2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.datamodel.SearchResultsI;
24 import jalview.datamodel.SequenceFeature;
25 import jalview.datamodel.SequenceI;
26 import jalview.jbgui.GFinder;
27 import jalview.util.MessageManager;
28 import jalview.viewmodel.AlignmentViewport;
30 import java.awt.event.ActionEvent;
31 import java.awt.event.KeyEvent;
32 import java.util.Vector;
33 import java.util.regex.Pattern;
34 import java.util.regex.PatternSyntaxException;
36 import javax.swing.AbstractAction;
37 import javax.swing.JComponent;
38 import javax.swing.JInternalFrame;
39 import javax.swing.JLayeredPane;
40 import javax.swing.JOptionPane;
41 import javax.swing.KeyStroke;
44 * Performs the menu option for searching the alignment, for the next or all
45 * matches. If matches are found, they are highlighted, and the user has the
46 * option to create a new feature on the alignment for the matched positions.
48 * Searches can be for a simple base sequence, or may use a regular expression.
49 * Any gaps are ignored.
54 public class Finder extends GFinder
56 private static final int HEIGHT = 110;
58 private static final int WIDTH = 340;
70 SearchResultsI searchResults;
73 * Creates a new Finder object with no associated viewport or panel.
82 * Constructor given an associated viewport and alignment panel. Constructs
83 * and displays an internal frame where the user can enter a search string.
88 public Finder(AlignmentViewport viewport, AlignmentPanel alignPanel)
93 frame = new JInternalFrame();
94 frame.setContentPane(this);
95 frame.setLayer(JLayeredPane.PALETTE_LAYER);
97 Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
100 textfield.requestFocus();
104 * Add a handler for the Escape key when the window has focus
106 private void addEscapeHandler()
108 getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
109 KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel");
110 getRootPane().getActionMap().put("Cancel", new AbstractAction()
113 public void actionPerformed(ActionEvent e)
115 escapeActionPerformed();
121 * Close the panel on Escape key press
123 protected void escapeActionPerformed()
130 * Performs the 'Find Next' action.
135 public void findNext_actionPerformed(ActionEvent e)
137 if (getFocusedViewport())
144 * Performs the 'Find All' action.
149 public void findAll_actionPerformed(ActionEvent e)
151 if (getFocusedViewport())
160 * do we only search a given alignment view ?
162 private boolean focusfixed;
165 * if !focusfixed and not in a desktop environment, checks that av and ap are
166 * valid. Otherwise, gets the topmost alignment window and sets av and ap
169 * @return false if no alignment window was found
171 boolean getFocusedViewport()
173 if (focusfixed || Desktop.desktop == null)
175 if (ap != null && av != null)
179 // we aren't in a desktop environment, so give up now.
182 // now checks further down the window stack to fix bug
183 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
184 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
185 for (int f = 0; f < frames.length; f++)
187 JInternalFrame frame = frames[f];
188 if (frame != null && frame instanceof AlignFrame)
190 av = ((AlignFrame) frame).viewport;
191 ap = ((AlignFrame) frame).alignPanel;
205 public void createNewGroup_actionPerformed(ActionEvent e)
207 SequenceI[] seqs = new SequenceI[searchResults.getSize()];
208 SequenceFeature[] features = new SequenceFeature[searchResults
211 for (int i = 0; i < searchResults.getSize(); i++)
213 seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();
215 features[i] = new SequenceFeature(textfield.getText().trim(),
216 "Search Results", null, searchResults.getResultStart(i),
217 searchResults.getResultEnd(i), "Search Results");
220 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
223 ap.alignFrame.showSeqFeatures.setSelected(true);
224 av.setShowSequenceFeatures(true);
225 ap.highlightSearchResults(null);
230 * Search the alignment for the next or all matches. If 'all matches', a
231 * dialog is shown with the number of sequence ids and subsequences matched.
235 void doSearch(boolean findAll)
237 createNewGroup.setEnabled(false);
239 String searchString = textfield.getText().trim();
241 if (isInvalidSearchString(searchString))
245 // TODO: extend finder to match descriptions, features and annotation, and
247 // TODO: add switches to control what is searched - sequences, IDS,
248 // descriptions, features
249 jalview.analysis.Finder finder = new jalview.analysis.Finder(
250 av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
251 finder.setCaseSensitive(caseSensitive.isSelected());
252 finder.setIncludeDescription(searchDescription.isSelected());
254 finder.setFindAll(findAll);
256 finder.find(searchString); // returns true if anything was actually found
258 seqIndex = finder.getSeqIndex();
259 resIndex = finder.getResIndex();
261 searchResults = finder.getSearchResults(); // find(regex,
262 // caseSensitive.isSelected(), )
263 Vector<SequenceI> idMatch = finder.getIdMatch();
264 boolean haveResults = false;
265 // set or reset the GUI
266 if ((idMatch.size() > 0))
269 ap.getIdPanel().highlightSearchResults(idMatch);
273 ap.getIdPanel().highlightSearchResults(null);
276 if (searchResults.getSize() > 0)
279 createNewGroup.setEnabled(true);
283 searchResults = null;
286 // if allResults is null, this effectively switches displaySearch flag in
288 ap.highlightSearchResults(searchResults);
289 // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
290 // 'SelectRegion' selection
293 JOptionPane.showInternalMessageDialog(this,
294 MessageManager.getString("label.finished_searching"), null,
295 JOptionPane.INFORMATION_MESSAGE);
303 // then we report the matches that were found
304 String message = (idMatch.size() > 0) ? "" + idMatch.size()
306 if (searchResults != null)
308 if (idMatch.size() > 0 && searchResults.getSize() > 0)
312 message += searchResults.getSize()
313 + " subsequence matches found.";
315 JOptionPane.showInternalMessageDialog(this, message, null,
316 JOptionPane.INFORMATION_MESSAGE);
325 * Displays an error dialog, and answers false, if the search string is
326 * invalid, else answers true.
328 * @param searchString
331 protected boolean isInvalidSearchString(String searchString)
333 String error = getSearchValidationError(searchString);
338 JOptionPane.showInternalMessageDialog(this, error,
339 MessageManager.getString("label.invalid_search"), // $NON-NLS-1$
340 JOptionPane.ERROR_MESSAGE);
345 * Returns an error message string if the search string is invalid, else
348 * Currently validation is limited to checking the string is not empty, and is
349 * a valid regular expression (simple searches for base sub-sequences will
350 * pass this test). Additional validations may be added in future if the
351 * search syntax is expanded.
353 * @param searchString
356 protected String getSearchValidationError(String searchString)
359 if (searchString == null || searchString.length() == 0)
361 error = MessageManager.getString("label.invalid_search");
365 Pattern.compile(searchString);
366 } catch (PatternSyntaxException e)
368 error = MessageManager.getString("error.invalid_regex") + ": "
369 + e.getDescription();