org.systemsbiology.inference
Class ObservationsData

java.lang.Object
  org.systemsbiology.inference.ObservationsData

All Implemented Interfaces:

Cloneable

public class ObservationsData

extends Object

implements Cloneable

A data structure containing a set of observations for M elements, and N types of evidence. Missing obesrvations are stored as a null in the data matrix, and can be denoted by either an empty cell or the string "null". Non-missing observations are stored as a Double object. This class is used by the SignificanceCalculatorDriver class.

Author:

sramsey

Field Summary

static String

NULL_OBSERVATION_STRING

Constructor Summary

ObservationsData()

ObservationsData(cern.colt.matrix.ObjectMatrix2D pObservations, String[] pElementNames, String[] pEvidenceNames)

Method Summary

Object	clone()
Double[]	getColumn(int pColumn)
String	getElementName(int pRow)
String[]	getElementNames()
String	getEvidenceName(int pColumn)
String[]	getEvidenceNames()
double	getMissingDataRate()
cern.colt.list.DoubleArrayList	getNonMissingColumnVals(int pColumn)
int	getNumElements()
int	getNumEvidences()
int	getNumObservations(int pEvidenceNum)
Double	getValueAt(int pRow, int pColumn)
void	loadFromFile(BufferedReader pBufferedReader, DataFileDelimiter pDelimiter)
void	mergeDataArray(ObservationsData[] pObservationsDataArray, boolean pAllowDuplicates)
void	setElementName(int pElementNumber, String pElementName)
void	setEvidenceName(int pEvidenceNumber, String pEvidenceName)
void	setValueAt(int pRow, int pColumn, Double pValue)
void	writeToFile(PrintWriter pPrintWriter, DataFileDelimiter pDelimiter, NumberFormat pNumberFormat)

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

NULL_OBSERVATION_STRING

public static final String NULL_OBSERVATION_STRING

See Also:

Constant Field Values

Constructor Detail

ObservationsData

public ObservationsData()

ObservationsData

public ObservationsData(cern.colt.matrix.ObjectMatrix2D pObservations,
                        String[] pElementNames,
                        String[] pEvidenceNames)

Method Detail

setElementName

public void setElementName(int pElementNumber,
                           String pElementName)

setEvidenceName

public void setEvidenceName(int pEvidenceNumber,
                            String pEvidenceName)

mergeDataArray

public void mergeDataArray(ObservationsData[] pObservationsDataArray,
                           boolean pAllowDuplicates)

clone

public Object clone()

getNumElements

public int getNumElements()

getNumEvidences

public int getNumEvidences()

getEvidenceName

public String getEvidenceName(int pColumn)

getElementName

public String getElementName(int pRow)

getElementNames

public String[] getElementNames()

getMissingDataRate

public double getMissingDataRate()

getEvidenceNames

public String[] getEvidenceNames()

setValueAt

public void setValueAt(int pRow,
                       int pColumn,
                       Double pValue)

getValueAt

public Double getValueAt(int pRow,
                         int pColumn)

getColumn

public Double[] getColumn(int pColumn)

getNonMissingColumnVals

public cern.colt.list.DoubleArrayList getNonMissingColumnVals(int pColumn)

writeToFile

public void writeToFile(PrintWriter pPrintWriter,
                        DataFileDelimiter pDelimiter,
                        NumberFormat pNumberFormat)

loadFromFile

public void loadFromFile(BufferedReader pBufferedReader,
                         DataFileDelimiter pDelimiter)
                  throws IOException,
                         InvalidInputException

Throws:

IOException

InvalidInputException

getNumObservations

public int getNumObservations(int pEvidenceNum)