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.SearchResultMatchI;
24 import jalview.datamodel.SearchResultsI;
25 import jalview.datamodel.SequenceFeature;
26 import jalview.datamodel.SequenceI;
27 import jalview.jbgui.GFinder;
28 import jalview.util.MessageManager;
29 import jalview.viewmodel.AlignmentViewport;
31 import java.awt.event.ActionEvent;
32 import java.awt.event.KeyEvent;
33 import java.util.Vector;
34 import java.util.regex.Pattern;
35 import java.util.regex.PatternSyntaxException;
37 import javax.swing.AbstractAction;
38 import javax.swing.JComponent;
39 import javax.swing.JInternalFrame;
40 import javax.swing.JLayeredPane;
41 import javax.swing.KeyStroke;
42 import javax.swing.event.InternalFrameEvent;
45 * Performs the menu option for searching the alignment, for the next or all
46 * matches. If matches are found, they are highlighted, and the user has the
47 * option to create a new feature on the alignment for the matched positions.
49 * Searches can be for a simple base sequence, or may use a regular expression.
50 * Any gaps are ignored.
55 public class Finder extends GFinder
57 private static final int HEIGHT = 110;
59 private static final int WIDTH = 340;
71 SearchResultsI searchResults;
74 * Creates a new Finder object with no associated viewport or panel.
83 * Constructor given an associated viewport and alignment panel. Constructs
84 * and displays an internal frame where the user can enter a search string.
89 public Finder(AlignmentViewport viewport, AlignmentPanel alignPanel)
94 frame = new JInternalFrame();
95 frame.setContentPane(this);
96 frame.setLayer(JLayeredPane.PALETTE_LAYER);
97 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
100 public void internalFrameClosing(InternalFrameEvent e)
106 Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
109 searchBox.requestFocus();
113 * Add a handler for the Escape key when the window has focus
115 private void addEscapeHandler()
117 getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
118 KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel");
119 getRootPane().getActionMap().put("Cancel", new AbstractAction()
122 public void actionPerformed(ActionEvent e)
124 escapeActionPerformed();
130 * Close the panel on Escape key press
132 protected void escapeActionPerformed()
139 * Performs the 'Find Next' action.
144 public void findNext_actionPerformed(ActionEvent e)
146 if (getFocusedViewport())
153 * Performs the 'Find All' action.
158 public void findAll_actionPerformed(ActionEvent e)
160 if (getFocusedViewport())
169 * do we only search a given alignment view ?
171 private boolean focusfixed;
174 * if !focusfixed and not in a desktop environment, checks that av and ap are
175 * valid. Otherwise, gets the topmost alignment window and sets av and ap
178 * @return false if no alignment window was found
180 boolean getFocusedViewport()
182 if (focusfixed || Desktop.desktop == null)
184 if (ap != null && av != null)
188 // we aren't in a desktop environment, so give up now.
191 // now checks further down the window stack to fix bug
192 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
193 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
194 for (int f = 0; f < frames.length; f++)
196 JInternalFrame frame = frames[f];
197 if (frame != null && frame instanceof AlignFrame)
199 av = ((AlignFrame) frame).viewport;
200 ap = ((AlignFrame) frame).alignPanel;
214 public void createNewGroup_actionPerformed(ActionEvent e)
216 SequenceI[] seqs = new SequenceI[searchResults.getSize()];
217 SequenceFeature[] features = new SequenceFeature[searchResults
221 for (SearchResultMatchI match : searchResults.getResults())
223 seqs[i] = match.getSequence().getDatasetSequence();
225 features[i] = new SequenceFeature(searchBox.getEditor().getItem()
227 "Search Results", null, match.getStart(), match.getEnd(),
232 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
235 ap.alignFrame.showSeqFeatures.setSelected(true);
236 av.setShowSequenceFeatures(true);
237 ap.highlightSearchResults(null);
242 * Search the alignment for the next or all matches. If 'all matches', a
243 * dialog is shown with the number of sequence ids and subsequences matched.
247 void doSearch(boolean findAll)
249 createNewGroup.setEnabled(false);
251 String searchString = searchBox.getEditor().getItem().toString().trim();
253 if (isInvalidSearchString(searchString))
257 // TODO: extend finder to match descriptions, features and annotation, and
259 // TODO: add switches to control what is searched - sequences, IDS,
260 // descriptions, features
261 jalview.analysis.Finder finder = new jalview.analysis.Finder(
262 av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
263 finder.setCaseSensitive(caseSensitive.isSelected());
264 finder.setIncludeDescription(searchDescription.isSelected());
266 finder.setFindAll(findAll);
268 finder.find(searchString); // returns true if anything was actually found
270 seqIndex = finder.getSeqIndex();
271 resIndex = finder.getResIndex();
273 searchResults = finder.getSearchResults(); // find(regex,
274 // caseSensitive.isSelected(), )
275 Vector<SequenceI> idMatch = finder.getIdMatch();
276 boolean haveResults = false;
277 // set or reset the GUI
278 if ((idMatch.size() > 0))
281 ap.getIdPanel().highlightSearchResults(idMatch);
285 ap.getIdPanel().highlightSearchResults(null);
288 if (searchResults.getSize() > 0)
291 createNewGroup.setEnabled(true);
295 searchResults = null;
298 // if allResults is null, this effectively switches displaySearch flag in
300 ap.highlightSearchResults(searchResults);
301 // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
302 // 'SelectRegion' selection
305 JvOptionPane.showInternalMessageDialog(this,
306 MessageManager.getString("label.finished_searching"), null,
307 JvOptionPane.INFORMATION_MESSAGE);
315 // then we report the matches that were found
316 String message = (idMatch.size() > 0) ? "" + idMatch.size()
318 if (searchResults != null)
320 if (idMatch.size() > 0 && searchResults.getSize() > 0)
324 message += searchResults.getSize()
325 + " subsequence matches found.";
327 JvOptionPane.showInternalMessageDialog(this, message, null,
328 JvOptionPane.INFORMATION_MESSAGE);
333 searchBox.updateCache();
337 * Displays an error dialog, and answers false, if the search string is
338 * invalid, else answers true.
340 * @param searchString
343 protected boolean isInvalidSearchString(String searchString)
345 String error = getSearchValidationError(searchString);
350 JvOptionPane.showInternalMessageDialog(this, error,
351 MessageManager.getString("label.invalid_search"), // $NON-NLS-1$
352 JvOptionPane.ERROR_MESSAGE);
357 * Returns an error message string if the search string is invalid, else
360 * Currently validation is limited to checking the string is not empty, and is
361 * a valid regular expression (simple searches for base sub-sequences will
362 * pass this test). Additional validations may be added in future if the
363 * search syntax is expanded.
365 * @param searchString
368 protected String getSearchValidationError(String searchString)
371 if (searchString == null || searchString.length() == 0)
373 error = MessageManager.getString("label.invalid_search");
377 Pattern.compile(searchString);
378 } catch (PatternSyntaxException e)
380 error = MessageManager.getString("error.invalid_regex") + ": "
381 + e.getDescription();
386 protected void closeAction()
389 searchBox.persistCache();