added javadoc for interfaces

src/main/java/model/events/SimulationEvent.java

@@ -4,12 +4,35 @@ import model.genes.RegulatoryGene;
 
 import java.util.List;
 
+/**
+ * This interface represents an event in a simulation that involves updating genes.
+ */
 public interface SimulationEvent {
+
+  /**
+   * Update the state of genes associated with this event.
+   */
   void updateGenes();
+
+  /**
+   * Get the time at which this event occurs in the simulation.
+   *
+   * @return The time of the event.
+   */
   double getTime();
 
+  /**
+   * Get the list of regulatory genes affected by this event.
+   *
+   * @return A list of regulatory genes associated with this event.
+   */
   List<RegulatoryGene> getGenes();
 
-  String getInfo();
-
+  /**
+   * Get a description of this simulation event.
+   *
+   * @return A string describing the event.
+   */
+  String description();
 }
+

src/main/java/model/genes/Gene.java

 package model.genes;
 
+/**
+ * This interface represents a gene that encodes a protein. It manages the protein concentration.
+ */
 public interface Gene {
+
+  /**
+   * Get the current protein concentration encoded by this gene.
+   *
+   * @return The current protein concentration.
+   */
   double getProteinConcentration();
+
+  /**
+   * Get the initial protein concentration encoded by this gene.
+   *
+   * @return The initial protein concentration.
+   */
   double getInitialProteinConcentration();
+
+  /**
+   * Set the protein concentration encoded by this gene to the specified value.
+   *
+   * @param proteinConcentration The new protein concentration to set.
+   */
   void setProteinConcentration(double proteinConcentration);
+
+  /**
+   * Get the name of this gene.
+   *
+   * @return The name of the gene.
+   */
   String getName();
+
+  /**
+   * Update the behavior of this gene for the specified duration.
+   * The protein concentration encoded by this gene is updated according
+   * to the production of the gene and the degradation rate of the protein.
+   *
+   * @param duration The duration for which to update the gene's behavior.
+   */
   void update(double duration);
+
+  /**
+   * Get the maximal production rate of protein by this gene.
+   *
+   * @return The maximal protein production rate.
+   */
   double getMaximalProduction();
+
+  /**
+   * Get the degradation rate of the protein encoded by this gene.
+   *
+   * @return The protein degradation rate.
+   */
   double getDegradationRate();
 }
+

src/main/java/model/genes/RegulatoryGene.java

@@ -2,10 +2,37 @@ package model.genes;
 
 import model.regulators.Regulator;
 
+/**
+ * This interface represents a regulatory gene, which extends the basic gene interface and includes methods
+ * for managing a gene's regulation.
+ */
 public interface RegulatoryGene extends Gene {
+
+  /**
+   * Get the regulator associated with this regulatory gene.
+   *
+   * @return The regulator linked to this gene.
+   */
   Regulator getRegulator();
+
+  /**
+   * Set the regulator associated with this regulatory gene.
+   *
+   * @param regulator The regulator to associate with this gene.
+   */
   void setRegulator(Regulator regulator);
+
+  /**
+   * Check if this regulatory gene is currently signaled, i.e., is influenced by its regulator.
+   *
+   * @return {@code true} if the gene is signaled, {@code false} otherwise.
+   */
   boolean isSignaled();
-  void setSignaled(boolean isSignaled);
 
+  /**
+   * Set the signaling status of this regulatory gene.
+   *
+   * @param isSignaled {@code true} to signal the gene, {@code false} to deactivate it.
+   */
+  void setSignaled(boolean isSignaled);
 }

src/main/java/model/network/RegulatoryNetworkDataManager.java

@@ -32,7 +32,7 @@ public class RegulatoryNetworkDataManager {
         eventString.append(genes.get(index));
       }
       eventString.append(" ");
-      eventString.append(event.getInfo()).append("\n");
+      eventString.append(event.description()).append("\n");
       bufferedWriter.write(eventString.toString());
     }
   }

src/main/java/model/regulators/Regulator.java

 package model.regulators;
 
+/**
+ * This interface represents a regulator, which defines methods for controlling and providing input to a regulatory
+ * gene.
+ */
 public interface Regulator {
+
+  /**
+   * Compute and provide an input value for a regulatory gene.
+   *
+   * @return The input value generated by the regulator.
+   */
   double inputFunction();
-  public String getInfo();
+
+  /**
+   * Get a description of this regulator.
+   *
+   * @return A string describing the regulator.
+   */
+  public String description();
 }
+