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.DistanceScoreModelI;
24 import jalview.api.analysis.SimilarityParamsI;
25 import jalview.datamodel.AlignmentView;
26 import jalview.math.Matrix;
27 import jalview.math.MatrixI;
28 import jalview.util.Comparison;
31 * @deprecated superseded by PIDModel
34 public class PIDDistanceModel implements DistanceScoreModelI
38 public MatrixI findDistances(AlignmentView seqData,
39 SimilarityParamsI options)
41 String[] sequenceString = seqData
42 .getSequenceStrings(Comparison.GAP_SPACE);
43 int noseqs = sequenceString.length;
44 double[][] distance = new double[noseqs][noseqs];
45 for (int i = 0; i < (noseqs - 1); i++)
47 for (int j = i; j < noseqs; j++)
55 distance[i][j] = 100 - Comparison.PID(sequenceString[i],
58 distance[j][i] = distance[i][j];
62 return new Matrix(distance);
66 public String getName()
72 public boolean isDNA()
78 public boolean isProtein()
84 public String toString()
86 return "Percentage identity of sequences";