/*
 * 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.analysis;

import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.gui.AlignViewport;

/**
 * @author kjvanderheide
 *
 */
public class TreeCalculator extends Thread// add threading
{
  SimilarityParamsI similarityParams;

  String treeType;

  String scoreModelName; // if tree computed

  /**
   * 
   * @param treeAlgo
   * @param substitutionMatrix
   * @param calculateParams
   */
  public TreeCalculator(String treeAlgo, String substitutionMatrix,
          SimilarityParamsI calculateParams)
  {
    this.treeType = treeAlgo;
    this.scoreModelName = substitutionMatrix;
    this.similarityParams = calculateParams;
  }

  /**
   * 
   * @param alignViewport
   * @return
   */
  public TreeBuilder makeTree(AlignViewport alignViewport)
  {
    ScoreModelI sm = ScoreModels.getInstance().getScoreModel(scoreModelName,
            alignViewport.getAlignPanel());

    TreeBuilder builtTree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
            ? new NJTree(alignViewport, sm, similarityParams)
            : new AverageDistanceTree(alignViewport, sm, similarityParams);

    return builtTree;

  }

  public SimilarityParamsI getSimilarityParams()
  {
    return similarityParams;
  }

  public void setSimilarityParams(SimilarityParamsI similarityParams)
  {
    this.similarityParams = similarityParams;
  }

  public String getTreeType()
  {
    return treeType;
  }

  public void setTreeType(String treeType)
  {
    this.treeType = treeType;
  }

  public String getScoreModelName()
  {
    return scoreModelName;
  }

  public void setScoreModelName(String scoreModelName)
  {
    this.scoreModelName = scoreModelName;
  }




}