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.DistanceModelI;
24 import jalview.datamodel.AlignmentView;
25 import jalview.util.Comparison;
27 public class PairwiseDistanceModel implements DistanceModelI
29 PairwiseScoreModelI scoreModel;
32 * Constructor given something to provide pairwise scores for residues
36 public PairwiseDistanceModel(PairwiseScoreModelI sm)
42 * Returns a matrix of [i][j] values representing distances between pairs of
46 public float[][] findDistances(AlignmentView seqData)
48 String[] sequenceString = seqData
49 .getSequenceStrings(Comparison.GAP_SPACE);
50 int noseqs = sequenceString.length;
51 float[][] distance = new float[noseqs][noseqs];
54 * calculate similarity scores for the upper half of the matrix
55 * as [i, j] = the sum of pairwise scores of corresponding
56 * positions of sequence[i] and sequence[j]
59 int end = sequenceString[0].length();
60 for (int i = 0; i < (noseqs - 1); i++)
62 for (int j = i; j < noseqs; j++)
66 for (int k = 0; k < end; k++)
70 score += scoreModel.getPairwiseScore(
71 sequenceString[i].charAt(k),
72 sequenceString[j].charAt(k));
73 } catch (Exception ex)
75 System.err.println("err creating " + getName() + " tree");
80 distance[i][j] = score;
90 * subtract similarity scores from the maximum value to
91 * convert to a distance measure; also populate the lower
92 * half of the result matrix with this value
94 // FIXME this assumes the score matrix is symmetric - it may not be?
95 for (int i = 0; i < (noseqs - 1); i++)
97 for (int j = i; j < noseqs; j++)
99 distance[i][j] = maxscore - distance[i][j];
100 distance[j][i] = distance[i][j];
107 public String getName()
109 return scoreModel.getName();
113 public boolean isDNA()
115 return scoreModel.isDNA();
119 public boolean isProtein()
121 return scoreModel.isProtein();
124 public PairwiseScoreModelI getScoreModel()