/*
 * 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;

import jalview.analysis.AlignSeq;
import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.SeqsetUtils;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.Annotation;
import jalview.datamodel.ContiguousI;
import jalview.datamodel.Mapping;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.IProgressIndicator;
import jalview.gui.IProgressIndicatorHandler;
import jalview.gui.JvOptionPane;
import jalview.gui.WebserviceInfo;
import jalview.schemes.FeatureSettingsAdapter;
import jalview.schemes.ResidueProperties;
import jalview.util.MapList;
import jalview.util.MessageManager;
import jalview.workers.AlignCalcWorker;
import jalview.ws.JobStateSummary;
import jalview.ws.api.CancellableI;
import jalview.ws.api.JalviewServiceEndpointProviderI;
import jalview.ws.api.JobId;
import jalview.ws.api.SequenceAnnotationServiceI;
import jalview.ws.api.ServiceWithParameters;
import jalview.ws.api.WSAnnotationCalcManagerI;
import jalview.ws.gui.AnnotationWsJob;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;

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

public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
        implements WSAnnotationCalcManagerI
{

  protected ServiceWithParameters service;

  protected WsParamSetI preset;

  protected List<ArgumentI> arguments;

  protected IProgressIndicator guiProgress;

  protected boolean submitGaps = true;

  /**
   * by default, we filter out non-standard residues before submission
   */
  protected boolean filterNonStandardResidues = true;

  /**
   * Recover any existing parameters for this service
   */
  protected void initViewportParams()
  {
    if (getCalcId() != null)
    {
      ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
              getCalcId(),
              new AAConSettings(true, service, this.preset, arguments),
              true);
    }
  }

  /**
   * 
   * @return null or a string used to recover all annotation generated by this
   *         worker
   */
  public String getCalcId()
  {
    return service.getAlignAnalysisUI() == null ? null
            : service.getAlignAnalysisUI().getCalcId();
  }

  public WsParamSetI getPreset()
  {
    return preset;
  }

  public List<ArgumentI> getArguments()
  {
    return arguments;
  }

  /**
   * reconfigure and restart the AAConClient. This method will spawn a new
   * thread that will wait until any current jobs are finished, modify the
   * parameters and restart the conservation calculation with the new values.
   * 
   * @param newpreset
   * @param newarguments
   */
  public void updateParameters(final WsParamSetI newpreset,
          final List<ArgumentI> newarguments)
  {
    preset = newpreset;
    arguments = newarguments;
    calcMan.startWorker(this);
    initViewportParams();
  }
  protected boolean alignedSeqs = true;

  protected boolean nucleotidesAllowed = false;

  protected boolean proteinAllowed = false;

  /**
   * record sequences for mapping result back to afterwards
   */
  protected boolean bySequence = false;

  protected Map<String, SequenceI> seqNames;

  // TODO: convert to bitset
  protected boolean[] gapMap;

  int realw;

  protected int start;

  int end;

  private AlignFrame alignFrame;

  public boolean[] getGapMap()
  {
    return gapMap;
  }

  public SeqAnnotationServiceCalcWorker(AlignViewportI alignViewport,
          AlignmentViewPanel alignPanel)
  {
    super(alignViewport, alignPanel);
  }

  public SeqAnnotationServiceCalcWorker(ServiceWithParameters service,
          AlignFrame alignFrame,
          WsParamSetI preset, List<ArgumentI> paramset)
  {
    this(alignFrame.getCurrentView(), alignFrame.alignPanel);
    // TODO: both these fields needed ?
    this.alignFrame = alignFrame;
    this.guiProgress = alignFrame;
    this.preset = preset;
    this.arguments = paramset;
    this.service = service;
    try
    {
      annotService = (jalview.ws.api.SequenceAnnotationServiceI) ((JalviewServiceEndpointProviderI) service)
              .getEndpoint();
    } catch (ClassCastException cce)
    {
      JvOptionPane.showMessageDialog(Desktop.desktop,
              MessageManager.formatMessage(
                      "label.service_called_is_not_an_annotation_service",
                      new String[]
                      { service.getName() }),
              MessageManager.getString("label.internal_jalview_error"),
              JvOptionPane.WARNING_MESSAGE);

