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joelib.desc.data
Class MoleculesDescriptorMatrix  

java.lang.Object
  joelib.desc.data.MoleculesDescriptorMatrix

All Implemented Interfaces:

java.io.Serializable

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public class MoleculesDescriptorMatrix

extends java.lang.Object

implements java.io.Serializable

Purpose: Holds all native value descriptors as double matrix for all known molecules.

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Field Summary
private  java.util.Hashtable	binning
private  java.util.Hashtable	booleanValues
private  java.util.Vector	desc2ignore
private  java.util.Hashtable	descNamesIndex
private  java.lang.String[]	descriptorNames
private static java.lang.String	FILE_EXT
private static org.apache.log4j.Category	logger           Obtain a suitable logger.
private  java.lang.String	moleculeIdentifier
private  java.lang.String[]	moleculeIDs
private  java.lang.String[]	moleculeNames
private  java.util.Hashtable	molIDsIndex
private  java.util.Hashtable	molNamesIndex
private static java.lang.String	NORM_FILE_EXT
private  boolean	normalizeOnLoad
private  java.lang.String	normalizeStatFile
private  java.util.Hashtable	notBooleanValues
private  joelib.process.types.DescStatistic	statistic
private  double[][]	values           Description of the Field

 

Constructor Summary

MoleculesDescriptorMatrix()           Constructor for the MoleculesDescriptorMatrix object

MoleculesDescriptorMatrix(joelib.io.IOType _inType, java.lang.String _inFile)           Constructor for the IntResult object

 

Method Summary
boolean	calcVarianceNorm(joelib.process.types.DescStatistic _statistic)           Description of the Method Description of the Method Description of the Method Description of the Method Description of the Method Gets the statistic attribute of the MoleculesDescriptorMatrix object Description of the Method Description of the Method Description of the Method Description of the Method Gets the statistic attribute of the MoleculesDescriptorMatrix object Description of the Method Description of the Method Description of the Method Gets the statistic attribute of the MoleculesDescriptorMatrix object Description of the Method Description of the Method Gets the statistic attribute of the MoleculesDescriptorMatrix object Description of the Method
MoleculesDescriptorMatrix	clone(MoleculesDescriptorMatrix target)           Description of the Method
boolean	existsMatrixFileFor(java.lang.String fileName)           Description of the Method
private  boolean	fromFile(java.lang.String fileName)           Description of the Method
boolean	fromFileFor(java.lang.String fileName)           Description of the Method
java.util.Hashtable	getBinning(int _bins)
java.util.Hashtable	getBinning(int _bins, boolean forceCalculation)           Description of the Method
java.lang.String[]	getDescContainsNaN()           Gets the descContainsNaN attribute of the MoleculesDescriptorMatrix object
double[]	getDescFromMolByIdentifier(java.lang.String _moleculeIdentifier)           Gets the descFromMolByIdentifier attribute of the MoleculesDescriptorMatrix object
double[]	getDescFromMolByIdentifier(java.lang.String _moleculeIdentifier, boolean replaceNaN)           Gets the descFromMol attribute of the MoleculesDescriptorMatrix object
double[]	getDescFromMolByIndex(int position)           Gets the descFromMolByIndex attribute of the MoleculesDescriptorMatrix object
double[]	getDescFromMolByIndex(int position, boolean replaceNaN)           Gets the descFromMol attribute of the MoleculesDescriptorMatrix object
double[]	getDescFromMolByName(java.lang.String _moleculeName)           Gets the descFromMolByName attribute of the MoleculesDescriptorMatrix object
double[]	getDescFromMolByName(java.lang.String _moleculeName, boolean replaceNaN)           Gets the descFromMol attribute of the MoleculesDescriptorMatrix object
java.lang.String[]	getDescNames()           Gets the descNames attribute of the MoleculesDescriptorMatrix object
double[]	getDescValues(java.lang.String _descriptorName)           Gets the descValues attribute of the MoleculesDescriptorMatrix object
double[][]	getDescValues(java.lang.String[] _descriptorNames)           Gets the descValues attribute of the MoleculesDescriptorMatrix object
double[][]	getDescValues(java.lang.String[] _descriptorNames, boolean replaceNaN, int[] ifMolID, int[] ifNotMolID)           Gets the descValues attribute of the MoleculesDescriptorMatrix object
double[]	getDescValues(java.lang.String _descriptorName, boolean replaceNaN)           Gets the descValues attribute of the MoleculesDescriptorMatrix object
double[][]	getMatrix()           Gets the matrix attribute of the MoleculesDescriptorMatrix object
double[][]	getMatrix(boolean replaceNaN)           Gets the molDescMatrix attribute of the MoleculesDescriptorMatrix object
java.lang.String[]	getMolNames()           Gets the moleculeNames attribute of the MoleculesDescriptorMatrix object
joelib.process.types.DescStatistic	getStatistic()           Description of the Method Description of the Method Description of the Method Description of the Method Description of the Method Gets the statistic attribute of the MoleculesDescriptorMatrix object
boolean	isBooleanValue(java.lang.String descriptor)
private  boolean	loadDescFromMols(joelib.io.IOType _inType, java.lang.String _inFile)           Description of the Method
boolean	loadMatrix(joelib.io.IOType _inType, java.lang.String _inFile)           Description of the Method
boolean	loadMatrix(joelib.io.IOType _inType, java.lang.String _inFile, boolean useCaching)           Description of the Method
int	numberOfDescriptors()           Description of the Method
int	numberOfMolecules()           Description of the Method
boolean	setMoleculeDescriptors(joelib.molecule.JOEMol mol, int moleculeEntry)           Adds a feature to the MoleculeDescriptors attribute of the MoleculesDescriptorMatrix object
void	setMolIdentifier(java.lang.String _moleculeIdentifier)           Sets the molIdentifier attribute of the MoleculesDescriptorMatrix object
java.lang.String	toString()           Description of the Method
void	writeMatrixFileFor(java.lang.String _inFile)           Description of the Method

