/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */

package org.biojavax;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;

import org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver;
import org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder;
import org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler;
import org.biojavax.bio.seq.DummyRichSequenceHandler;
import org.biojavax.bio.seq.PositionResolver;
import org.biojavax.bio.seq.RichSequenceHandler;
import org.biojavax.bio.seq.PositionResolver.AverageResolver;
import org.biojavax.ontology.ComparableOntology;
import org.biojavax.ontology.SimpleComparableOntology;


/**
 * Runs a service that builds rich objects, and provides some default values
 * for things like default ontology, default namespace, etc.
 * @author Richard Holland
 * @since 1.5
 */
public class RichObjectFactory {
    
    private static RichObjectBuilder builder = new SimpleRichObjectBuilder();
    
    private static String defaultOntologyName = "biojavax";
    private static String defaultNamespaceName = "lcl";
    private static PositionResolver defaultPositionResolver = new AverageResolver();
    private static CrossReferenceResolver defaultCrossRefResolver = new DummyCrossReferenceResolver();
    private static RichSequenceHandler defaultRichSequenceHandler = new DummyRichSequenceHandler();
    
    // the LRU cache - keys are classes, entries are maps of param sets to objects
    private static int defaultLRUcacheSize = 20;
    private static Map LRUcacheSizes = new HashMap();
    private static Map cache = new HashMap();
    private final static Map applicationClassMap = new HashMap();
    
    // Constructor is private as this is all static.
    private RichObjectFactory() {}
    
    /**
     * Sets the builder to use when instantiating new Rich objects. The basic,
     * default, one is a SimpleRichObjectBuilder, which just calls the constructor.
     * Another useful one is BioSQLRichObjectBuilder, which attempts to load
     * objects from the database. The latter is required if you are working with
     * Hibernate as it will not work without it.
     * @param b the builder to use.
     * @see SimpleRichObjectBuilder
     * @see org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder
     */
    public static synchronized void setRichObjectBuilder(RichObjectBuilder b) {
        builder = b;
    }
    
    /**
     * Delegates to a RichObjectBuilder to construct/retrieve the object, and returns it.
     * To increase efficiency, it keeps a list of recently requested objects. If it
     * receives further requests for the same object, it returns them from the cache. The
     * size of the cache can be altered using setLRUCacheSize(). The default cache size is 20
     * objects for each type of class requested.
     * @param clazz the class to build
     * @param params the parameters to pass to the class' constructor
     * @return the instantiated object
     */
    public static synchronized Object getObject(final Class clazz, Object[] params) {
        List paramsList = Arrays.asList(params);
        final Class applicationClass = getApplicationClass(clazz);
        if (!cache.containsKey(applicationClass)) {
            int LRUcacheSize = defaultLRUcacheSize;
            if (LRUcacheSizes.containsKey(applicationClass)) LRUcacheSize = ((Integer)LRUcacheSizes.get(applicationClass)).intValue();
            else LRUcacheSizes.put(applicationClass,new Integer(LRUcacheSize));
            cache.put(applicationClass, new LinkedHashMap(LRUcacheSize, 0.75f, true) {
                protected boolean removeEldestEntry(Map.Entry eldest) {
                    return this.size() > ((Integer)LRUcacheSizes.get(applicationClass)).intValue();
                }
            });
        }
        Map m = (Map)cache.get(applicationClass);
       if (!m.containsKey(paramsList)) {
           m.put(paramsList,builder.buildObject(applicationClass, paramsList));
       }
        return m.get(paramsList);
    }
    
    private final static Map getApplicationClassMap() {
    	return applicationClassMap;
    }
    
	/**
	 * Allow application to override the default biojava class created in getObject - subclass restriction is checked in the builder.
	 * @param theBiojavaClass one of the well-known builder classes: SimpleNamespace, SimpleComparableOntology, SimpleNCBITaxon, SimpleCrossRef, or SimpleDocRef
	 * @param theApplicationClass - a subclass of theBiojavaClass
	 */
    public final static void setApplicationClass(final Class theBiojavaClass, final Class theApplicationClass) {
    	if (theApplicationClass==null || theBiojavaClass.isAssignableFrom(theApplicationClass) == false) throw new IllegalArgumentException("RichObjectFactory.setApplicationClass-theApplicationClass: <"+theApplicationClass+"> must be assignable to the biojava class: <"+theBiojavaClass+">");
    	getApplicationClassMap().put(theBiojavaClass, theApplicationClass);
    }
    
    private final static Class getApplicationClass(final Class theBiojavaClass) {
    	final Class applicationClass = (Class) getApplicationClassMap().get(theBiojavaClass);
    	return applicationClass!=null?applicationClass:theBiojavaClass;
    }
    
    /**
     * Removes all objects from the LRU cache.
     */
    public static synchronized void clearLRUCache(){
        cache.clear();
    }
    
    /**
     * Removes all objects of the specified class from the LRU cache.
     * @param clazz The class of the objects to remove.
     */
    public static synchronized void clearLRUCache(Class clazz){
        cache.remove(clazz);
    }
    
