Class providing methods of parsing the XML simulation protocol file. More...

Inheritance diagram for utils.XMLParser:

Public Member Functions
	XMLParser (Element localRoot)
	Create an XML parser for a given XML local grouping. More...

	XMLParser (String fileName)

	XMLParser (String activePath, String protocolFile)
	Used to parse an XML file before a simulation log file is generated, when the simulation is being initialised. More...

void	openXMLDocument (String fileName, boolean testDTD)
	Creates a DOM document for an XML protocol file of a given name. More...

void	openXMLDocument (String activePath, String protocolFile, boolean testDTD)
	Used to open an XML file in simulation initialisation - where the log file has yet to be created. More...

LinkedList< Element >	buildSetMarkUp (String childMarkup)
	Returns a linked list of all XML elements of a given tag name. More...

LinkedList< XMLParser >	buildSetParser (String childMarkup)
	Returns a list of XML parsers from combining nodes in the protocol file. Used for boundary conditions. More...

XMLParser	getChild (String childName)
	Returns the child node for a given XML tag name. More...

String	getParam (String paramName)
	Searches the child nodes of a given tag for a particular parameter name. Returns the assigned string value if present. More...

Element	getParamMarkUp (String paramName)
	Searches the child nodes of a given tag for a particular parameter name. Returns the XML element for that tag if present. More...

String	getParam (String paramName, StringBuffer unit)
	Searches the child nodes of a given tag for a particular parameter name and a specified unit. Returns the String value of that tag if present. More...

double	getParamDbl (String paramName)
	Returns the double value assigned to an XML tag in the protocol file. More...

double	getParamDbl (String paramName, StringBuffer unit)
	For a given XML tag name, returns the value in the specified unit (if that tag exists) More...

int	getParamInt (String paramName)
	For a given XML tag name, returns the value it is assigned (if that tag exists) More...

int	getParamInt (String paramName, StringBuffer unit)
	For a given XML tag name, and a given unit of measurement, returns the value the tag is assigned (if that tag exists) More...

double	getParamLength (String paramName)
	Returns a length parameter from the XML, converting to the correct unit as required. More...

double	getParamMass (String paramName)
	Returns the mass of a specified parameter from the XML, calculating this using the unit of measurement for that parameter. More...

double	getParamTime (String paramName)
	Gets a given parameter from the protocol file and converts into a double representing time. More...

double	getParamConc (String paramName)
	Reads a concentration from the protocol file and converts this to the required unit. More...

DiscreteVector	getParamXYZ (String paramName)
	Converts coordinates specified in the protocol file into a discrete vector. More...

Boolean	getParamBool (String paramName)
	Read in boolean value of specified parameter from the XML file. More...

Boolean	getParamBool (String paramName, StringBuffer unit)
	Read in boolean value and unit of measurement of a specified parameter from the XML file. More...

String	getParamSuch (String paramName, String detailName)
	Searches through the attributes of the XML tags of a given parameter name to find the String value of a specified detail within that tag. More...

String	getParamSuch (String paramName, String detailName, StringBuffer unit)
	Searches through the attributes of the XML tags of a given parameter name, in a specified unit to find the String value of a specified detail within that tag. More...

double	getParamSuchDbl (String paramName, String detailName)
	Searches through the attributes of the XML tags of a given parameter name to find the Double value of a specified detail within that tag. More...

Boolean	getParamSuchBool (String paramName, String detailName)
	Searches through the attributes of the XML tags of a given parameter name to find the boolean value of a specified detail within that tag. More...

double	getParamSuchDbl (String paramName, String detailName, StringBuffer unit)
	Searches through the attributes of the XML tags of a given parameter name, in a specified unit to find the Double value of a specified detail within that tag. More...

Boolean	getParamSuchBool (String paramName, String detailName, StringBuffer unit)
	Searches through the attributes of the XML tags of a given parameter name, in a specified unit to find the boolean value of a specified detail within that tag. More...

