/*
 * 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;

import jalview.util.MapList;
import jalview.util.MappingUtils;

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

/**
 * Stores mapping between the columns of a protein alignment and a DNA alignment
 * and a list of individual codon to amino acid mappings between sequences.
 */
public class AlignedCodonFrame
{

  /*
   * Data bean to hold mappings from one sequence to another
   */
  private class SequenceToSequenceMapping
  {
    private SequenceI fromSeq;

    private Mapping mapping;

    SequenceToSequenceMapping(SequenceI from, Mapping map)
    {
      this.fromSeq = from;
      this.mapping = map;
    }

    /**
     * Readable representation for debugging only, not guaranteed not to change
     */
    @Override
    public String toString()
    {
      return String.format("From %s %s", fromSeq.getName(),
              mapping.toString());
    }
  }

  private List<SequenceToSequenceMapping> mappings;

  /**
   * Constructor
   */
  public AlignedCodonFrame()
  {
    mappings = new ArrayList<SequenceToSequenceMapping>();
  }

  /**
   * Adds a mapping between the dataset sequences for the associated dna and
   * protein sequence objects
   * 
   * @param dnaseq
   * @param aaseq
   * @param map
   */
  public void addMap(SequenceI dnaseq, SequenceI aaseq, MapList map)
  {
    // JBPNote DEBUG! THIS !
    // dnaseq.transferAnnotation(aaseq, mp);
    // aaseq.transferAnnotation(dnaseq, new Mapping(map.getInverse()));

    SequenceI fromSeq = (dnaseq.getDatasetSequence() == null) ? dnaseq
            : dnaseq.getDatasetSequence();
    SequenceI toSeq = (aaseq.getDatasetSequence() == null) ? aaseq : aaseq
            .getDatasetSequence();

    /*
     * if we already hold a mapping between these sequences, just add to it 
     */
    for (SequenceToSequenceMapping ssm : mappings)
    {
      if (ssm.fromSeq == fromSeq && ssm.mapping.to == toSeq)
      {
        ssm.mapping.map.addMapList(map);
        return;
      }
    }

    /*
     * otherwise, add a new sequence mapping
     */
    Mapping mp = new Mapping(toSeq, map);
    mappings.add(new SequenceToSequenceMapping(fromSeq, mp));
  }

  public SequenceI[] getdnaSeqs()
  {
    // TODO return a list instead?
    // return dnaSeqs;
    List<SequenceI> seqs = new ArrayList<SequenceI>();
    for (SequenceToSequenceMapping ssm : mappings)
    {
      seqs.add(ssm.fromSeq);
    }
    return seqs.toArray(new SequenceI[seqs.size()]);
  }

  public SequenceI[] getAaSeqs()
  {
    // TODO not used - remove?
    List<SequenceI> seqs = new ArrayList<SequenceI>();
    for (SequenceToSequenceMapping ssm : mappings)
    {
      seqs.add(ssm.mapping.to);
    }
    return seqs.toArray(new SequenceI[seqs.size()]);
  }

  public MapList[] getdnaToProt()
  {
    List<MapList> maps = new ArrayList<MapList>();
    for (SequenceToSequenceMapping ssm : mappings)
    {
      maps.add(ssm.mapping.map);
    }
    return maps.toArray(new MapList[maps.size()]);
  }

  public Mapping[] getProtMappings()
  {
    List<Mapping> maps = new ArrayList<Mapping>();
    for (SequenceToSequenceMapping ssm : mappings)
    {
      maps.add(ssm.mapping);
    }
    return maps.toArray(new Mapping[maps.size()]);
  }

  /**
   * Returns the first mapping found which is to or from the given sequence, or
   * null.
   * 
   * @param seq
   * @return
   */
  public Mapping getMappingForSequence(SequenceI seq)
  {
    SequenceI seqDs = seq.getDatasetSequence();
    seqDs = seqDs != null ? seqDs : seq;

    for (SequenceToSequenceMapping ssm : mappings)
    {
      if (ssm.fromSeq == seqDs || ssm.mapping.to == seqDs)
      {
        return ssm.mapping;
      }
    }
    return null;
  }

