chemaxon.descriptors
Class MDParameters

java.lang.Object
  chemaxon.descriptors.MDParameters

Direct Known Subclasses:

BCUTParameters, CDParameters, CFParameters, ECFPParameters, PFParameters, RFParameters, SDParameters, ShapeParameters

public class MDParameters
extends java.lang.Object

MolecularDescriptor parameter settings. This class serves as the base class for the parameter classes of specific MolecularDescriptor derivatives.
Descriptor objects of the same type share one common MDParameter object that stores all parameters.
Besides storing parameters and other internal data that are better kept in this class than in individual MolecularDescriptor objects for the sake of memory efficiency.
The naming convention - similarly to the derivates of the MolecularDescriptor class - is as follows: derived class name begins with the name of the corresponding MolecularDescriptor class and postfixed by Parameters. For instance that parameters class of the descriptor class MDXyZ is XyZParameters.
Parameters are read from configuration files. MDParameters provides an extensive functionality to process XML configuration files, however, further parameter classes extending MDParameters do not necessarily have to use XML for storing parameters.
MDParameters plays an important role in providing so called Screening Configurations for the dissimilarity calculations. Such configurations contain so called parameterized metrics that are based on dissimilarity metrics implemented in classes that extend the MolecularDescriptor class. It is important to make clear distinction between the above two cathegories: dissimilarity metrics are the basis of the parametrized metrics. MDParameters stores metrics parameters and provides services for retrieving and storing parametrized metrics, access them by either name or index.
Another important functionality of this class is to allow the creation of new parametrized metrics and write them into the XML document.

Since:

JChem 2.2

Author:

Miklos Vargyas

Field Summary

protected java.util.ArrayList	asymmetryFactors asymmetry ratio of parametrized asymmetric metrics
protected int	cellSize size - number of bits - of one descriptor cell
protected java.util.ArrayList	cellwiseWeights is cell weights for parametrized metrics
protected java.lang.String	configFilePath location of the configuration file
protected int	currentMetricIndex index of the parametrized metric currently in use
protected byte[]	data buffer for external data format generation, used in MolecularDescriptor.toData()
protected java.text.NumberFormat	decForm to format floating point output
static float	DEFAULT_ASYMMETRY_FACTOR
static int	DEFAULT_OUTPUT_PRECISION
static float	DEFAULT_SCALE_FACTOR constants, default parameter values
static float	DEFAULT_WEIGHT
protected float	defaultWeight value for all missing weight parameters
protected org.dom4j.Document	document contains the XML document
protected MDGenerator	generator generates MolecularDescriptors
protected int	internalSize required memory size of one descriptor instance
protected int	length the length of the descriptor: the number of cells
protected MolecularDescriptor	md this object is needed to access default dissimilarity functions
protected java.util.ArrayList	metricIndexes convert parameterized indexes to MolecularDescriptor metric indexes
protected java.util.ArrayList	normalized flags indicating if the metric is normalized or not
protected int	outputPrecision number of fraction digits in floating point output format
protected java.util.List	parametrizedMetricNodes
protected java.util.ArrayList	parametrizedMetrics symbolic names (mnemonics) of parametrized metrics
protected org.dom4j.Element	parametrizedMetricsNode
protected java.util.ArrayList	scaleFactors scale factor of scalable parametrized metrics
protected org.dom4j.Node	screeningConfigurationNode
protected org.dom4j.Element	similarityNode node holding the similarity calculations related parameters
protected Standardizer	standardizer transform molecules into standard form before descriptor generation
protected org.dom4j.Node	standardizerConfigurationNode node defining the Standardizer configuration
protected java.util.ArrayList	thresholds dissimilarity thresholds values
protected java.util.ArrayList<java.lang.Float>	tverskyA alpha values for tversky dissimilarity
protected java.util.ArrayList<java.lang.Float>	tverskyB beta values for tversky dissimilarity
protected java.util.ArrayList	weights weights for parametrized metrics

Constructor Summary

protected

MDParameters() Creates and initializes an empty object.

