/*
 * 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.gui.AlignFrame;
import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;

import java.util.List;

public abstract class JabawsMsaInterfaceAlignCalcWorker
        extends SeqAnnotationServiceCalcWorker
{

  public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service,
          AlignFrame alignFrame, WsParamSetI preset,
          List<ArgumentI> paramset)
  {
    super(service, alignFrame, preset, paramset);
    // TODO Auto-generated constructor stub
  }

  // TODO: REFACTOR if needed !
  // may be able to get away with overriding run() only, but maybe not.
  /***
   * @SuppressWarnings("unchecked") protected MsaWS msaservice;
   * 
   * protected Alignment msascoreset;
   * 
   * public JabawsMsaInterfaceAlignCalcWorker(AlignViewportI alignViewport,
   * AlignmentViewPanel alignPanel) { super(alignViewport, alignPanel); }
   * 
   * public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service, AlignFrame
   * alignFrame, WsParamSetI preset, List<ArgumentI> paramset) {
   * this(alignFrame.getCurrentView(), alignFrame.alignPanel); this.guiProgress
   * = alignFrame; this.preset = preset; this.arguments = paramset; this.service
   * = service; msaservice = (MsaWS) service.service;
   * 
   * }
   * 
   * @Override ChunkHolder pullExecStatistics(String rslt, long rpos) { return
   *           msaservice.pullExecStatistics(rslt, rpos); }
   * 
   * @Override boolean collectAnnotationResultsFor(String rslt) throws
   *           ResultNotAvailableException { msascoreset =
   *           msaservice.getResult(rslt); if (msascoreset != null) { return
   *           true; } return false; }
   * 
   * @Override boolean cancelJob(String rslt) throws Exception { return
   *           msaservice.cancelJob(rslt); }
   * 
   * @Override protected JobStatus getJobStatus(String rslt) throws Exception {
   *           return msaservice.getJobStatus(rslt); }
   * 
   * @Override boolean hasService() { return msaservice != null; }
   * 
   * @Override protected boolean isInteractiveUpdate() { return false; // this
   *           instanceof AAConClient; }
   * 
   * @Override protected String submitToService(
   *           List<compbio.data.sequence.FastaSequence> seqs) throws
   *           JobSubmissionException { String rslt; if (preset == null &&
   *           arguments == null) { rslt = msaservice.align(seqs); } else { try
   *           { rslt = msaservice.customAlign(seqs, getJabaArguments()); }
   *           catch (WrongParameterException x) { throw new
   *           JobSubmissionException(MessageManager.getString(
   *           "exception.jobsubmission_invalid_params_set"), x); } } return
   *           rslt; }
   * 
   *           protected void createAnnotationRowsForScores(
   *           List<AlignmentAnnotation> ourAnnot, String calcId, int alWidth,
   *           Score scr) { // simple annotation row AlignmentAnnotation
   *           annotation = alignViewport.getAlignment()
   *           .findOrCreateAnnotation(scr.getMethod(), calcId, true, null,
   *           null); if (alWidth == gapMap.length) // scr.getScores().size()) {
   *           constructAnnotationFromScore(annotation, 0, alWidth, scr);
   *           ourAnnot.add(annotation); } }
   * 
   *           protected AlignmentAnnotation createAnnotationRowsForScores(
   *           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 = alignViewport.getAlignment()
   *           .findOrCreateAnnotation(typeName, calcId, false, dseq, null);
   *           constructAnnotationFromScore(annotation, 0, dseq.getLength(),
   *           scr); annotation.createSequenceMapping(dseq, base, false);
   *           annotation.adjustForAlignment();
   *           dseq.addAlignmentAnnotation(annotation);
   *           ourAnnot.add(annotation); return annotation; }
   * 
   *           private void constructAnnotationFromScore(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) { 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();
   *           }
   ***/
}