/*
 * 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.datamodel;

/**
 * BH 2018 SwingJS note: If additional final static Strings are added to this
 * file, they should be added to public static final String[] allTypes.
 * 
 * Defines internal constants for unambiguous annotation of DbRefEntry source
 * strings and describing the data retrieved from external database sources (see
 * jalview.ws.DbSourcProxy) <br/>
 * TODO: replace with ontology to allow recognition of particular attributes
 * (e.g. protein coding, alignment (ortholog db, paralog db, domain db),
 * genomic, transcriptomic, 3D structure providing (PDB, MODBASE, etc) ..).
 * 
 * 
 * 
 * @author JimP
 * 
 */
import java.util.Locale;

public class DBRefSource
{
  
  
  
  public static final String UNIPROT = "UNIPROT";
  public static final String UP_NAME = "UNIPROT_NAME".toUpperCase(Locale.ROOT);
  /**
   * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
   */
  public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase(Locale.ROOT);

  public static final String ENSEMBL        = "ENSEMBL";
  public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
  
  public static final String EMBL           = "EMBL";
  public static final String EMBLCDS        = "EMBLCDS";
  public static final String EMBLCDSProduct = "EMBLCDSProtein".toUpperCase(Locale.ROOT);

  public static final String PDB    = "PDB";
  public static final String PFAM   = "PFAM";
  public static final String RFAM   = "RFAM";
  public static final String GENEDB = "GeneDB".toUpperCase(Locale.ROOT);

  public static final String PDB_CANONICAL_NAME = PDB;


  public static final String[] allSources = new String[] {
      UNIPROT, 
      UP_NAME, UNIPROTKB, 
      ENSEMBL, ENSEMBLGENOMES, 
      EMBL, EMBLCDS, EMBLCDSProduct, 
      PDB, PFAM, RFAM, GENEDB 
      };  

	public static final int UNIPROT_MASK          = 1<<0;
	public static final int UP_NAME_MASK          = 1<<1;
	public static final int UNIPROT_KB_MASK       = 1<<2;
	public static final int ENSEMBL_MASK          = 1<<3;
	public static final int ENSEMBL_GENOMES_MASK  = 1<<4;
	public static final int EMBL_MASK             = 1<<5;
	public static final int EMBL_CDS_MASK         = 1<<6;
	public static final int EMBL_CDS_PRODUCT_MASK = 1<<7;
	public static final int PDB_MASK              = 1<<8;
	public static final int PFAM_MASK             = 1<<9;
	public static final int RFAM_MASK             = 1<<10;
	public static final int GENE_DB_MASK          = 1<<11;

    public static final int MASK_COUNT = 12;
	  
    public static final int ALL_MASKS = (1 << MASK_COUNT) - 1;

	public static int getSourceKey(String name) {
		  for (int i = 0; i < MASK_COUNT; i++) {
			  if (name.equals(allSources[i]))
        {
          return 1<<i;
        }
		  }
		  return 0;	  
	  }

	public static final int PRIMARY_MASK = UNIPROT_MASK | ENSEMBL_MASK;

	  /**
	  * List of databases whose sequences might have coding regions annotated
	  */
	 public static final String[] DNACODINGDBS = { 
		     ENSEMBL, ENSEMBLGENOMES,
			 EMBL, EMBLCDS, GENEDB
	     };
	
     public static final int DNA_CODING_MASK = 
    		 ENSEMBL_MASK | ENSEMBL_GENOMES_MASK
    	  | EMBL_MASK | EMBL_CDS_MASK | GENE_DB_MASK;

    
     
    public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };

    public static final int CODING_MASK = EMBL_CDS_MASK | GENE_DB_MASK | ENSEMBL_MASK;
  
   
  
    public static final String[] PROTEINDBS = { 
    		UNIPROT, UNIPROTKB,
    		ENSEMBL, EMBLCDSProduct }; // Ensembl ENSP* entries are protein

    public static final int PROTEIN_MASK = 
    		  UNIPROT_MASK | UNIPROT_KB_MASK 
    		| ENSEMBL_MASK | EMBL_CDS_PRODUCT_MASK ;


    // for SequenceAnnotationReport only
    
//    public static final String[][] PRIMARY_SOURCES = new String[][] {
//  	  CODINGDBS, DNACODINGDBS, PROTEINDBS };
//  	  
  	public static final int PRIMARY_SOURCES_MASK = CODING_MASK | DNA_CODING_MASK | PROTEIN_MASK;
      	
    public static boolean isPrimarySource(String source)
    {
    	return ((PRIMARY_SOURCES_MASK & getSourceKey(source)) != 0);
    }

  public static boolean isPrimaryCandidate(String ucversion) {	
    // tricky - this test really needs to search the sequence's set of dbrefs to
    // see if there is a primary reference that derived this reference.
    for (int i = allSources.length; --i >= 0;)
    {
      if (ucversion.startsWith(allSources[i])) // BH 2019.01.25 .toUpperCase(Locale.ROOT) unnecessary here for allSources
      {
        // by convention, many secondary references inherit the primary
        // reference's
        // source string as a prefix for any version information from the
        // secondary reference.
        return false;
      }
    }
    return true;
}



  
}