/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview 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.
 *  
 * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.ws;

import jalview.bin.ApplicationSingletonProvider;
import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.datamodel.DBRefSource;
import jalview.ext.ensembl.EnsemblGene;
import jalview.ws.dbsources.Uniprot;
import jalview.ws.seqfetcher.ASequenceFetcher;
import jalview.ws.seqfetcher.DbSourceProxy;

import java.util.ArrayList;
import java.util.Collections;
import java.util.List;

/**
 * Thread safe construction of database proxies. This implements the run-time
 * discovery of sequence database clients.
 * 
 * TODO: extend to a configurable database plugin mechanism where classes are
 * instantiated by reflection and queried for their DbRefSource and version
 * association.
 */
public class SequenceFetcher extends ASequenceFetcher implements ApplicationSingletonI
{
  /*
   * set a mock fetcher here for testing only - reset to null afterwards
   */
  private static SequenceFetcher mockFetcher;

  /**
   * Returns a new SequenceFetcher singleton, or a mock object if one has been
   * set.
   * 
   * @return
   */
  public static SequenceFetcher getInstance()
  {
    return mockFetcher != null ? mockFetcher
            : (SequenceFetcher) ApplicationSingletonProvider
                    .getInstance(SequenceFetcher.class);
  }

  /**
   * Set the instance object to use (intended for unit testing with mock
   * objects).
   * 
   * Be sure to reset to null in the tearDown method of any tests!
   * 
   * @param sf
   */
  public static void setSequenceFetcher(SequenceFetcher sf)
  {
    mockFetcher = sf;
  }

  /**
   * 
   * This public constructor is only is for use by testng to anonymously
   * subclass SequenceFetcher.
   * 
   * 
   */
  public SequenceFetcher()
  {
    addAllDatabases();
  }

  public void addAllDatabases()
  {
    addDBRefSourceImpl(EnsemblGene.class); // includes EnsemblGenomes.class
    addDBRefSourceImpl(Uniprot.class); // includes UniprotName.class
    // addDBRefSourceImpl(EmblSource.class);
    // addDBRefSourceImpl(EmblCdsSource.class);
    // addDBRefSourceImpl(Pdb.class);
    // addDBRefSourceImpl(PfamFull.class);
    // addDBRefSourceImpl(PfamSeed.class);
    // addDBRefSourceImpl(RfamSeed.class);
    addDBRefSourceImpl(DBRefSource.EMBL,
            "jalview.ws.dbsources.EmblSource");
    addDBRefSourceImpl(DBRefSource.EMBLCDS,
            "jalview.ws.dbsources.EmblCdsSource");
    addDBRefSourceImpl(DBRefSource.PDB, "jalview.ws.dbsources.Pdb");
    addDBRefSourceImpl(DBRefSource.PFAM_FULL,
            "jalview.ws.dbsources.PfamFull");
    addDBRefSourceImpl(DBRefSource.PFAM_SEED,
            "jalview.ws.dbsources.PfamSeed");
    addDBRefSourceImpl(DBRefSource.RFAM_SEED,
            "jalview.ws.dbsources.RfamSeed");
  }

  /**
   * return an ordered list of database sources excluding alignment only
   * databases
   */
  public String[] getNonAlignmentSources()
  {
    String[] srcs = this.getSupportedDb();
    List<String> src = new ArrayList<>();
    outer: for (int i = 0; i < srcs.length; i++)
    {
      for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
      {
        // Skip the alignment databases for the moment - they're not useful for
        // verifying a single sequence against its reference source
        if (dbs.isAlignmentSource())
        {
          continue outer;
        }
      }
      src.add(srcs[i]);
    }
    Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
    return src.toArray(new String[src.size()]);
  }
}