2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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20 package jalview.appletgui;
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24 import java.awt.event.*;
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26 import jalview.analysis.*;
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27 import jalview.datamodel.*;
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30 public class PairwiseAlignPanel
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33 Vector sequences = new Vector();
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36 public PairwiseAlignPanel(AlignmentPanel ap)
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44 e.printStackTrace();
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47 float scores[][] = new float[ap.av.alignment.getHeight()][ap.av.alignment.
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49 double totscore = 0;
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50 int count = ap.av.getSelectionGroup().getSize();
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53 for (int i = 1; i < count; i++)
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55 for (int j = 0; j < i; j++)
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58 AlignSeq as = new AlignSeq(ap.av.getSelectionGroup().getSequenceAt(i),
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59 ap.av.getSelectionGroup().getSequenceAt(j),
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62 as.calcScoreMatrix();
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63 as.traceAlignment();
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64 as.printAlignment(System.out);
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65 scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
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66 totscore = totscore + scores[i][j];
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68 textarea.append(as.getOutput());
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69 sequences.addElement(new Sequence(as.getS1().getName(), as.getAStr1()));
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70 sequences.addElement(new Sequence(as.getS2().getName(), as.getAStr2()));
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77 for (int i = 0; i < count; i++)
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79 for (int j = 0; j < i; j++)
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81 jalview.util.Format.print(System.out, "%7.3f",
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82 scores[i][j] / totscore);
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88 protected void viewInEditorButton_actionPerformed(ActionEvent e)
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91 Sequence[] seq = new Sequence[sequences.size()];
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93 for (int i = 0; i < sequences.size(); i++)
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95 seq[i] = (Sequence) sequences.elementAt(i);
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98 new AlignFrame(new Alignment(seq),
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99 ap.alignFrame.applet,
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100 "Pairwise Aligned Sequences");
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103 protected ScrollPane scrollPane = new ScrollPane();
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104 protected TextArea textarea = new TextArea();
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105 protected Button viewInEditorButton = new Button();
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106 Panel jPanel1 = new Panel();
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107 BorderLayout borderLayout1 = new BorderLayout();
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109 private void jbInit() throws Exception {
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110 this.setLayout(borderLayout1);
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111 textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
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112 textarea.setText("");
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113 viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
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114 viewInEditorButton.setLabel("View in alignment editor");
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115 viewInEditorButton.addActionListener(new java.awt.event.ActionListener() {
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116 public void actionPerformed(ActionEvent e) {
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117 viewInEditorButton_actionPerformed(e);
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120 this.add(scrollPane, BorderLayout.CENTER);
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121 scrollPane.add(textarea);
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122 this.add(jPanel1, BorderLayout.SOUTH);
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123 jPanel1.add(viewInEditorButton, null);
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