/*
 * 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.workers;

import jalview.analysis.AAFrequency;
import jalview.analysis.Conservation;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
import jalview.util.MappingUtils;

import java.util.ArrayList;
import java.util.ConcurrentModificationException;
import java.util.Hashtable;
import java.util.List;

/**
 * A thread to compute the columnwise correspondence between aligned positions
 * and their positions in a linked alignment
 * 
 * @author jprocter
 *
 */
public class AlignmentComparisonThread extends AlignCalcWorker
{

  public AlignmentComparisonThread(AlignViewportI alignViewport,
          AlignmentViewPanel alignPanel)
  {
    super(alignViewport, alignPanel);
  }

  Annotation[] correspondence = new Annotation[] {};
  AlignmentAnnotation comparisonAnnot=null;
  int alWidth;

  @Override
  public void run()
  {
    try
    {
      calcMan.notifyStart(this); // updatingConservation = true;

      while ((calcMan != null) && (!calcMan.notifyWorking(this)))
      {
        try
        {
          if (ap != null)
          {
            // ap.paintAlignment(false);
          }
          Thread.sleep(200);
        } catch (Exception ex)
        {
          ex.printStackTrace();
        }
      }
      if ((alignViewport == null) || (calcMan == null)
              || (alignViewport.isClosed()))
      {
        abortAndDestroy();
        return;
      }
      List<AlignmentAnnotation> ourAnnot = new ArrayList<>();

      AlignmentI alignment = alignViewport.getAlignment();
      AlignViewportI codingComplement = alignViewport.getCodingComplement();
      if (alignment == null || (alWidth = alignment.getWidth()) < 0
              || (codingComplement == null))
      {
        calcMan.workerComplete(this);
        // .updatingConservation = false;
        // AlignViewport.UPDATING_CONSERVATION = false;

        return;
      }
      comparisonAnnot = alignViewport.getAlignment().findOrCreateAnnotation("Comparison", "CORRESPONDENCE", true, null, null);
      comparisonAnnot.annotations=correspondence;
      ourAnnot.add(comparisonAnnot);
      ourAnnots = ourAnnot;

      try
      {
        computeColumnCorrespondence(alignViewport, codingComplement);
      } catch (IndexOutOfBoundsException x)
      {
        // probable race condition. just finish and return without any fuss.
        calcMan.workerComplete(this);
        return;
      }
      updateResultAnnotation(true);
    } catch (OutOfMemoryError error)
    {
      ap.raiseOOMWarning("calculating conservation", error);
      calcMan.disableWorker(this);
      // alignViewport.conservation = null;
      // this.alignViewport.quality = null;

    }
    calcMan.workerComplete(this);

    if ((alignViewport == null) || (calcMan == null)
            || (alignViewport.isClosed()))
    {
      abortAndDestroy();
      return;
    }
    if (ap != null)
    {
      ap.paintAlignment(true, true);
    }

  }

  private void computeColumnCorrespondence(AlignViewportI alignViewport,
          AlignViewportI codingComplement)
  {
    List<SequenceI> us = alignViewport.getAlignment().getSequences();
    List<AlignedCodonFrame> ourMappings = alignViewport.getAlignment()
            .getCodonFrames();
    List<SequenceI> them = codingComplement.getAlignment().getSequences();
    List<AlignedCodonFrame> theirMappings = codingComplement.getAlignment()
            .getCodonFrames();
    if (us == null || them == null || us.isEmpty() || them.isEmpty())
    {
      return;
    }

    int colEnd = alignViewport.getAlignment().getWidth();
    Annotation[] colCorrsp = new Annotation[colEnd];
    for (int col = 0; col < colEnd; col++)
    {
      int[] theirWidth = MappingUtils.findMappedColumns(col, ourMappings,
              us, them, alignViewport.getGapCharacter());
      colCorrsp[col] = new Annotation(
              theirWidth != null ? Math.abs(theirWidth[1] - theirWidth[0])
                      : 0);
    }
    correspondence=colCorrsp;
  }

  private void updateResultAnnotation(boolean b)
  {
    if (b || !calcMan.isWorking(this) && correspondence!=null)
    {
      comparisonAnnot.annotations = correspondence;
      comparisonAnnot.validateRangeAndDisplay();
    }
  }

  @Override
  public void updateAnnotation()
  {
    updateResultAnnotation(false);

  }

}