/*
 * Jalview - A Sequence Alignment Editor and Viewer (2.11.2.6)
 * Copyright (C) 2023 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.Locale;
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(Locale.ROOT),
              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(Locale.ROOT));
    }

    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(Locale.ROOT)))
      {
        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(Locale.ROOT));
    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(cand.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());
          }
        }
      }
    }
  }

}
