Extend the new QueryChemObject

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

Author: egonw

src/main/org/openscience/cdk/isomorphism/matchers/QueryAtom.java

@@ -19,25 +19,18 @@
  */
 package org.openscience.cdk.isomorphism.matchers;
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
 import javax.vecmath.Point2d;
 import javax.vecmath.Point3d;
 
 import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.event.ChemObjectChangeEvent;
-import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomType;
 import org.openscience.cdk.interfaces.IBond;
-import org.openscience.cdk.interfaces.IChemObjectBuilder;
-import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
-import org.openscience.cdk.interfaces.IChemObjectListener;
 
-public abstract class QueryAtom implements IQueryAtom {
+/**
+ * @cdk.module  isomorphism
+ * @cdk.githash
+ */
+public abstract class QueryAtom extends QueryChemObject implements IQueryAtom {
 
     /**
      *  The partial charge of the atom.
@@ -134,26 +127,6 @@ public abstract class QueryAtom implements IQueryAtom {
     /** The atomic number for this element giving their position in the periodic table. */
     protected Integer atomicNumber = (Integer) CDKConstants.UNSET;
 
-    /**
-     * List for listener administration.
-     */
-    private List<IChemObjectListener> chemObjectListeners;
-
-    /**
-     *  A hashtable for the storage of any kind of properties of this IChemObject.
-     */
-    private Map<Object, Object> properties;
-
-    /**
-     *  You will frequently have to use some flags on a IChemObject. For example, if
-     *  you want to draw a molecule and see if you've already drawn an atom, or in
-     *  a ring search to check whether a vertex has been visited in a graph
-     *  traversal. Use these flags while addressing particular positions in the
-     *  flag array with self-defined constants (flags[VISITED] = true). 100 flags
-     *  per object should be more than enough.
-     */
-    private boolean[] flags;
-
     public QueryAtom(String symbol) {
         this.symbol = symbol;
     }
@@ -661,294 +634,4 @@ public Integer getValency()
        return this.electronValency;
    }
 
