Constructor Detail

Method Detail

• addLayer

   abstract void addLayer(Molecule m, Layer<T, P> l)

  Add a Layer to the Environment.

  Parameters:

  m - the Molecule of the Layer

  l - the Layer

• addNode

   abstract void addNode(Node<T> node, P p)

  This method allows to add a new node to this environment. The environment is responsible to call the right method of the simulation in order to ensure that the reaction is properly scheduled.

  Parameters:

  node - The node to add

  p - The position where to place it

• addTerminator

   abstract void addTerminator(Predicate<Environment<T, P>> terminator)

  Parameters:

  terminator - a Predicate indicating whether the simulation should be considered finished

• getDimensions

   abstract int getDimensions()

  The number of dimensions of this environment.

• getDistanceBetweenNodes

   abstract double getDistanceBetweenNodes(Node<T> n1, Node<T> n2)

  Measures the distance between two nodes in the environment.

  Parameters:

  n1 - the first node

  n2 - the second node

• getIncarnation

  @Nonnull() abstract Incarnation<T, P> getIncarnation()

• getLayer

   abstract Optional<Layer<T, P>> getLayer(Molecule m)

  Get the layer associate to the given molecule. If no Layer is associated with the given molecule, return an empty optional.

  Parameters:

  m - the Molecule

• getLayers

   abstract ListSet<Layer<T, P>> getLayers()

  Return all the Layers in this Environment.

• getLinkingRule

   abstract LinkingRule<T, P> getLinkingRule()

• getNeighborhood

   abstract Neighborhood<T> getNeighborhood(Node<T> center)

  Given a node, this method returns its neighborhood.

  Parameters:

  center - The node you want the neighbors to be found

• getNodeByID

   abstract Node<T> getNodeByID(int id)

  Allows to access a node known its id. Depending on the implementation, this method may or not be optimized (namely, id could run in constant or linear time with the number of nodes).

  Parameters:

  id - the node's ID

• getNodes

   abstract ListSet<Node<T>> getNodes()

  All the nodes that exist in current environment.

• getNodeCount

   abstract int getNodeCount()

• getNodesWithinRange

   abstract ListSet<Node<T>> getNodesWithinRange(Node<T> center, double range)

  Given a node (center) this method returns a list of all the surroundings nodes within the given range. Note that this method (depending on the implementation) might be not optimized and it's consequently much better to use getNeighborhood and filter the neighborhood if you are sure that all the nodes within the range are connected to the center.

  Parameters:

  center - the node to consider as center

  range - the exploration range

• getNodesWithinRange

   abstract ListSet<Node<T>> getNodesWithinRange(P center, double range)

  Given a Position(center) this method returns a list of all the surroundings nodes within the given range. Note that this method (depending on the implementation) might be not optimized.

  Parameters:

  center - the Position to consider as center

  range - the exploration range

• getOffset

   abstract Array<double> getOffset()

  This method allows to know which are the smallest coordinates represented.

• getPosition

  @Nonnull() abstract P getPosition(Node<T> node)

  Calculates the position of a node.

  Parameters:

  node - the node you want to know the position

• getSimulation

   abstract Simulation<T, P> getSimulation()

• getSize

   abstract Array<double> getSize()

  This method returns the size of the environment as an array of length getDimensions. This method must return distance measured with the same unit used by the positions. No non-euclidean distance metrics are allowed.

• getSizeInDistanceUnits

   abstract Array<double> getSizeInDistanceUnits()

  This method returns the size of the environment as an array of length getDimensions. This method must return distance measured with the same unit used for measuring distances. It may or may not return the same result of getSize

• isTerminated

   abstract boolean isTerminated()

• makePosition

   abstract P makePosition(Array<Number> coordinates)

  Parameters:

  coordinates - the coordinates of the point

• moveNodeToPosition

   abstract void moveNodeToPosition(Node<T> node, P position)

  This method moves a node in the environment to some position. If node move is unsupported, it does nothing.

  Parameters:

  node - The node to move

  position - The absolute position in which this node will be moved.

• removeNode

   abstract void removeNode(Node<T> node)

  This method allows to remove a node. If node removal is unsupported, it does nothing.

  Parameters:

  node - the node to remove

• setLinkingRule

   abstract void setLinkingRule(LinkingRule<T, P> rule)

  Parameters:

  rule - the rule to set

• setSimulation

   abstract void setSimulation(Simulation<T, P> s)

  Parameters:

  s - the simulation