RealUseCase1.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.codesamples;

import com.bio4j.neo4jdb.model.nodes.InterproNode;
import com.bio4j.neo4jdb.model.nodes.OrganismNode;
import com.bio4j.neo4jdb.model.nodes.ProteinNode;
import com.bio4j.neo4jdb.model.nodes.TaxonNode;
import com.bio4j.neo4jdb.model.nodes.refseq.CDSNode;
import com.bio4j.neo4jdb.model.nodes.refseq.GenomeElementNode;
import com.bio4j.neo4jdb.model.relationships.protein.ProteinInterproRel;
import com.bio4j.neo4jdb.model.relationships.protein.ProteinOrganismRel;
import com.bio4j.neo4jdb.model.util.Bio4jManager;
import com.bio4j.neo4jdb.model.util.NodeRetriever;

import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;

import org.neo4j.graphdb.Direction;
import org.neo4j.graphdb.Relationship;

/**
 *
 * Retrieving all nucleotide sequences of CDS corresponding to LysR family 
 * proteins of Uniprot (IPR000847 positive) belonging to 
 * enterobacteriaceae (taxonomy)
 * 
 * @author Pablo Pareja Tobes <ppareja@era7.com>
 */
public class RealUseCase1 {

    public static void main(String[] args) {

    	
    	if (args.length != 1) {
            System.out.println("The program expects the following parameters: \n"
                    + "1. Bio4j DB folder\n");
        } else {
        	Bio4jManager manager = null;

            try {
                
                //--creating manager and node retriever----
                manager = new Bio4jManager(args[0]);
                NodeRetriever nodeRetriever = new NodeRetriever(manager);

                //First we get the taxon node we're interested in
                TaxonNode taxonNode = nodeRetriever.getTaxonByName("Enterobacteriaceae");
                
                System.out.println("taxonNode = " + taxonNode);

                //In this list we're gonna store the organism nodes
                ArrayList<OrganismNode> organisms = new ArrayList<OrganismNode>();

                System.out.println("Getting organisms...");
                
                //Now we get the organisms
                getAllSubOrganisms(taxonNode,organisms);
                
                //Here we'll store selected proteins
                ArrayList<ProteinNode> proteins = new ArrayList<ProteinNode>();
                
                //getting proteins for those organisms and selecting the ones
                //that have the interpro value = IPR000847
                ProteinOrganismRel proteinOrganismRel = new ProteinOrganismRel(null);
                ProteinInterproRel proteinInterproRel = new ProteinInterproRel(null);
                
                System.out.println("looping through organisms...");
                
                //----------looping through organisms checking every associated protein----
                for (OrganismNode organismNode : organisms) {
                    
                    System.out.println("organismNode = " + organismNode);
                    
                    Iterator<Relationship> iterator = organismNode.getNode().getRelationships(proteinOrganismRel, Direction.INCOMING).iterator();
                    while(iterator.hasNext()){                    
                        ProteinNode tempProt = new ProteinNode(iterator.next().getStartNode());
                        
                        Iterator<Relationship> interProIterator = tempProt.getNode().getRelationships(proteinInterproRel, Direction.OUTGOING).iterator();
                        boolean interproFound = false;
                        while(interProIterator.hasNext() && !interproFound){
                            InterproNode interpro = new InterproNode(interProIterator.next().getEndNode());
                            if(interpro.getId().equals("IPR000847")){
                                interproFound = true;
                            }
                        }
                        
                        //---the protein is selected in case it has the interpro id---
                        if(interproFound){
                            proteins.add(tempProt);
                        }
                    }
                }
                
                System.out.println("looping through proteins...");
                
                //At this point we should already have the proteins we want
                //now it's time to retrieve their CDS sequences
                for (ProteinNode proteinNode : proteins) {
                    
                    System.out.println("protein = " + proteinNode.getAccession());
                    
                    List<GenomeElementNode> genomeElements = proteinNode.getGenomeElements();
                    
                    for (GenomeElementNode genomeElementNode : genomeElements) {
                        
                        System.out.println("genomeElement = " + genomeElementNode.getVersion());
                        
                        List<CDSNode> cdsList = genomeElementNode.getCDS();
                        for (CDSNode cDSNode : cdsList) {
                            System.out.println("cDSNode = " + cDSNode);
                        }
                    }
                }
                
                System.out.println("Done! :)");
                



            } catch (Exception e) {
                //deal somehow with the exception
                e.printStackTrace();
            } finally {

                //---closing the manager----
                manager.shutDown();

            }
        }     


    }

    private static void getAllSubOrganisms(TaxonNode taxonNode,
            ArrayList<OrganismNode> organisms) {

        System.out.println(taxonNode);

        organisms.addAll(taxonNode.getOrganisms());
        List<TaxonNode> children = taxonNode.getChildren();
        
        for (TaxonNode child : children) {
            getAllSubOrganisms(child, organisms);
        }

    }
}