fern.network.sbml

Class MathTree

java.lang.Object

fern.network.sbml.MathTree

public class MathTree
extends Object

Representation of am evaluation tree. Within a sbml file, MathML branches may occur at different positions. These are represented as MathTrees in FERN.

Author:

Florian Erhard

Field Summary

Fields

Modifier and Type	Field and Description
static String	TEMP_VALUE

Constructor Summary

Constructors

Constructor and Description
MathTree(SBMLinterpreter interpreter, org.sbml.jsbml.ASTNode ast) Creates a MathTree ASTNode.

Method Summary

Modifier and Type	Method and Description
double	calculate(AmountManager amount, Simulator sim) Evaluate the MathTree.
org.sbml.jsbml.ASTNode	getCopiedAST() Gets the ASTNode of this MathTree.
List<Integer>	getSpecies() Gets the species present in this tree.

Methods inherited from class java.lang.Object

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

Field Detail

TEMP_VALUE

public static final String TEMP_VALUE

See Also:

Constant Field Values

Constructor Detail

MathTree

public MathTree(SBMLinterpreter interpreter,
                org.sbml.jsbml.ASTNode ast)

Creates a MathTree ASTNode.

Parameters:

interpreter - sbmlInterpreter instance for calculating the nodes

ast - ASTNode

Method Detail

getSpecies

public List<Integer> getSpecies()

Gets the species present in this tree.

Returns:

indices of the species.

getCopiedAST

public org.sbml.jsbml.ASTNode getCopiedAST()

Gets the ASTNode of this MathTree.

Returns:

the copiedAST of this MathTree

calculate

public double calculate(AmountManager amount,
                        Simulator sim)

Evaluate the MathTree.

Parameters:

amount - AmountManager

sim - Simulator

Returns:

value of the expression