/*
 * 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.util;

import java.util.ArrayList;
import java.util.BitSet;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;

import com.stevesoft.pat.Regex;

import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.Mapping;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;

/**
 * Utilities for handling DBRef objects and their collections.
 */
public class DBRefUtils
{
  /*
   * lookup from lower-case form of a name to its canonical (standardised) form
   */
  private static Map<String, String> canonicalSourceNameLookup = new HashMap<>();

	public final static int DB_SOURCE = 1;
	public final static int DB_VERSION = 2;
	public final static int DB_ID = 4;
	public final static int DB_MAP = 8;

	public final static int SEARCH_MODE_NO_MAP_NO_VERSION = DB_SOURCE | DB_ID;
	public final static int SEARCH_MODE_FULL = DB_SOURCE | DB_VERSION | DB_ID | DB_MAP;

	static 
	{
		// TODO load these from a resource file?
		canonicalSourceNameLookup.put("uniprotkb/swiss-prot", DBRefSource.UNIPROT);
		canonicalSourceNameLookup.put("uniprotkb/trembl", DBRefSource.UNIPROT);

		// Ensembl values for dbname in xref REST service:
		canonicalSourceNameLookup.put("uniprot/sptrembl", DBRefSource.UNIPROT);
		canonicalSourceNameLookup.put("uniprot/swissprot", DBRefSource.UNIPROT);

		canonicalSourceNameLookup.put("pdb", DBRefSource.PDB);
		canonicalSourceNameLookup.put("ensembl", DBRefSource.ENSEMBL);
		// Ensembl Gn and Tr are for Ensembl genomic and transcript IDs as served
		// from ENA.
		canonicalSourceNameLookup.put("ensembl-tr", DBRefSource.ENSEMBL);
		canonicalSourceNameLookup.put("ensembl-gn", DBRefSource.ENSEMBL);

	    // guarantee we always have lowercase entries for canonical string lookups
	    for (String k : canonicalSourceNameLookup.keySet())
	    {
	      canonicalSourceNameLookup.put(k.toLowerCase(),
	              canonicalSourceNameLookup.get(k));
	    }
   }

  /**
   * Returns those DBRefEntry objects whose source identifier (once converted to
   * Jalview's canonical form) is in the list of sources to search for. Returns
   * null if no matches found.
   * 
   * @param dbrefs  DBRefEntry objects to search
   * @param sources array of sources to select
   * @return
   */
  public static List<DBRefEntry> selectRefs(List<DBRefEntry> dbrefs, String[] sources) 
  {
    if (dbrefs == null || sources == null) 
	{
	  return dbrefs;
	}

	// BH TODO (what?)
	HashSet<String> srcs = new HashSet<String>();
	for (String src : sources) 
	{
	  srcs.add(src.toUpperCase());
	}

	int nrefs = dbrefs.size();
	List<DBRefEntry> res = new ArrayList<DBRefEntry>();
	for (int ib = 0; ib < nrefs; ib++) 
	{
	  DBRefEntry dbr = dbrefs.get(ib);
	  String source = getCanonicalName(dbr.getSource());
	  if (srcs.contains(source.toUpperCase())) 
	  {
	    res.add(dbr);
	  }
	}
	if (res.size() > 0) 
	{
		// List<DBRefEntry> reply = new DBRefEntry[res.size()];
		return res;// .toArray(reply);
	}
	return null;
  }

  private static boolean selectRefsBS(List<DBRefEntry> dbrefs, int sourceKeys, BitSet bsSelect) 
  {
	if (dbrefs == null || sourceKeys == 0) 
	{
	  return false;
	}
	for (int i = 0, n = dbrefs.size(); i < n; i++) 
	{
	  DBRefEntry dbr = dbrefs.get(i);
	  if ((dbr.getSourceKey() & sourceKeys) != 0) 
	  {
	    bsSelect.clear(i);
	  }
	}
	return !bsSelect.isEmpty();
  }

  /**
   * Returns a (possibly empty) list of those references that match the given
   * entry, according to the given comparator.
   * 
   * @param refs
   *          an array of database references to search
   * @param entry
   *          an entry to compare against
   * @param comparator
   * @return
   */
  static List<DBRefEntry> searchRefs(DBRefEntry[] refs, DBRefEntry entry,
          DbRefComp comparator)
  {
    List<DBRefEntry> rfs = new ArrayList<>();
    if (refs == null || entry == null)
    {
      return rfs;
    }
    for (int i = 0; i < refs.length; i++)
    {
      if (comparator.matches(entry, refs[i]))
      {
        rfs.add(refs[i]);
      }
    }
    return rfs;
  }