    /**
     * Sets the size of the LRU cache. This is the size per class of object requested, so
     * if you set it to 20 and request 3 different types of object, you will get 20*3=60
     * entries in the cache. The default cache size is 20. Setting this value will undo 
     * any previous changes made using the setLRUCacheSize(Class,int) method below, but will not
     * override future ones.
     * @param size the size of the cache.
     */
    public static void setLRUCacheSize(int size) {
        defaultLRUcacheSize = size;
        for (Iterator i = LRUcacheSizes.keySet().iterator(); i.hasNext(); ) LRUcacheSizes.put(i.next(), new Integer(size));
    }
    
    /**
     * Sets the size of the LRU cache. This is the size for the specific class of object 
     * requested, so does not affect the size of caches of other objects.
     * If this method is not called, then the cache size defaults to 20, or whatever value
     * was passed to setLRUCacheSize(int) above.
     * @param size the size of the cache.
     */
    public static void setLRUCacheSize(Class clazz, int size) {
        LRUcacheSizes.put(clazz,new Integer(size));
    }
    
    /**
     * Sets the default namespace name to use when loading sequences. Defaults to "lcl".
     * @param name the namespace name to use.
     */
    public static void setDefaultNamespaceName(String name) { defaultNamespaceName = name; }
    
    /**
     * Sets the default ontology name to use when loading sequences. Defaults to "biojavax".
     * @param name the ontology name to use.
     */
    public static void setDefaultOntologyName(String name) { defaultOntologyName = name; }
    
    /**
     * Sets the default position resolver to use when creating new rich feature locations.
     * Defaults to the AverageResolver
     * @param pr the position resolver to use.
     * @see org.biojavax.bio.seq.PositionResolver
     * @see org.biojavax.bio.seq.PositionResolver.AverageResolver
     * @see org.biojavax.bio.seq.RichLocation
     */
    public static void setDefaultPositionResolver(PositionResolver pr) { defaultPositionResolver = pr; }
    
    /**
     * Sets the default crossref resolver to use when resolving remote entries.
     * Defaults to the DummyCrossReferenceResolver.
     * @param crr the resolver to use.
     * @see org.biojavax.CrossReferenceResolver
     * @see org.biojavax.DummyCrossReferenceResolver
     */
    public static void setDefaultCrossReferenceResolver(CrossReferenceResolver crr) { defaultCrossRefResolver = crr; }
    
    /**
     * Sets the default sequence handler to use when performing sequence manipulation.
     * Defaults to the DummyRichSequenceHandler.
     * @param rsh the resolver to use.
     * @see org.biojavax.bio.seq.RichSequenceHandler
     * @see org.biojavax.bio.seq.DummyRichSequenceHandler
     */
    public static void setDefaultRichSequenceHandler(RichSequenceHandler rsh) { defaultRichSequenceHandler = rsh; }
    
    /**
     * Returns the default namespace object. Defaults to "lcl".
     * @return the default namespace.
     */
    public static Namespace getDefaultNamespace() {
        return (Namespace)getObject(SimpleNamespace.class, new Object[]{defaultNamespaceName});
    }
    
    /**
     * Returns the default ontology object. Defaults to "biojavax".
     * @return the default ontology.
     */
    public static ComparableOntology getDefaultOntology() {
        return (ComparableOntology)getObject(SimpleComparableOntology.class, new Object[]{defaultOntologyName});
    }
    
    /**
     * Returns the default position resolver object. Defaults to PositionResolver.AverageResolver
     * @return the default position resolver.
     * @see org.biojavax.bio.seq.PositionResolver.AverageResolver
     */
    public static PositionResolver getDefaultPositionResolver() { return defaultPositionResolver; }
    
    /**
     * Returns the default cross ref resolver object. Defaults to DummyCrossReferenceResolver
     * @return the default resolver.
     * @see org.biojavax.DummyCrossReferenceResolver
     */
    public static CrossReferenceResolver getDefaultCrossReferenceResolver() { return defaultCrossRefResolver; }
    
    /**
     * Returns the default sequence resolver object. Defaults to DummyRichSequenceHandler.
     * @return the default resolver.
     * @see org.biojavax.bio.seq.DummyRichSequenceHandler
     */
    public static RichSequenceHandler getDefaultRichSequenceHandler() { return defaultRichSequenceHandler; }
        
    /** 
     * A utility method that configures the RichObjectFactory for use with a Hibernate session.
     * @param session an object containing a Hibernate session.
     */
    public static void connectToBioSQL(Object session) {
    	clearLRUCache();
        RichObjectFactory.setRichObjectBuilder(new BioSQLRichObjectBuilder(session));
        RichObjectFactory.setDefaultCrossReferenceResolver(new BioSQLCrossReferenceResolver(session));      
        RichObjectFactory.setDefaultRichSequenceHandler(new BioSQLRichSequenceHandler(session));        
    }
}