  /**
   * Return the corresponding aligned or dataset aa sequence for given dna
   * sequence, null if not found.
   * 
   * @param sequenceRef
   * @return
   */
  public SequenceI getAaForDnaSeq(SequenceI dnaSeqRef)
  {
    SequenceI dnads = dnaSeqRef.getDatasetSequence();
    for (SequenceToSequenceMapping ssm : mappings)
    {
      if (ssm.fromSeq == dnaSeqRef || ssm.fromSeq == dnads)
      {
        return ssm.mapping.to;
      }
    }
    return null;
  }

  /**
   * 
   * @param sequenceRef
   * @return null or corresponding aaSeq entry for dnaSeq entry
   */
  public SequenceI getDnaForAaSeq(SequenceI aaSeqRef)
  {
    SequenceI aads = aaSeqRef.getDatasetSequence();
    for (SequenceToSequenceMapping ssm : mappings)
    {
      if (ssm.mapping.to == aaSeqRef || ssm.mapping.to == aads)
      {
        return ssm.fromSeq;
      }
    }
    return null;
  }

  /**
   * test to see if codon frame involves seq in any way
   * 
   * @param seq
   *          a nucleotide or protein sequence
   * @return true if a mapping exists to or from this sequence to any translated
   *         sequence
   */
  public boolean involvesSequence(SequenceI seq)
  {
    return getAaForDnaSeq(seq) != null || getDnaForAaSeq(seq) != null;
  }

  /**
   * Add search results for regions in other sequences that translate or are
   * translated from a particular position in seq
   * 
   * @param seq
   * @param index
   *          position in seq
   * @param results
   *          where highlighted regions go
   */
  public void markMappedRegion(SequenceI seq, int index,
          SearchResults results)
  {
    int[] codon;
    SequenceI ds = seq.getDatasetSequence();
    for (SequenceToSequenceMapping ssm : mappings)
    {
      if (ssm.fromSeq == seq || ssm.fromSeq == ds)
      {
        codon = ssm.mapping.map.locateInTo(index, index);
        if (codon != null)
        {
          for (int i = 0; i < codon.length; i += 2)
          {
            results.addResult(ssm.mapping.to, codon[i], codon[i + 1]);
          }
        }
      }
      else if (ssm.mapping.to == seq || ssm.mapping.to == ds)
      {
        {
          codon = ssm.mapping.map.locateInFrom(index, index);
          if (codon != null)
          {
            for (int i = 0; i < codon.length; i += 2)
            {
              results.addResult(ssm.fromSeq, codon[i], codon[i + 1]);
            }
          }
        }
      }
    }
  }

  /**
   * Returns the DNA codon positions (base 1) for the given position (base 1) in
   * a mapped protein sequence, or null if no mapping is found.
   * 
   * Intended for use in aligning cDNA to match aligned protein. Only the first
   * mapping found is returned, so not suitable for use if multiple protein
   * sequences are mapped to the same cDNA (but aligning cDNA as protein is
   * ill-defined for this case anyway).
   * 
   * @param seq
   *          the DNA dataset sequence
   * @param aaPos
   *          residue position (base 1) in a protein sequence
   * @return
   */
  public int[] getDnaPosition(SequenceI seq, int aaPos)
  {
    /*
     * Adapted from markMappedRegion().
     */
    MapList ml = null;
    int i = 0;
    for (SequenceToSequenceMapping ssm : mappings)
    {
      if (ssm.fromSeq == seq)
      {
        ml = getdnaToProt()[i];
        break;
      }
      i++;
    }
    return ml == null ? null : ml.locateInFrom(aaPos, aaPos);
  }

  /**
   * Convenience method to return the first aligned sequence in the given
   * alignment whose dataset has a mapping with the given (aligned or dataset)
   * sequence.
   * 
   * @param seq
   * 
   * @param al
   * @return
   */
  public SequenceI findAlignedSequence(SequenceI seq, AlignmentI al)
  {
    /*
     * Search mapped protein ('to') sequences first.
     */
    for (SequenceToSequenceMapping ssm : mappings)
    {
      if (ssm.fromSeq == seq || ssm.fromSeq == seq.getDatasetSequence())
      {
        for (SequenceI sourceAligned : al.getSequences())
        {
          if (ssm.mapping.to == sourceAligned.getDatasetSequence()
                  || ssm.mapping.to == sourceAligned)
          {
            return sourceAligned;
          }
        }
      }
    }