Element	getChildSuchAttribute (String childName, String attrName, String attrValue)
	Returns the XML element matching the specified tag name, attribute name, and attribute value. If not find return the local root. More...

String	getAttributeStr (String attributeName)
	Return the string value of an attribute of the current localroot of the XML file. More...

double	getAttributeDbl (String attributeName)
	Return the double value of an attribute of the current localroot of the XML file. More...

String	getChildAttrStr (String childName, String attrName)
	Return the string value of a child attribute of the current localroot of the XML file. More...

double	getChildAttrDbl (String childName, String attrName)
	Returns the value assigned to an attribute within a child node. More...

List< Element >	getChildren (String childName)
	Returns a list of the children of a given XML child tag name. More...

Element	getChildElement (String childName)
	Returns the XML element of a given child node tag name. More...

String	getAttribute (String attributeName)
	Return the value assigned to a given XML tag. More...

Element	getElement ()
	Return the current XML local root element. More...

Object	instanceCreator (String prefix)
	Creates an instance of a class using a string containing that class name. More...

double	getDblAttrOfChildSuchAttribute (String childName, String attrName, String attrValue, String attr2Name)
	Used for Epi-Bac scenarios - retrieving list of environments to which this species is sensitive to and the correspondent probability of dying if under the influence of that environment. More...

Detailed Description

Class providing methods of parsing the XML simulation protocol file.

In iDynoMiCS, protocol files are used to create the conditions under which a simulation is run. This is specified in XML. During initialisation, the simulation will require access to tags within this file. This class provides a means of accessing the data in these tags

Constructor & Destructor Documentation

utils.XMLParser.XMLParser ( Element localRoot )

Create an XML parser for a given XML local grouping.

Create an XML parser for a given XML local grouping

Parameters

localRoot An element that is the root of a group of XML tags

utils.XMLParser.XMLParser ( String fileName )

Create an XML parser object for an XML file of a given name

Parameters

fileName The name of the XML file to be processed

utils.XMLParser.XMLParser	(	String	activePath,
		String	protocolFile
	)

Used to parse an XML file before a simulation log file is generated, when the simulation is being initialised.

There are some checks the simulation needs to do on initialisation (with the protocol file). This is before the simulation log is generated. These errors get stored in a separate log file

Parameters

activePath	The path to the protocol file to open
protocolFile	The protocol file to read in

Member Function Documentation

LinkedList<Element> utils.XMLParser.buildSetMarkUp ( String childMarkup )

Returns a linked list of all XML elements of a given tag name.

Returns a linked list of all XML elements within that protocol file that have a given tag name

Parameters

childMarkup The tag name of the elements to put in the list

Returns: A linked list of all the elements of the given tag name

LinkedList<XMLParser> utils.XMLParser.buildSetParser ( String childMarkup )

Returns a list of XML parsers from combining nodes in the protocol file. Used for boundary conditions.

Returns a list of XML parsers from combining nodes in the protocol file. Used for boundary conditions

Parameters

childMarkup The XML tag for which many nodes may exist. boundaryCondition is a good example

Returns: Linked list of XML parsers for each of the nodes of this name that are found in the protocol file

String utils.XMLParser.getAttribute ( String attributeName )

Return the value assigned to a given XML tag.

Returns the value assigned to a given XML tag in a protocol file

Parameters

attributeName The XML tag for which the associated value is needed

Returns: The string value assigned to that tag in the protocol file

double utils.XMLParser.getAttributeDbl ( String attributeName )

Return the double value of an attribute of the current localroot of the XML file.

Return the double value of an attribute of the current localroot of the XML file

Parameters

attributeName The attribute name for which the value is being sought

Returns: The double value of that attribute, if present

String utils.XMLParser.getAttributeStr ( String attributeName )

Return the string value of an attribute of the current localroot of the XML file.

