2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
22 import java.awt.event.*;
24 import jalview.analysis.*;
25 import jalview.datamodel.*;
26 import jalview.jbgui.*;
27 import jalview.util.MessageManager;
35 public class PairwiseAlignPanel extends GPairwiseAlignPanel
43 * Creates a new PairwiseAlignPanel object.
48 public PairwiseAlignPanel(AlignViewport av)
53 sequences = new Vector();
56 String[] seqStrings = av.getViewAsString(true);
58 if (av.getSelectionGroup() == null)
60 seqs = av.getAlignment().getSequencesArray();
64 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
67 String type = (av.getAlignment().isNucleotide()) ? AlignSeq.DNA
70 float[][] scores = new float[seqs.length][seqs.length];
72 int count = seqs.length;
76 for (int i = 1; i < count; i++)
78 for (int j = 0; j < i; j++)
81 AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
84 if (as.s1str.length() == 0 || as.s2str.length() == 0)
92 as.printAlignment(System.out);
93 scores[i][j] = (float) as.getMaxScore()
94 / (float) as.getASeq1().length;
95 totscore = totscore + scores[i][j];
97 textarea.append(as.getOutput());
98 seq = new Sequence(as.getS1().getName(), as.getAStr1(), as.getS1()
99 .getStart(), as.getS1().getEnd());
102 seq = new Sequence(as.getS2().getName(), as.getAStr2(), as.getS2()
103 .getStart(), as.getS2().getEnd());
111 .println("Pairwise alignment scaled similarity score matrix\n");
113 for (int i = 0; i < count; i++)
115 jalview.util.Format.print(System.out, "%s \n", ("" + i) + " "
116 + seqs[i].getName());
119 System.out.println("\n");
121 for (int i = 0; i < count; i++)
123 for (int j = 0; j < i; j++)
125 jalview.util.Format.print(System.out, "%7.3f", scores[i][j]
130 System.out.println("\n");
140 protected void viewInEditorButton_actionPerformed(ActionEvent e)
142 Sequence[] seq = new Sequence[sequences.size()];
144 for (int i = 0; i < sequences.size(); i++)
146 seq[i] = (Sequence) sequences.elementAt(i);
149 AlignFrame af = new AlignFrame(new Alignment(seq),
150 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
152 Desktop.addInternalFrame(af, MessageManager.getString("label.pairwise_aligned_sequences"),
153 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);