Constructor Detail

• MoleculeReader

  MoleculeReader(String moleculeName, String property, Incarnation<?, ?> incarnation, FilteringPolicy filter, List<String> aggregatorNames)

  Parameters:

  moleculeName -

      the target molecule

  property -

      the target property

  incarnation -

      the target incarnation

  filter -

      the [FilteringPolicy] to use

  aggregatorNames -

      the names of the [UnivariateStatistic] to use for
      aggregating data. If an empty list is passed, then the values
      will be logged indipendently for each node.

Method Detail

• getColumnNames

   List<String> getColumnNames()

• extractData

   <T extends Any> Map<String, Double> extractData(Environment<T, ?> environment, Reaction<T> reaction, Time time, Long step)

  Extracts properties from an environment. The returned map must either:

  • contain a single element,

  • have the keys matching columnNames, or

  • be iterable in predictable order (namely, implement SortedMap or extend one of LinkedHashMap or ConcurrentLinkedHashMap).

  Parameters:

  environment -

      the {@link Environment}

  reaction -

      the last executed {@link Reaction}

  time -

      the current {@link Time}

  step -

      the simulation step