chemaxon.descriptors

Class SDParameters

java.lang.Object

chemaxon.descriptors.MDParameters

chemaxon.descriptors.SDParameters

Direct Known Subclasses:

HBParameters, LDParameters

@PublicAPI
public class SDParameters
extends MDParameters

Manages ScalarDescriptor parameters. This class reads, stores and provides parameters for the ScalarDescriptor class. The native format of the parameter configuraton is XML.

Since:

JChem 2.2

Author:

Miklos Vargyas

Field Summary

Fields inherited from class chemaxon.descriptors.MDParameters

asymmetryFactors, cellSize, cellwiseWeights, configFilePath, currentMetricIndex, data, decForm, DEFAULT_ASYMMETRY_FACTOR, DEFAULT_OUTPUT_PRECISION, DEFAULT_SCALE_FACTOR, DEFAULT_WEIGHT, defaultWeight, document, generator, internalSize, length, md, metricIndexes, normalized, outputPrecision, parametrizedMetricNodes, parametrizedMetrics, parametrizedMetricsNode, scaleFactors, screeningConfigurationNode, similarityNode, standardizer, standardizerConfigurationNode, thresholds, tverskyA, tverskyB, weights

Constructor Summary

Constructors

Constructor and Description
SDParameters() Creates an empty object.
SDParameters(java.io.File configFile) Creates a new object from the given configuration file.
SDParameters(java.lang.String XMLconfig) Creates a new object from the given configuration string.

Method Summary

Modifier and Type	Method and Description
void	fromFile(java.io.File parameterFile) Sets parameters from an XML file.
void	fromString(java.lang.String parameterString) Sets parameters from a string representation.
int	getNumberOfMetrics() Gets the total number of parametrized metrics available in the present configuration.
java.lang.String	getType()
protected void	init() This method is called by the constructors before processing the XML configuration.
protected void	initParameters() Initializes those data members that depend on the XML configuration but are not directly taken from it.
protected void	processDocument(boolean all) Processes parts of the XML configuration specific to ScalarDescriptor.
protected void	readValues(boolean all) Reads attribute values form the XML configuration.
void	setLength(int length) Sets the length (number of cells) of the descriptor.

Methods inherited from class chemaxon.descriptors.MDParameters

addParameters, addParameters, addParametrizedMetric, addParametrizedMetricNode, addParametrizedMetricsNode, appendParametrizedMetric, checkDocumentVersion, getAsymmetryFactor, getCellSize, getCurrentMetricIndex, getData, getDecForm, getDefaultDocumentFrame, getDefaultStandardizerConfiguration, getDescriptorTypeName, getInternalMetricIndex, getInternalSize, getLength, getMetricIndex, getMetricName, getMetricName, getNumberOfWeights, getNumberOfWeights, getScaleFactor, getScalingHypothesis, getScreeningConfigurationString, getThreshold, getThreshold, getTverskyAlpha, getTverskyBeta, getWeights, importNodes, isAsymmetric, isCellwiseWeights, isNormalized, isScaled, isStandardizationMandatory, isWeighted, readFromXmlFile, readFromXmlString, readMetricParameters, readMetricWeights, setAsymmetryFactor, setCellSize, setCellwiseWeights, setCreateStatistics, setCurrentParametrizedMetric, setNormalized, setOutputPrecision, setParameters, setParameters, setScaleFactor, setScalingHypothesis, setThreshold, setWeights, standardize, toString, toString, writeMetricParameter

Methods inherited from class java.lang.Object

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

Constructor Detail

SDParameters

public SDParameters()

Creates an empty object.

SDParameters

public SDParameters(java.io.File configFile)
             throws MDParametersException

Creates a new object from the given configuration file.

Parameters:

configFile - XML configuration file

Throws:

MDParametersException - missing or bad XML configuration

SDParameters

public SDParameters(java.lang.String XMLconfig)
             throws MDParametersException

Creates a new object from the given configuration string.

Parameters:

XMLconfig - XML configuration string

Throws:

MDParametersException - missing or bad XML configuration

Method Detail

fromString

public void fromString(java.lang.String parameterString)
                throws MDParametersException

Sets parameters from a string representation. This method processes an XML format, but derived classes may overload this and define their own formats.

Overrides:

fromString in class MDParameters

Parameters:

parameterString - parameters in string

Throws:

MDParametersException - when the parameter string is not well-formed

fromFile

public void fromFile(java.io.File parameterFile)
              throws MDParametersException

Sets parameters from an XML file. Derived classes may overload this and define their own format (other than XML).

Overrides:

fromFile in class MDParameters

Parameters:

parameterFile - initialized parameter file

Throws:

MDParametersException - failed to process parameter file

setLength

public void setLength(int length)
               throws MDParametersException

Description copied from class: MDParameters

Sets the length (number of cells) of the descriptor.

Overrides:

setLength in class MDParameters

Parameters:

length - the required length (cell count)

Throws:

MDParametersException - if argument is not positive

getNumberOfMetrics

public int getNumberOfMetrics()

Gets the total number of parametrized metrics available in the present configuration.

Overrides:

getNumberOfMetrics in class MDParameters

Returns:

number of metrics

init

protected void init()

This method is called by the constructors before processing the XML configuration. It creates a ScalarDescriptor object stored in MDParameters.md.

initParameters

protected void initParameters()

Initializes those data members that depend on the XML configuration but are not directly taken from it.

Overrides:

initParameters in class MDParameters

processDocument

protected void processDocument(boolean all)
                        throws MDParametersException

Processes parts of the XML configuration specific to ScalarDescriptor. Find the node in the DOM tree and leaves the rest of the work to the parent class.

Overrides:

processDocument in class MDParameters

Parameters:

all - indicates if the entire document has to be processed in which case the existing configuration is overwritten

Throws:

MDParametersException

getType

public java.lang.String getType()

readValues

protected void readValues(boolean all)
                   throws MDParametersException

Reads attribute values form the XML configuration.

Overrides:

readValues in class MDParameters

Parameters:

all - process the complete document or only the ScreeningConfiguration tag

Throws:

MDParametersException