package jalview.workers;

import jalview.analysis.AAFrequency;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;

import java.util.ConcurrentModificationException;
import java.util.Hashtable;

/**
 * A thread to recompute the consensus of the cDNA complement for a linked
 * protein alignment.
 * 
 * @author gmcarstairs
 *
 */
public class ComplementConsensusThread extends ConsensusThread
{

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

  @Override
  protected AlignmentAnnotation getConsensusAnnotation()
  {
    return alignViewport.getComplementConsensusAnnotation();
  }

  @Override
  protected Hashtable[] getViewportConsensus()
  {
    return alignViewport.getComplementConsensusHash();
  }

  /**
   * Calculate the cDNA consensus and store it on the Viewport
   */
  @Override
  protected void computeConsensus(AlignmentI alignment)
  {
    Hashtable[] hconsensus = new Hashtable[alignment.getWidth()];

    SequenceI[] aseqs = getSequences();

    /*
     * Allow 3 tries at this, since this thread can start up while we are still
     * modifying protein-codon mappings on the alignment
     */
    for (int i = 0; i < 3; i++)
    {
      try
      {
        AAFrequency.calculateCdna(alignment, hconsensus);
        break;
      } catch (ConcurrentModificationException e)
      {
        // try again
      }
    }

    alignViewport.setComplementConsensusHash(hconsensus);
  }

  /**
   * Convert the computed consensus data into the desired annotation for
   * display.
   * 
   * @param consensusAnnotation
   *          the annotation to be populated
   * @param consensusData
   *          the computed consensus data
   */
  @Override
  protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
          Hashtable[] consensusData)
  {
    AAFrequency.completeCdnaConsensus(consensusAnnotation, consensusData,
            alignViewport.isShowSequenceLogo(), getSequences().length);
  }

}