getModulatorInfoMap()

addToSortkeyMap

public void addToSortkeyMap(java.text.Collator myCollator,
                            DSGeneMarker target)
used for sorting

Parameters:
myCollator -
target -

addToTargetInfoMap

public void addToTargetInfoMap(double correlation,
                               DSGeneMarker target)
used for sorting

Parameters:
myCollator -
target -

calcPearsonCorrelation

public double calcPearsonCorrelation(DSGeneMarker target)
Pearson correlation between target and TF

Parameters:
target -

createArrayForMindyRun

public static java.util.ArrayList<DSMicroarray> createArrayForMindyRun(DSMicroarraySet inSet,
                                                                       DSPanel<DSMicroarray> arraySet)

isAnnotated

public boolean isAnnotated()

setAnnotated

public void setAnnotated(boolean annotated)

getArraySet

public CSMicroarraySet getArraySet()

getArrayForMindyRun

public java.util.ArrayList<DSMicroarray> getArrayForMindyRun()

convertToMindyGeneMarker

public java.util.ArrayList<MindyGeneMarker> convertToMindyGeneMarker(java.util.List<DSGeneMarker> list)

convertToDSGeneMarker

public java.util.ArrayList<DSGeneMarker> convertToDSGeneMarker(java.util.List<MindyGeneMarker> list)

getDataSize

public int getDataSize()

getFilteredDataSize

public int getFilteredDataSize()

getStatistics

public ModulatorStatistics getStatistics(DSGeneMarker modulator)
Get the statics for the specified modulator.

Parameters:
modulator - - modulator for which to get the statistics
Returns:
- ModulatorStatistics object

getFilteredStatistics

public ModulatorStatistics getFilteredStatistics(DSGeneMarker modulator)

getTranscriptionFactor

public DSGeneMarker getTranscriptionFactor()
Get the transcription factor specified for MINDY data.

Returns:
the transcription factor gene marker

getSetFraction

public float getSetFraction()
Get the fraction of the sample to display on the heat map.

Returns:
fraction of the sample to display

getModulators

public java.util.List<DSGeneMarker> getModulators()
Get the list of mondulators.

Returns:
list of modulators

getRows

public java.util.List<MindyResultRow> getRows(DSGeneMarker modulator)
Get the list of MINDY result rows

Parameters:
modulator -
Returns:
list of MINDY result rows

isEmpty

public boolean isEmpty()

getRows

public java.util.List<MindyResultRow> getRows(DSGeneMarker modulator,
                                              java.util.List<DSGeneMarker> limitTargets)
Get the list of MINDY result rows

Parameters:
modulator -
limitTargets - - target marker set being displayed
Returns:
list of MINDY result rows one row for each marker, all rows for modulator if limitTargets is null

getCorrelation

public double getCorrelation(DSGeneMarker target)
Pearson correlation between the transcription factor and the target gene. Used primarily for the heat map.

Returns:
result of Pearson correlation

getGeneNameSortKey

public java.text.CollationKey getGeneNameSortKey(DSGeneMarker target)
Gene name CollationKey that is used for sorting

Returns:
CollationKey

getTargets

public java.util.List<DSGeneMarker> getTargets(DSGeneMarker modulator)
Get a list of targets for one modulator

Parameters:
modulator -
Returns:
list of targets

getTargets

public java.util.List<DSGeneMarker> getTargets(java.util.List<DSGeneMarker> modulatorsList)
Get a list of targets for all modulator in the list

Parameters:
modulatorsList -
Returns:
list of targets

getScore

public float getScore(DSGeneMarker modulator,
                      DSGeneMarker target)
Get the score

Parameters:
modulator -
target -
Returns:
the score used in MINDY data