    }
    // configure submission flags
    proteinAllowed = service.isProteinService();
    nucleotidesAllowed = service.isNucleotideService();
    alignedSeqs = service.isNeedsAlignedSequences();
    bySequence = !service.isAlignmentAnalysis();
    filterNonStandardResidues = service.isFilterSymbols();
    min_valid_seqs = service.getMinimumInputSequences();
    submitGaps = service.isAlignmentAnalysis();

    if (service.isInteractiveUpdate())
    {
      initViewportParams();
    }
  }

  /**
   * 
   * @return true if the submission thread should attempt to submit data
   */
  public boolean hasService()
  {
    return annotService != null;
  }

  protected jalview.ws.api.SequenceAnnotationServiceI annotService = null;

  volatile JobId rslt = null;

  AnnotationWsJob running = null;

  private int min_valid_seqs;

  @Override
  public void run()
  {
    if (!hasService())
    {
      return;
    }

    long progressId = -1;

    int serverErrorsLeft = 3;
    final boolean cancellable = CancellableI.class
            .isAssignableFrom(annotService.getClass());
    StringBuffer msg = new StringBuffer();
    JobStateSummary job = new JobStateSummary();
    WebserviceInfo info = new WebserviceInfo("foo", "bar", false);
    try
    {
      if (checkDone())
      {
        return;
      }
      List<SequenceI> seqs = getInputSequences(
              alignViewport.getAlignment(),
              bySequence ? alignViewport.getSelectionGroup() : null);

      if (seqs == null || !checkValidInputSeqs(seqs))
      {
        jalview.bin.Cache.log.debug(
                "Sequences for analysis service were null or not valid");
        calcMan.workerComplete(this);
        return;
      }

      if (guiProgress != null)
      {
        guiProgress.setProgressBar(service.getActionText(),
                progressId = System.currentTimeMillis());
      }
      jalview.bin.Cache.log.debug("submitted " + seqs.size()
              + " sequences to " + service.getActionText());

      rslt = annotService.submitToService(seqs, getPreset(),
              getArguments());
      if (rslt == null)
      {
        return;
      }
      // TODO: handle job submission error reporting here.
      
      // ///
      // otherwise, construct WsJob and any UI handlers
      running = new AnnotationWsJob();
      running.setJobHandle(rslt);
      running.setSeqNames(seqNames);
      running.setStartPos(start);
      running.setSeqs(seqs);
      job.updateJobPanelState(info, "", running);
      if (guiProgress != null)
      {
        guiProgress.registerHandler(progressId,
                new IProgressIndicatorHandler()
                {

                  @Override
                  public boolean cancelActivity(long id)
                  {
                    ((CancellableI) annotService).cancel(running);
                    return true;
                  }

                  @Override
                  public boolean canCancel()
                  {
                    return cancellable;
                  }
                });
      }
      
      // ///
      // and poll for updates until job finishes, fails or becomes stale
      
      boolean finished = false;
      do
      {
        Cache.log.debug("Updating status for annotation service.");
        annotService.updateStatus(running);
        job.updateJobPanelState(info, "", running);
        if (running.isSubjobComplete())
        {
          Cache.log.debug(
                  "Finished polling analysis service job: status reported is "
                          + running.getState());
          finished = true;
        }
        else
        {
          Cache.log.debug("Status now " + running.getState());
        }

        if (calcMan.isPending(this) && isInteractiveUpdate())
        {
          Cache.log.debug("Analysis service job is stale. aborting.");
          // job has become stale.
          if (!finished) {
            finished = true;
            // cancel this job and yield to the new job
            try
            {
              if (cancellable
                        && ((CancellableI) annotService).cancel(running))
              {
                System.err.println("Cancelled job: " + rslt);
              }
              else
              {
                System.err.println("FAILED TO CANCEL job: " + rslt);
              }
  
            } catch (Exception x)
            {
  
            }
          }
          rslt = running.getJobHandle();
          return;
        }

