Class SBMLRule
- java.lang.Object
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- de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
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- de.unirostock.sems.bives.sbml.parser.SBMLSBase
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- de.unirostock.sems.bives.sbml.parser.SBMLRule
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- 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
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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
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Method Summary
All Methods Instance Methods Concrete Methods 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 class de.unirostock.sems.bives.sbml.parser.SBMLSBase
addOntologyLink, flagMetaModifcations, getAnnotation, getMetaId, getNotes, getOntologyLinks, getSBOTerm
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Methods inherited from class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
getDocumentNode, getModel
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Field Detail
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ASSIGNMENT_RULE
public static final int ASSIGNMENT_RULE
The flag ASSIGNMENT_RULE.- See Also:
- Constant Field Values
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ALGEBRAIC_RULE
public static final int ALGEBRAIC_RULE
The flag ALGEBRAIC_RULE.- See Also:
- Constant Field Values
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RATE_RULE
public static final int RATE_RULE
The flag RATE_RULE.- See Also:
- Constant Field Values
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math
protected de.unirostock.sems.bives.ds.MathML math
The math.
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type
protected int type
The type flag encoding the type of rule.
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Constructor Detail
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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 treesbmlModel
- the SBML model- Throws:
BivesSBMLParseException
- the bives sbml parse exception
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Method Detail
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getMath
public de.unirostock.sems.bives.ds.MathML getMath()
Gets the math.- Returns:
- the math
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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
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getRuleType
public int getRuleType()
Gets the rule type. (see static flags)- Returns:
- the rule type
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