Return the string value of an attribute of the current localroot of the XML file

Parameters

attributeName The attribute name for which the value is being sought

Returns: The string value of that attribute, if present

XMLParser utils.XMLParser.getChild ( String childName )

Returns the child node for a given XML tag name.

Returns the child node for a given XML tag name

Parameters

childName The XML tag name to return

Returns: An XML parser containing the tags relating to this XML child tag

double utils.XMLParser.getChildAttrDbl	(	String	childName,
		String	attrName
	)

Returns the value assigned to an attribute within a child node.

Returns the value assigned to an attribute within a child node. Checking computation domain dimension is one example of its use

Parameters

childName	The name of the child node of which the attribute value is being sought
attrName	The name of the attribute for which the value is required

Returns: Double value assigned to that attribute, if present

String utils.XMLParser.getChildAttrStr	(	String	childName,
		String	attrName
	)

Return the string value of a child attribute of the current localroot of the XML file.

Return the string value of a child attribute of the current localroot of the XML file

Parameters

childName	Name of the XML child tag
attrName	The attribute of that tag for which the value is being sought

Returns: The string value of that attribute, if present

Element utils.XMLParser.getChildElement ( String childName )

Returns the XML element of a given child node tag name.

Returns the XML element of a given child node tag name

Parameters

childName The child tag name for which the XML element is required

Returns: An XML element containing the tags for the specified child name

List<Element> utils.XMLParser.getChildren ( String childName )

Returns a list of the children of a given XML child tag name.

Returns a list of the children of a given XML child tag name

Parameters

childName The name of a child tag in the XML file for which the list of children is required

Returns: List of XML elements containing the children of the specified tag name

Element utils.XMLParser.getChildSuchAttribute	(	String	childName,
		String	attrName,
		String	attrValue
	)

Returns the XML element matching the specified tag name, attribute name, and attribute value. If not find return the local root.

Returns the XML element matching the specified tag name, attribute name, and attribute value. If not find return the local root

Parameters

childName	The XML tag required
attrName	The name of the attribute within that tag
attrValue	The value of the attribute within that tag

Returns: The XML element that matches these three criteria

double utils.XMLParser.getDblAttrOfChildSuchAttribute	(	String	childName,
		String	attrName,
		String	attrValue,
		String	attr2Name
	)

Used for Epi-Bac scenarios - retrieving list of environments to which this species is sensitive to and the correspondent probability of dying if under the influence of that environment.

Used for Epi-Bac scenarios - retrieving list of environments to which this species is sensitive to and the correspondent probability of dying if under the influence of that environment

Parameters

childName	The name of the XML tag that contains the information on this parameter
attrName	The name of the first attribute within that XML tag
attrValue	The value of the first attribute
attr2Name	The name of the related attribute that is required to find this value

Returns: Double value assigned to this tag

Element utils.XMLParser.getElement ( )

Return the current XML local root element.

Return the current XML local root element

Returns: XML Element for the current local root

String utils.XMLParser.getParam ( String paramName )

Searches the child nodes of a given tag for a particular parameter name. Returns the assigned string value if present.

Searches the child nodes of a given tag for a particular parameter name. Returns the assigned string value if present

Parameters

paramName The name of the parameter for which a String value is being sought

Returns: String value assigned to that parameter, if present

String utils.XMLParser.getParam	(	String	paramName,
		StringBuffer	unit
	)

Searches the child nodes of a given tag for a particular parameter name and a specified unit. Returns the String value of that tag if present.

Searches the child nodes of a given tag for a particular parameter name and a specified unit. Returns the String value of that tag if present

Parameters

paramName	The name of the parameter for which a String value is being sought
unit	The unit that this parameter should be

Returns: The value assigned to this tag in the protocol file, if present

Boolean utils.XMLParser.getParamBool ( String paramName )

Read in boolean value of specified parameter from the XML file.

Reads in boolean value of specified parameter from the XML file

Parameters

paramName The parameter to be retrieved from the XML file

Returns: Boolean value assigned to this parameter

Boolean utils.XMLParser.getParamBool	(	String	paramName,
		StringBuffer	unit
	)

Read in boolean value and unit of measurement of a specified parameter from the XML file.

