getModel method added to BioEntity

model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java

@@ -4,6 +4,8 @@ import java.io.Serializable;
 import java.util.Collection;
 import java.util.List;
 
+import lcsb.mapviewer.model.map.model.Model;
+
 /**
  * Interface that describes bio entity on the map (like Protein or Reaction).
  * 
@@ -11,149 +13,149 @@ import java.util.List;
  * 
  */
 public interface BioEntity extends Serializable {
-	/**
-	 * Returns list of {@link MiriamData annotations} for the object.
-	 * 
-	 * @return list of {@link MiriamData annotations} for the object
-	 */
-	Collection<MiriamData> getMiriamData();
-
-	/**
-	 * Adds miriam annotations to the element.
-	 * 
-	 * @param miriamData
-	 *          set of miriam annotations to be added
-	 */
-	void addMiriamData(Collection<MiriamData> miriamData);
-
-	/**
-	 * Adds miriam annotation to the element.
-	 * 
-	 * @param md
-	 *          miriam annotation to be added
-	 */
-	void addMiriamData(MiriamData md);
-
-	/**
-	 * Returns the name of the object.
-	 * 
-	 * @return the name of the object
-	 */
-	String getName();
-
-	/**
-	 * Returns notes about the object.
-	 * 
-	 * @return notes about the object
-	 */
-	String getNotes();
-
-	/**
-	 * Sets notes about the object.
-	 * 
-	 * @param notes
-	 *          new notes
-	 */
-	void setNotes(String notes);
-
-	/**
-	 * Returns the symbol of the element.
-	 * 
-	 * @return the symbol of the element
-	 */
-	String getSymbol();
-
-	/**
-	 * Sets symbol of the element.
-	 * 
-	 * @param symbol
-	 *          new symbol
-	 */
-	void setSymbol(String symbol);
-
-	/**
-	 * Get list of synonyms.
-	 * 
-	 * @return list of synonyms
-	 */
-	List<String> getSynonyms();
-
-	/**
-	 * Sets list of synonyms to the element.
-	 * 
-	 * @param synonyms
-	 *          new list
-	 */
-	void setSynonyms(List<String> synonyms);
-
-	/**
-	 * Returns the abbreviation.
-	 * 
-	 * @return the abbreviation
-	 */
-	String getAbbreviation();
-
-	/**
-	 * Sets abbreviation.
-	 * 
-	 * @param abbreviation
-	 *          new abbreviation
-	 */
-	void setAbbreviation(String abbreviation);
-
-	/**
-	 * Sets formula.
-	 * 
-	 * @param formula
-	 *          new formula
-	 */
-	void setFormula(String formula);
-
-	/**
-	 * Returns the formula.
-	 * 
-	 * @return the formula
-	 */
-	String getFormula();
-
-	/**
-	 * Sets the name to the object.
-	 * 
-	 * @param name
-	 *          name of the object
-	 * 
-	 */
-	void setName(String name);
-
-	/**
-	 * Returns database identifier of the object.
-	 * 
-	 * @return database identifier of the object
-	 */
-	int getId();
-
-	/**
-	 * Return human readable {@link String} representing class.
-	 * 
-	 * @return human readable {@link String} representing class
-	 */
-	String getStringType();
-
-	/**
-	 * Sets semantic zoom level visibility.
-	 * 
-	 * @param zoomLevelVisibility
-	 *          semantic zoom level visibility
-	 */
-	void setVisibilityLevel(String zoomLevelVisibility);
-	
-	/**
-	 * Sets semantic zoom level visibility.
-	 * 
-	 * @param zoomLevelVisibility
-	 *          semantic zoom level visibility
-	 */
-	void setVisibilityLevel(Integer zoomLevelVisibility);
+  /**
+   * Returns list of {@link MiriamData annotations} for the object.
+   *
+   * @return list of {@link MiriamData annotations} for the object
+   */
+  Collection<MiriamData> getMiriamData();
+
+  /**
+   * Adds miriam annotations to the element.
+   *
+   * @param miriamData
+   *          set of miriam annotations to be added
+   */
+  void addMiriamData(Collection<MiriamData> miriamData);