Method Summary

void	addParameters(java.io.File parameterFile) Sets parameters from an XML config file keeping all previous settings.
void	addParameters(java.lang.String parameterString) Sets parameters from an XML string representation keeping all previous settings.
int	addParametrizedMetric(java.lang.String name, java.lang.String metric, java.lang.String activeFamily) Expands the set of parametrized metrics with a new item.
protected org.dom4j.Element	addParametrizedMetricNode(java.lang.String name, java.lang.String activeFamily, java.lang.String metric) Adds a ParametrizedMetric node to the DOM tree.
protected void	addParametrizedMetricsNode() Adds the ParametrizedMetrics node to the DOM tree.
protected int	appendParametrizedMetric(java.lang.String name, java.lang.String metric) Extends internal data with a new parametrized metric.
protected void	checkDocumentVersion(java.lang.String docType, java.lang.String version) Checks if the document is the right version
void	fromFile(java.io.File parameterFile) Sets parameters from an XML file.
void	fromString(java.lang.String parameterString) Sets parameters from a string representation.
float	getAsymmetryFactor() Gets the asymmetry factor used in the current parametrized asymmetric metrics.
int	getCellSize() Gets the number of bits of an atomic cell in the descriptor.
int	getCurrentMetricIndex()
byte[]	getData() Gets the byte array which is used for conversions between internal and external data formats.
java.text.DecimalFormat	getDecForm() Gets the formatter object that is capable of formatting fractions with given precision.
java.lang.String	getDefaultDocumentFrame() Gets the default XML configuration string.
static java.lang.String	getDefaultStandardizerConfiguration() Gets the default configuration of the standardizer.
static java.lang.String	getDescriptorTypeName(java.lang.String xmlConfig) Takes the descriptor type name from the root element of the XML configuration.
int	getInternalMetricIndex() Gets the MolecularDescriptor specific metric index of the current parametrized metric.
int	getInternalSize() Gets the required memory size to store the descriptor according to the specified parameters.
int	getLength() Returns the number of cells forming the descriptor.
int	getMetricIndex(java.lang.String name) Gets the index of the given parametrized metric.
java.lang.String	getMetricName() Gets the user defined symbolic name of the current parametrized metric.
java.lang.String	getMetricName(int metricIndex) Gets the user defined symbolic name of the specified parametrized metric.
int	getNumberOfMetrics() Gets the total number of parametrized metrics available in the present configuration.
int	getNumberOfWeights() Gets the number of weights the current parametrized metric takes.
protected int	getNumberOfWeights(int parametrizedMetricIndex) Gets the number of weight factors used by the specified metric.
float	getScaleFactor() Gets the scale factor used in the current parametrized scalable metrics.
MolecularDescriptor	getScalingHypothesis() Gets the scaling hypothesis used in scaled metrics.
java.lang.String	getScreeningConfigurationString(java.lang.String nodeName, java.lang.String attrib, java.lang.String value) Returns parts of the parameter values in string.
float	getThreshold() Gets the threshold value being set for the current parametrized version.
float	getThreshold(int metricIndex) Gets a metric dependent threshold value.
float	getTverskyAlpha() Gets Tversky alpha value for the given parametrized metric.
float	getTverskyBeta() Gets Tversky beta value for the given parametrized metric.
float[]	getWeights() Gets all weights for the given parametrized metric.
