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The main project for the external domain-specific modeling language ML-Rules, which is used to model hierarchical biochemical reaction networks with nested and attributed species

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/*
 *   Copyright 2015 University of Rostock
 *
 *   Licensed under the Apache License, Version 2.0 (the "License");
 *   you may not use this file except in compliance with the License.
 *   You may obtain a copy of the License at
 *
 *   http://www.apache.org/licenses/LICENSE-2.0
 *
 *   Unless required by applicable law or agreed to in writing, software
 *   distributed under the License is distributed on an "AS IS" BASIS,
 *   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *   See the License for the specific language governing permissions and
 *   limitations under the License.
 */

package org.jamesii.mlrules.model.species;

import java.io.Serializable;

/**
 * A {@link LeafSpecies} is a species that cannot contain other species, i.e.,
 * it is always a leaf is a species tree. {@link LeafSpecies} are treated
 * population-based.
 * 
 * @author Tobias Helms
 *
 */
public class LeafSpecies extends Species implements Serializable {

  /**
   * The amount of a species saved as a floating point number. Floating point
   * numbers are needed in case a simulation is computed deterministically with
   * numerical integration methods.
   */
  private double amount;

  public LeafSpecies(SpeciesType type, Object[] attributes, Compartment context, double amount) {
    super(type, attributes, context);
    this.amount = amount;
  }

  @Override
  public double getAmount() {
    return amount;
  }

  private void checkAmount(double amount) {
    if (amount < 0) {
      throw new IllegalArgumentException(
          String.format("Negative amount %s for %s is not allowed.", amount, toString()));
    }
  }

  public void setAmount(double amount) {
    checkAmount(amount);
    this.amount = amount;
  }

  public void changeAmount(double change) {
    double result = amount + change;
    checkAmount(result);
    this.amount = result;
  }

  @Override
  public Species copy() {
    Object[] attributes = new Object[getType().getAttributesSize()];
    for (int i = 0; i < getType().getAttributesSize(); ++i) {
      attributes[i] = getAttribute(i);
    }
    Species result = new LeafSpecies(getType(), attributes, getContext(), amount);
    return result;
  }

  @Override
  public boolean equals(Object o) {
    if (o == this) {
      return true;
    }
    if (o instanceof LeafSpecies) {
      LeafSpecies s = (LeafSpecies) o;
      if (!s.getType().equals(getType())) {
        return false;
      }
      for (int i = 0; i < getType().getAttributesSize(); ++i) {
        if (!getAttribute(i).equals(s.getAttribute(i))) {
          return false;
        }
      }
      return true;
    }
    return false;
  }

  @Override
  public String toString() {
    return amount + " " + super.toString();
  }

}