    /*
     * Then try mapped dna sequences.
     */
    for (SequenceToSequenceMapping ssm : mappings)
    {
      if (ssm.mapping.to == seq
              || ssm.mapping.to == seq.getDatasetSequence())
      {
        for (SequenceI sourceAligned : al.getSequences())
        {
          if (ssm.fromSeq == sourceAligned.getDatasetSequence())
          {
            return sourceAligned;
          }
        }
      }
    }

    return null;
  }

  /**
   * Returns the region in the target sequence's dataset that is mapped to the
   * given position (base 1) in the query sequence's dataset. The region is a
   * set of start/end position pairs.
   * 
   * @param target
   * @param query
   * @param queryPos
   * @return
   */
  public int[] getMappedRegion(SequenceI target, SequenceI query,
          int queryPos)
  {
    SequenceI targetDs = target.getDatasetSequence() == null ? target
            : target.getDatasetSequence();
    SequenceI queryDs = query.getDatasetSequence() == null ? query : query
            .getDatasetSequence();
    if (targetDs == null || queryDs == null /*|| dnaToProt == null*/)
    {
      return null;
    }
    for (SequenceToSequenceMapping ssm : mappings)
    {
      /*
       * try mapping from target to query
       */
      if (ssm.fromSeq == targetDs && ssm.mapping.to == queryDs)
      {
        int[] codon = ssm.mapping.map.locateInFrom(queryPos, queryPos);
        if (codon != null)
        {
          return codon;
        }
      }
      /*
       * else try mapping from query to target
       */
      else if (ssm.fromSeq == queryDs && ssm.mapping.to == targetDs)
      {
        int[] codon = ssm.mapping.map.locateInTo(queryPos, queryPos);
        if (codon != null)
        {
          return codon;
        }
      }
    }
    return null;
  }

  /**
   * Returns the mapped DNA codons for the given position in a protein sequence,
   * or null if no mapping is found. Returns a list of (e.g.) ['g', 'c', 't']
   * codons. There may be more than one codon mapped to the protein if (for
   * example), there are mappings to cDNA variants.
   * 
   * @param protein
   *          the peptide dataset sequence
   * @param aaPos
   *          residue position (base 1) in the peptide sequence
   * @return
   */
  public List<char[]> getMappedCodons(SequenceI protein, int aaPos)
  {
    MapList ml = null;
    SequenceI dnaSeq = null;
    List<char[]> result = new ArrayList<char[]>();

    for (SequenceToSequenceMapping ssm : mappings)
    {
      if (ssm.mapping.to == protein)
      {
        ml = ssm.mapping.map;
        dnaSeq = ssm.fromSeq;

        int[] codonPos = ml.locateInFrom(aaPos, aaPos);
        if (codonPos == null)
        {
          return null;
        }

        /*
         * Read off the mapped nucleotides (converting to position base 0)
         */
        codonPos = MappingUtils.flattenRanges(codonPos);
        char[] dna = dnaSeq.getSequence();
        int start = dnaSeq.getStart();
        result.add(new char[] { dna[codonPos[0] - start],
            dna[codonPos[1] - start], dna[codonPos[2] - start] });
      }
    }
    return result.isEmpty() ? null : result;
  }

  /**
   * Returns any mappings found which are from the given sequence, and to
   * distinct sequences.
   * 
   * @param seq
   * @return
   */
  public List<Mapping> getMappingsFromSequence(SequenceI seq)
  {
    List<Mapping> result = new ArrayList<Mapping>();
    List<SequenceI> related = new ArrayList<SequenceI>();
    SequenceI seqDs = seq.getDatasetSequence();
    seqDs = seqDs != null ? seqDs : seq;

    for (SequenceToSequenceMapping ssm : mappings)
    {
      final Mapping mapping = ssm.mapping;
      if (ssm.fromSeq == seqDs)
      {
        if (!related.contains(mapping.to))
        {
          result.add(mapping);
          related.add(mapping.to);
        }
      }
    }
    return result;
  }

  /**
   * Test whether the given sequence is substitutable for one or more dummy
   * sequences in this mapping
   * 
   * @param map
   * @param seq
   * @return
   */
  public boolean isRealisableWith(SequenceI seq)
  {
    return realiseWith(seq, false) > 0;
  }