Read in boolean value and unit of measurement of a specified parameter from the XML file

Parameters

paramName	The parameter to be retrieved from the XML file
unit	The unit of measurement specified for this parameter

Returns: Boolean value assigned to this parameter

double utils.XMLParser.getParamConc ( String paramName )

Reads a concentration from the protocol file and converts this to the required unit.

Reads a concentration from the protocol file and converts this to the required unit

Parameters

paramName The concentration of the parameter to be retrieved from the protocol file

Returns: The calculated concentration level for this simulation parameter

double utils.XMLParser.getParamDbl ( String paramName )

Returns the double value assigned to an XML tag in the protocol file.

Returns the double value assigned to an XML tag in the protocol file, if the tag is present

Parameters

paramName The XML parameter for which the value is required

Returns: Double value assigned to that XML tag

double utils.XMLParser.getParamDbl	(	String	paramName,
		StringBuffer	unit
	)

For a given XML tag name, returns the value in the specified unit (if that tag exists)

Parameters

paramName	The name of the XML tag for which a value is required
unit	The unit that this parameter is required to be within

Returns: The double value assigned to that parameter, in the required unit

int utils.XMLParser.getParamInt ( String paramName )

For a given XML tag name, returns the value it is assigned (if that tag exists)

Parameters

paramName The name of the XML tag for which a value is required

Returns: The int value assigned to that parameter

int utils.XMLParser.getParamInt	(	String	paramName,
		StringBuffer	unit
	)

For a given XML tag name, and a given unit of measurement, returns the value the tag is assigned (if that tag exists)

Parameters

paramName	The name of the XML tag for which a value is required
unit	The unif of measurement specified for this parameter

Returns: The int value assigned to that parameter

double utils.XMLParser.getParamLength ( String paramName )

Returns a length parameter from the XML, converting to the correct unit as required.

Returns a length parameter from the XML, converting to the correct unit as required

Parameters

paramName The name of the parameter for which the length value should be returned

Returns: The length value assigned to this parameter in the protocol file

Element utils.XMLParser.getParamMarkUp ( String paramName )

Searches the child nodes of a given tag for a particular parameter name. Returns the XML element for that tag if present.

Searches the child nodes of a given tag for a particular parameter name. Returns the XML element for that tag if present

Parameters

paramName The name of the parameter for which a String value is being sought

Returns: XML Element contains the tags relating to that parameter, if present

double utils.XMLParser.getParamMass ( String paramName )

Returns the mass of a specified parameter from the XML, calculating this using the unit of measurement for that parameter.

Returns the mass of a specified parameter from the XML, calculating this using the unit of measurement for that parameter

Parameters

paramName The name of the parameter for which the mass should be returned

Returns: The calculated mass of this parameter

String utils.XMLParser.getParamSuch	(	String	paramName,
		String	detailName
	)

Searches through the attributes of the XML tags of a given parameter name to find the String value of a specified detail within that tag.

Searches through the attributes of the XML tags of a given parameter name to find the value of a specified detail within that tag

Parameters

paramName	The parameter name for which the value is required
detailName	The name of the detail element which is part of that tag, if present

Returns: The text associated with the specified detail of this tag

String utils.XMLParser.getParamSuch	(	String	paramName,
		String	detailName,
		StringBuffer	unit
	)

Searches through the attributes of the XML tags of a given parameter name, in a specified unit to find the String value of a specified detail within that tag.

Searches through the attributes of the XML tags of a given parameter name to find the value of a specified detail within that tag

Parameters

paramName	The parameter name for which the value is required
detailName	The name of the detail element which is part of that tag, if present
unit	The unit that this parameter should be measured in

Returns: The text associated with the specified detail of this tag

Boolean utils.XMLParser.getParamSuchBool	(	String	paramName,
		String	detailName
	)

Searches through the attributes of the XML tags of a given parameter name to find the boolean value of a specified detail within that tag.

