/**
 * Copyright (C) 2010-2015 The Roslin Institute <contact andy.law@roslin.ed.ac.uk>
 *
 * This file is part of JEnsembl: a Java API to Ensembl data sources developed by the
 * Bioinformatics Group at The Roslin Institute, The Royal (Dick) School of
 * Veterinary Studies, University of Edinburgh.
 *
 * Project hosted at: http://jensembl.sourceforge.net
 *
 * This is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License (version 3) as published by
 * the Free Software Foundation.
 *
 * This software 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
 * in this software distribution. If not, see: http://opensource.org/licenses/gpl-3.0.html
 */
package uk.ac.roslin.ensembl.demo;

import java.util.ArrayList;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.TreeSet;
import uk.ac.roslin.ensembl.config.DBConnection.DataSource;
import uk.ac.roslin.ensembl.config.EnsemblDBType;
import uk.ac.roslin.ensembl.dao.database.*;
import uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome;
import uk.ac.roslin.ensembl.exception.NonUniqueException;
import uk.ac.roslin.ensembl.model.database.CollectionDatabase;

public class BacteriaConnection {

    //demonstrated connection to the Bacterial collections in EnsemblesGenomes datasource

    //various standard operations demonstrated 
    public static void main(String[] args) throws Exception {

        System.out.println("uninitialized bacterial registry report: ");
        
        DBRegistry uRegistry = DBRegistry.createUninitializedRegistryForDataSource(DataSource.ENSEMBLBACTERIA);       
        System.out.println(uRegistry.getVersionReport());
        System.out.println(uRegistry.getBriefRegistryReport());
        
        DBRegistry bacterialRegistry =DBRegistry.createRegistryForDataSourceAtReleaseVersion(DataSource.ENSEMBLBACTERIA, uRegistry.getHighestReleaseVersion());
       
        System.out.println("current bacterial registry report: ");
        System.out.println(bacterialRegistry.getVersionReport());
        System.out.println(bacterialRegistry.getBriefRegistryReport());       
        
        System.out.println("******************************* ");

        //the 'standard' species in the database
        System.out.println("all DBSpecies");
        for (DBSpecies s : bacterialRegistry.getSpecies()) {
            System.out.println(s.getCommonName() + "\n\t ["+s.getShortName()+"]" +" ("+s.getSpeciesBinomial()+")");
        }
        if (bacterialRegistry.getSpecies().isEmpty()) {
            System.out.println("No DBSpecies!");
        }
        //bacterial species that are organised into collections
        System.out.println("all DBCollectionSpecies");
        for (DBCollectionSpecies s : bacterialRegistry.getCollectionSpecies()) {
            System.out.println(s.getCommonName()+ "\n\t ["+s.getShortName()+"]" +" ("+s.getSpeciesBinomial()+")");
        }
        System.out.println("");

        //get all the CollectionSpecies ( which currently are Bacteria ) 
        //which are in the CURRENT HIGHEST release configured
        List<DBSpecies> bactSpeciess = new ArrayList<DBSpecies>();
        for (DBCollection c : bacterialRegistry.getCollectionsByDBVersion(
                "" + bacterialRegistry.getHighestReleaseVersion())) {
            bactSpeciess.addAll(c.getSpecies());
        }
        System.out.println("bacteria in : " + bacterialRegistry.getHighestReleaseVersion());
        for (DBSpecies s : bactSpeciess) {
            System.out.println(s);
        }

        //will print out details of each collection
        
        for (DBCollection c : bacterialRegistry.getCollections()) {
            System.out.println(c.getCollectionName() + " (version " + c.getDBVersion() + ")");
            int i = 1;
            for (DBCollectionSpecies s : c.getSpecies()) {
                System.out.println(i++ + ":\t" + s.getComparaName(c.getDBVersion()));
            }
        }


        System.out.println("TESTING LIVE ENSEMBLBACTERIA");

       

        System.out.println("all  of the collection databases are:");
        System.out.println("*************************************\n");

//        for (CollectionOfSpecies r : bacterialRegistry.getCollectionsByDBVersion(bacterialRegistry.getMostRecentDBVersion())) {        
        for (DBCollection coll : bacterialRegistry.getCollections()) {

            System.out.println("collection name: " + coll.getCollectionName());
            System.out.println("\tschema version: " + coll.getSchemaVersion());
            System.out.println("\tdb version: " + coll.getDBVersion());
            System.out.println("\tSpecies: "+ coll.getSpecies().size());
//          System.out.println("\t_________________________________\n Species included:\n");
//
//            for (CollectionSpecies sp : r.getSpecies()) {
//                System.out.println("\t\t" + sp.getSpeciesBinomial() + " : " + sp.getCommonName());
//            }

            System.out.println("\t\tDatabases");

            for (CollectionDatabase d : coll.getDatabases()) {
                System.out.println("\t\t\t" + d.getdBName());
            }

            System.out.println("\t\t" + EnsemblDBType.collection_core);

            for (CollectionDatabase d : coll.getDatabasesByType(EnsemblDBType.collection_core)) {
                System.out.println("\t\t\t" + d.getdBName());
            }
            System.out.println("\t\t" + EnsemblDBType.collection_funcgen);

            for (CollectionDatabase d : coll.getDatabasesByType(EnsemblDBType.collection_funcgen)) {
                System.out.println("\t\t\t" + d.getdBName());
            }
            System.out.println("\t\t" + EnsemblDBType.collection_variation);

            for (CollectionDatabase d : coll.getDatabasesByType(EnsemblDBType.collection_variation)) {
                System.out.println("\t\t\t" + d.getdBName());
            }
            System.out.println("*************************************\n");
        }

