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

---

joelib.util
Class ComparisonHelper  

java.lang.Object
  joelib.util.ComparisonHelper

---

public class ComparisonHelper

extends java.lang.Object

Example for converting molecules.

---

Field Summary
private static int	BINARY_COMPARISON
private  int	comparisonType
private  java.util.Vector	descBinaryValue
private  java.lang.String[]	descriptors
private  java.util.Vector	descValues
private static int	DIST_METRIC_COMPARISON
private  java.util.Vector	distMetricValue
private static int	EUKLIDIAN_COMPARISON
private static org.apache.log4j.Category	logger
private static int	NOT_DEFINED
private  java.lang.String	targetFile
private  java.util.Vector	targetMols
private  double[]	tmpValues

 

Constructor Summary

ComparisonHelper()

ComparisonHelper(joelib.io.IOType inType, java.lang.String _targetFile)

ComparisonHelper(joelib.io.IOType inType, java.lang.String _targetFile, int _initialSize)           Constructor for the ComparisonHelper object

ComparisonHelper(joelib.molecule.JOEMol _targetMolecule)           Constructor for the ComparisonHelper object

 

Method Summary
double[]	compare(joelib.molecule.JOEMol mol)           Description of the Method
double	compare(joelib.molecule.JOEMol source, joelib.molecule.JOEMol target)
double[]	compare(joelib.molecule.JOEMol mol, java.lang.String _distResultName, double[] distances)           Description of the Method.
private  double	distance(joelib.desc.DistanceMetricValue source, joelib.desc.DistanceMetricValue target)
private  double	distance(joelib.desc.DistanceMetricValue dMetricValue, int index)           Description of the Method
private  double	distance(double[] source, double[] target)
private  double	distance(double[] ds, int index)           Description of the Method
private  double	distance(JOEBitVec bitset, int index)           Description of the Method
private  double	distance(JOEBitVec source, JOEBitVec target)
private  JOEBitVec	getBitset(joelib.molecule.JOEMol mol)
private  double[]	getDescriptors(joelib.molecule.JOEMol mol, double[] vals)
private  joelib.desc.DistanceMetricValue	getDistMetricValue(joelib.molecule.JOEMol mol)
private  double	getDoubleDesc(joelib.molecule.JOEMol mol, java.lang.String _descName)           Gets the doubleDesc attribute of the ComparisonHelper object
java.util.Vector	getTargetMols()
boolean	setComparisonDescriptor(java.lang.String _descriptor)           Sets the comparisonDescriptor attribute of the ComparisonHelper object
boolean	setComparisonDescriptors(java.lang.String[] _descriptors)           Sets the comparisonDescriptors attribute of the ComparisonHelper object

 

Methods inherited from class java.lang.Object

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

 

Field Detail

logger

private static org.apache.log4j.Category logger

---

NOT_DEFINED

private static final int NOT_DEFINED

See Also:

Constant Field Values

---

BINARY_COMPARISON

private static final int BINARY_COMPARISON

See Also:

Constant Field Values

---

EUKLIDIAN_COMPARISON

private static final int EUKLIDIAN_COMPARISON

See Also:

Constant Field Values

---

DIST_METRIC_COMPARISON

private static final int DIST_METRIC_COMPARISON

See Also:

Constant Field Values

---

targetFile

private java.lang.String targetFile

---

descBinaryValue

private java.util.Vector descBinaryValue

---

descValues

private java.util.Vector descValues

---

distMetricValue

private java.util.Vector distMetricValue

---

targetMols

private java.util.Vector targetMols

---

descriptors

private java.lang.String[] descriptors

---

tmpValues

private double[] tmpValues

---

comparisonType

private int comparisonType

Constructor Detail

ComparisonHelper

public ComparisonHelper(joelib.io.IOType inType,
                        java.lang.String _targetFile)

---

ComparisonHelper

public ComparisonHelper(joelib.io.IOType inType,
                        java.lang.String _targetFile,
                        int _initialSize)

Constructor for the ComparisonHelper object

---

ComparisonHelper

public ComparisonHelper(joelib.molecule.JOEMol _targetMolecule)

Constructor for the ComparisonHelper object

---

ComparisonHelper

public ComparisonHelper()

Method Detail

setComparisonDescriptor

public boolean setComparisonDescriptor(java.lang.String _descriptor)

Sets the comparisonDescriptor attribute of the ComparisonHelper object

---

setComparisonDescriptors

public boolean setComparisonDescriptors(java.lang.String[] _descriptors)

Sets the comparisonDescriptors attribute of the ComparisonHelper object

---

getTargetMols

public final java.util.Vector getTargetMols()

---

compare

public double[] compare(joelib.molecule.JOEMol mol)

Description of the Method

---

compare

public double[] compare(joelib.molecule.JOEMol mol,
                        java.lang.String _distResultName,
                        double[] distances)

Description of the Method. Double.NaN is returned if no comparison value could be calulated

---

compare

public double compare(joelib.molecule.JOEMol source,
                      joelib.molecule.JOEMol target)

---

getBitset

private final JOEBitVec getBitset(joelib.molecule.JOEMol mol)

---

getDescriptors

private final double[] getDescriptors(joelib.molecule.JOEMol mol,
                                      double[] vals)

---

getDistMetricValue

private final joelib.desc.DistanceMetricValue getDistMetricValue(joelib.molecule.JOEMol mol)

---

getDoubleDesc

private final double getDoubleDesc(joelib.molecule.JOEMol mol,
                                   java.lang.String _descName)
                            throws joelib.desc.DescriptorException

Gets the doubleDesc attribute of the ComparisonHelper object

---

distance

private final double distance(JOEBitVec bitset,
                              int index)

Description of the Method

---

distance

private final double distance(JOEBitVec source,
                              JOEBitVec target)

---

distance

private final double distance(joelib.desc.DistanceMetricValue dMetricValue,
                              int index)

Description of the Method

---

distance

private final double distance(joelib.desc.DistanceMetricValue source,
                              joelib.desc.DistanceMetricValue target)

---

distance

private final double distance(double[] ds,
                              int index)

Description of the Method

---

distance

private final double distance(double[] source,
                              double[] target)

---

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

---