chemaxon.descriptors
Class ShapeParameters

java.lang.Object
  chemaxon.descriptors.MDParameters
      chemaxon.descriptors.ShapeParameters

public class ShapeParameters
extends MDParameters

Author:

adrian

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

ShapeParameters()

ShapeParameters(java.io.File configFile)

ShapeParameters(java.lang.String XMLconfig)
Creates a new object based on a given configuration string.

Method Summary

void	fromFile(java.io.File parameterFile) Sets parameters from an XML file.
void	fromString(java.lang.String parameterString) Sets parameters from a string representation.
java.lang.String	getDefaultDocumentFrame() Get the default XML configuration string.
static java.lang.String	getDefaultStandardizerConfiguration() Gets the default configuration of the standardizer.
protected void	initEmbeddedMD() This method is called by the constructors before processing the XML configuration.
protected void	initGenerator() Initializes the fingerprint generator.
protected void	processDocument(boolean all) Processes pars of the XML configuration specific to Shape.
protected void	readValues(boolean all) Picks attribute values from the document tree that are relevant to the actual MDParameters sub-class.
void	setFlexible(boolean flexible)

Methods inherited from class chemaxon.descriptors.MDParameters

addParameters, addParameters, addParametrizedMetric, addParametrizedMetricNode, addParametrizedMetricsNode, appendParametrizedMetric, checkDocumentVersion, getAsymmetryFactor, getCellSize, getCurrentMetricIndex, getData, getDecForm, getDescriptorTypeName, getInternalMetricIndex, getInternalSize, getLength, getMetricIndex, getMetricName, getMetricName, getNumberOfMetrics, getNumberOfWeights, getNumberOfWeights, getScaleFactor, getScalingHypothesis, getScreeningConfigurationString, getThreshold, getThreshold, getTverskyAlpha, getTverskyBeta, getWeights, importNodes, initParameters, isAsymmetric, isCellwiseWeights, isNormalized, isScaled, isStandardizationMandatory, isWeighted, readFromXmlFile, readFromXmlString, readMetricParameters, readMetricWeights, setAsymmetryFactor, setCellSize, setCellwiseWeights, setCreateStatistics, setCurrentParametrizedMetric, setLength, 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

ShapeParameters

public ShapeParameters()

ShapeParameters

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

Throws:

MDParametersException

ShapeParameters

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

Creates a new object based on a 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

Description copied from class: MDParameters

Sets parameters from a string representation. This method assumes that parameters are described in XML format.

Overrides:

fromString in class MDParameters

Parameters:

parameterString - configuration parameters in string

Throws:

MDParametersException - when the parameter string is not well-formed

setFlexible

public void setFlexible(boolean flexible)

initGenerator

protected final void initGenerator()
                            throws MDParametersException

Initializes the fingerprint generator.

Throws:

MDParametersException

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 (even other than XML).

Overrides:

fromFile in class MDParameters

Parameters:

parameterFile - initialized parameter file

Throws:

MDParametersException - failed to process parameter file

initEmbeddedMD

protected final void initEmbeddedMD()

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

getDefaultDocumentFrame

public java.lang.String getDefaultDocumentFrame()

Get the default XML configuration string. This is needed when the optional Shape XML configuration is not specified.

Overrides:

getDefaultDocumentFrame in class MDParameters

Returns:

default XML configuration string of the ShapeParameters class

getDefaultStandardizerConfiguration

public static java.lang.String getDefaultStandardizerConfiguration()

Gets the default configuration of the standardizer. This method is called if no standardizer configuration is set in the parameters configuration. The default standardization for Shape includes aromatization.

Returns:

standardizer configuration XML string

processDocument

protected void processDocument(boolean all)
                        throws MDParametersException

Processes pars of the XML configuration specific to Shape. 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

readValues

protected void readValues(boolean all)
                   throws MDParametersException

Description copied from class: MDParameters

Picks attribute values from the document tree that are relevant to the actual MDParameters sub-class.

Overrides:

readValues in class MDParameters

Parameters:

all - process the complete document or only the ScreeningConfiguration tag

Throws:

MDParametersException