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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19 package jalview.jbgui;
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22 import java.awt.event.*;
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23 import javax.swing.*;
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24 import javax.swing.event.*;
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25 import jalview.io.FormatAdapter;
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26 import jalview.datamodel.SequenceI;
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27 import java.awt.datatransfer.DataFlavor;
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28 import jalview.io.IdentifyFile;
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30 public class GFinder
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33 JLabel jLabel1 = new JLabel();
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34 protected JButton findAll = new JButton();
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35 protected JButton findNext = new JButton();
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36 JPanel jPanel1 = new JPanel();
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37 GridLayout gridLayout1 = new GridLayout();
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38 protected JButton createNewGroup = new JButton();
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39 JScrollPane jScrollPane1 = new JScrollPane();
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40 protected JTextArea textfield = new JTextArea();
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41 BorderLayout borderLayout1 = new BorderLayout();
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42 JPanel jPanel2 = new JPanel();
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43 JPanel jPanel3 = new JPanel();
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44 JPanel jPanel4 = new JPanel();
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45 BorderLayout borderLayout2 = new BorderLayout();
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46 JPanel jPanel5 = new JPanel();
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47 JPanel jPanel6 = new JPanel();
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56 e.printStackTrace();
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60 private void jbInit()
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63 jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
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64 jLabel1.setText("Find");
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65 this.setLayout(borderLayout1);
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66 findAll.setFont(new java.awt.Font("Verdana", 0, 12));
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67 findAll.setText("Find all");
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68 findAll.addActionListener(new java.awt.event.ActionListener()
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70 public void actionPerformed(ActionEvent e)
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72 findAll_actionPerformed(e);
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75 findNext.setEnabled(false);
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76 findNext.setFont(new java.awt.Font("Verdana", 0, 12));
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77 findNext.setText("Find Next");
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78 findNext.addActionListener(new java.awt.event.ActionListener()
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80 public void actionPerformed(ActionEvent e)
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82 findNext_actionPerformed(e);
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85 jPanel1.setLayout(gridLayout1);
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86 gridLayout1.setHgap(0);
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87 gridLayout1.setRows(3);
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88 gridLayout1.setVgap(2);
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89 createNewGroup.setEnabled(false);
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90 createNewGroup.setFont(new java.awt.Font("Verdana", 0, 12));
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91 createNewGroup.setToolTipText("");
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92 createNewGroup.setMargin(new Insets(0, 0, 0, 0));
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93 createNewGroup.setText("Create new group");
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94 createNewGroup.addActionListener(new java.awt.event.ActionListener()
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96 public void actionPerformed(ActionEvent e)
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98 createNewGroup_actionPerformed(e);
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101 textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 12));
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102 textfield.setText("");
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103 textfield.setLineWrap(true);
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104 textfield.addCaretListener(new CaretListener()
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106 public void caretUpdate(CaretEvent e)
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108 textfield_caretUpdate(e);
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111 textfield.addKeyListener(new java.awt.event.KeyAdapter() {
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112 public void keyPressed(KeyEvent e) {
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113 textfield_keyPressed(e);
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117 borderLayout1.setHgap(5);
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118 borderLayout1.setVgap(5);
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119 jPanel4.setLayout(borderLayout2);
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120 jPanel2.setPreferredSize(new Dimension(10, 1));
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121 jPanel3.setPreferredSize(new Dimension(10, 1));
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122 jPanel1.add(findNext, null);
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123 jPanel1.add(findAll, null);
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124 jPanel1.add(createNewGroup, null);
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125 this.add(jLabel1, java.awt.BorderLayout.WEST);
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126 this.add(jPanel1, java.awt.BorderLayout.EAST);
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127 this.add(jPanel2, java.awt.BorderLayout.SOUTH);
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128 this.add(jPanel3, java.awt.BorderLayout.NORTH);
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129 this.add(jPanel4, java.awt.BorderLayout.CENTER);
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130 jPanel4.add(jScrollPane1, java.awt.BorderLayout.CENTER);
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131 jPanel4.add(jPanel5, java.awt.BorderLayout.SOUTH);
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132 jPanel4.add(jPanel6, java.awt.BorderLayout.NORTH);
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133 jScrollPane1.getViewport().add(textfield);
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136 protected void findNext_actionPerformed(ActionEvent e)
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140 protected void findAll_actionPerformed(ActionEvent e)
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145 protected void textfield_keyPressed(KeyEvent e)
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148 if(e.getKeyCode()==KeyEvent.VK_ENTER)
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151 findNext_actionPerformed(null);
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153 findNext.setEnabled(true);
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156 public void createNewGroup_actionPerformed(ActionEvent e)
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160 public void textfield_caretUpdate(CaretEvent e)
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162 if (textfield.getText().indexOf(">") > -1)
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164 SwingUtilities.invokeLater(new Runnable()
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168 String str = textfield.getText();
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169 SequenceI[] sequences = FormatAdapter.readFile(str, "Paste", "FASTA");
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170 if(sequences!=null && sequences.length>0)
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172 str = jalview.analysis.AlignSeq.extractGaps(
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173 jalview.util.Comparison.GapChars, sequences[0].getSequence());
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175 textfield.setText(str);
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