        // pull any stats - some services need to flush log output before
        // results are available
        Cache.log.debug("Updating progress log for annotation service.");

        try
        {
        annotService.updateJobProgress(running);
        } catch (Throwable thr)
        {
          Cache.log.debug("Ignoring exception during progress update.",
                  thr);
        }
        Cache.log.trace("Result of poll: " + running.getStatus());

        if (!finished && !running.isFailed())
        {
          try
          {
            Cache.log.debug("Analysis service job thread sleeping.");
            Thread.sleep(200);
            Cache.log.debug("Analysis service job thread woke.");
          } catch (InterruptedException x)
          {
          }
          ;
        }
      } while (!finished);

      Cache.log.debug("Job poll loop exited. Job is " + running.getState());
      // TODO: need to poll/retry
      if (serverErrorsLeft > 0)
      {
        try
        {
          Thread.sleep(200);
        } catch (InterruptedException x)
        {
        }
      }
      if (running.isFinished())
      {
        // expect there to be results to collect
        // configure job with the associated view's feature renderer, if one
        // exists.
        // TODO: here one would also grab the 'master feature renderer' in order
        // to enable/disable
        // features automatically according to user preferences
        running.setFeatureRenderer(
                ((jalview.gui.AlignmentPanel) ap).cloneFeatureRenderer());
        Cache.log.debug("retrieving job results.");
        final Map<String, FeatureColourI> featureColours = new HashMap<>();
        final Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
        List<AlignmentAnnotation> returnedAnnot = annotService
                .getAnnotationResult(running.getJobHandle(), seqs,
                        featureColours, featureFilters);

        Cache.log.debug("Obtained " + (returnedAnnot == null ? "no rows"
                : ("" + returnedAnnot.size())));
        Cache.log.debug("There were " + featureColours.size()
                + " feature colours and " + featureFilters.size()
                + " filters defined.");

        // TODO
        // copy over each annotation row reurned and also defined on each
        // sequence, excluding regions not annotated due to gapMap/column
        // visibility

        running.setAnnotation(returnedAnnot);

        if (running.hasResults())
        {
          jalview.bin.Cache.log.debug("Updating result annotation from Job "
                  + rslt + " at " + service.getUri());
          updateResultAnnotation(true);
          if (running.isTransferSequenceFeatures())
          {
            // TODO
            // look at each sequence and lift over any features, excluding
            // regions
            // not annotated due to gapMap/column visibility

            jalview.bin.Cache.log.debug(
                    "Updating feature display settings and transferring features from Job "
                            + rslt + " at " + service.getUri());
            // TODO: consider merge rather than apply here
            alignViewport.applyFeaturesStyle(new FeatureSettingsAdapter()
            {
              @Override
              public FeatureColourI getFeatureColour(String type)
              {
                return featureColours.get(type);
              }

              @Override
              public FeatureMatcherSetI getFeatureFilters(String type)
              {
                return featureFilters.get(type);
              }

              @Override
              public boolean isFeatureDisplayed(String type)
              {
                return featureColours.containsKey(type);
              }

            });
            // TODO: JAL-1150 - create sequence feature settings API for
            // defining
            // styles and enabling/disabling feature overlay on alignment panel

            if (alignFrame.alignPanel == ap)
            {
              alignViewport.setShowSequenceFeatures(true);
              alignFrame.setMenusForViewport();
            }
          }
          ap.adjustAnnotationHeight();
        }
      }
      Cache.log.debug("Annotation Service Worker thread finished.");
    }
// TODO: use service specitic exception handlers
//    catch (JobSubmissionException x)
//    {
//
//      System.err.println(
//              "submission error with " + getServiceActionText() + " :");
//      x.printStackTrace();
//      calcMan.disableWorker(this);
//    } catch (ResultNotAvailableException x)
//    {
//      System.err.println("collection error:\nJob ID: " + rslt);
//      x.printStackTrace();
//      calcMan.disableWorker(this);
//
//    } catch (OutOfMemoryError error)
//    {
//      calcMan.disableWorker(this);
//
//      ap.raiseOOMWarning(getServiceActionText(), error);
//    } 
    catch (Throwable x)
    {
      calcMan.disableWorker(this);

