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.analysis.AlignSeq;
24 import jalview.api.analysis.SimilarityParamsI;
25 import jalview.api.analysis.SimilarityScoreModelI;
26 import jalview.datamodel.AlignmentView;
27 import jalview.datamodel.SequenceI;
28 import jalview.math.Matrix;
29 import jalview.math.MatrixI;
30 import jalview.util.Comparison;
33 * A class that computes pairwise similarity scores using the Smith-Waterman
36 public class SmithWatermanModel implements SimilarityScoreModelI
38 private static final String NAME = "Smith Waterman Score";
41 public MatrixI findSimilarities(AlignmentView seqData,
42 SimilarityParamsI options)
44 SequenceI[] sequenceString = seqData.getVisibleAlignment(
45 Comparison.GAP_SPACE).getSequencesArray();
46 int noseqs = sequenceString.length;
47 double[][] distances = new double[noseqs][noseqs];
51 for (int i = 0; i < (noseqs - 1); i++)
53 for (int j = i; j < noseqs; j++)
55 AlignSeq as = new AlignSeq(sequenceString[i], sequenceString[j],
56 seqData.isNa() ? "dna" : "pep");
59 as.printAlignment(System.out);
60 distances[i][j] = as.maxscore;
62 if (max < distances[i][j])
64 max = distances[i][j];
69 return new Matrix(distances);
73 public String getName()
79 public boolean isDNA()
85 public boolean isProtein()
91 public String toString()
93 return "Score between two sequences aligned with Smith Waterman with default Peptide/Nucleotide matrix";