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.appletgui;
23 import jalview.analysis.AlignSeq;
24 import jalview.datamodel.Alignment;
25 import jalview.datamodel.Sequence;
26 import jalview.datamodel.SequenceI;
27 import jalview.util.Format;
28 import jalview.util.MessageManager;
30 import java.awt.BorderLayout;
31 import java.awt.Button;
32 import java.awt.Panel;
33 import java.awt.ScrollPane;
34 import java.awt.TextArea;
35 import java.awt.event.ActionEvent;
36 import java.awt.event.ActionListener;
37 import java.util.Vector;
39 public class PairwiseAlignPanel extends Panel implements ActionListener
41 Vector sequences = new Vector();
45 public PairwiseAlignPanel(AlignmentPanel ap)
55 sequences = new Vector();
58 String[] seqStrings = ap.av.getViewAsString(true);
60 if (ap.av.getSelectionGroup() == null)
62 seqs = ap.av.getAlignment().getSequencesArray();
66 seqs = ap.av.getSelectionGroup().getSequencesInOrder(
67 ap.av.getAlignment());
70 float scores[][] = new float[seqs.length][seqs.length];
72 int count = ap.av.getSelectionGroup().getSize();
73 String type = (ap.av.getAlignment().isNucleotide()) ? AlignSeq.DNA
77 for (int i = 1; i < count; i++)
79 for (int j = 0; j < i; j++)
82 AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
85 if (as.s1str.length() == 0 || as.s2str.length() == 0)
93 as.printAlignment(System.out);
94 scores[i][j] = (float) as.getMaxScore()
95 / (float) as.getASeq1().length;
96 totscore = totscore + scores[i][j];
98 textarea.append(as.getOutput());
99 sequences.add(as.getAlignedSeq1());
100 sequences.add(as.getAlignedSeq1());
107 .println("Pairwise alignment scaled similarity score matrix\n");
109 for (int i = 0; i < count; i++)
111 Format.print(System.out, "%s \n",
113 + seqs[i].getName());
116 System.out.println("\n");
118 for (int i = 0; i < count; i++)
120 for (int j = 0; j < i; j++)
122 Format.printDouble(System.out, "%7.3f", scores[i][j]
127 System.out.println("\n");
131 public void actionPerformed(ActionEvent evt)
133 if (evt.getSource() == viewInEditorButton)
135 viewInEditorButton_actionPerformed();
139 protected void viewInEditorButton_actionPerformed()
142 Sequence[] seq = new Sequence[sequences.size()];
144 for (int i = 0; i < sequences.size(); i++)
146 seq[i] = (Sequence) sequences.elementAt(i);
149 new AlignFrame(new Alignment(seq), ap.av.applet,
150 "Pairwise Aligned Sequences", false);
154 protected ScrollPane scrollPane = new ScrollPane();
156 protected TextArea textarea = new TextArea();
158 protected Button viewInEditorButton = new Button();
160 Panel jPanel1 = new Panel();
162 BorderLayout borderLayout1 = new BorderLayout();
164 private void jbInit() throws Exception
166 this.setLayout(borderLayout1);
167 textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
168 textarea.setText("");
169 viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
170 viewInEditorButton.setLabel(MessageManager
171 .getString("label.view_alignment_editor"));
172 viewInEditorButton.addActionListener(this);
173 this.add(scrollPane, BorderLayout.CENTER);
174 scrollPane.add(textarea);
175 this.add(jPanel1, BorderLayout.SOUTH);
176 jPanel1.add(viewInEditorButton, null);