protected boolean	importNodes(org.dom4j.Document doc, boolean merge) Imports nodes from the specified Document into the current (main) Document.
protected void	initParameters() Initializes object after configuration parameters are loaded.
boolean	isAsymmetric() Returns whether current parametrized metric is asymmetric or not.
boolean	isCellwiseWeights() Gets boolean telling whether cell weights are to be generated for current parametrized metric.
boolean	isNormalized() Returns whether current parametrized metric is normalized or not.
boolean	isScaled() Returns whether current parametrized metric is scaled or not.
boolean	isStandardizationMandatory() Checks is Standardization of molecules is mandatory for the corresponding MolecularDescriptor before descriptor generation.
boolean	isWeighted() Returns whether current parametrized metric is weighted or not.
protected void	processDocument(boolean all) Searches the DOM tree for relevant nodes and sets internal variables to some these nodes for the sake of easier information processing.
protected void	readFromXmlFile(java.io.File file, boolean merge, boolean all) Reads configuration from XML file.
protected void	readFromXmlString(java.lang.String xml, boolean merge, boolean all) Reads configuration from XML string.
protected void	readMetricParameters() Processes all ParametrizedMetric nodes in the DOM tree.
protected void	readMetricWeights(org.dom4j.Element parametrizedMetric, int metricIndex)
protected void	readValues(boolean all) Picks attribute values from the document tree that are relevant to the actual MDParameters sub-class.
void	setAsymmetryFactor(float af) Sets the value of the asymmetry factor of the current parametrized metric.
void	setCellSize(int cellSize) Sets the size (number of bits) of the bins (cells).
void	setCellwiseWeights(boolean c) Sets boolean telling whether cell weights are to be generated for current parametrized metric.
void	setCreateStatistics(boolean createStatistics) Toggles the create statistics flag of the MDGenerator object.
void	setCurrentParametrizedMetric(int metricIndex) Selects the specified parametrized metric to be the current.
void	setLength(int length) Sets the length (number of cells) of the descriptor.
void	setNormalized(boolean yes) Toggles the normalized flag of the current parametrized metric.
void	setOutputPrecision(int precision) Specifies the output precision for floating point values.
void	setParameters(java.io.File parametersFile) Sets parameters from an XML file representation overwriting all previous settings with the new ones.
void	setParameters(java.lang.String parametersString) Sets parameters from an XML string representation overwriting all previous parameters settings with the new ones.
void	setScaleFactor(float scaleFactor) Sets scaleFactor used with the current parametrized metrics.
void	setScalingHypothesis(MolecularDescriptor scalingHypothesis) Sets (stores) the specified scaling hypothesis.
void	setThreshold(float th) Sets the value of the threshold of the current parametrized metric.
void	setWeights(float[] w) Sets the cell-wise weight factors for the current parametrized metric.
Molecule	standardize(Molecule m) Standardizes the Molecule and returns the standardized form.
java.lang.String	toString() Returns the parameter values in string.
protected java.lang.String	toString(org.dom4j.Node node) Returns parts of the parameter values in string.
protected void	writeMetricParameter(java.util.ArrayList pl, java.lang.String attr, int mi, boolean useDecForm) Writes a given parameter of the specified metric into the corresponding tree node.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_SCALE_FACTOR

