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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25 import java.awt.event.*;
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27 import jalview.datamodel.*;
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29 public class Finder extends Panel
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34 SuperGroup searchGroup;
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35 Vector searchResults;
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39 public Finder(final AlignmentPanel ap)
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47 e.printStackTrace();
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52 frame = new Frame();
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54 jalview.bin.JalviewLite.addFrame(frame, "Find", 340, 120);
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56 frame.addWindowListener(new WindowAdapter()
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58 public void windowClosing(WindowEvent evt)
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60 ap.highlightSearchResults(null);
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65 public void textfield_actionPerformed(ActionEvent e)
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70 public void findNext_actionPerformed(ActionEvent e)
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75 public void findAll_actionPerformed(ActionEvent e)
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82 public void cancel_actionPerformed(ActionEvent e)
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86 // if allResults is null, this effectively switches displaySearch flag in seqCanvas
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87 ap.highlightSearchResults(null);
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88 ap.idPanel.highlightSearchResults(null);
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89 // frame.setClosed(true);
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91 catch (Exception ex)
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95 public void createNewGroup_actionPerformed(ActionEvent e)
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97 Color[] newColors = new Color[24];
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98 for (int i = 0; i < 24; i++)
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100 newColors[i] = new Color(60, 160, 115);
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103 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
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105 String searchString = textfield.getText();
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107 searchGroup = new SuperGroup(searchString, ucs, true, true, false);
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109 for (int i = 0; i < searchResults.size(); i += 3)
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111 // its possible edits may have occurred since search was performed
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112 // account for this here
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114 SequenceI seq = av.alignment.getSequenceAt(Integer.parseInt(searchResults.
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115 elementAt(i).toString()));
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116 int startRes = seq.findIndex(Integer.parseInt(searchResults.elementAt(i +
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117 1).toString())) - 1;
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118 int endRes = seq.findIndex(Integer.parseInt(searchResults.elementAt(i + 2).
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121 SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,
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123 sg.addSequence(seq, false);
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124 av.alignment.addGroup(sg);
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125 searchGroup.addGroup(sg);
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129 ap.av.alignment.addSuperGroup(searchGroup);
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130 ap.highlightSearchResults(null);
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133 void doSearch(boolean findAll)
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135 createNewGroup.setEnabled(false);
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137 String searchString = textfield.getText().toUpperCase();
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139 com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
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141 searchResults = new Vector();
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142 int[] allResults = null;
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145 String item = null;
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146 boolean found = false;
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148 ////// is the searchString a residue number?
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151 int res = Integer.parseInt(searchString);
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154 if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)
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156 seq = (Sequence) av.getAlignment().getSequenceAt(0);
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160 seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
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163 searchResults.addElement(Integer.toString(av.getAlignment().findIndex(seq)));
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164 searchResults.addElement(String.valueOf(res));
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165 searchResults.addElement(String.valueOf(res));
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168 catch (NumberFormatException ex)
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170 ///////////////////////////////////////////////
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173 int end = av.alignment.getHeight();
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175 SequenceGroup selection = av.getSelectionGroup();
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176 if (selection != null)
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178 if (selection.getSize() < 1 ||
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179 (selection.getEndRes() - selection.getStartRes() < 2))
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185 while (!found && seqIndex < end)
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187 seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
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189 if (selection != null && !selection.sequences.contains(seq))
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196 item = seq.getSequence().toUpperCase();
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198 if (selection != null && selection.getEndRes() < av.alignment.getWidth())
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200 item = item.substring(0, selection.getEndRes() + 1);
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203 ///Shall we ignore gaps????
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204 StringBuffer noGaps = new StringBuffer();
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205 int insertCount = 0;
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206 Vector spaces = new Vector();
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208 for (int j = 0; j < item.length(); j++)
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211 if (!jalview.util.Comparison.isGap(item.charAt(j)))
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213 noGaps.append(item.charAt(j));
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214 spaces.addElement(new Integer(insertCount));
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222 for (int r = resIndex; r < noGaps.length(); r++)
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225 if (regex.searchFrom(noGaps.toString(), r))
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227 resIndex = regex.matchedFrom();
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228 if (selection != null &&
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229 (resIndex + Integer.parseInt(spaces.elementAt(resIndex).toString())) <
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230 selection.getStartRes())
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235 searchResults.addElement(Integer.toString(seqIndex));
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236 int sres = seq.findPosition(resIndex +
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237 Integer.parseInt(spaces.