      System.err
              .println("Blacklisting worker due to unexpected exception:");
      x.printStackTrace();
    } finally
    {

      calcMan.workerComplete(this);
      if (ap != null)
      {
        calcMan.workerComplete(this);
        if (guiProgress != null && progressId != -1)
        {
          guiProgress.setProgressBar("", progressId);
        }
        // TODO: may not need to paintAlignment again !
        ap.paintAlignment(false, false);
      }
      if (msg.length() > 0)
      {
        // TODO: stash message somewhere in annotation or alignment view.
        // code below shows result in a text box popup
        /*
         * jalview.gui.CutAndPasteTransfer cap = new
         * jalview.gui.CutAndPasteTransfer(); cap.setText(msg.toString());
         * jalview.gui.Desktop.addInternalFrame(cap,
         * "Job Status for "+getServiceActionText(), 600, 400);
         */
      }
    }

  }

  /**
   * validate input for dynamic/non-dynamic update context TODO: move to
   * analysis interface ?
   * @param seqs
   * 
   * @return true if input is valid
   */
  boolean checkValidInputSeqs(List<SequenceI> seqs)
  {
    int nvalid = 0;
    for (SequenceI sq : seqs)
    {
      if (sq.getStart() <= sq.getEnd()
              && (sq.isProtein() ? proteinAllowed : nucleotidesAllowed))
      {
        if (submitGaps
                || sq.getLength() == (sq.getEnd() - sq.getStart() + 1))
        {
          nvalid++;
        }
      }
    }
    return nvalid >= min_valid_seqs;
  }

  public void cancelCurrentJob()
  {
    try
    {
      String id = running.getJobId();
      if (((CancellableI) annotService).cancel(running))
      {
        System.err.println("Cancelled job " + id);
      }
      else
      {
        System.err.println("Job " + id + " couldn't be cancelled.");
      }
    } catch (Exception q)
    {
      q.printStackTrace();
    }
  }

  /**
   * Interactive updating. Analysis calculations that work on the currently
   * displayed alignment data should cancel existing jobs when the input data
   * has changed.
   * 
   * @return true if a running job should be cancelled because new input data is
   *         available for analysis
   */
  boolean isInteractiveUpdate()
  {
    return service.isInteractiveUpdate();
  }

  /**
   * decide what sequences will be analysed TODO: refactor to generate
   * List<SequenceI> for submission to service interface
   * 
   * @param alignment
   * @param inputSeqs
   * @return
   */
  public List<SequenceI> getInputSequences(AlignmentI alignment,
          AnnotatedCollectionI inputSeqs)
  {
    if (alignment == null || alignment.getWidth() <= 0
            || alignment.getSequences() == null || alignment.isNucleotide()
                    ? !nucleotidesAllowed
                    : !proteinAllowed)
    {
      return null;
    }
    if (inputSeqs == null || inputSeqs.getWidth() <= 0
            || inputSeqs.getSequences() == null
            || inputSeqs.getSequences().size() < 1)
    {
      inputSeqs = alignment;
    }

    List<SequenceI> seqs = new ArrayList<>();