public static final float DEFAULT_SCALE_FACTOR

constants, default parameter values

See Also:

Constant Field Values

DEFAULT_ASYMMETRY_FACTOR

public static final float DEFAULT_ASYMMETRY_FACTOR

See Also:

Constant Field Values

DEFAULT_WEIGHT

public static final float DEFAULT_WEIGHT

See Also:

Constant Field Values

DEFAULT_OUTPUT_PRECISION

public static final int DEFAULT_OUTPUT_PRECISION

See Also:

Constant Field Values

cellSize

protected int cellSize

size - number of bits - of one descriptor cell

length

protected int length

the length of the descriptor: the number of cells

internalSize

protected int internalSize

required memory size of one descriptor instance

data

protected byte[] data

buffer for external data format generation, used in MolecularDescriptor.toData()

configFilePath

protected java.lang.String configFilePath

location of the configuration file

document

protected org.dom4j.Document document

contains the XML document

standardizerConfigurationNode

protected org.dom4j.Node standardizerConfigurationNode

node defining the Standardizer configuration

similarityNode

protected org.dom4j.Element similarityNode

node holding the similarity calculations related parameters

screeningConfigurationNode

protected org.dom4j.Node screeningConfigurationNode

parametrizedMetricsNode

protected org.dom4j.Element parametrizedMetricsNode

parametrizedMetricNodes

protected java.util.List parametrizedMetricNodes

parametrizedMetrics

protected java.util.ArrayList parametrizedMetrics

symbolic names (mnemonics) of parametrized metrics

metricIndexes

protected java.util.ArrayList metricIndexes

convert parameterized indexes to MolecularDescriptor metric indexes

scaleFactors

protected java.util.ArrayList scaleFactors

scale factor of scalable parametrized metrics

tverskyA

protected java.util.ArrayList<java.lang.Float> tverskyA

alpha values for tversky dissimilarity

tverskyB

protected java.util.ArrayList<java.lang.Float> tverskyB

beta values for tversky dissimilarity

asymmetryFactors

protected java.util.ArrayList asymmetryFactors

asymmetry ratio of parametrized asymmetric metrics

thresholds

protected java.util.ArrayList thresholds

dissimilarity thresholds values

normalized

protected java.util.ArrayList normalized

flags indicating if the metric is normalized or not

defaultWeight

protected float defaultWeight

value for all missing weight parameters

weights

protected java.util.ArrayList weights

weights for parametrized metrics

cellwiseWeights

protected java.util.ArrayList cellwiseWeights

is cell weights for parametrized metrics

outputPrecision

protected int outputPrecision

number of fraction digits in floating point output format

currentMetricIndex

protected int currentMetricIndex

index of the parametrized metric currently in use

md

protected MolecularDescriptor md

this object is needed to access default dissimilarity functions

decForm

protected java.text.NumberFormat decForm

to format floating point output

generator

protected MDGenerator generator

generates MolecularDescriptors

standardizer

protected Standardizer standardizer

transform molecules into standard form before descriptor generation

Constructor Detail

MDParameters

protected MDParameters()

Creates and initializes an empty object. This class is not allowed to be instantiated directly. Only its derived classes can call the superclass constructors.

Method Detail

initParameters

protected void initParameters()

Initializes object after configuration parameters are loaded.

fromString

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

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

Parameters:

parameterString - configuration 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. Stores filepath in configFilePath.

Parameters:

parameterFile - initialized parameter file

Throws:

MDParametersException - failed to process parameter file

addParameters

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

Sets parameters from an XML string representation keeping all previous settings.

Parameters:

parameterString - parameters in string

Throws:

MDParametersException - when the parameter string is not well-formed

addParameters

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

Sets parameters from an XML config file keeping all previous settings.

Parameters:

parameterFile - parameter file

Throws:

MDParametersException - when the parameter string is not well-formed

setParameters

public void setParameters(java.lang.String parametersString)
                   throws MDParametersException

Sets parameters from an XML string representation overwriting all previous parameters settings with the new ones.

Parameters:

parametersString - parameters in string

Throws:

MDParametersException - when the parameter string is not well-formed

setParameters

public void setParameters(java.io.File parametersFile)
                   throws MDParametersException

Sets parameters from an XML file representation overwriting all previous settings with the new ones. Stores filepath in configFilePath.

Parameters:

parametersFile - parameters File

Throws:

MDParametersException - when the parameter string is not well-formed

toString

public java.lang.String toString()

Returns the parameter values in string. This implementation uses XML for the external format of parameters, however derived classes may use different formats.

Overrides:

toString in class java.lang.Object

Returns:

parameter string

Throws:

MDParametersException - when creating the parameter string fails

getScreeningConfigurationString

public java.lang.String getScreeningConfigurationString(java.lang.String nodeName,
                                                        java.lang.String attrib,
                                                        java.lang.String value)
                                                 throws MDParametersException

Returns parts of the parameter values in string. Selects a sub-tree of the DOM tree specified by the tagname of one of its nodes, and writes the subtree into an XML string.

Parameters:

nodeName - name of the node to be printed

attrib - attribute name

value - value of the attribute

Returns:

parameter string

Throws:

MDParametersException - when creating the parameter string fails

toString

protected java.lang.String toString(org.dom4j.Node node)
                             throws MDParametersException

Returns parts of the parameter values in string. Selects a sub-tree of the DOM tree specified by a node, and writes the subtree into an XML string.

Parameters:

node - rootnode of the subtree to be printed

Returns:

parameter string

Throws:

MDParametersException - when creating the parameter string fails

setCellSize

public void setCellSize(int cellSize)

Sets the size (number of bits) of the bins (cells). This has to be at least 1, but should not exceed 32.

Parameters:

cellSize - the width of one (and each) cell (bin) in bits

setLength

public void setLength(int length)
               throws MDParametersException

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

Parameters:

length - the required length (cell count)

Throws:

MDParametersException - if argument is not positive

setScalingHypothesis

public void setScalingHypothesis(MolecularDescriptor scalingHypothesis)

Sets (stores) the specified scaling hypothesis. It is used by various scaled metrics. It cannot be passed to these metrics directly as an argument, because of the uniform method header of metric functions (which has to be preserved).