        DBSpecies s = bacterialRegistry.getSpeciesByAlias("Bacillus anthracis str. CDC 684");
        List<DBCollectionSpecies> accessioned = bacterialRegistry.getGCAccessionedCollectionSpecies();
        List<DBCollectionSpecies> named = bacterialRegistry.getNamedCollectionSpecies();
        
        
        if (accessioned.contains(s)) {
            System.out.println("sp is in accessioned list: "+s.getSpeciesBinomial()+" "+s.hashCode());
            System.out.println("dbname "+s.getDatabaseStyleName());
            System.out.println("url "+s.getUrlName());
            System.out.println("stem "+s.getAssemblyAccessionStem());
            System.out.println("aliases "+s.getAliases().toString());
            System.out.println("most recent core "+s.getMostRecentCoreDatabase().getdBName());
            System.out.println("databases: "+s.getDatabases().toString());
            System.out.println("----------------------------------------------\n");
        } else {
            System.out.println("sp is NOT in accessioned list");
        }
        
        if (named.contains(s)) {
            System.out.println("sp is in named list: "+s.getSpeciesBinomial()+" "+s.hashCode());
        } else {
            System.out.println("sp is NOT in named list");
        }
        DBCollectionSpecies s2= bacterialRegistry.getCSpeciesByGCAccessionStem(s.getAssemblyAccessionStem());
        
        if (s.equals(s2)) {
            System.out.println("retrieval by accession is identical: "+s.getSpeciesBinomial()+" "+s.hashCode());   
        } else {
            System.out.println("retrieval by accession is NOT identical");   
        }
        
        String st2 = bacterialRegistry.getGCAssemblyAccessionForAlias(s.getSpeciesBinomial());
        String st = bacterialRegistry.getEnsemblNameForAlias(s.getSpeciesBinomial());
        
        DBSpecies s3 = bacterialRegistry.getSpeciesByAlias(st);
        
        if (s.equals(s3)) {
            System.out.println("retrieval by alias is identical: "+s.getSpeciesBinomial()+" "+s.hashCode());   
        } else {
            System.out.println("retrieval by alias is NOT identical");   
        }
        
        for (DBCollectionSpecies sp:named) {
            if (sp.getAliases().contains(st)) {
                System.out.println(" name indexed species with this ensembl name "+st+" = "+sp.getSpeciesBinomial()
                        + " "+sp.hashCode());
                System.out.println("stem "+sp.getAssemblyAccessionStem());
                System.out.println("dbname "+sp.getDatabaseStyleName());
                System.out.println("url "+sp.getUrlName());
                System.out.println("aliases "+sp.getAliases().toString());
                System.out.println("most recent core "+sp.getMostRecentCoreDatabase().getdBName());
                System.out.println("databases: "+sp.getDatabases().toString());
                
                if (s.equals(sp)) {
                    System.out.println("which is the same object as the accession indexed species");
                    
                } else {
                    System.out.println("which is NOT the same object as the accession indexed species"); 
                }
                System.out.println("-----------------------------------------------------\n");
            }
        }
          

        DBCollectionSpecies pumi = (DBCollectionSpecies) bacterialRegistry.getSpeciesByAlias("Bacillus pumilus SAFR-032");

        System.out.println("DB for Bacillus pumilus SAFR-032");

        TreeSet<Integer> versions = new TreeSet<Integer>();

        for (DBCollectionDatabase d : pumi.getDatabasesByType(EnsemblDBType.collection_core)) {

            System.out.println("core version " + d.getDBVersion());
            versions.add(Integer.parseInt(d.getDBVersion()));

        }


        DAChromosome chrP = (DAChromosome) ((DBCollectionCoreDatabase) pumi.getDatabaseByTypeAndVersion(EnsemblDBType.collection_core, versions.last().toString())).getCoreFactory(pumi).getChromosomeDAO().getChromosomeByName("Chromosome");

        System.out.println(chrP.getSpecies().getSpeciesBinomial() + " : " + chrP.getId() + " : " + chrP.getChromosomeName());

        
        
        
        
        DBSpecies spG3;
        DBSpecies spG4;
        
          try {
            spG3 = bacterialRegistry.getSpeciesByAlias("h37rv");

            
            
            
        } catch (NonUniqueException nonUniqueException) {
            System.out.print("Mycobacterium tuberculosis H37Rv is not unique....");
            HashSet<DBSpecies> allHits = (HashSet<DBSpecies>) nonUniqueException.getAllHits();
            System.out.println(allHits.size());
            Iterator<DBSpecies> iterator = allHits.iterator();
            
            int count = 0;
            for (DBSpecies sp: allHits) {
              System.out.println(count++ +": "+sp.getDatabaseStyleName()+" "+sp.getComparaName(null));  
            }

        }
        
        
        
        
        
        
        
        
        System.out.println("\n\n*****************************\n* COMPLETED FUNCTIONAL TEST *\n*****************************\n");

    }
}