    int minlen = 10;
    int ln = -1;
    if (bySequence)
    {
      seqNames = new HashMap<>();
    }
    gapMap = new boolean[0];
    start = inputSeqs.getStartRes();
    end = inputSeqs.getEndRes();
    // TODO: URGENT! unify with JPred / MSA code to handle hidden regions
    // correctly
    // TODO: push attributes into WsJob instance (so they can be safely
    // persisted/restored
    for (SequenceI sq : (inputSeqs.getSequences()))
    {
      if (bySequence
              ? sq.findPosition(end + 1)
                      - sq.findPosition(start + 1) > minlen - 1
              : sq.getEnd() - sq.getStart() > minlen - 1)
      {
        String newname = SeqsetUtils.unique_name(seqs.size() + 1);
        // make new input sequence with or without gaps
        if (seqNames != null)
        {
          seqNames.put(newname, sq);
        }
        SequenceI seq;
        if (submitGaps)
        {
          seqs.add(seq = new jalview.datamodel.Sequence(newname,
                  sq.getSequenceAsString()));
          if (gapMap == null || gapMap.length < seq.getLength())
          {
            boolean[] tg = gapMap;
            gapMap = new boolean[seq.getLength()];
            System.arraycopy(tg, 0, gapMap, 0, tg.length);
            for (int p = tg.length; p < gapMap.length; p++)
            {
              gapMap[p] = false; // init as a gap
            }
          }
          for (int apos : sq.gapMap())
          {
            char sqc = sq.getCharAt(apos);
            if (!filterNonStandardResidues
                    || (sq.isProtein() ? ResidueProperties.aaIndex[sqc] < 20
                            : ResidueProperties.nucleotideIndex[sqc] < 5))
            {
              gapMap[apos] = true; // aligned and real amino acid residue
            }
            ;
          }
        }
        else
        {
          // TODO: add ability to exclude hidden regions
          seqs.add(seq = new jalview.datamodel.Sequence(newname,
                  AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
                          sq.getSequenceAsString(start, end + 1))));
          // for annotation need to also record map to sequence start/end
          // position in range
          // then transfer back to original sequence on return.
        }
        if (seq.getLength() > ln)
        {
          ln = seq.getLength();
        }
      }
    }
    if (alignedSeqs && submitGaps)
    {
      realw = 0;
      for (int i = 0; i < gapMap.length; i++)
      {
        if (gapMap[i])
        {
          realw++;
        }
      }
      // try real hard to return something submittable
      // TODO: some of AAcon measures need a minimum of two or three amino
      // acids at each position, and AAcon doesn't gracefully degrade.
      for (int p = 0; p < seqs.size(); p++)
      {
        SequenceI sq = seqs.get(p);
        // strip gapped columns
        char[] padded = new char[realw],
                orig = sq.getSequence();
        for (int i = 0, pp = 0; i < realw; pp++)
        {
          if (gapMap[pp])
          {
            if (orig.length > pp)
            {
              padded[i++] = orig[pp];
            }
            else
            {
              padded[i++] = '-';
            }
          }
        }
        seqs.set(p, new jalview.datamodel.Sequence(sq.getName(),
                new String(padded)));
      }
    }
    return seqs;
  }

  @Override
  public void updateAnnotation()
  {
    updateResultAnnotation(false);
  }

  public void updateResultAnnotation(boolean immediate)
  {
    if ((immediate || !calcMan.isWorking(this)) && running != null
            && running.hasResults())
    {
      List<AlignmentAnnotation> ourAnnot = running.getAnnotation(),
              newAnnots = new ArrayList<>();
      //
      // update graphGroup for all annotation
      //
      /**
       * find a graphGroup greater than any existing ones this could be a method
       * provided by alignment Alignment.getNewGraphGroup() - returns next
       * unused graph group
       */
      int graphGroup = 1;
      if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
      {
        for (AlignmentAnnotation ala : alignViewport.getAlignment()
                .getAlignmentAnnotation())
        {
          if (ala.graphGroup > graphGroup)
          {
            graphGroup = ala.graphGroup;
          }
        }
      }
      /**
       * update graphGroup in the annotation rows returned from service
       */
      // TODO: look at sequence annotation rows and update graph groups in the
      // case of reference annotation.
      for (AlignmentAnnotation ala : ourAnnot)
      {
        if (ala.graphGroup > 0)
        {
          ala.graphGroup += graphGroup;
        }
        SequenceI aseq = null;

