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Extend the new QueryChemObject
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Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
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@egonw @rajarshi
egonw authored and rajarshi committed Feb 13, 2011
1 parent b98f650 commit b0a97a6
Showing 1 changed file with 5 additions and 322 deletions.
327 changes: 5 additions & 322 deletions src/main/org/openscience/cdk/isomorphism/matchers/QueryAtom.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand Down Expand Up @@ -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;
}
Expand Down Expand Up @@ -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();
}
}

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