/*
 * Jalview - A Sequence Alignment Editor and Viewer (2.11.2.4)
 * Copyright (C) 2022 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;

import jalview.api.FeatureColourI;
import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.schemes.FeatureColour;
import jalview.util.ColorUtils;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;

import java.awt.Color;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
import java.util.Map;

import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.Range;
import compbio.data.sequence.Score;
import compbio.data.sequence.ScoreManager.ScoreHolder;
import compbio.metadata.Argument;

public class AADisorderClient extends JabawsCalcWorker
{

  private static final String THRESHOLD = "THRESHOLD";

  private static final String RANGE = "RANGE";

  String typeName;

  String methodName;

  String groupName;

  AlignFrame af;

  public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
          WsParamSetI thePreset, List<Argument> paramset)
  {
    super(sh, alignFrame, thePreset, paramset);
    af = alignFrame;
    typeName = sh.action;
    methodName = sh.serviceType;

    submitGaps = false;
    alignedSeqs = false;
    nucleotidesAllowed = false;
    proteinAllowed = true;
    bySequence = true;
  }

  @Override
  public String getServiceActionText()
  {
    return "Submitting amino acid sequences for disorder prediction.";
  }

  @Override
  boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
  {
    return (seqs.size() > 0);
  }

  private static Map<String, Map<String, String[]>> featureMap;

  private static Map<String, Map<String, Map<String, Object>>> annotMap;

  private static String DONTCOMBINE = "DONTCOMBINE";

  private static String INVISIBLE = "INVISIBLE";
  static
  {
    // TODO: turn this into some kind of configuration file that's a bit easier
    // to edit
    featureMap = new HashMap<>();
    Map<String, String[]> fmap;
    featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
            fmap = new HashMap<>());
    fmap.put("Glob",
            new String[]
            { "Globular Domain", "Predicted globular domain" });
    featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
            fmap = new HashMap<>());
    featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
            fmap = new HashMap<>());
    fmap.put("REM465", new String[] { "REM465", "Missing density" });
    fmap.put("HOTLOOPS", new String[] { "HOTLOOPS", "Flexible loops" });
    fmap.put("COILS", new String[] { "COILS", "Random coil" });
    featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
            fmap = new HashMap<>());
    fmap.put("GlobDoms",
            new String[]
            { "Globular Domain", "Predicted globular domain" });
    fmap.put("Disorder",
            new String[]
            { "Protein Disorder", "Probable unstructured peptide region" });
    Map<String, Map<String, Object>> amap;
    annotMap = new HashMap<>();
    annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
            amap = new HashMap<>());
    amap.put("Dydx", new HashMap<String, Object>());
    amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
    amap.get("Dydx").put(THRESHOLD, new double[] { 1, 0 });
    amap.get("Dydx").put(RANGE, new float[] { -1, +1 });

    amap.put("SmoothedScore", new HashMap<String, Object>());
    amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
    amap.put("RawScore", new HashMap<String, Object>());
    amap.get("RawScore").put(INVISIBLE, INVISIBLE);
    annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
            amap = new HashMap<>());
    amap.put("COILS", new HashMap<String, Object>());
    amap.put("HOTLOOPS", new HashMap<String, Object>());
    amap.put("REM465", new HashMap<String, Object>());
    amap.get("COILS").put(THRESHOLD, new double[] { 1, 0.516 });
    amap.get("COILS").put(RANGE, new float[] { 0, 1 });

    amap.get("HOTLOOPS").put(THRESHOLD, new double[] { 1, 0.6 });
    amap.get("HOTLOOPS").put(RANGE, new float[] { 0, 1 });
    amap.get("REM465").put(THRESHOLD, new double[] { 1, 0.1204 });
    amap.get("REM465").put(RANGE, new float[] { 0, 1 });

    annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
            amap = new HashMap<>());
    amap.put("Long", new HashMap<String, Object>());
    amap.put("Short", new HashMap<String, Object>());
    amap.get("Long").put(THRESHOLD, new double[] { 1, 0.5 });
    amap.get("Long").put(RANGE, new float[] { 0, 1 });
    amap.get("Short").put(THRESHOLD, new double[] { 1, 0.5 });
    amap.get("Short").put(RANGE, new float[] { 0, 1 });
    annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
            amap = new HashMap<>());
    amap.put("JRonn", new HashMap<String, Object>());
    amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5 });
    amap.get("JRonn").put(RANGE, new float[] { 0, 1 });
  }

  @Override
  public void updateResultAnnotation(boolean immediate)
  {

    if (immediate || !calcMan.isWorking(this) && scoremanager != null)
    {
      Map<String, String[]> featureTypeMap = featureMap
              .get(service.serviceType);
      Map<String, Map<String, Object>> annotTypeMap = annotMap
              .get(service.serviceType);
      boolean dispFeatures = false;
      Map<String, Object> fc = new Hashtable<>();
      List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
      /**
       * grouping for any annotation rows created
       */
      int graphGroup = 1;
      if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
      {
        for (AlignmentAnnotation ala : alignViewport.getAlignment()
                .getAlignmentAnnotation())
        {
          if (ala.graphGroup > graphGroup)
          {
            graphGroup = ala.graphGroup;
          }
        }
      }