Parameters:

scalingHypothesis - the consensus hypothesis used for scaling

setScaleFactor

public void setScaleFactor(float scaleFactor)

Sets scaleFactor used with the current parametrized metrics.

Parameters:

scaleFactor - the new value of the scaleFactor

setAsymmetryFactor

public void setAsymmetryFactor(float af)

Sets the value of the asymmetry factor of the current parametrized metric.

Parameters:

af - asymmetry factor

setThreshold

public void setThreshold(float th)

Sets the value of the threshold of the current parametrized metric.

Parameters:

th - dissimilarity threshold value

setWeights

public void setWeights(float[] w)

Sets the cell-wise weight factors for the current parametrized metric.

Parameters:

w - weights

setCellwiseWeights

public void setCellwiseWeights(boolean c)

Sets boolean telling whether cell weights are to be generated for current parametrized metric.

Parameters:

c - true if cell weights

setNormalized

public void setNormalized(boolean yes)

Toggles the normalized flag of the current parametrized metric.

Parameters:

yes - true, if the metric is normalized

setOutputPrecision

public void setOutputPrecision(int precision)

Specifies the output precision for floating point values. This method can be used in conjunction with getDecForm().

Parameters:

precision - number of digits after the decimal point

setCurrentParametrizedMetric

public void setCurrentParametrizedMetric(int metricIndex)

Selects the specified parametrized metric to be the current.

Parameters:

metricIndex - index of the selected parametrized metric

setCreateStatistics

public void setCreateStatistics(boolean createStatistics)

Toggles the create statistics flag of the MDGenerator object.

Parameters:

createStatistics - new value for the create statistics flag

addParametrizedMetric

public int addParametrizedMetric(java.lang.String name,
                                 java.lang.String metric,
                                 java.lang.String activeFamily)
                          throws MDParametersException

Expands the set of parametrized metrics with a new item. The first parameter is optional, if not specified the symbolic name is formed from the second and the third parameters (both of these are mandatory).

Parameters:

name - symbolic name of the parametrized metric

metric - name of the metric (like Tanimoto, Euclidean etc)

activeFamily - name of the active compounds family

Throws:

MDParametersException

getCellSize

public int getCellSize()

Gets the number of bits of an atomic cell in the descriptor.

Returns:

the number of bits in one single descriptor cell

getLength

public int getLength()

Returns the number of cells forming the descriptor.

getInternalSize

public int getInternalSize()

Gets the required memory size to store the descriptor according to the specified parameters.

Returns:

size of a suitable array that can store one descriptor

getData

public byte[] getData()

Gets the byte array which is used for conversions between internal and external data formats. Internal is the memory representation, while external is used for storing descriptors in files.

Returns:

an array large enough to hold the descriptor in external format

getCurrentMetricIndex

public int getCurrentMetricIndex()

getNumberOfMetrics

public int getNumberOfMetrics()

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

Returns:

number of metrics

getNumberOfWeights

public int getNumberOfWeights()

Gets the number of weights the current parametrized metric takes.

Returns:

number of weight factors corresponding to the current metric

getNumberOfWeights

protected int getNumberOfWeights(int parametrizedMetricIndex)
                          throws java.lang.IllegalArgumentException

Gets the number of weight factors used by the specified metric. This method can be applied to the dissimilarity metrics provided by the MolecularDescriptor class or its derived classes, but not to parametrized metric.

Parameters:

parametrizedMetricIndex - parametrized metric index

Returns:

number of weights the metric uses

Throws:

java.lang.IllegalArgumentException - if the given parameter is not a valid metric index

getThreshold

public float getThreshold(int metricIndex)

Gets a metric dependent threshold value. Ideally, this value should be based on statistics, though the actual value is not too critical, since these are only used in user interfaces to simplify the use of applications for beginners. Note: this parametrized version of getThreshold() is kept for compatibility reasons.

