package jalview.ws2.actions.alignment;

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

import jalview.analysis.AlignSeq;
import jalview.analysis.SeqsetUtils;
import jalview.analysis.SeqsetUtils.SequenceInfo;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import jalview.ws2.actions.BaseJob;
import jalview.ws2.api.WebServiceJobHandle;

/**
 * A wrapper class that extends basic job container with data specific to
 * alignment services. It stores input and empty sequences (with uniquified
 * names) along the original sequence information. {@link AlignmentJob} objects
 * are created by {@link AlignmentTask} during a preparation stage.
 * 
 * @author mmwarowny
 *
 */
class AlignmentJob extends BaseJob
{
  private final List<SequenceI> emptySeqs;

  private final Map<String, SequenceInfo> names;

  private AlignmentI alignmentResult;

  AlignmentJob(List<SequenceI> inputSeqs, List<SequenceI> emptySeqs,
      Map<String, SequenceInfo> names)
  {
    super(Collections.unmodifiableList(inputSeqs));
    this.emptySeqs = Collections.unmodifiableList(emptySeqs);
    this.names = Collections.unmodifiableMap(names);
  }

  public static AlignmentJob create(SequenceI[] seqs, int minlen, boolean keepGaps)
  {
    int nseqs = 0;
    for (int i = 0; i < seqs.length; i++)
    {
      if (seqs[i].getEnd() - seqs[i].getStart() >= minlen)
        nseqs++;
    }
    boolean valid = nseqs > 1; // need at least two sequences
    Map<String, SequenceInfo> names = new LinkedHashMap<>();
    List<SequenceI> inputSeqs = new ArrayList<>();
    List<SequenceI> emptySeqs = new ArrayList<>();
    for (int i = 0; i < seqs.length; i++)
    {
      SequenceI seq = seqs[i];
      String newName = SeqsetUtils.unique_name(i);
      names.put(newName, SeqsetUtils.SeqCharacterHash(seq));
      if (valid && seq.getEnd() - seq.getStart() >= minlen)
      {
        // make new input sequence
        String seqString = seq.getSequenceAsString();
        if (!keepGaps)
          seqString = AlignSeq.extractGaps(Comparison.GapChars, seqString);
        inputSeqs.add(new Sequence(newName, seqString));
      }
      else
      {
        String seqString = "";
        if (seq.getEnd() >= seq.getStart()) // true if gaps only
        {
          seqString = seq.getSequenceAsString();
          if (!keepGaps)
            seqString = AlignSeq.extractGaps(Comparison.GapChars, seqString);
        }
        emptySeqs.add(new Sequence(newName, seqString));
      }
    }
    return new AlignmentJob(inputSeqs, emptySeqs, names);
  }

  @Override
  public boolean isInputValid()
  {
    return inputSeqs.size() >= 2;
  }

  List<SequenceI> getEmptySequences()
  {
    return emptySeqs;
  }

  Map<String, SequenceInfo> getNames()
  {
    return names;
  }

  boolean hasResult()
  {
    return alignmentResult != null;
  }

  AlignmentI getAlignmentResult()
  {
    return alignmentResult;
  }

  void setAlignmentResult(AlignmentI alignment)
  {
    this.alignmentResult = alignment;
  }
}