package jalview.ws.jws2.jabaws2;

import jalview.api.FeatureColourI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.util.MessageManager;
import jalview.ws.api.JobId;
import jalview.ws.api.SequenceAnnotationServiceI;
import jalview.ws.jws2.JabaParamStore;
import jalview.ws.jws2.JabaPreset;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;

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

import compbio.data.msa.SequenceAnnotation;
import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.Score;
import compbio.data.sequence.ScoreManager;
import compbio.metadata.JobSubmissionException;
import compbio.metadata.WrongParameterException;

public abstract class JabawsAnnotationInstance
        extends JabawsServiceInstance<SequenceAnnotation>
        implements SequenceAnnotationServiceI
{

  /**
   * holds last results obtained when non-null. TODO: remove this as a field ?
   */
  protected ScoreManager scoremanager = null;

  public JabawsAnnotationInstance(Jws2Instance handle)
  {
    super(handle);
  }


  /**
   * 
   * @return the calcId for this Jabaws Service (convenience method).
   * 
   *         TODO: decide if this is really convenient since manager and
   *         instance have same method !
   */
  public String getCalcId()
  {
    return our.getAlignAnalysisUI() == null ? null
            : our.getAlignAnalysisUI().getCalcId();
  }

  @Override
  public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset,
          List<ArgumentI> arguments) throws Throwable
  {
    String rslt = null;
    scoremanager = null;
    List<FastaSequence> jabaseqs = new ArrayList(seqs.size());
    for (SequenceI seq : seqs)
    {
      jabaseqs.add(
              new FastaSequence(seq.getName(), seq.getSequenceAsString()));
    }
    if (preset == null && arguments == null)
    {
      rslt = service.analize(jabaseqs);
    }
    if (preset != null)
    {
      if (preset instanceof JabaPreset)
      {
        // TODO: verify behaviour is really the same, since preset analyze was
        // never called in Jalview 2.11.x
        rslt = service.presetAnalize(jabaseqs,
                ((JabaPreset) preset).getJabaPreset());
      }
      else
      {
        rslt = service.customAnalize(jabaseqs,
                JabaParamStore.getJabafromJwsArgs(preset.getArguments()));
      }
    }
    else if (arguments != null && arguments.size() > 0)
    {
      try
      {
        rslt = service.customAnalize(jabaseqs,
                JabaParamStore.getJabafromJwsArgs(arguments));
      } catch (WrongParameterException x)
      {
        throw new JobSubmissionException(MessageManager.getString(
                "exception.jobsubmission_invalid_params_set"), x);

      }
    }

    if (rslt == null)
    {
      return null;
    }
    return new JobId(our.getServiceType(), our.getName(), rslt);
  }


  @Override
  public
  List<AlignmentAnnotation> getAnnotationResult(JobId job,
          List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
          Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
  {
    if (scoremanager == null)
    {
      // TODO: raise annotation unavailable exception ?
      scoremanager = service.getAnnotation(job.getJobId());
    }
    if (scoremanager == null)
    {
      return List.of();
    }
    /**
     * dummy alignment to perform annotation on
     */
    AlignmentI newal = new Alignment(seqs.toArray(new SequenceI[0]));
    List<AlignmentAnnotation> ourAnnot = annotationFromScoreManager(newal,
            featureColours, featureFilters);
    return ourAnnot;
  }

  /**
   * service specific annotation creation method
   * 
   * @param seqs
   *          - sequences to be annotated with results
   * @param featureColours
   *          - - updated with any colours imported during result processing
   * @param featureFilters
   *          - updated with any filters imported during result processing
   * 
   * @return
   */
  abstract List<AlignmentAnnotation> annotationFromScoreManager(
          AlignmentI seqs, Map<String, FeatureColourI> featureColours,
          Map<String, FeatureMatcherSetI> featureFilters);


  /**
   * create and complete an annotation row from a JABAWS score object
   * 
   * @param alignViewport
   * @param gapMap
   * @param ourAnnot
   * @param calcId
   * @param alWidth
   * @param scr
   */

  protected void createAnnotationRowsForScores(AlignmentI al_result,
          boolean[] gapMap, List<AlignmentAnnotation> ourAnnot,
          String calcId,
          int alWidth, Score scr)
  {
    // simple annotation row
    AlignmentAnnotation annotation = al_result
            .findOrCreateAnnotation(scr.getMethod(), calcId, true, null,
                    null);
    if (gapMap == null || alWidth == gapMap.length) // scr.getScores().size())
    {
      constructAnnotationFromScore(gapMap, annotation, 0,
              alWidth, scr);
      ourAnnot.add(annotation);
    }
  }

  /**
   * create a sequence associated annotation row for JABAWS score object scr
   * 
   * @param alignViewport
   * @param gapMap
   * @param ourAnnot
   * @param typeName
   * @param calcId
   * @param dseq
   * @param base
   * @param scr
   * @return
   */
  protected AlignmentAnnotation createAnnotationRowsForScores(
          AlignmentI alignment, boolean[] gapMap,
          List<AlignmentAnnotation> ourAnnot, String typeName,
          String calcId, SequenceI dseq, int base, Score scr)
  {
    System.out.println("Creating annotation on dseq:" + dseq.getStart()
            + " base is " + base + " and length=" + dseq.getLength()
            + " == " + scr.getScores().size());
    // AlignmentAnnotation annotation = new AlignmentAnnotation(
    // scr.getMethod(), typeName, new Annotation[]
    // {}, 0, -1, AlignmentAnnotation.LINE_GRAPH);
    // annotation.setCalcId(calcId);
    AlignmentAnnotation annotation = alignment
            .findOrCreateAnnotation(typeName, calcId, false, dseq, null);
    constructAnnotationFromScore(gapMap, annotation, 0, dseq.getLength(),
            scr);
    annotation.createSequenceMapping(dseq, base, false);
    annotation.adjustForAlignment();
    dseq.addAlignmentAnnotation(annotation);
    ourAnnot.add(annotation);
    return annotation;
  }

  /**
   * create column annotation elements from Jabaws score object
   * 
   * @param gapMap
   * @param annotation
   * @param base
   * @param alWidth
   * @param scr
   *          JABAWS score object
   */
  protected void constructAnnotationFromScore(boolean[] gapMap,
          AlignmentAnnotation annotation,
          int base, int alWidth, Score scr)
  {
    Annotation[] elm = new Annotation[alWidth];
    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)
      {
        // if gapMap is a different length to the result then it may be out of
        // sync with the job.
        while (i < gapMap.length && !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();
  }

}