	/**
	 * look up source in an internal list of database reference sources and return
	 * the canonical jalview name for the source, or the original string if it has
	 * no canonical form.
	 * 
	 * @param source
	 * @return canonical jalview source (one of jalview.datamodel.DBRefSource.*) or
	 *         original source
	 */
	public static String getCanonicalName(String source) 
	{
	  if (source == null) 
	  {
		return null;
	  }
	  String canonical = canonicalSourceNameLookup.get(source.toLowerCase());
	  return canonical == null ? source : canonical;
	}

	/**
	 * Returns a (possibly empty) list of those references that match the given
	 * entry. Currently uses a comparator which matches if
	 * <ul>
	 * <li>database sources are the same</li>
	 * <li>accession ids are the same</li>
	 * <li>both have no mapping, or the mappings are the same</li>
	 * </ul>
	 * 
	 * @param ref   Set of references to search
	 * @param entry pattern to match
	 * @param mode  SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION optional
	 * @return
	 */
	public static List<DBRefEntry> searchRefs(List<DBRefEntry> ref, DBRefEntry entry, int mode) {
		return searchRefs(ref, entry, matchDbAndIdAndEitherMapOrEquivalentMapList, mode);
	}

	/**
	 * Returns a list of those references that match the given accession id
	 * <ul>
	 * <li>database sources are the same</li>
	 * <li>accession ids are the same</li>
	 * <li>both have no mapping, or the mappings are the same</li>
	 * </ul>
	 * 
	 * @param refs  Set of references to search
	 * @param accId accession id to match
	 * @return
	 */
	public static List<DBRefEntry> searchRefs(List<DBRefEntry> refs, String accId) {
		List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
		if (refs == null || accId == null) {
			return rfs;
		}
		for (int i = 0, n = refs.size(); i < n; i++) {
			DBRefEntry e = refs.get(i);
			if (accId.equals(e.getAccessionId())) {
				rfs.add(e);
			}
		}
		return rfs;
//    return searchRefs(refs, new DBRefEntry("", "", accId), matchId, SEARCH_MODE_FULL);
	}

	/**
	 * Returns a (possibly empty) list of those references that match the given
	 * entry, according to the given comparator.
	 * 
	 * @param refs       an array of database references to search
	 * @param entry      an entry to compare against
	 * @param comparator
	 * @param mode       SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION
	 *                   optional
	 * @return
	 */
	static List<DBRefEntry> searchRefs(List<DBRefEntry> refs, DBRefEntry entry, DbRefComp comparator, int mode) {
		List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
		if (refs == null || entry == null) {
			return rfs;
		}
		for (int i = 0, n = refs.size(); i < n; i++) {
			DBRefEntry e = refs.get(i);
			if (comparator.matches(entry, e, SEARCH_MODE_FULL)) {
				rfs.add(e);
			}
		}
		return rfs;
	}

	interface DbRefComp {
		default public boolean matches(DBRefEntry refa, DBRefEntry refb) {
			return matches(refa, refb, SEARCH_MODE_FULL);
		};

		public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode);
	}

	/**
	 * match on all non-null fields in refa
	 */
	// TODO unused - remove? would be broken by equating "" with null
	public static DbRefComp matchNonNullonA = new DbRefComp() {
		@Override
		public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
			if ((mode & DB_SOURCE) != 0 && 
					(refa.getSource() == null || DBRefUtils.getCanonicalName(refb.getSource())
					.equals(DBRefUtils.getCanonicalName(refa.getSource())))) {
				if ((mode & DB_VERSION) != 0 && 
						(refa.getVersion() == null || refb.getVersion().equals(refa.getVersion()))) {
					if ((mode & DB_ID) != 0 && 
							(refa.getAccessionId() == null || refb.getAccessionId().equals(refa.getAccessionId()))) {
						if ((mode & DB_MAP) != 0 && 
								(refa.getMap() == null || (refb.getMap() != null && refb.getMap().equals(refa.getMap())))) {
							return true;
						}
					}
				}
			}
			return false;
		}
	};

