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 implements ActionListener
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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 actionPerformed(ActionEvent evt)
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67 if (evt.getSource() == textfield)
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70 else if (evt.getSource() == findNext)
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73 else if (evt.getSource() == findAll)
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79 else if(evt.getSource() == createNewGroup)
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80 createNewGroup_actionPerformed();
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84 public void createNewGroup_actionPerformed()
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86 Color[] newColors = new Color[24];
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87 for (int i = 0; i < 24; i++)
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89 newColors[i] = new Color(60, 160, 115);
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92 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
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94 String searchString = textfield.getText();
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96 searchGroup = new SuperGroup(searchString, ucs, true, true, false);
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98 for (int i = 0; i < searchResults.size(); i += 3)
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100 // its possible edits may have occurred since search was performed
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101 // account for this here
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103 SequenceI seq = av.alignment.getSequenceAt(Integer.parseInt(searchResults.
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104 elementAt(i).toString()));
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105 int startRes = seq.findIndex(Integer.parseInt(searchResults.elementAt(i +
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106 1).toString())) - 1;
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107 int endRes = seq.findIndex(Integer.parseInt(searchResults.elementAt(i + 2).
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110 SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,
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112 sg.addSequence(seq, false);
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113 av.alignment.addGroup(sg);
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114 searchGroup.addGroup(sg);
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118 ap.av.alignment.addSuperGroup(searchGroup);
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119 ap.highlightSearchResults(null);
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122 void doSearch(boolean findAll)
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124 createNewGroup.setEnabled(false);
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126 String searchString = textfield.getText().toUpperCase();
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128 com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
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130 searchResults = new Vector();
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131 int[] allResults = null;
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134 String item = null;
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135 boolean found = false;
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137 ////// is the searchString a residue number?
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140 int res = Integer.parseInt(searchString);
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143 if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)
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145 seq = (Sequence) av.getAlignment().getSequenceAt(0);
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149 seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
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152 searchResults.addElement(Integer.toString(av.getAlignment().findIndex(seq)));
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153 searchResults.addElement(String.valueOf(res));
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154 searchResults.addElement(String.valueOf(res));
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157 catch (NumberFormatException ex)
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159 ///////////////////////////////////////////////
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162 int end = av.alignment.getHeight();
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164 SequenceGroup selection = av.getSelectionGroup();
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165 if (selection != null)
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167 if (selection.getSize() < 1 ||
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168 (selection.getEndRes() - selection.getStartRes() < 2))
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174 while (!found && seqIndex < end)
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176 seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
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178 if (selection != null && !selection.sequences.contains(seq))
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185 item = seq.getSequence().toUpperCase();
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187 if (selection != null && selection.getEndRes() < av.alignment.getWidth())
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189 item = item.substring(0, selection.getEndRes() + 1);
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192 ///Shall we ignore gaps????
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193 StringBuffer noGaps = new StringBuffer();
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194 int insertCount = 0;
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195 Vector spaces = new Vector();
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197 for (int j = 0; j < item.length(); j++)
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200 if (!jalview.util.Comparison.isGap(item.charAt(j)))
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202 noGaps.append(item.charAt(j));
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203 spaces.addElement(new Integer(insertCount));
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211 for (int r = resIndex; r < noGaps.length(); r++)
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214 if (regex.searchFrom(noGaps.toString(), r))
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216 resIndex = regex.matchedFrom();
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217 if (selection != null &&
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218 (resIndex + Integer.parseInt(spaces.elementAt(resIndex).toString())) <
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219 selection.getStartRes())
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224 searchResults.addElement(Integer.toString(seqIndex));
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225 int sres = seq.findPosition(resIndex +
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226 Integer.parseInt(spaces.
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227 elementAt(resIndex).toString()));
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228 int eres = seq.findPosition(regex.matchedTo() - 1 +
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230 spaces.elementAt(regex.matchedTo() - 1).
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232 searchResults.addElement(sres + "");
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233 searchResults.addElement(eres + "");
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237 // thats enough, break and display the result
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255 Vector idMatch = new Vector();
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256 for (int id = 0; id < av.alignment.getHeight(); id++)
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258 if (regex.search(av.alignment.getSequenceAt(id).getName()))
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260 idMatch.addElement(av.alignment.getSequenceAt(id));
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264 if (searchResults.size() == 0 && idMatch.size() > 0)
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266 ap.idPanel.highlightSearchResults(idMatch);
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269 if (searchResults.size() > 0)
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271 allResults = new int[searchResults.size()];
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272 for (int i = 0; i < searchResults.size(); i++)
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274 allResults[i] = Integer.parseInt(searchResults.elementAt(i).toString());
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277 createNewGroup.setEnabled(true);
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285 // if allResults is null, this effectively switches displaySearch flag in seqCanvas
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286 ap.highlightSearchResults(allResults);
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290 String message = (searchResults.size() / 3) + " matches found.";
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291 System.out.println(message);
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296 Label jLabel1 = new Label();
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297 protected TextField textfield = new TextField();
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298 protected Button findAll = new Button();
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299 protected Button findNext = new Button();
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300 Panel jPanel1 = new Panel();
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301 GridLayout gridLayout1 = new GridLayout();
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302 protected Button createNewGroup = new Button();
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305 private void jbInit() throws Exception {
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306 jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
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307 jLabel1.setText("Find");
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308 jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
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309 this.setLayout(null);
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310 textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
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311 textfield.setText("");
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312 textfield.setBounds(new Rectangle(40, 27, 133, 21));
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313 textfield.addKeyListener(new java.awt.event.KeyAdapter() {
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314 public void keyTyped(KeyEvent e) {
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315 textfield_keyTyped(e);
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318 textfield.addActionListener(this);
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319 findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
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320 findAll.setLabel("Find all");
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321 findAll.addActionListener(this);
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322 findNext.setEnabled(false);
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323 findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
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324 findNext.setLabel("Find Next");
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325 findNext.addActionListener(this);
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326 jPanel1.setBounds(new Rectangle(180, 5, 141, 64));
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327 jPanel1.setLayout(gridLayout1);
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328 gridLayout1.setHgap(0);
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329 gridLayout1.setRows(3);
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330 gridLayout1.setVgap(2);
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331 createNewGroup.setEnabled(false);
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332 createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
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333 createNewGroup.setLabel("Create new group");
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334 createNewGroup.addActionListener(this);
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335 jPanel1.add(findNext, null);
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336 jPanel1.add(findAll, null);
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337 jPanel1.add(createNewGroup, null);
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338 this.add(textfield, null);
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339 this.add(jLabel1, null);
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340 this.add(jPanel1, null);
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343 void textfield_keyTyped(KeyEvent e) {
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344 findNext.setEnabled(true);
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