+
+  /**
+   * Adds miriam annotation to the element.
+   *
+   * @param md
+   *          miriam annotation to be added
+   */
+  void addMiriamData(MiriamData md);
+
+  /**
+   * Returns the name of the object.
+   *
+   * @return the name of the object
+   */
+  String getName();
+
+  /**
+   * Returns notes about the object.
+   *
+   * @return notes about the object
+   */
+  String getNotes();
+
+  /**
+   * Sets notes about the object.
+   *
+   * @param notes
+   *          new notes
+   */
+  void setNotes(String notes);
+
+  /**
+   * Returns the symbol of the element.
+   *
+   * @return the symbol of the element
+   */
+  String getSymbol();
+
+  /**
+   * Sets symbol of the element.
+   *
+   * @param symbol
+   *          new symbol
+   */
+  void setSymbol(String symbol);
+
+  /**
+   * Get list of synonyms.
+   *
+   * @return list of synonyms
+   */
+  List<String> getSynonyms();
+
+  /**
+   * Sets list of synonyms to the element.
+   *
+   * @param synonyms
+   *          new list
+   */
+  void setSynonyms(List<String> synonyms);
+
+  /**
+   * Returns the abbreviation.
+   *
+   * @return the abbreviation
+   */
+  String getAbbreviation();
+
+  /**
+   * Sets abbreviation.
+   *
+   * @param abbreviation
+   *          new abbreviation
+   */
+  void setAbbreviation(String abbreviation);
+
+  /**
+   * Sets formula.
+   *
+   * @param formula
+   *          new formula
+   */
+  void setFormula(String formula);
+
+  /**
+   * Returns the formula.
+   *
+   * @return the formula
+   */
+  String getFormula();
+
+  /**
+   * Sets the name to the object.
+   *
+   * @param name
+   *          name of the object
+   *
+   */
+  void setName(String name);
+
+  /**
+   * Returns database identifier of the object.
+   *
+   * @return database identifier of the object
+   */
+  int getId();
+
+  /**
+   * Return human readable {@link String} representing class.
+   *
+   * @return human readable {@link String} representing class
+   */
+  String getStringType();
+
+  /**
+   * Sets semantic zoom level visibility.
+   *
+   * @param zoomLevelVisibility
+   *          semantic zoom level visibility
+   */
+  void setVisibilityLevel(String zoomLevelVisibility);
+
+  /**
+   * Sets semantic zoom level visibility.
+   *
+   * @param zoomLevelVisibility
+   *          semantic zoom level visibility
+   */
+  void setVisibilityLevel(Integer zoomLevelVisibility);
 
 	/**
 	 * Returns semantic zoom level visibility.
@@ -161,6 +163,14 @@ public interface BioEntity extends Serializable {
 	 * @return semantic zoom level visibility
 	 */
     String getVisibilityLevel();
-    
+
     String getElementId();
+
+  /**
+   * Returns the {@link Model} where BioEntity is located.
+   *
+   * @return the model
+   */
+  Model getModel();
+
 }

model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java

@@ -727,12 +727,8 @@ public class Reaction implements BioEntity {
     this.model = model2.getModelData();
   }
 
-  /**
-   * Returns model where reaction is locacted.
-   * 
-   * @return model where reaction is locacted.
-   */
   @XmlTransient
+  @Override
   public Model getModel() {
     return model.getModel();
   }

model/src/main/java/lcsb/mapviewer/model/map/species/Element.java

@@ -767,11 +767,8 @@ public abstract class Element implements BioEntity, Serializable {
     this.transparencyLevel = transparencyLevel;
   }
 
-  /**
-   * @return the model
-   * @see #model
-   */
   @XmlTransient
+  @Override
   public Model getModel() {
     return model.getModel();
   }