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.analysis.AlignSeq;
24 import jalview.api.analysis.ScoreModelI;
25 import jalview.datamodel.AlignmentView;
26 import jalview.datamodel.SequenceI;
27 import jalview.util.Comparison;
29 public class SWScoreModel implements ScoreModelI
33 public float[][] findDistances(AlignmentView seqData)
35 SequenceI[] sequenceString = seqData.getVisibleAlignment(
36 Comparison.GapChars.charAt(0)).getSequencesArray();
37 int noseqs = sequenceString.length;
38 float[][] distance = new float[noseqs][noseqs];
42 for (int i = 0; i < (noseqs - 1); i++)
44 for (int j = i; j < noseqs; j++)
46 AlignSeq as = new AlignSeq(sequenceString[i], sequenceString[j],
47 seqData.isNa() ? "dna" : "pep");
50 as.printAlignment(System.out);
51 distance[i][j] = (float) as.maxscore;
53 if (max < distance[i][j])
60 for (int i = 0; i < (noseqs - 1); i++)
62 for (int j = i; j < noseqs; j++)
64 distance[i][j] = max - distance[i][j];
65 distance[j][i] = distance[i][j];
73 public String getName()
75 return "Smith Waterman Score";
79 public boolean isDNA()
85 public boolean isProtein()
90 public String toString()
92 return "Score between two sequences aligned with Smith Waterman with default Peptide/Nucleotide matrix";