Searches through the attributes of the XML tags of a given parameter name to find the boolean value of a specified detail within that tag

Parameters

paramName	The parameter name for which the value is required
detailName	The name of the detail element which is part of that tag, if present

Returns: The boolean value associated with the specified detail of this tag

Boolean utils.XMLParser.getParamSuchBool	(	String	paramName,
		String	detailName,
		StringBuffer	unit
	)

Searches through the attributes of the XML tags of a given parameter name, in a specified unit to find the boolean value of a specified detail within that tag.

Searches through the attributes of the XML tags of a given parameter name to find the boolean value of a specified detail within that tag

Parameters

paramName	The parameter name for which the value is required
detailName	The name of the detail element which is part of that tag, if present
unit	The unit that this parameter should be measured in

Returns: The boolean value associated with the specified detail of this tag

double utils.XMLParser.getParamSuchDbl	(	String	paramName,
		String	detailName
	)

Searches through the attributes of the XML tags of a given parameter name to find the Double value of a specified detail within that tag.

Searches through the attributes of the XML tags of a given parameter name to find the Double value of a specified detail within that tag

Parameters

paramName	The parameter name for which the value is required
detailName	The name of the detail element which is part of that tag, if present

Returns: The double value associated with the specified detail of this tag

double utils.XMLParser.getParamSuchDbl	(	String	paramName,
		String	detailName,
		StringBuffer	unit
	)

Searches through the attributes of the XML tags of a given parameter name, in a specified unit to find the Double value of a specified detail within that tag.

Searches through the attributes of the XML tags of a given parameter name to find the Double value of a specified detail within that tag

Parameters

paramName	The parameter name for which the value is required
detailName	The name of the detail element which is part of that tag, if present
unit	The unit that this parameter should be measured in

Returns: The double value associated with the specified detail of this tag

double utils.XMLParser.getParamTime ( String paramName )

Gets a given parameter from the protocol file and converts into a double representing time.

Gets a given parameter from the protocol file and converts into a double representing time

Parameters

paramName The parameter to be retrieved from the XML file

Returns: Double of the value of this parameter converted into a unit of time

DiscreteVector utils.XMLParser.getParamXYZ ( String paramName )

Converts coordinates specified in the protocol file into a discrete vector.

Converts coordinates specified in the protocol file into a discrete vector. Used for boundary conditions and specifications of birth area of agents

Parameters

paramName The protocol file parameter specified as X,Y,and Z coordinated

Returns: A discrete vector containing these three coordinates

Object utils.XMLParser.instanceCreator ( String prefix )

Creates an instance of a class using a string containing that class name.

Creates an instance of a class using a string containing that class name. Useful for a set of boundary conditions, for example

Parameters

prefix The class for which a new instance is being created

Returns: An object of the class stated in the prefix string

void utils.XMLParser.openXMLDocument	(	String	fileName,
		boolean	testDTD
	)

Creates a DOM document for an XML protocol file of a given name.

Creates a DOM document for an XML protocol file of a given name

Parameters

fileName	The name of the XML protocol file being processed
testDTD	Boolean stating whether or not schema validation should be applied on reading the XML file

void utils.XMLParser.openXMLDocument	(	String	activePath,
		String	protocolFile,
		boolean	testDTD
	)

Used to open an XML file in simulation initialisation - where the log file has yet to be created.

Used to open an XML file in simulation initialisation - where the log file has yet to be created. This is the case as the simulation log file location is specified in the protocol file. If that can't be read then there is a problem

Parameters

activePath	String of path to protocol file being processed
protocolFile	The protocol file to be read
testDTD	Boolean stating whether or not schema validation should be applied on reading the XML file

The documentation for this class was generated from the following file:

/home/kieran/Dropbox/workspace/iDynoMiCS/src/utils/XMLParser.java

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation