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.schemes;
23 import jalview.api.analysis.ScoreModelI;
24 import jalview.gui.JvOptionPane;
28 import org.testng.annotations.BeforeClass;
30 public class ScoreMatrixPrinter
33 @BeforeClass(alwaysRun = true)
34 public void setUpJvOptionPane()
36 JvOptionPane.setInteractiveMode(false);
37 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
40 public void printAllMatrices()
42 for (Map.Entry<String, ScoreModelI> sm : ResidueProperties.scoreMatrices
45 System.out.println("Matrix " + sm.getKey());
46 System.out.println(sm.getValue().toString());
50 public void printHTMLMatrices()
52 for (Map.Entry<String, ScoreModelI> _sm : ResidueProperties.scoreMatrices
55 if (_sm.getValue() instanceof ScoreMatrix)
57 ScoreMatrix sm = (ScoreMatrix) _sm.getValue();
58 System.out.println("Matrix " + _sm.getKey());
59 System.out.println(sm.outputMatrix(true));