package jalview.ws.jws2;

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

import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
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];
  }

  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)
    {
      AlignmentAnnotation annotation;
      ;
      Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
      int alWidth = alignViewport.getAlignment().getWidth();
      AlignmentI alignment;
      int ann = (alignment = alignViewport.getAlignment())
              .getAlignmentAnnotation().length;
      ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
      for (String score : scoremap.keySet())
      {
        TreeSet<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
          {
            // simple annotation row
            annotation = alignViewport.getAlignment().findOrCreateAnnotation(scr.getMethod(), true, null, null);
            Annotation[] elm = new Annotation[alWidth];
            if (alWidth == gapMap.length) // scr.getScores().size())
            {
              Iterator<Float> vals = scr.getScores().iterator();
              float m = 0f, x = 0f;
              for (int i = 0; vals.hasNext(); i++)
              {
                float val = vals.next().floatValue();
                if (i == 0)
                {
                  m = val;
                  x = val;
                }
                else
                {
                  if (m > val)
                  {
                    m = val;
                  }
                  ;
                  if (x < val)
                  {
                    x = val;
                  }
                }
                // if we're at a gapped column then skip to next ungapped position
                if (gapMap != null && gapMap.length > 0)
                {
                  while (!gapMap[i])
                  {
                    elm[i++]=new Annotation("", "" , ' ', Float.NaN);
                  }
                }
                elm[i] = new Annotation("", "" + val, ' ', val);
              }

              annotation.annotations = elm;
              annotation.belowAlignment = true;
              if (x < 0)
              {
                x = 0;
              }
              x += (x - m) * 0.1;
              annotation.graphMax = x;
              annotation.graphMin = m;
              annotation.validateRangeAndDisplay();
              ourAnnot.add(annotation);
            }
          }
        }
      }
      if (ourAnnot.size() > 0)
      {
        List<AlignmentAnnotation> our = ourAnnots;
        ourAnnots = ourAnnot;
        if (our != null)
        {
          if (our.size() > 0)
          {
            for (AlignmentAnnotation an : our)
            {
              if (!ourAnnots.contains(an))
              {
                // remove the old annotation
                alignment.deleteAnnotation(an);
              }
            }
          }
          our.clear();
        }
      }
      // if (ann !=
      // alignViewport.getAlignment().getAlignmentAnnotation().length)
      {
        ap.adjustAnnotationHeight();
      }
      /*
       * else { ap.paintAlignment(true); }
       */
    }
  }

  public static void removeAAConsAnnotation(AlignmentPanel alignPanel)
  {
    // List<AlignmentAnnotation>
    // ourannots=alignPanel.getAlignment().findAnnotation(Screen3D.)
    // TODO Auto-generated method stub

  }
}