	/**
	 * either field is null or field matches for all of source, version, accession
	 * id and map.
	 */
	// TODO unused - remove?
	public static DbRefComp matchEitherNonNull = new DbRefComp() {
		@Override
		public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
			if (nullOrEqualSource(refa.getSource(), refb.getSource())
					&& nullOrEqual(refa.getVersion(), refb.getVersion())
					&& nullOrEqual(refa.getAccessionId(), refb.getAccessionId())
					&& nullOrEqual(refa.getMap(), refb.getMap())) {
				return true;
			}
			return false;
		}

	};

  /**
   * Parses a DBRefEntry and adds it to the sequence, also a PDBEntry if the
   * database is PDB.
   * <p>
   * Used by file parsers to generate DBRefs from annotation within file (eg
   * Stockholm)
   * 
   * @param dbname
   * @param version
   * @param acn
   * @param seq
   *          where to annotate with reference
   * @return parsed version of entry that was added to seq (if any)
   */
  public static DBRefEntry parseToDbRef(SequenceI seq, String dbname,
          String version, String acn)
  {
    DBRefEntry ref = null;
    if (dbname != null)
    {
      String locsrc = DBRefUtils.getCanonicalName(dbname);
      if (locsrc.equals(DBRefSource.PDB))
      {
        /*
         * Check for PFAM style stockhom PDB accession id citation e.g.
         * "1WRI A; 7-80;"
         */
        Regex r = new com.stevesoft.pat.Regex(
                "([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)");
        if (r.search(acn.trim()))
        {
          String pdbid = r.stringMatched(1);
          String chaincode = r.stringMatched(2);
          if (chaincode == null)
          {
            chaincode = " ";
          }
          // String mapstart = r.stringMatched(3);
          // String mapend = r.stringMatched(4);
          if (chaincode.equals(" "))
          {
            chaincode = "_";
          }
          // construct pdb ref.
          ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
          PDBEntry pdbr = new PDBEntry();
          pdbr.setId(pdbid);
          pdbr.setType(PDBEntry.Type.PDB);
          pdbr.setChainCode(chaincode);
          seq.addPDBId(pdbr);
        }
        else
        {
          System.err.println("Malformed PDB DR line:" + acn);
        }
      }
      else
      {
        // default:
        ref = new DBRefEntry(locsrc, version, acn.trim());
      }
    }
    if (ref != null)
    {
      seq.addDBRef(ref);
    }
    return ref;
  }

	/**
	 * accession ID and DB must be identical. Version is ignored. Map is either not
	 * defined or is a match (or is compatible?)
	 */
	// TODO unused - remove?
	public static DbRefComp matchDbAndIdAndEitherMap = new DbRefComp() {
		@Override
		public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
			if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource())
					.equals(DBRefUtils.getCanonicalName(refa.getSource()))) {
				// We dont care about version
				if (refa.getAccessionId() != null && refb.getAccessionId() != null
						// FIXME should be && not || here?
						|| refb.getAccessionId().equals(refa.getAccessionId())) {
					if ((refa.getMap() == null || refb.getMap() == null) || (refa.getMap() != null
							&& refb.getMap() != null && refb.getMap().equals(refa.getMap()))) {
						return true;
					}
				}
			}
			return false;
		}
	};

	/**
	 * accession ID and DB must be identical. Version is ignored. No map on either
	 * or map but no maplist on either or maplist of map on a is the complement of
	 * maplist of map on b.
	 */
	// TODO unused - remove?
	public static DbRefComp matchDbAndIdAndComplementaryMapList = new DbRefComp() {
		@Override
		public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
			if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource())
					.equals(DBRefUtils.getCanonicalName(refa.getSource()))) {
				// We dont care about version
				if (refa.getAccessionId() != null && refb.getAccessionId() != null
						|| refb.getAccessionId().equals(refa.getAccessionId())) {
					if ((refa.getMap() == null && refb.getMap() == null)
							|| (refa.getMap() != null && refb.getMap() != null)) {
						if ((refb.getMap().getMap() == null && refa.getMap().getMap() == null)
								|| (refb.getMap().getMap() != null && refa.getMap().getMap() != null
										&& refb.getMap().getMap().getInverse().equals(refa.getMap().getMap()))) {
							return true;
						}
					}
				}
			}
			return false;
		}
	};