Parameters:

metricIndex - index of a parametrized metric

Returns:

threshold corresponding to the given metric index

getThreshold

public float getThreshold()

Gets the threshold value being set for the current parametrized version.

Returns:

dissimilarity threshold corresponding to the curent metric

getScalingHypothesis

public MolecularDescriptor getScalingHypothesis()

Gets the scaling hypothesis used in scaled metrics.

Returns:

the scaling hypothesis

getInternalMetricIndex

public int getInternalMetricIndex()

Gets the MolecularDescriptor specific metric index of the current parametrized metric.

Returns:

metric index

getMetricName

public java.lang.String getMetricName()

Gets the user defined symbolic name of the current parametrized metric.

Returns:

metric name

getMetricName

public java.lang.String getMetricName(int metricIndex)

Gets the user defined symbolic name of the specified parametrized metric.

Returns:

metric name

getMetricIndex

public int getMetricIndex(java.lang.String name)

Gets the index of the given parametrized metric.

Parameters:

name - name of the parametrized metric

Returns:

metric index

getScaleFactor

public float getScaleFactor()

Gets the scale factor used in the current parametrized scalable metrics.

Returns:

the scale factor

getAsymmetryFactor

public float getAsymmetryFactor()

Gets the asymmetry factor used in the current parametrized asymmetric metrics.

Returns:

the value of the asymmetry factor

getWeights

public float[] getWeights()

Gets all weights for the given parametrized metric. If the specified metric is not a weighted metric or correspong weights are not set, null is returned.

Returns:

all weights as float values

getTverskyAlpha

public float getTverskyAlpha()

Gets Tversky alpha value for the given parametrized metric.

Returns:

alpha as float value

getTverskyBeta

public float getTverskyBeta()

Gets Tversky beta value for the given parametrized metric.

Returns:

beta as float value

isCellwiseWeights

public boolean isCellwiseWeights()

Gets boolean telling whether cell weights are to be generated for current parametrized metric.

Returns:

true if weights are assigned to each individual descriptor cell

getDecForm

public java.text.DecimalFormat getDecForm()

Gets the formatter object that is capable of formatting fractions with given precision. Precision can be set by calling setOutputPrecision( int precision ) .

Returns:

decimal number formatter object (not localized)

isScaled

public boolean isScaled()

Returns whether current parametrized metric is scaled or not.

Returns:

true if the metric is scaled

isAsymmetric

public boolean isAsymmetric()

Returns whether current parametrized metric is asymmetric or not.

Returns:

true if the metric is asymmetric

isWeighted

public boolean isWeighted()

Returns whether current parametrized metric is weighted or not.

Returns:

true if the metric is weighted

isNormalized

public boolean isNormalized()

Returns whether current parametrized metric is normalized or not.

Returns:

true if the metric is normalized

isStandardizationMandatory

public boolean isStandardizationMandatory()

Checks is Standardization of molecules is mandatory for the corresponding MolecularDescriptor before descriptor generation. This method always returns true. Derived classes should override in case when standardization is not obligatory.

Returns:

whether or not standardization of molecules is needed

Since:

JChem 2.2

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 but standardization is mandatory for the corresponding MolecularDescriptor. The default on this top level is aromatization and dehydrogenization, but derived parameter classes may overload this behaviour.

Returns:

standardizar confiuration XML string

Since:

JChem 2.2

getDefaultDocumentFrame

public java.lang.String getDefaultDocumentFrame()

Gets the default XML configuration string. This is needed when an optional XML configuration is not specified. Descriptor files and descriptor tables always store the configuration that corresponds to the descriptors stored, thus sg. has to be storedeven when nothing is specified.

Returns:

default XML configuration string of the actual Parameters class

Since:

JChem 2.2

standardize

public Molecule standardize(Molecule m)

Standardizes the Molecule and returns the standardized form. The standardization is configured via XML. StandardizerConfiguration is the corresponding XML tag. If no standardizar is set up, null is returned.

