/*
 * 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.workers;

import jalview.analysis.Conservation;
import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.schemes.ResidueProperties;

import java.util.ArrayList;
import java.util.List;

public class ConservationThread extends AlignCalcWorker implements
        AlignCalcWorkerI
{

  private int ConsPercGaps = 25; // JBPNote : This should be a configurable
                                 // property!

  public ConservationThread(AlignViewportI alignViewport,
          AlignmentViewPanel alignPanel)
  {
    super(alignViewport, alignPanel);
    ConsPercGaps = alignViewport.getConsPercGaps();
  }

  private Conservation cons;

  AlignmentAnnotation conservation, quality;

	@Override
	protected void run1(int state) {
		while (!interrupted()) {
			try {
				switch (state) {
				case INIT:
					if (calcMan.isPending(this))
						return;
					calcMan.notifyStart(this);
					state = LOOP_STANDBY;
					break;
				case LOOP_STANDBY:
					while (!calcMan.notifyWorking(this)) {
						if (ap != null) {
							ap.paintAlignment(false);
						}
						try {
							if (sleepAndReturn(200, state))
								return;
						} catch (InterruptedException e) {
							state = DONE;
							break;
						}
					}
					if (alignViewport.isClosed()) {
						abortAndDestroy();
						state = DONE;
						break;
					}
		      List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
		      alignment = alignViewport.getAlignment();
		      conservation = alignViewport.getAlignmentConservationAnnotation();
		      quality = alignViewport.getAlignmentQualityAnnot();
		      ourAnnot.add(conservation);
		      ourAnnot.add(quality);
		      ourAnnots = ourAnnot;
		      ConsPercGaps = alignViewport.getConsPercGaps();
		      // AlignViewport.UPDATING_CONSERVATION = true;

		      if (alignment == null || (aWidth = alignment.getWidth()) < 0)
		      {
		        calcMan.workerComplete(this);
		        // .updatingConservation = false;
		        // AlignViewport.UPDATING_CONSERVATION = false;

		        return;
		      }
					state = LOOP_CALCULATE;
					break;
				case LOOP_CALCULATE:
					iFirst = iLast;
					nPer = aWidth  + 1; // for now - one big chunk
					iLast = Math.min(iLast + nPer, aWidth);
					if (iLast == iFirst) {
						state = DONE;
					} else {
						computeConsensus();
						if (sleepAndReturn(0, state))
							return;
					}
					break;
				case DONE:
		      updateResultAnnotation(true);
					return;
				}
			} catch (OutOfMemoryError error) {
				calcMan.workerCannotRun(this);
	      ap.raiseOOMWarning("calculating conservation", error);
			} catch (Throwable e) {
				System.out.println("Error in ConsensusThread: " + e);
				e.printStackTrace();
				calcMan.workerComplete(this);
			}
		}
	}

	private void computeConsensus() {
    cons = Conservation.calculateConservation("All",
        ResidueProperties.propHash, 3,
        alignment.getSequences(), 0, aWidth - 1, false,
        ConsPercGaps, quality != null);
	}


  private void updateResultAnnotation(boolean b)
  {
    if (b || !calcMan.isWorking(this) && cons != null
            && conservation != null && quality != null)
    {
      alignViewport.setConservation(cons);
      cons.completeAnnotations(conservation, quality, 0, aWidth);
    }
  }

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

  }

}