	/**
	 * accession ID and DB must be identical. Version is ignored. No map on both or
	 * or map but no maplist on either or maplist of map on a is equivalent to the
	 * maplist of map on b.
	 */
	// TODO unused - remove?
	public static DbRefComp matchDbAndIdAndEquivalentMapList = new DbRefComp() {
		@Override
		public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
			if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource())
					.equals(DBRefUtils.getCanonicalName(refa.getSource()))) {
				// We dont care about version
				// if ((refa.getVersion()==null || refb.getVersion()==null)
				// || refb.getVersion().equals(refa.getVersion()))
				// {
				if (refa.getAccessionId() != null && refb.getAccessionId() != null
						|| refb.getAccessionId().equals(refa.getAccessionId())) {
					if (refa.getMap() == null && refb.getMap() == null) {
						return true;
					}
					if (refa.getMap() != null && refb.getMap() != null
							&& ((refb.getMap().getMap() == null && refa.getMap().getMap() == null)
									|| (refb.getMap().getMap() != null && refa.getMap().getMap() != null
											&& refb.getMap().getMap().equals(refa.getMap().getMap())))) {
						return true;
					}
				}
			}
			return false;
		}
	};

	/**
	 * accession ID and DB must be identical, or null on a. Version is ignored. No
	 * map on either or map but no maplist on either or maplist of map on a is
	 * equivalent to the maplist of map on b.
	 */
	public static DbRefComp matchDbAndIdAndEitherMapOrEquivalentMapList = new DbRefComp() 
	{
		@Override
		public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) 
		{
			if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource())
					.equals(DBRefUtils.getCanonicalName(refa.getSource()))) 
			{
				// We dont care about version
				if (refa.getAccessionId() == null || refa.getAccessionId().equals(refb.getAccessionId())) 
				{
					if (refa.getMap() == null || refb.getMap() == null) 
					{
						return true;
					}
					if ((refa.getMap() != null && refb.getMap() != null)
							&& (refb.getMap().getMap() == null && refa.getMap().getMap() == null)
							|| (refb.getMap().getMap() != null && refa.getMap().getMap() != null
									&& (refb.getMap().getMap().equals(refa.getMap().getMap())))) 
					{
						return true;
					}
				}
			}
			return false;
		}
	};

	/**
   * Returns the (possibly empty) list of those supplied dbrefs which have the
   * specified source database, with a case-insensitive match of source name
   * 
   * @param dbRefs
   * @param source
   * @return
   */
  public static List<DBRefEntry> searchRefsForSource(DBRefEntry[] dbRefs,
          String source)
  {
    List<DBRefEntry> matches = new ArrayList<>();
    if (dbRefs != null && source != null)
    {
      for (DBRefEntry dbref : dbRefs)
      {
        if (source.equalsIgnoreCase(dbref.getSource()))
        {
          matches.add(dbref);
        }
      }
    }
    return matches;
  }

	/**
	 * Returns true if either object is null, or they are equal
	 * 
	 * @param o1
	 * @param o2
	 * @return
	 */
	public static boolean nullOrEqual(Object o1, Object o2) {
		if (o1 == null || o2 == null) {
			return true;
		}
		return o1.equals(o2);
	}

	/**
	 * canonicalise source string before comparing. null is always wildcard
	 * 
	 * @param o1 - null or source string to compare
	 * @param o2 - null or source string to compare
	 * @return true if either o1 or o2 are null, or o1 equals o2 under
	 *         DBRefUtils.getCanonicalName
	 *         (o1).equals(DBRefUtils.getCanonicalName(o2))
	 */
	public static boolean nullOrEqualSource(String o1, String o2) {
		if (o1 == null || o2 == null) {
			return true;
		}
		return DBRefUtils.getCanonicalName(o1).equals(DBRefUtils.getCanonicalName(o2));
	}

	/**
	 * Selects just the DNA or protein references from a set of references
	 * 
	 * @param selectDna if true, select references to 'standard' DNA databases, else
	 *                  to 'standard' peptide databases
	 * @param refs      a set of references to select from
	 * @return
	 */
	public static List<DBRefEntry> selectDbRefs(boolean selectDna, List<DBRefEntry> refs) {
		return selectRefs(refs, selectDna ? DBRefSource.DNACODINGDBS : DBRefSource.PROTEINDBS);
		// could attempt to find other cross
		// refs here - ie PDB xrefs
		// (not dna, not protein seq)
	}

	/**
	 * Returns the (possibly empty) list of those supplied dbrefs which have the
	 * specified source database, with a case-insensitive match of source name
	 * 
	 * @param dbRefs
	 * @param source
	 * @return
	 */
	public static List<DBRefEntry> searchRefsForSource(List<DBRefEntry> dbRefs, String source) {
		List<DBRefEntry> matches = new ArrayList<DBRefEntry>();
		if (dbRefs != null && source != null) {
			for (DBRefEntry dbref : dbRefs) {
				if (source.equalsIgnoreCase(dbref.getSource())) {
					matches.add(dbref);
				}
			}
		}
		return matches;
	}

