/*
 * 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.ws.jws2.jabaws2;

import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.util.MessageManager;
import jalview.ws.uimodel.AlignAnalysisUIText;

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;

public class AAConClient extends JabawsAnnotationInstance
{
  // configuration for factory
  public static String getServiceActionText()
  {
    return "calculating Amino acid consensus using AACon service";
  }



  private static String CALC_ID = "jabaws2.AACon";

  public static AlignAnalysisUIText getAlignAnalysisUIText()
  {
    return new AlignAnalysisUIText(
            compbio.ws.client.Services.AAConWS.toString(),
            AAConClient.class, CALC_ID, false, true, true, true,
            true, 2, MessageManager.getString("label.aacon_calculations"),
            MessageManager.getString("tooltip.aacon_calculations"),
            MessageManager.getString("label.aacon_settings"),
            MessageManager.getString("tooltip.aacon_settings"));
  }

  // instance
  public AAConClient(Jws2Instance handle)
  {
    super(handle);
  }

  @Override
  List<AlignmentAnnotation> annotationFromScoreManager(AlignmentI seqs,
          Map<String, FeatureColourI> featureColours,
          Map<String, FeatureMatcherSetI> featureFilters)
  {
    return aacons_annotation(seqs.getWidth(), seqs, null);
  }

  private List<AlignmentAnnotation> aacons_annotation(int alWidth,
          AlignmentI alignViewport, boolean[] gapMap)
  {
    Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
    ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<>();
    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(alignViewport, null, ourAnnot,
                  getCalcId(),
                  scr.getScores().size(), scr);
        }
      }
    }
    return ourAnnot;
  }

}