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.gui;
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21 import jalview.datamodel.*;
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23 import jalview.jbgui.*;
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26 import java.awt.event.*;
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30 import javax.swing.*;
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31 import javax.swing.event.*;
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38 * @version $Revision$
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40 public class Finder extends GFinder
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44 JInternalFrame frame;
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45 SuperGroup searchGroup;
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46 Vector searchResults;
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51 * Creates a new Finder object.
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53 * @param av DOCUMENT ME!
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54 * @param ap DOCUMENT ME!
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55 * @param f DOCUMENT ME!
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57 public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)
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63 // all a big pain, but we need to wait until the frame is visible before the textfield can
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64 // obtain the focus/////////////////////////
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65 frame.addInternalFrameListener(new InternalFrameAdapter()
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67 public void internalFrameOpened(InternalFrameEvent evt)
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69 SwingUtilities.invokeLater(new Runnable()
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73 textfield.requestFocus();
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81 * @param evt DOCUMENT ME!
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83 public void internalFrameClosing(InternalFrameEvent evt)
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85 cancel_actionPerformed(null);
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94 * @param e DOCUMENT ME!
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96 public void findNext_actionPerformed(ActionEvent e)
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104 * @param e DOCUMENT ME!
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106 public void findAll_actionPerformed(ActionEvent e)
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116 * @param e DOCUMENT ME!
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118 public void cancel_actionPerformed(ActionEvent e)
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122 // if allResults is null, this effectively switches displaySearch flag in seqCanvas
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123 ap.highlightSearchResults(null);
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124 ap.idPanel.highlightSearchResults(null);
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126 // frame.setClosed(true);
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128 catch (Exception ex)
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136 * @param e DOCUMENT ME!
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138 public void createNewGroup_actionPerformed(ActionEvent e)
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140 Color[] newColors = new Color[24];
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142 for (int i = 0; i < 24; i++)
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144 newColors[i] = new Color(60, 160, 115);
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147 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
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148 String searchString = textfield.getText();
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150 searchGroup = new SuperGroup(searchString, ucs, true, true, false);
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152 for (int i = 0; i < searchResults.size(); i += 3)
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154 // its possible edits may have occurred since search was performed
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155 // account for this here
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156 SequenceI seq = av.alignment.getSequenceAt(Integer.parseInt(
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157 searchResults.elementAt(i).toString()));
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158 int startRes = seq.findIndex(Integer.parseInt(
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159 searchResults.elementAt(i + 1).toString())) - 1;
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160 int endRes = seq.findIndex(Integer.parseInt(
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161 searchResults.elementAt(i + 2).toString())) - 1;
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163 SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true,
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164 false, startRes, endRes);
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165 sg.addSequence(seq, false);
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166 av.alignment.addGroup(sg);
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167 searchGroup.addGroup(sg);
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170 ap.av.alignment.addSuperGroup(searchGroup);
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171 ap.highlightSearchResults(null);
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177 * @param findAll DOCUMENT ME!
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179 void doSearch(boolean findAll)
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181 createNewGroup.setEnabled(false);
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183 String searchString = textfield.getText().toUpperCase().trim();
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185 com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
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187 searchResults = new Vector();
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189 int[] allResults = null;
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192 String item = null;
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193 boolean found = false;
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195 ////// is the searchString a residue number?
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198 int res = Integer.parseInt(searchString);
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201 if (av.getSelectionGroup().getSize() > 0)
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203 seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
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207 seq = (Sequence) av.getAlignment().getSequenceAt(0);
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210 searchResults.add(Integer.toString(av.getAlignment().findIndex(seq)));
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211 searchResults.add(Integer.toString(seq.findIndex(res) - 1));
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212 searchResults.add(Integer.toString(seq.findIndex(res) - 1));
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214 catch (NumberFormatException ex)
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218 ///////////////////////////////////////////////
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219 Color[] newColors = new Color[24];
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221 for (int i = 0; i < 24; i++)
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223 newColors[i] = new Color(60, 160, 115);
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226 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
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228 searchGroup = new SuperGroup(searchString, ucs, true, true, false);
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230 int end = av.alignment.getHeight();
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232 SequenceGroup selection = av.getSelectionGroup();
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234 if (selection != null)
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236 if ((selection.getSize() < 1) ||
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237 ((selection.getEndRes() - selection.getStartRes()) < 2))
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243 while (!found && (seqIndex < end))
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245 seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
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247 if ((selection != null) && !selection.sequences.contains(seq))
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255 item = seq.getSequence().toUpperCase();
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257 if ((selection != null) &&
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258 (selection.getEndRes() < av.alignment.getWidth()))
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260 item = item.substring(0, selection.getEndRes() + 1);
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263 ///Shall we ignore gaps????
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264 StringBuffer noGaps = new StringBuffer();
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265 int insertCount = 0;
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266 Vector spaces = new Vector();
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268 for (int j = 0; j < item.length(); j++)
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270 if (!jalview.util.Comparison.isGap(item.charAt(j)))
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272 noGaps.append(item.charAt(j));
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273 spaces.add(new Integer(insertCount));
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281 for (int r = resIndex; r < noGaps.length(); r++)
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283 if (regex.searchFrom(noGaps.toString(), r))
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285 resIndex = regex.matchedFrom();
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287 if ((selection != null) &&
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289 Integer.parseInt(spaces.get(resIndex).toString())) < selection.getStartRes()))
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294 searchResults.add(Integer.toString(seqIndex));
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296 int sres = seq.findPosition(resIndex +
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297 Integer.parseInt(spaces.elementAt(resIndex)
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299 int eres = seq.findPosition(regex.matchedTo() - 1 +
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300 Integer.parseInt(spaces.elementAt(regex.matchedTo() -
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303 searchResults.addElement(sres + "");
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304 searchResults.addElement(eres + "");
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308 // thats enough, break and display the result
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326 Vector idMatch = new Vector();
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328 for (int id = 0; id < av.alignment.getHeight(); id++)
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330 if (regex.search(av.alignment.getSequenceAt(id).getName()))
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332 idMatch.add(av.alignment.getSequenceAt(id));
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336 if ((searchResults.size() == 0) && (idMatch.size() > 0))
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338 ap.idPanel.highlightSearchResults(idMatch);
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341 if (searchResults.size() > 0)
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343 allResults = new int[searchResults.size()];
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345 for (int i = 0; i < searchResults.size(); i++)
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347 allResults[i] = Integer.parseInt(searchResults.get(i).toString());
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350 createNewGroup.setEnabled(true);
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354 JOptionPane.showInternalMessageDialog(this, "Finished searching",
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355 null, JOptionPane.INFORMATION_MESSAGE);
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360 // if allResults is null, this effectively switches displaySearch flag in seqCanvas
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361 ap.highlightSearchResults(allResults);
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365 String message = (searchResults.size() / 3) + " matches found.";
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366 JOptionPane.showInternalMessageDialog(this, message, null,
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367 JOptionPane.INFORMATION_MESSAGE);
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