2 * Jalview - A Sequence Alignment Editor and Viewer ($Version-Rel$)
3 * Copyright (C) $Year-Rel$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.analysis;
23 import jalview.analysis.scoremodels.ScoreModels;
24 import jalview.api.analysis.ScoreModelI;
25 import jalview.api.analysis.SimilarityParamsI;
26 import jalview.gui.AlignViewport;
29 * @author kjvanderheide
32 public class TreeCalculator extends Thread// add threading
34 SimilarityParamsI similarityParams;
38 String scoreModelName; // if tree computed
43 * @param substitutionMatrix
44 * @param calculateParams
46 public TreeCalculator(String treeAlgo, String substitutionMatrix,
47 SimilarityParamsI calculateParams)
49 this.treeType = treeAlgo;
50 this.scoreModelName = substitutionMatrix;
51 this.similarityParams = calculateParams;
56 * @param alignViewport
59 public TreeBuilder makeTree(AlignViewport alignViewport)
61 ScoreModelI sm = ScoreModels.getInstance().getScoreModel(scoreModelName,
62 alignViewport.getAlignPanel());
64 TreeBuilder builtTree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
65 ? new NJTree(alignViewport, sm, similarityParams)
66 : new AverageDistanceTree(alignViewport, sm, similarityParams);
72 public SimilarityParamsI getSimilarityParams()
74 return similarityParams;
77 public void setSimilarityParams(SimilarityParamsI similarityParams)
79 this.similarityParams = similarityParams;
82 public String getTreeType()
87 public void setTreeType(String treeType)
89 this.treeType = treeType;
92 public String getScoreModelName()
94 return scoreModelName;
97 public void setScoreModelName(String scoreModelName)
99 this.scoreModelName = scoreModelName;