  /**
   * Replace any matchable mapped dummy sequences with the given real one.
   * Returns the count of sequence mappings instantiated.
   * 
   * @param seq
   * @return
   */
  public int realiseWith(SequenceI seq)
  {
    return realiseWith(seq, true);
  }

  /**
   * Returns the number of mapped dummy sequences that could be replaced with
   * the given real sequence.
   * 
   * @param seq
   *          a dataset sequence
   * @param doUpdate
   *          if true, performs replacements, else only counts
   * @return
   */
  protected int realiseWith(SequenceI seq, boolean doUpdate)
  {
    SequenceI ds = seq.getDatasetSequence() != null ? seq
            .getDatasetSequence() : seq;
    int count = 0;

    /*
     * check for replaceable DNA ('map from') sequences
     */
    for (SequenceToSequenceMapping ssm : mappings)
    {
      SequenceI dna = ssm.fromSeq;
      if (dna instanceof SequenceDummy
              && dna.getName().equals(ds.getName()))
      {
        Mapping mapping = ssm.mapping;
        int mapStart = mapping.getMap().getFromLowest();
        int mapEnd = mapping.getMap().getFromHighest();
        boolean mappable = couldRealiseSequence(dna, ds, mapStart, mapEnd);
        if (mappable)
        {
          count++;
          if (doUpdate)
          {
            // TODO: new method ? ds.realise(dna);
            // might want to copy database refs as well
            ds.setSequenceFeatures(dna.getSequenceFeatures());
            // dnaSeqs[i] = ds;
            ssm.fromSeq = ds;
            System.out.println("Realised mapped sequence " + ds.getName());
          }
        }
      }

      /*
       * check for replaceable protein ('map to') sequences
       */
      Mapping mapping = ssm.mapping;
      SequenceI prot = mapping.getTo();
      int mapStart = mapping.getMap().getToLowest();
      int mapEnd = mapping.getMap().getToHighest();
      boolean mappable = couldRealiseSequence(prot, ds, mapStart, mapEnd);
      if (mappable)
      {
        count++;
        if (doUpdate)
        {
          // TODO: new method ? ds.realise(dna);
          // might want to copy database refs as well
          ds.setSequenceFeatures(dna.getSequenceFeatures());
          ssm.mapping.setTo(ds);
        }
      }
    }
    return count;
  }

  /**
   * Helper method to test whether a 'real' sequence could replace a 'dummy'
   * sequence in the map. The criteria are that they have the same name, and
   * that the mapped region overlaps the candidate sequence.
   * 
   * @param existing
   * @param replacement
   * @param mapStart
   * @param mapEnd
   * @return
   */
  protected static boolean couldRealiseSequence(SequenceI existing,
          SequenceI replacement, int mapStart, int mapEnd)
  {
    if (existing instanceof SequenceDummy
            && !(replacement instanceof SequenceDummy)
            && existing.getName().equals(replacement.getName()))
    {
      int start = replacement.getStart();
      int end = replacement.getEnd();
      boolean mappingOverlapsSequence = (mapStart >= start && mapStart <= end)
              || (mapEnd >= start && mapEnd <= end);
      if (mappingOverlapsSequence)
      {
        return true;
      }
    }
    return false;
  }

  /**
   * Change any mapping to the given sequence to be to its dataset sequence
   * instead. For use when mappings are created before their referenced
   * sequences are instantiated, for example when parsing GFF data.
   * 
   * @param seq
   */
  public void updateToDataset(SequenceI seq)
  {
    if (seq == null || seq.getDatasetSequence() == null)
    {
      return;
    }
    SequenceI ds = seq.getDatasetSequence();

    for (SequenceToSequenceMapping ssm : mappings)
    /*
     * 'from' sequences
     */
    {
      if (ssm.fromSeq == seq)
      {
        ssm.fromSeq = ds;
      }

      /*
       * 'to' sequences
       */
      if (ssm.mapping.to == seq)
      {
        ssm.mapping.to = ds;
      }
    }
  }

  /**
   * Answers true if this object contains no mappings
   * 
   * @return
   */
  public boolean isEmpty()
  {
    return mappings.isEmpty();
  }

  /**
   * Method for debug / inspection purposes only, may change in future
   */
  @Override
  public String toString()
  {
    return mappings == null ? "null" : mappings.toString();
  }
}