      for (String seqId : seqNames.keySet())
      {
        boolean sameGroup = false;
        SequenceI dseq, aseq, seq = seqNames.get(seqId);
        int base = seq.findPosition(start) - 1;
        aseq = seq;
        while ((dseq = seq).getDatasetSequence() != null)
        {
          seq = seq.getDatasetSequence();
        }
        ScoreHolder scores = null;
        try
        {
          scores = scoremanager.getAnnotationForSequence(seqId);
        } catch (Exception q)
        {
          Console.info("Couldn't recover disorder prediction for sequence "
                  + seq.getName() + "(Prediction name was " + seqId + ")"
                  + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
        }
        float last = Float.NaN, val = Float.NaN;
        int lastAnnot = ourAnnot.size();
        if (scores != null && scores.scores != null)
        {
          for (Score scr : scores.scores)
          {

            if (scr.getRanges() != null && scr.getRanges().size() > 0)
            {
              Iterator<Float> vals = scr.getScores().iterator();
              // make features on sequence
              for (Range rn : scr.getRanges())
              {

                SequenceFeature sf;
                String[] type = featureTypeMap.get(scr.getMethod());
                if (type == null)
                {
                  // create a default type for this feature
                  type = new String[] {
                      typeName + " (" + scr.getMethod() + ")",
                      service.getActionText() };
                }
                if (vals.hasNext())
                {
                  val = vals.next().floatValue();
                  sf = new SequenceFeature(type[0], type[1], base + rn.from,
                          base + rn.to, val, methodName);
                }
                else
                {
                  sf = new SequenceFeature(type[0], type[1], base + rn.from,
                          base + rn.to, methodName);
                }
                dseq.addSequenceFeature(sf);
                if (last != val && !Float.isNaN(last))
                {
                  fc.put(sf.getType(), sf);
                }
                last = val;
                dispFeatures = true;
              }
            }
            else
            {
              if (scr.getScores().size() == 0)
              {
                continue;
              }
              String typename, calcName;
              AlignmentAnnotation annot = createAnnotationRowsForScores(
                      ourAnnot,
                      typename = service.serviceType + " ("
                              + scr.getMethod() + ")",
                      calcName = service.getServiceTypeURI() + "/"
                              + scr.getMethod(),
                      aseq, base + 1, scr);
              annot.graph = AlignmentAnnotation.LINE_GRAPH;

              Map<String, Object> styleMap = (annotTypeMap == null) ? null
                      : annotTypeMap.get(scr.getMethod());

              annot.visible = (styleMap == null
                      || styleMap.get(INVISIBLE) == null);
              double[] thrsh = (styleMap == null) ? null
                      : (double[]) styleMap.get(THRESHOLD);
              float[] range = (styleMap == null) ? null
                      : (float[]) styleMap.get(RANGE);
              if (range != null)
              {
                annot.graphMin = range[0];
                annot.graphMax = range[1];
              }
              if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
              {
                {
                  if (!sameGroup)
                  {
                    graphGroup++;
                    sameGroup = true;
                  }

                  annot.graphGroup = graphGroup;
                }
              }

              annot.description = "<html>" + service.getActionText()
                      + " - raw scores";
              if (thrsh != null)
              {
                String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
                        + thrsh[1] + " indicates disorder";
                annot.threshold = new GraphLine((float) thrsh[1],
                        threshNote, Color.red);
                annot.description += "<br/>" + threshNote;
              }
              annot.description += "</html>";
              Color col = ColorUtils
                      .createColourFromName(typeName + scr.getMethod());
              for (int p = 0, ps = annot.annotations.length; p < ps; p++)
              {
                if (annot.annotations[p] != null)
                {
                  annot.annotations[p].colour = col;
                }
              }
              annot._linecolour = col;
              // finally, update any dataset annotation
              replaceAnnotationOnAlignmentWith(annot, typename, calcName,
                      aseq);
            }
          }
        }
        if (lastAnnot + 1 == ourAnnot.size())
        {
          // remove singleton alignment annotation row
          ourAnnot.get(lastAnnot).graphGroup = -1;
        }
      }
      {
        if (dispFeatures)
        {
          jalview.api.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
                  .cloneFeatureRenderer();
          for (String ft : fc.keySet())
          {
            FeatureColourI gc = fr.getFeatureStyle(ft);
            if (gc.isSimpleColour())
            {
              // set graduated color as fading to white for minimum, and
              // autoscaling to values on alignment
              FeatureColourI ggc = new FeatureColour(gc.getColour(),
                      Color.white, gc.getColour(), Color.white,
                      Float.MIN_VALUE, Float.MAX_VALUE);
              ggc.setAutoScaled(true);
              fr.setColour(ft, ggc);
            }
          }
          // TODO: JAL-1150 - create sequence feature settings API for defining
          // styles and enabling/disabling feature overlay on alignment panel
          ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
          if (af.alignPanel == ap)
          {
            // only do this if the alignFrame is currently showing this view.
            af.setShowSeqFeatures(true);
          }
        }
        if (ourAnnot.size() > 0)
        {
          // Modify the visible annotation on the alignment viewport with the
          // new alignment annotation rows created.
          updateOurAnnots(ourAnnot);
          ap.adjustAnnotationHeight();
          ap.paintAlignment(true, true);
        }
      }
    }
  }

  @Override
  public String getCalcId()
  {
    // Disorder predictions are not dynamically updated so we return null
    return null;
  }

}