 

Methods inherited from class java.lang.Object

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

 

Field Detail

logger

private static org.apache.log4j.Category logger

Obtain a suitable logger.

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FILE_EXT

private static final java.lang.String FILE_EXT

See Also:

Constant Field Values

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NORM_FILE_EXT

private static final java.lang.String NORM_FILE_EXT

See Also:

Constant Field Values

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statistic

private joelib.process.types.DescStatistic statistic

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binning

private java.util.Hashtable binning

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descNamesIndex

private java.util.Hashtable descNamesIndex

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molIDsIndex

private java.util.Hashtable molIDsIndex

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molNamesIndex

private java.util.Hashtable molNamesIndex

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moleculeIdentifier

private java.lang.String moleculeIdentifier

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normalizeStatFile

private java.lang.String normalizeStatFile

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desc2ignore

private java.util.Vector desc2ignore

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descriptorNames

private java.lang.String[] descriptorNames

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moleculeIDs

private java.lang.String[] moleculeIDs

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moleculeNames

private java.lang.String[] moleculeNames

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booleanValues

private java.util.Hashtable booleanValues

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notBooleanValues

private java.util.Hashtable notBooleanValues

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values

private double[][] values

Description of the Field

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normalizeOnLoad

private boolean normalizeOnLoad

Constructor Detail

MoleculesDescriptorMatrix

public MoleculesDescriptorMatrix()

Constructor for the MoleculesDescriptorMatrix object

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MoleculesDescriptorMatrix

public MoleculesDescriptorMatrix(joelib.io.IOType _inType,
                                 java.lang.String _inFile)
                          throws java.lang.Exception

Constructor for the IntResult object

Method Detail

getBinning

public java.util.Hashtable getBinning(int _bins)

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getBinning

public java.util.Hashtable getBinning(int _bins,
                                      boolean forceCalculation)

Description of the Method

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getDescContainsNaN

public java.lang.String[] getDescContainsNaN()

Gets the descContainsNaN attribute of the MoleculesDescriptorMatrix object

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getDescFromMolByIdentifier

public double[] getDescFromMolByIdentifier(java.lang.String _moleculeIdentifier)

Gets the descFromMolByIdentifier attribute of the MoleculesDescriptorMatrix object

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getDescFromMolByIdentifier

public double[] getDescFromMolByIdentifier(java.lang.String _moleculeIdentifier,
                                           boolean replaceNaN)

Gets the descFromMol attribute of the MoleculesDescriptorMatrix object

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getDescFromMolByIndex

public double[] getDescFromMolByIndex(int position)

Gets the descFromMolByIndex attribute of the MoleculesDescriptorMatrix object

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getDescFromMolByIndex

public double[] getDescFromMolByIndex(int position,
                                      boolean replaceNaN)

