GoTermNode.java

/*
 * Copyright (C) 2010-2011  "Bio4j"
 *
 * This file is part of Bio4j
 *
 * Bio4j is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero 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 Affero General Public License for more details.
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>
 */

package com.bio4j.neo4jdb.model.nodes;

import com.bio4j.neo4jdb.model.relationships.go.*;
import com.bio4j.neo4jdb.model.relationships.protein.ProteinGoRel;
import com.bio4j.neo4jdb.BasicEntity;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import org.neo4j.graphdb.Direction;
import org.neo4j.graphdb.Node;
import org.neo4j.graphdb.Relationship;

/**
 * Gene ontology term
 * @author Pablo Pareja Tobes <ppareja@era7.com>
 */
public class GoTermNode extends BasicEntity{

    public static final String GO_TERM_ID_INDEX = "go_term_id_index";
    public static final String NODE_TYPE = GoTermNode.class.getCanonicalName();
    
    public static final String MOLECULAR_FUNCTION_GO_ID = "GO:0003674";
    public static final String BIOLOGICAL_PROCESS_GO_ID = "GO:0008150";
    public static final String CELLULAR_COMPONENT_GO_ID = "GO:0005575";

    /** GO Term id **/
    public static final String ID_PROPERTY = "go_term_id";
    /** Go Term name **/
    public static final String NAME_PROPERTY = "go_term_name";
    /** Go Term definition **/
    public static final String DEFINITION_PROPERTY = "go_term_definition";
    /** Go Term namespace.<br>
        One of these:<br>
        - Biological process<br>
        - Molecular function<br>
        - Cellular component<br>**/
    public static final String NAMESPACE_PROPERTY = "go_term_namespace";
    /**
     * Boolean value indicating whether the term is obsolete or not
     */
    public static final String OBSOLETE_PROPERTY = "go_term_obsolete";
    public static final String COMMENT_PROPERTY = "go_term_comment";
    public static final String ALTERNATIVE_IDS_PROPERTY = "go_term_alternative_ids";

    public static final String BIOLOGICAL_PROCESS_NAMESPACE = "biological_process";
    public static final String MOLECULAR_FUNCTION_NAMESPACE = "molecular_function";
    public static final String CELLULAR_COMPONENT_NAMESPACE = "cellular_component";


    public GoTermNode(Node n){
        super(n);
    }


    public String getId(){  return String.valueOf(node.getProperty(ID_PROPERTY));}
    public String getName(){    return String.valueOf(node.getProperty(NAME_PROPERTY));}
    public String getDefinition(){  return String.valueOf(node.getProperty(DEFINITION_PROPERTY));}
    public String getNamespace(){   return String.valueOf(node.getProperty(NAMESPACE_PROPERTY));}
    public Boolean getObsolete(){    return Boolean.parseBoolean(String.valueOf(node.getProperty(OBSOLETE_PROPERTY)));}
    public String getComment(){ return String.valueOf(node.getProperty(COMMENT_PROPERTY));}
    public String[] getAlternativeIds(){    return (String[]) node.getProperty(ALTERNATIVE_IDS_PROPERTY);}


    public void setId(String value){    node.setProperty(ID_PROPERTY, value);}
    public void setName(String value){  node.setProperty(NAME_PROPERTY, value);}
    public void setDefinition(String value){    node.setProperty(DEFINITION_PROPERTY, value);}
    public void setNamespace(String value){ node.setProperty(NAMESPACE_PROPERTY, value);}
    public void setObsolete(Boolean value){ node.setProperty(OBSOLETE_PROPERTY, String.valueOf(value));}
    public void setComment(String value){   node.setProperty(COMMENT_PROPERTY, value);}
    public void setAlternativeIds(String[] value){  node.setProperty(ALTERNATIVE_IDS_PROPERTY, value);}
  
    
    public List<ProteinNode> getAssociatedProteins(){
        List<ProteinNode> proteins = new LinkedList<ProteinNode>();
        
        Iterator<Relationship> iterator = node.getRelationships(new ProteinGoRel(null), Direction.INCOMING).iterator();
        while(iterator.hasNext()){
            ProteinNode protein = new ProteinNode(iterator.next().getStartNode());
            proteins.add(protein);                        
        }
        return proteins;  
    }
    
    /**
     * 
     * @return "Is a go" linked nodes 
     */
    public List<GoTermNode> getIsAGoNodes(){
        List<GoTermNode> list = new ArrayList<GoTermNode>();
        Iterator<Relationship> iterator = this.node.getRelationships(new IsAGoRel(null), Direction.OUTGOING).iterator();
        while(iterator.hasNext()){
            list.add(new GoTermNode(iterator.next().getEndNode()));
        }
        return list;
    }    
    /**
     * 
     * @return 
     */
    public List<GoTermNode> getNegativelyRegulatesNodes(){
        List<GoTermNode> list = new ArrayList<GoTermNode>();
        Iterator<Relationship> iterator = this.node.getRelationships(new NegativelyRegulatesGoRel(null), Direction.OUTGOING).iterator();
        while(iterator.hasNext()){
            list.add(new GoTermNode(iterator.next().getEndNode()));
        }
        return list;
    }
    /**
     * 
     * @return 
     */
    public List<GoTermNode> getPositivelyRegulatesNodes(){
        List<GoTermNode> list = new ArrayList<GoTermNode>();
        Iterator<Relationship> iterator = this.node.getRelationships(new PositivelyRegulatesGoRel(null), Direction.OUTGOING).iterator();
        while(iterator.hasNext()){
            list.add(new GoTermNode(iterator.next().getEndNode()));
        }
        return list;
    }
    /**
     * 
     * @return 
     */
    public List<GoTermNode> getPartOfNodes(){
        List<GoTermNode> list = new ArrayList<GoTermNode>();
        Iterator<Relationship> iterator = this.node.getRelationships(new PartOfGoRel(null), Direction.OUTGOING).iterator();
        while(iterator.hasNext()){
            list.add(new GoTermNode(iterator.next().getEndNode()));
        }
        return list;
    }
    /**
     * 
     * @return 
     */
    public List<GoTermNode> getHasPartOfNodes(){
        List<GoTermNode> list = new ArrayList<GoTermNode>();
        Iterator<Relationship> iterator = this.node.getRelationships(new HasPartOfGoRel(null), Direction.OUTGOING).iterator();
        while(iterator.hasNext()){
            list.add(new GoTermNode(iterator.next().getEndNode()));
        }
        return list;
    }
    
    
    @Override
    public int hashCode(){
        return super.hashCode();
    }

    @Override
    public boolean equals(Object obj) {
        if(obj instanceof GoTermNode){
            GoTermNode other = (GoTermNode) obj;
            return this.node.equals(other.node);
        }else{
            return false;
        }
    }

    @Override
    public String toString(){
        return "id = " + getId() +
                "\nnamespace = " + getNamespace() + 
                "\nname = " + getName() +
                "\ndefinition = " + getDefinition();
    }

}