ambit2.model.structure

Class DataCoverageFingerprints

java.lang.Object

ambit2.model.numeric.DataCoverage<List<BitSet>>

ambit2.model.structure.DataCoverageFingerprints

All Implemented Interfaces:

IDataCoverage<List<BitSet>>, Serializable

Direct Known Subclasses:

DataCoverageFingeprintsMissingFragments, DataCoverageFingerprintsTanimoto

public abstract class DataCoverageFingerprints
extends DataCoverage<List<BitSet>>

A class to estimate applicability domain by fingerprints

Author:

Nina Jeliazkova
Modified 2005-4-7

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected BitSet	consensusFingerprint
protected int	fingerPrintLength
protected int	fingerprintsCalculated
protected double[]	fpProfile

Fields inherited from class ambit2.model.numeric.DataCoverage

appDomainMethodType, logger, object, pThreshold, threshold

Constructor Summary

Constructors

Constructor and Description
DataCoverageFingerprints()

Method Summary

Modifier and Type	Method and Description
static String	arrayToString(double[] array)
boolean	build(List<BitSet> bitsets)
boolean	buildStart()
void	clear()
protected void	clearProfile(double[] profile)
protected void	estimateConsensusFP(double[] profile, double athreshold)
abstract void	evaluate(List<BitSet> bitsets)
int	getDomain(double coverage)
int[]	getDomain(double[] coverage)
int	getFingerPrintLength()
int	getFingerprintsCalculated()
String	getName()
String	histToString(double[][] hist)
boolean	isEmpty()
double[][]	profileToHistogram(int bins)
String	profileToString()
void	setFingerPrintLength(int fpLength)

Methods inherited from class ambit2.model.numeric.DataCoverage

clone, getAppDomainMethodType, getDomainName, getId, getMetricName, getPoints, getPThreshold, setAppDomainMethodType, setDomainName, setMetricName, setMode, setParameters, setPThreshold, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface ambit2.model.numeric.IDataCoverage

predict

Field Detail

fingerPrintLength

protected int fingerPrintLength

fingerprintsCalculated

protected int fingerprintsCalculated

consensusFingerprint

protected BitSet consensusFingerprint

fpProfile

protected double[] fpProfile

Constructor Detail

DataCoverageFingerprints

public DataCoverageFingerprints()

Parameters:

mode -

Method Detail

clear

public void clear()

Overrides:

clear in class DataCoverage<List<BitSet>>

clearProfile

protected void clearProfile(double[] profile)

buildStart

public boolean buildStart()

evaluate

public abstract void evaluate(List<BitSet> bitsets)

build

public boolean build(List<BitSet> bitsets)

estimateConsensusFP

protected void estimateConsensusFP(double[] profile,
                                   double athreshold)

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface IDataCoverage<List<BitSet>>

Overrides:

isEmpty in class DataCoverage<List<BitSet>>

getFingerPrintLength

public int getFingerPrintLength()

setFingerPrintLength

public void setFingerPrintLength(int fpLength)

arrayToString

public static String arrayToString(double[] array)

histToString

public String histToString(double[][] hist)

profileToString

public String profileToString()

getFingerprintsCalculated

public int getFingerprintsCalculated()

profileToHistogram

public double[][] profileToHistogram(int bins)

getName

public String getName()

Overrides:

getName in class DataCoverage<List<BitSet>>

getDomain

public int getDomain(double coverage)

Specified by:

getDomain in interface IDataCoverage<List<BitSet>>

Overrides:

getDomain in class DataCoverage<List<BitSet>>

getDomain

public int[] getDomain(double[] coverage)

Specified by:

getDomain in interface IDataCoverage<List<BitSet>>

Overrides:

getDomain in class DataCoverage<List<BitSet>>