package jalview.ws.jws2;

import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignmentPanel;
import jalview.ws.jws2.dm.AAConsSettings;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;

import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeSet;

import compbio.data.sequence.Score;
import compbio.metadata.Argument;

public class AAConsClient extends JabawsAlignCalcWorker
{

  public AAConsClient(Jws2Instance service, AlignFrame alignFrame,
          WsParamSetI preset, List<Argument> paramset)
  {
    super(service, alignFrame, preset, paramset);
    submitGaps = true;
    alignedSeqs = true;
    nucleotidesAllowed = false;
    proteinAllowed = true;
    gapMap=new boolean[0];
    initViewportParams();
  }

  protected void initViewportParams()
  {
    ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(getCalcId(), new AAConsSettings(true, service, this.preset, (arguments!=null) ?  JabaParamStore.getJwsArgsfromJaba(arguments) : null), true);
  }
  @Override
  public void updateParameters(WsParamSetI newpreset, java.util.List<Argument> newarguments) {
    super.updateParameters(newpreset, newarguments);
    initViewportParams();
  };
  public String getServiceActionText()
  {
    return "calculating Amino acid consensus using AACons service";
  }

  /**
   * update the consensus annotation from the sequence profile data using
   * current visualization settings.
   */

  public void updateResultAnnotation(boolean immediate)
  {
    if (immediate || !calcMan.isWorking(this) && scoremanager != null)
    {
      Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
      int alWidth = alignViewport.getAlignment().getWidth();
      ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
      for (String score : scoremap.keySet())
      {
        Set<Score> scores = scoremap.get(score);
        for (Score scr : scores)
        {
          if (scr.getRanges() != null && scr.getRanges().size() > 0)
          {
            /**
             * annotation in range annotation = findOrCreate(scr.getMethod(),
             * true, null, null); Annotation[] elm = new Annotation[alWidth];
             * Iterator<Float> vals = scr.getScores().iterator(); for (Range rng
             * : scr.getRanges()) { float val = vals.next().floatValue(); for
             * (int i = rng.from; i <= rng.to; i++) { elm[i] = new
             * Annotation("", "", ' ', val); } } annotation.annotations = elm;
             * annotation.validateRangeAndDisplay();
             */
          }
          else
          {
            createAnnotationRowsForScores(ourAnnot, getCalcId(), alWidth,
                    scr);
          }
        }
      }

      if (ourAnnot.size() > 0)
      {
        updateOurAnnots(ourAnnot);
      }
    }
  }

  public String getCalcId()
  {
    return SequenceAnnotationWSClient.AAConsCalcId;
  }

  public static void removeAAConsAnnotation(AlignmentPanel alignPanel)
  {
    for (AlignmentAnnotation aa: alignPanel.getAlignment().findAnnotation(SequenceAnnotationWSClient.AAConsCalcId))
    {
      alignPanel.getAlignment().deleteAnnotation(aa);
    }
    // List<AlignmentAnnotation>
    // ourannots=alignPanel.getAlignment().findAnnotation(Screen3D.)
    // TODO Auto-generated method stub

  }
}