/*
 *  Copyright (C) 2011 apurv
 * 
 *  This program is free software: you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation, either version 3 of the License, or
 *  (at your option) any later version.
 * 
 *  This program is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 * 
 *  You should have received a copy of the GNU General Public License
 *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

package nescent.phylogeoref.reader;

import static java.lang.System.out;
import java.util.HashMap;
import java.util.Map;
import nescent.phylogeoref.reader.utility.PhyloUtility;
import nescent.phylogeoref.reader.utility.PhylogenyFactory;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
import org.nexml.model.Edge;
import org.nexml.model.FloatEdge;
import org.nexml.model.Network;
import org.nexml.model.Node;


/**
 * Provides methods that can construct a Phylogeny object from a Tree or Network.
 * @author apurv
 */
public class NeXMLEngine {

    private Map<String,PhylogenyNode> map = null;
    private Map<String,PhylogenyMould> mouldMap = null;

    /**
     * Should be strictly called after invoking the method
     * constructPhylogenyFromNetwork()
     * @return
     */
    public Map<String, PhylogenyNode> getMap() {
        return map;
    }

    
    /**
     * Constructs the Phylogeny object representation of the network
     *
     * @param network represents the tree from which the Phylogeny object is to be constructed.
     * @return the fully built Phylogeny object representing this tree.
     */
    public Phylogeny constructPhylogenyFromNetwork(Network<FloatEdge> network){

        Phylogeny phy = PhylogenyFactory.newInstance(network);
        map= new HashMap<String,PhylogenyNode>();

        Node rootNode = PhyloUtility.getRootNode(network);

        map.put(rootNode.getId(), phy.getRoot());
        
        for(Node node:network.getNodes()){
            if(node.isRoot()){
                continue;
            }
            PhylogenyNode phyNode = PhyloUtility.toPhylogenyNode(node);

            map.put(node.getId(), phyNode);


        }

        for(Edge edge:network.getEdges()){
            Node sourceNode = edge.getSource();
            Node targetNode = edge.getTarget();
            
            PhylogenyNode phySourceNode = map.get(sourceNode.getId());
            PhylogenyNode phyTargetNode = map.get(targetNode.getId());

            phySourceNode.addAsChild(phyTargetNode);

            PhyloUtility.setDistanceToParent(edge, phyTargetNode);
        }

        //Attach the metadata information that is available from the NeXML file.
        for(Node node:network.getNodes()){
            PhylogenyNode phyNode = map.get(node.getId());
            this.attachMetadataFromNeXML(node, phyNode);
        }

        return phy;        
    }

    /**
     * Finds any metadata attached to the node in the NeXML and attaches to the PhylogenyNode.
     * @param node
     * @param phyNode
     */
    private void attachMetadataFromNeXML(Node node, PhylogenyNode phyNode){
        PhyloUtility.attachOtherMetadata(node, phyNode);

        if(phyNode.isExternal()){
            PhyloUtility.attachLocationMetadata(node, phyNode);
        }
    }
      
}