	/**
	 * promote direct database references to primary for nucleotide or protein
	 * sequences if they have an appropriate primary ref
	 * <table>
	 * <tr>
	 * <th>Seq Type</th>
	 * <th>Primary DB</th>
	 * <th>Direct which will be promoted</th>
	 * </tr>
	 * <tr align=center>
	 * <td>peptides</td>
	 * <td>Ensembl</td>
	 * <td>Uniprot</td>
	 * </tr>
	 * <tr align=center>
	 * <td>peptides</td>
	 * <td>Ensembl</td>
	 * <td>Uniprot</td>
	 * </tr>
	 * <tr align=center>
	 * <td>dna</td>
	 * <td>Ensembl</td>
	 * <td>ENA</td>
	 * </tr>
	 * </table>
	 * 
	 * @param sequence
	 */
	public static void ensurePrimaries(SequenceI sequence, List<DBRefEntry> pr) {
		if (pr.size() == 0) {
			// nothing to do
			return;
		}
		int sstart = sequence.getStart();
		int send = sequence.getEnd();
		boolean isProtein = sequence.isProtein();
		BitSet bsSelect = new BitSet();

//    List<DBRefEntry> selfs = new ArrayList<DBRefEntry>();
//    {

//      List<DBRefEntry> selddfs = selectDbRefs(!isprot, sequence.getDBRefs());
//      if (selfs == null || selfs.size() == 0)
//      {
//        // nothing to do
//        return;
//      }

		List<DBRefEntry> dbrefs = sequence.getDBRefs();
		bsSelect.set(0, dbrefs.size());

		if (!selectRefsBS(dbrefs, isProtein ? DBRefSource.PROTEIN_MASK : DBRefSource.DNA_CODING_MASK, bsSelect))
			return;

//      selfs.addAll(selfArray);
//    }

		// filter non-primary refs
		for (int ip = pr.size(); --ip >= 0;) {
			DBRefEntry p = pr.get(ip);
			for (int i = bsSelect.nextSetBit(0); i >= 0; i = bsSelect.nextSetBit(i + 1)) {
				if (dbrefs.get(i) == p)
					bsSelect.clear(i);
			}
//      while (selfs.contains(p))
//      {
//        selfs.remove(p);
//      }
		}
//    List<DBRefEntry> toPromote = new ArrayList<DBRefEntry>();

		for (int ip = pr.size(), keys = 0; --ip >= 0 && keys != DBRefSource.PRIMARY_MASK;) {
			DBRefEntry p = pr.get(ip);
			if (isProtein) {
				switch (getCanonicalName(p.getSource())) {
				case DBRefSource.UNIPROT:
					keys |= DBRefSource.UNIPROT_MASK;
					break;
				case DBRefSource.ENSEMBL:
					keys |= DBRefSource.ENSEMBL_MASK;
					break;
				}
			} else {
				// TODO: promote transcript refs ??
			}
			if (keys == 0 || !selectRefsBS(dbrefs, keys, bsSelect))
				return;
//      if (candidates != null)
			{
				for (int ic = bsSelect.nextSetBit(0); ic >= 0; ic = bsSelect.nextSetBit(ic + 1))
//        for (int ic = 0, n = candidates.size(); ic < n; ic++)
				{
					DBRefEntry cand = dbrefs.get(ic);// candidates.get(ic);
					if (cand.hasMap()) {
						Mapping map = cand.getMap();
						SequenceI cto = map.getTo();
						if (cto != null && cto != sequence) {
							// can't promote refs with mappings to other sequences
							continue;
						}
						MapList mlist = map.getMap();
						if (mlist.getFromLowest() != sstart && mlist.getFromHighest() != send) {
							// can't promote refs with mappings from a region of this sequence
							// - eg CDS
							continue;
						}
					}
					// and promote - not that version must be non-null here, 
					// as p must have passed isPrimaryCandidate()
					cand.setVersion(p.getVersion() + " (promoted)");
					bsSelect.clear(ic);
					// selfs.remove(cand);
//          toPromote.add(cand);
					if (!cand.isPrimaryCandidate()) {
						System.out.println("Warning: Couldn't promote dbref " + cand.toString() + " for sequence "
								+ sequence.toString());
					}
				}
			}
		}
	}

}