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.scoremodels;
23 import jalview.api.analysis.ScoreModelI;
24 import jalview.datamodel.AlignmentView;
25 import jalview.util.Comparison;
27 public class PIDScoreModel implements ScoreModelI
31 public float[][] findDistances(AlignmentView seqData)
33 String[] sequenceString = seqData
34 .getSequenceStrings(Comparison.GapChars.charAt(0));
35 int noseqs = sequenceString.length;
36 float[][] distance = new float[noseqs][noseqs];
37 for (int i = 0; i < (noseqs - 1); i++)
39 for (int j = i; j < noseqs; j++)
47 distance[i][j] = 100 - Comparison.PID(sequenceString[i],
50 distance[j][i] = distance[i][j];
58 public String getName()
64 public boolean isDNA()
70 public boolean isProtein()