2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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.schemes.ScoreMatrix;
26 import jalview.util.Comparison;
28 public abstract class PairwiseSeqScoreModel implements ScoreModelI
30 abstract public int getPairwiseScore(char c, char d);
32 public float[][] findDistances(AlignmentView seqData)
34 String[] sequenceString = seqData
35 .getSequenceStrings(Comparison.GapChars.charAt(0));
36 int noseqs = sequenceString.length;
37 float[][] distance = new float[noseqs][noseqs];
40 int end = sequenceString[0].length();
41 for (int i = 0; i < (noseqs - 1); i++)
43 for (int j = i; j < noseqs; j++)
47 for (int k = 0; k < end; k++)
51 score += getPairwiseScore(sequenceString[i].charAt(k),
52 sequenceString[j].charAt(k));
53 } catch (Exception ex)
55 System.err.println("err creating " + getName() + " tree");
60 distance[i][j] = (float) score;
69 for (int i = 0; i < (noseqs - 1); i++)
71 for (int j = i; j < noseqs; j++)
73 distance[i][j] = (float) maxscore - distance[i][j];
74 distance[j][i] = distance[i][j];
80 abstract public int[][] getMatrix();