Parameters:

m - molecular structure to be standardized

Returns:

standardized form of the input structure, or null if standardization is mandatory for the corresponding descriptor

Since:

JChem 2.2

readFromXmlFile

protected void readFromXmlFile(java.io.File file,
                               boolean merge,
                               boolean all)
                        throws MDParametersException

Reads configuration from XML file. Builds a DOM tree, picks nodes, elements that store information that can be processed on this level (leaves others for derived classes), and processes this information by converting values in to internal format and stores them in data members of this class. Stores filepath in configFilePath.

Parameters:

file - the XML file to read configuration data from

merge - merge config from file into already existing parameters or overwrite existing parameter values

all - process the complete document or only the ScreeningConfiguration tag

Throws:

MDParametersException - in the case of any failure

readFromXmlString

protected void readFromXmlString(java.lang.String xml,
                                 boolean merge,
                                 boolean all)
                          throws MDParametersException

Reads configuration from XML string. Builds a DOM tree, picks nodes, elements that store information that can be processed on this level (leaves others for derived classes), and processes this information by converting values in to internal format and stores them in data members of this class.

Parameters:

xml - the XML string to get the configuration data from

merge - merge config from file into already existing parameters or overwrite existing parameter values

all - process the complete document or only the ScreeningConfiguration tag

Throws:

MDParametersException - in the case of any failure

checkDocumentVersion

protected void checkDocumentVersion(java.lang.String docType,
                                    java.lang.String version)
                             throws MDParametersException

Checks if the document is the right version

Parameters:

docType - the required document type

version - the expected version number

Throws:

MDParametersException

processDocument

protected void processDocument(boolean all)
                        throws MDParametersException

Searches the DOM tree for relevant nodes and sets internal variables to some these nodes for the sake of easier information processing.

Parameters:

all - process the complete document or only the ScreeningConfiguration tag

Throws:

MDParametersException

readValues

protected void readValues(boolean all)
                   throws MDParametersException

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

Parameters:

all - process the complete document or only the ScreeningConfiguration tag

Throws:

MDParametersException

readMetricParameters

protected void readMetricParameters()
                             throws MDParametersException

Processes all ParametrizedMetric nodes in the DOM tree. Reads parameterized metric names and associated parameter setting and stores them in data member for faster and easier access in getter methods.

Throws:

MDParametersException - if one of the nodes is not well-formed

readMetricWeights

protected void readMetricWeights(org.dom4j.Element parametrizedMetric,
                                 int metricIndex)
                          throws MDParametersException

Throws:

MDParametersException

writeMetricParameter

protected void writeMetricParameter(java.util.ArrayList pl,
                                    java.lang.String attr,
                                    int mi,
                                    boolean useDecForm)

Writes a given parameter of the specified metric into the corresponding tree node.

Parameters:

pl - list of parameters (for all metric indexes)

attr - name of the attribute which the parameter corresponds to

mi - index of the metric

useDecForm - use precision for writing floating point values

appendParametrizedMetric

protected int appendParametrizedMetric(java.lang.String name,
                                       java.lang.String metric)

Extends internal data with a new parametrized metric. Neither the DOM tree nor the XML document is modified.

Parameters:

name - name of the parametrized metric

metric - dissimilarity metric name (as defined in its implementor class

addParametrizedMetricsNode

protected void addParametrizedMetricsNode()

Adds the ParametrizedMetrics node to the DOM tree.

addParametrizedMetricNode

protected org.dom4j.Element addParametrizedMetricNode(java.lang.String name,
                                                      java.lang.String activeFamily,
                                                      java.lang.String metric)

Adds a ParametrizedMetric node to the DOM tree.

Parameters:

name - name of the parameterized metric, given by the user

activeFamily - name of the active compound family (e.g. ACE)

metric - name of the dissimilarity metric

importNodes

protected boolean importNodes(org.dom4j.Document doc,
                              boolean merge)

Imports nodes from the specified Document into the current (main) Document. New nodes can either merged into the existing ones without removing them, or new nodes may overwrite exisiting nodes.

Parameters:

doc - import nodes from this document

merge - merge (add new) or overwrite (replace with new) existing nodes

getDescriptorTypeName

public static java.lang.String getDescriptorTypeName(java.lang.String xmlConfig)

Takes the descriptor type name from the root element of the XML configuration.

Parameters:

xmlConfig - configuration string

Returns:

descriptor type name