-   /**
-    *  Lazy creation of chemObjectListeners List.
-    *
-    *@return    List with the ChemObjects associated.
-    */
-   private List<IChemObjectListener> lazyChemObjectListeners()
-   {
-       if (chemObjectListeners == null) {
-           chemObjectListeners = new ArrayList<IChemObjectListener>();
-       }
-       return chemObjectListeners;
-   }
-
-
-   /**
-    *  Use this to add yourself to this IChemObject as a listener. In order to do
-    *  so, you must implement the ChemObjectListener Interface.
-    *
-    *@param  col  the ChemObjectListener
-    *@see         #removeListener
-    */
-   public void addListener(IChemObjectListener col)
-   {
-       List<IChemObjectListener> listeners = lazyChemObjectListeners();
-
-       if (!listeners.contains(col))
-       {
-           listeners.add(col);
-       }
-       // Should we throw an exception if col is already in here or
-       // just silently ignore it?
-   }
-
-
-   /**
-    *  Returns the number of ChemObjectListeners registered with this object.
-    *
-    *@return    the number of registered listeners.
-    */
-   public int getListenerCount() {
-       if (chemObjectListeners == null) {
-           return 0;
-       }
-       return lazyChemObjectListeners().size();
-   }
-
-
-   /**
-    *  Use this to remove a ChemObjectListener from the ListenerList of this
-    *  IChemObject. It will then not be notified of change in this object anymore.
-    *
-    *@param  col  The ChemObjectListener to be removed
-    *@see         #addListener
-    */
-   public void removeListener(IChemObjectListener col) {
-       if (chemObjectListeners == null) {
-           return;
-       }
-       
-       List<IChemObjectListener> listeners = lazyChemObjectListeners();
-       if (listeners.contains(col)) {
-           listeners.remove(col);
-       }
-   }
-
-
-   /**
-    *  This should be triggered by an method that changes the content of an object
-    *  to that the registered listeners can react to it.
-    */
-   public void notifyChanged() {
-       if (getNotification() && getListenerCount() > 0) {
-           List<IChemObjectListener> listeners = lazyChemObjectListeners();
-           for (Object listener : listeners) {
-               ((IChemObjectListener) listener).stateChanged(
-                       new ChemObjectChangeEvent(this)
-               );
-           }
-       }
-   }
-
-
-   /**
-    *  This should be triggered by an method that changes the content of an object
-    *  to that the registered listeners can react to it. This is a version of
-    *  notifyChanged() which allows to propagate a change event while preserving
-    *  the original origin.
-    *
-    *@param  evt  A ChemObjectChangeEvent pointing to the source of where
-    *      the change happend
-    */
-   public void notifyChanged(IChemObjectChangeEvent evt) {
-       if (getNotification() && getListenerCount() > 0) {
-           List<IChemObjectListener> listeners = lazyChemObjectListeners();
-           for (Object listener : listeners) {
-               ((IChemObjectListener) listener).stateChanged(evt);
-           }
-       }
-   }
-
-
-   /**
-    * Lazy creation of properties hash.
-    *
-    * @return    Returns in instance of the properties
-    */
-   private Map<Object, Object> lazyProperties()
-   {
-       if (properties == null)
-       {
-           properties = new HashMap<Object, Object>();
-       }
-       return properties;
-   }
-
-
-   /**
-    *  Sets a property for a IChemObject.
-    *
-    *@param  description  An object description of the property (most likely a
-    *      unique string)
-    *@param  property     An object with the property itself
-    *@see                 #getProperty
-    *@see                 #removeProperty
-    */
-   public void setProperty(Object description, Object property)
-   {
-       lazyProperties().put(description, property);
-       notifyChanged();
-   }
-
-
-   /**
-    *  Removes a property for a IChemObject.
-    *
-    *@param  description  The object description of the property (most likely a
-    *      unique string)
-    *@see                 #setProperty
-    *@see                 #getProperty
-    */
-   public void removeProperty(Object description)
-   {
-       if (properties == null) {
-           return;
-       }
-       if (lazyProperties().remove(description) != null)
-           notifyChanged();
-   }
-
-   /**
-    *  Returns a property for the IChemObject.
-    *
-    *@param  description  An object description of the property (most likely a
-    *      unique string)
-    *@return              The object containing the property. Returns null if
-    *      propert is not set.
-    *@see                 #setProperty
-    *@see                 #removeProperty
-    */
-   public Object getProperty(Object description)
-   {
-       if (properties != null) {
-           return lazyProperties().get(description);
-       }
-       return null;
-   }
-
-   /**
-    *  Returns a Map with the IChemObject's properties.
-    *
-    *@return    The object's properties as an Hashtable
-    *@see       #setProperties
-    */
-   public Map<Object,Object> getProperties()
-   {
-       return lazyProperties();
-   }
-
-   /**
-    *  Returns the identifier (ID) of this object.
-    *
-    *@return    a String representing the ID value
-    *@see       #setID
-    */
-   public String getID()
-   {
-       return this.identifier;
-   }
-
-   /**
-    *  Sets the identifier (ID) of this object.
-    *
-    *@param  identifier  a String representing the ID value
-    *@see                #getID
-    */
-   public void setID(String identifier)
-   {
-       this.identifier = identifier;
-       notifyChanged();
-   }
-
-   /**
-    *  Sets the value of some flag.
-    *
-    *@param  flag_type   Flag to set
-    *@param  flag_value  Value to assign to flag
-    *@see                #getFlag
-    */
-   public void setFlag(int flag_type, boolean flag_value)
-   {
-       flags[flag_type] = flag_value;
-       notifyChanged();
-   }
-
-   /**
-    *  Returns the value of some flag.
-    *
-    *@param  flag_type  Flag to retrieve the value of
-    *@return            true if the flag <code>flag_type</code> is set
-    *@see               #setFlag
-    */
-   public boolean getFlag(int flag_type)
-   {
-       return flags[flag_type];
-   }
-
-   /**
-    *  Sets the properties of this object.
-    *
-    *@param  properties  a Hashtable specifying the property values
-    *@see                #getProperties
-    */
-   public void setProperties(Map<Object,Object> properties)
-   {
-       Iterator<Object> keys = properties.keySet().iterator();
-       while (keys.hasNext())
-       {
-           Object key = keys.next();
-           lazyProperties().put(key, properties.get(key));
-       }
-       notifyChanged();
-   }
-
-   private boolean doNotification = true;
-
-   /**
-    * Sets the whole set of flags.
-    *
-    * @param  flagsNew    the new flags.
-    * @see                #getFlags
-    */
-   public void setFlags(boolean[] flagsNew){
-       flags=flagsNew;
-   }
-
-   /**
-    * Returns the whole set of flags.
-    *
-    *@return    the flags.
-    *@see       #setFlags
-    */
-   public boolean[] getFlags(){
-       return(flags);
-   }
-
-   public void setNotification(boolean bool) {
-       this.doNotification = bool;
-   }
-
-   public boolean getNotification() {
-       return this.doNotification;
-   }
-
-   @Override
-    public IChemObjectBuilder getBuilder() {
-        // TODO Auto-generated method stub
-        return null;
-    }
-
-    @Override
-    public boolean matches(IAtom atom) {
-        // TODO Auto-generated method stub
-        return false;
-    }
-
-    @Override
-    public Object clone() throws CloneNotSupportedException {
-        // TODO Auto-generated method stub
-        return super.clone();
-    }
 }