Constructor Detail

Method Detail

• getProperty

   abstract double getProperty(Node<T> node, Molecule molecule, String property)

  Given an Node, an Molecule and a property expressed as a String, returns a numeric value. If a numeric value is not deducible, Double.NaN is returned.

  Parameters:

  node - the node

  molecule - the molecule to analyze

  property - the property to extract

• createMolecule

   abstract Molecule createMolecule(String s)

  Parses a String, and provides a Molecule.

  Parameters:

  s - the String to parse

• createConcentration

   abstract T createConcentration(String s)

  Creates a new concentration object of a specific concrete type.

  Parameters:

  s - the String to parse

• createNode

   abstract Node<T> createNode(RandomGenerator randomGenerator, Environment<T, P> environment, @Nullable() String parameter)

  Parameters:

  randomGenerator - the random engine

  environment - the environment that will host this object

  parameter - a String describing the object

• createTimeDistribution

   abstract TimeDistribution<T> createTimeDistribution(RandomGenerator randomGenerator, Environment<T, P> environment, Node<T> node, @Nullable() String parameter)

  Parameters:

  randomGenerator - the random engine

  environment - the environment that will host this object

  node - the node that will host this object

  parameter - a String describing the object

• createReaction

   abstract Reaction<T> createReaction(RandomGenerator randomGenerator, Environment<T, P> environment, Node<T> node, TimeDistribution<T> timeDistribution, String parameter)

  Parameters:

  randomGenerator - the random engine

  environment - the environment that will host this object

  node - the node that will host this object

  timeDistribution - the time distribution of the reaction

  parameter - a String describing the object

• createCondition

   abstract Condition<T> createCondition(RandomGenerator randomGenerator, Environment<T, P> environment, Node<T> node, TimeDistribution<T> time, Reaction<T> reaction, String additionalParameters)

  Parameters:

  randomGenerator - the random engine

  environment - the environment that will host this object

  node - the node that will host this object

  time - the time distribution of the reaction

  reaction - the reaction hosting this object

  additionalParameters - a String describing the object

• createAction

   abstract Action<T> createAction(RandomGenerator randomGenerator, Environment<T, P> environment, Node<T> node, TimeDistribution<T> time, Reaction<T> reaction, String additionalParameters)

  Parameters:

  randomGenerator - the random engine

  environment - the environment that will host this object

  node - the node that will host this object

  time - the time distribution of the reaction

  reaction - the reaction hosting this object

  additionalParameters - a String describing the object