Package de.unirostock.sems.bives.sbml.parser

Class SBMLRule

java.lang.Object

de.unirostock.sems.bives.sbml.parser.SBMLGenericObject

de.unirostock.sems.bives.sbml.parser.SBMLSBase

de.unirostock.sems.bives.sbml.parser.SBMLRule

All Implemented Interfaces:

de.unirostock.sems.bives.algorithm.DiffReporter

Direct Known Subclasses:

SBMLAlgebraicRule, SBMLAssignmentRule, SBMLRateRule

public abstract class SBMLRule
extends SBMLSBase
implements de.unirostock.sems.bives.algorithm.DiffReporter

The abstract Class SBMLRule. In SBML, Rules provide additional ways to define the values of variables in a model, their relationships, and the dynamical behaviors of those variables.

Author:

Martin Scharm

Field Summary

Fields

Modifier and Type	Field	Description
static int	ALGEBRAIC_RULE	The flag ALGEBRAIC_RULE.
static int	ASSIGNMENT_RULE	The flag ASSIGNMENT_RULE.
protected de.unirostock.sems.bives.ds.MathML	math	The math.
static int	RATE_RULE	The flag RATE_RULE.
protected int	type	The type flag encoding the type of rule.

Fields inherited from class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject

documentNode, sbmlModel

Constructor Summary

Constructors

Constructor	Description
SBMLRule(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode, SBMLModel sbmlModel)	Instantiates a new SBML rule.

Method Summary

Modifier and Type	Method	Description
de.unirostock.sems.bives.ds.MathML	getMath()	Gets the math.
int	getRuleType()	Gets the rule type.
protected SBMLSBase	resolveVariable(String ref)	Resolves a variable.

Methods inherited from interface de.unirostock.sems.bives.algorithm.DiffReporter

reportDelete, reportInsert, reportModification

Methods inherited from class java.lang.Object

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

Methods inherited from class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject

getDocumentNode, getModel

Methods inherited from class de.unirostock.sems.bives.sbml.parser.SBMLSBase

addOntologyLink, flagMetaModifcations, getAnnotation, getMetaId, getNotes, getOntologyLinks, getSBOTerm

Field Detail

ASSIGNMENT_RULE

public static final int ASSIGNMENT_RULE

The flag ASSIGNMENT_RULE.

See Also:

Constant Field Values

ALGEBRAIC_RULE

public static final int ALGEBRAIC_RULE

The flag ALGEBRAIC_RULE.

See Also:

Constant Field Values

RATE_RULE

public static final int RATE_RULE

The flag RATE_RULE.

See Also:

Constant Field Values

math

protected de.unirostock.sems.bives.ds.MathML math

The math.

type

protected int type

The type flag encoding the type of rule.

Constructor Detail

SBMLRule

public SBMLRule(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode,
                SBMLModel sbmlModel)
         throws BivesSBMLParseException

Instantiates a new SBML rule.

Parameters:

documentNode - the document node encoding this entity in the corresponding XML tree

sbmlModel - the SBML model

Throws:

BivesSBMLParseException - the bives sbml parse exception

Method Detail

getMath

public de.unirostock.sems.bives.ds.MathML getMath()

Gets the math.

Returns:

the math

resolveVariable

protected final SBMLSBase resolveVariable(String ref)
                                   throws BivesSBMLParseException

Resolves a variable.

Parameters:

ref - the reference name

Returns:

the SBML SBase node of this variable

Throws:

BivesSBMLParseException - the bives sbml parse exception

getRuleType

public int getRuleType()

Gets the rule type. (see static flags)

Returns:

the rule type