        /**
         * transfer sequence refs and adjust gapmap
         */
        if (ala.sequenceRef != null)
        {
          SequenceI seq = running.getSeqNames()
                  .get(ala.sequenceRef.getName());
          aseq = seq;
          while (seq.getDatasetSequence() != null)
          {
            seq = seq.getDatasetSequence();
          }
        }
        Annotation[] resAnnot = ala.annotations,
                gappedAnnot = new Annotation[Math.max(
                        alignViewport.getAlignment().getWidth(),
                        gapMap.length)];
        for (int p = 0, ap = start; ap < gappedAnnot.length; ap++)
        {
          if (gapMap != null && gapMap.length > ap && !gapMap[ap])
          {
            gappedAnnot[ap] = new Annotation("", "", ' ', Float.NaN);
          }
          else if (p < resAnnot.length)
          {
            gappedAnnot[ap] = resAnnot[p++];
          }
        }
        ala.sequenceRef = aseq;
        ala.annotations = gappedAnnot;
        AlignmentAnnotation newAnnot = getAlignViewport().getAlignment()
                .updateFromOrCopyAnnotation(ala);
        if (aseq != null)
        {

          aseq.addAlignmentAnnotation(newAnnot);
          newAnnot.adjustForAlignment();

          AlignmentAnnotationUtils.replaceAnnotationOnAlignmentWith(
                  newAnnot, newAnnot.label, newAnnot.getCalcId());
        }
        newAnnots.add(newAnnot);

      }
      for (SequenceI sq : running.getSeqs())
      {
        if (!sq.getFeatures().hasFeatures()
                && (sq.getDBRefs() == null || sq.getDBRefs().length == 0))
        {
          continue;
        }
        running.setTransferSequenceFeatures(true);
        SequenceI seq = running.getSeqNames().get(sq.getName());
        SequenceI dseq;
        ContiguousI seqRange = seq.findPositions(start, end);

        while ((dseq = seq).getDatasetSequence() != null)
        {
          seq = seq.getDatasetSequence();
        }
        List<ContiguousI> sourceRange = new ArrayList();
        if (gapMap != null && gapMap.length >= end)
        {
          int lastcol = start, col = start;
          do
          {
            if (col == end || !gapMap[col])
            {
              if (lastcol <= (col - 1))
              {
                seqRange = seq.findPositions(lastcol, col);
                sourceRange.add(seqRange);
              }
              lastcol = col + 1;
            }
          } while (++col <= end);
        }
        else
        {
          sourceRange.add(seq.findPositions(start, end));
        }
        int i = 0;
        int source_startend[] = new int[sourceRange.size() * 2];

        for (ContiguousI range : sourceRange)
        {
          source_startend[i++] = range.getBegin();
          source_startend[i++] = range.getEnd();
        }
        Mapping mp = new Mapping(
                new MapList(source_startend, new int[]
                { seq.getStart(), seq.getEnd() }, 1, 1));
        dseq.transferAnnotation(sq, mp);

      }
      updateOurAnnots(newAnnots);
    }
  }

  /**
   * notify manager that we have started, and wait for a free calculation slot
   * 
   * @return true if slot is obtained and work still valid, false if another
   *         thread has done our work for us.
   */
  protected boolean checkDone()
  {
    calcMan.notifyStart(this);
    ap.paintAlignment(false, false);
    while (!calcMan.notifyWorking(this))
    {
      if (calcMan.isWorking(this))
      {
        return true;
      }
      try
      {
        if (ap != null)
        {
          ap.paintAlignment(false, false);
        }

        Thread.sleep(200);
      } catch (Exception ex)
      {
        ex.printStackTrace();
      }
    }
    if (alignViewport.isClosed())
    {
      abortAndDestroy();
      return true;
    }
    return false;
  }

  protected void updateOurAnnots(List<AlignmentAnnotation> ourAnnot)
  {
    List<AlignmentAnnotation> our = ourAnnots;
    ourAnnots = ourAnnot;
    AlignmentI alignment = alignViewport.getAlignment();
    if (our != null)
    {
      if (our.size() > 0)
      {
        for (AlignmentAnnotation an : our)
        {
          if (!ourAnnots.contains(an))
          {
            // remove the old annotation
            alignment.deleteAnnotation(an);
          }
        }
      }
      our.clear();
    }

    // validate rows and update Alignmment state
    for (AlignmentAnnotation an : ourAnnots)
    {
      alignViewport.getAlignment().validateAnnotation(an);
    }
    // TODO: may need a menu refresh after this
    // af.setMenusForViewport();
    ap.adjustAnnotationHeight();

  }

  public SequenceAnnotationServiceI getService()
  {
    return annotService;
  }

}