2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 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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31 extends Panel implements ActionListener
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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 sequences = new Vector();
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50 String[] seqStrings = ap.av.getViewAsString(true);
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52 if (ap.av.getSelectionGroup() == null)
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54 seqs = ap.av.alignment.getSequencesArray();
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58 seqs = ap.av.getSelectionGroup().getSequencesInOrder(ap.av.alignment);
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61 float scores[][] = new float[seqs.length][seqs.length];
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62 double totscore = 0;
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63 int count = ap.av.getSelectionGroup().getSize(false);
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67 for (int i = 1; i < count; i++)
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69 for (int j = 0; j < i; j++)
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72 AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
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73 seqs[j], seqStrings[j], "pep");
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75 if (as.s1str.length() == 0 || as.s2str.length() == 0)
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80 as.calcScoreMatrix();
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81 as.traceAlignment();
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83 as.printAlignment(System.out);
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84 scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
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85 totscore = totscore + scores[i][j];
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87 textarea.append(as.getOutput());
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88 seq = new Sequence(as.getS1().getName(),
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90 as.getS1().getStart(),
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93 sequences.addElement(seq);
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95 seq = new Sequence(as.getS2().getName(),
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97 as.getS2().getStart(),
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98 as.getS2().getEnd());
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99 sequences.addElement(seq);
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105 System.out.println(
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106 "Pairwise alignment scaled similarity score matrix\n");
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108 for (int i = 0; i < count; i++)
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110 jalview.util.Format.print(System.out, "%s \n",
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112 seqs[i].getName());
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115 System.out.println("\n");
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117 for (int i = 0; i < count; i++)
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119 for (int j = 0; j < i; j++)
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121 jalview.util.Format.print(System.out, "%7.3f",
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122 scores[i][j] / totscore);
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126 System.out.println("\n");
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129 public void actionPerformed(ActionEvent evt)
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131 if(evt.getSource()==viewInEditorButton)
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132 viewInEditorButton_actionPerformed();
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135 protected void viewInEditorButton_actionPerformed()
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138 Sequence[] seq = new Sequence[sequences.size()];
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140 for (int i = 0; i < sequences.size(); i++)
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142 seq[i] = (Sequence) sequences.elementAt(i);
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145 new AlignFrame(new Alignment(seq),
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147 "Pairwise Aligned Sequences",
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151 protected ScrollPane scrollPane = new ScrollPane();
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152 protected TextArea textarea = new TextArea();
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153 protected Button viewInEditorButton = new Button();
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154 Panel jPanel1 = new Panel();
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155 BorderLayout borderLayout1 = new BorderLayout();
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157 private void jbInit() throws Exception {
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158 this.setLayout(borderLayout1);
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159 textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
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160 textarea.setText("");
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161 viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
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162 viewInEditorButton.setLabel("View in alignment editor");
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163 viewInEditorButton.addActionListener(this);
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164 this.add(scrollPane, BorderLayout.CENTER);
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165 scrollPane.add(textarea);
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166 this.add(jPanel1, BorderLayout.SOUTH);
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167 jPanel1.add(viewInEditorButton, null);
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