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

• addGlobalReaction

   abstract void addGlobalReaction(GlobalReaction<T> reaction)

  Add a GlobalReaction to the Environment.

  Parameters:

  reaction - the GlobalReaction to add.

• removeGlobalReaction

   abstract void removeGlobalReaction(GlobalReaction<T> reaction)

  Remove a GlobalReaction from the Environment.

  Parameters:

  reaction - GlobalReaction to remove.

• getGlobalReactions

   abstract ListSet<GlobalReaction<T>> getGlobalReactions()

  Get the Environment's GlobalReactions.

  Returns:

  the list of GlobalReactions in this Environment.

• addNode

   abstract boolean 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

  Returns:

  true if node is added in the environment

• 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.

  Returns:

  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

  Returns:

  the distance between the two nodes

• getIncarnation

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

  Returns:

  the Incarnation used to initialize the entities of this Environment, if it has been set.

• 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

  Returns:

  the Optional containing the Layer associated with the requested molecule

• getLayers

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

  Return all the Layers in this Environment.

  Returns:

  a ListSet of Layer.

• getLinkingRule

   abstract LinkingRule<T, P> getLinkingRule()

  Returns:

  the current linking rule

• setLinkingRule

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

  Parameters:

  rule - the rule to set

• 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

  Returns:

  the neighborhood

• 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

  Returns:

  the node with that id, or null if it does not exist in this environment

• getNodes

   abstract ListSet<Node<T>> getNodes()

  All the nodes that exist in current environment.

  Returns:

  All the nodes that exist in current environment

• getNodeCount

   abstract int getNodeCount()

  Returns:

  the number of nodes currently in the environment

• 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

  Returns:

  the list of nodes within the 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

  Returns:

  the list of nodes within the range

• getOffset

   abstract Array<double> getOffset()

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

  Returns:

  an array of length getDimensions() containing the smallest coordinates for each dimension.

• getPosition

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

  Calculates the position of a node.

  Parameters:

  node - the node you want to know the position

  Returns:

  The position

• getSimulation

   abstract Simulation<T, P> getSimulation()

  Returns:

  the current simulation, if present, or throws an IllegalStateException otherwise

• setSimulation

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

  Parameters:

  s - the simulation

• 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.

  Returns:

  the size of this environment

• 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

  Returns:

  the size of this environment

• isTerminated

   abstract boolean isTerminated()

  Returns:

  true if all the terminators are true

• makePosition

   abstract P makePosition(Array<Number> coordinates)

  Parameters:

  coordinates - the coordinates of the point

  Returns:

  a Position compatible with this environment

• moveNodeToPosition

  @Nonnull() abstract void moveNodeToPosition(@Nonnull() Node<T> node, @Nonnull() 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