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238 elementAt(resIndex).toString()));
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239 int eres = seq.findPosition(regex.matchedTo() - 1 +
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241 spaces.elementAt(regex.matchedTo() - 1).
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243 searchResults.addElement(sres + "");
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244 searchResults.addElement(eres + "");
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248 // thats enough, break and display the result
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266 Vector idMatch = new Vector();
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267 for (int id = 0; id < av.alignment.getHeight(); id++)
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269 if (regex.search(av.alignment.getSequenceAt(id).getName()))
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271 idMatch.addElement(av.alignment.getSequenceAt(id));
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275 if (searchResults.size() == 0 && idMatch.size() > 0)
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277 ap.idPanel.highlightSearchResults(idMatch);
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280 if (searchResults.size() > 0)
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282 allResults = new int[searchResults.size()];
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283 for (int i = 0; i < searchResults.size(); i++)
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285 allResults[i] = Integer.parseInt(searchResults.elementAt(i).toString());
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288 createNewGroup.setEnabled(true);
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296 // if allResults is null, this effectively switches displaySearch flag in seqCanvas
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297 ap.highlightSearchResults(allResults);
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301 String message = (searchResults.size() / 3) + " matches found.";
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302 System.out.println(message);
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307 Label jLabel1 = new Label();
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308 protected TextField textfield = new TextField();
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309 protected Button findAll = new Button();
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310 protected Button findNext = new Button();
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311 Panel jPanel1 = new Panel();
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312 GridLayout gridLayout1 = new GridLayout();
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313 protected Button createNewGroup = new Button();
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316 private void jbInit() throws Exception {
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317 jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
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318 jLabel1.setText("Find");
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319 jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
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320 this.setLayout(null);
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321 textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
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322 textfield.setText("");
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323 textfield.setBounds(new Rectangle(40, 27, 133, 21));
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324 textfield.addKeyListener(new java.awt.event.KeyAdapter() {
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325 public void keyTyped(KeyEvent e) {
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326 textfield_keyTyped(e);
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329 textfield.addActionListener(new java.awt.event.ActionListener() {
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330 public void actionPerformed(ActionEvent e) {
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331 textfield_actionPerformed(e);
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334 findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
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335 findAll.setLabel("Find all");
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336 findAll.addActionListener(new java.awt.event.ActionListener() {
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337 public void actionPerformed(ActionEvent e) {
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338 findAll_actionPerformed(e);
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341 findNext.setEnabled(false);
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342 findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
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343 findNext.setLabel("Find Next");
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344 findNext.addActionListener(new java.awt.event.ActionListener() {
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345 public void actionPerformed(ActionEvent e) {
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346 findNext_actionPerformed(e);
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349 jPanel1.setBounds(new Rectangle(180, 5, 141, 64));
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350 jPanel1.setLayout(gridLayout1);
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351 gridLayout1.setHgap(0);
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352 gridLayout1.setRows(3);
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353 gridLayout1.setVgap(2);
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354 createNewGroup.setEnabled(false);
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355 createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
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356 createNewGroup.setLabel("Create new group");
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357 createNewGroup.addActionListener(new java.awt.event.ActionListener() {
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358 public void actionPerformed(ActionEvent e) {
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359 createNewGroup_actionPerformed(e);
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362 jPanel1.add(findNext, null);
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363 jPanel1.add(findAll, null);
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364 jPanel1.add(createNewGroup, null);
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365 this.add(textfield, null);
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366 this.add(jLabel1, null);
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367 this.add(jPanel1, null);
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370 void textfield_keyTyped(KeyEvent e) {
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371 findNext.setEnabled(true);
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