Gets the descFromMol attribute of the MoleculesDescriptorMatrix object

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getDescFromMolByName

public double[] getDescFromMolByName(java.lang.String _moleculeName)

Gets the descFromMolByName attribute of the MoleculesDescriptorMatrix object

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getDescFromMolByName

public double[] getDescFromMolByName(java.lang.String _moleculeName,
                                     boolean replaceNaN)

Gets the descFromMol attribute of the MoleculesDescriptorMatrix object

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getDescNames

public java.lang.String[] getDescNames()

Gets the descNames attribute of the MoleculesDescriptorMatrix object

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getDescValues

public double[] getDescValues(java.lang.String _descriptorName)

Gets the descValues attribute of the MoleculesDescriptorMatrix object

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getDescValues

public double[] getDescValues(java.lang.String _descriptorName,
                              boolean replaceNaN)

Gets the descValues attribute of the MoleculesDescriptorMatrix object

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getDescValues

public double[][] getDescValues(java.lang.String[] _descriptorNames)

Gets the descValues attribute of the MoleculesDescriptorMatrix object

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getDescValues

public double[][] getDescValues(java.lang.String[] _descriptorNames,
                                boolean replaceNaN,
                                int[] ifMolID,
                                int[] ifNotMolID)

Gets the descValues attribute of the MoleculesDescriptorMatrix object

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getMatrix

public double[][] getMatrix()

Gets the matrix attribute of the MoleculesDescriptorMatrix object

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getMatrix

public double[][] getMatrix(boolean replaceNaN)

Gets the molDescMatrix attribute of the MoleculesDescriptorMatrix object

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setMolIdentifier

public void setMolIdentifier(java.lang.String _moleculeIdentifier)

Sets the molIdentifier attribute of the MoleculesDescriptorMatrix object

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getMolNames

public java.lang.String[] getMolNames()

Gets the moleculeNames attribute of the MoleculesDescriptorMatrix object

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isBooleanValue

public boolean isBooleanValue(java.lang.String descriptor)

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setMoleculeDescriptors

public boolean setMoleculeDescriptors(joelib.molecule.JOEMol mol,
                                      int moleculeEntry)

Adds a feature to the MoleculeDescriptors attribute of the MoleculesDescriptorMatrix object

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getStatistic

public joelib.process.types.DescStatistic getStatistic()

Description of the Method Description of the Method Description of the Method Description of the Method Description of the Method Gets the statistic attribute of the MoleculesDescriptorMatrix object

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calcVarianceNorm

public boolean calcVarianceNorm(joelib.process.types.DescStatistic _statistic)

Description of the Method Description of the Method Description of the Method Description of the Method Description of the Method Gets the statistic attribute of the MoleculesDescriptorMatrix object Description of the Method Description of the Method Description of the Method Description of the Method Gets the statistic attribute of the MoleculesDescriptorMatrix object Description of the Method Description of the Method Description of the Method Gets the statistic attribute of the MoleculesDescriptorMatrix object Description of the Method Description of the Method Gets the statistic attribute of the MoleculesDescriptorMatrix object Description of the Method

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clone

public MoleculesDescriptorMatrix clone(MoleculesDescriptorMatrix target)

Description of the Method

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existsMatrixFileFor

public boolean existsMatrixFileFor(java.lang.String fileName)

Description of the Method

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fromFileFor

public boolean fromFileFor(java.lang.String fileName)

Description of the Method

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loadMatrix

public boolean loadMatrix(joelib.io.IOType _inType,
                          java.lang.String _inFile)
                   throws java.lang.Exception

Description of the Method

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loadMatrix

public boolean loadMatrix(joelib.io.IOType _inType,
                          java.lang.String _inFile,
                          boolean useCaching)
                   throws java.lang.Exception

Description of the Method

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numberOfDescriptors

public int numberOfDescriptors()

Description of the Method

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numberOfMolecules

public int numberOfMolecules()

Description of the Method

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toString

public java.lang.String toString()

Description of the Method

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writeMatrixFileFor

public void writeMatrixFileFor(java.lang.String _inFile)

Description of the Method

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fromFile

private boolean fromFile(java.lang.String fileName)

Description of the Method

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loadDescFromMols

private boolean loadDescFromMols(joelib.io.IOType _inType,
                                 java.lang.String _inFile)
                          throws java.lang.Exception

Description of the Method

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> joelib >> desc >> [ data overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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