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.api.AlignViewportI;
24 import jalview.api.FinderI;
25 import jalview.datamodel.SearchResultMatchI;
26 import jalview.datamodel.SearchResultsI;
27 import jalview.datamodel.SequenceFeature;
28 import jalview.datamodel.SequenceI;
29 import jalview.jbgui.GFinder;
30 import jalview.util.MessageManager;
31 import jalview.viewmodel.AlignmentViewport;
33 import java.awt.Dimension;
34 import java.awt.event.ActionEvent;
35 import java.awt.event.KeyEvent;
36 import java.util.ArrayList;
37 import java.util.HashMap;
38 import java.util.List;
40 import java.util.regex.Pattern;
41 import java.util.regex.PatternSyntaxException;
43 import javax.swing.AbstractAction;
44 import javax.swing.JComponent;
45 import javax.swing.JInternalFrame;
46 import javax.swing.JLayeredPane;
47 import javax.swing.KeyStroke;
48 import javax.swing.event.InternalFrameAdapter;
49 import javax.swing.event.InternalFrameEvent;
52 * Performs the menu option for searching the alignment, for the next or all
53 * matches. If matches are found, they are highlighted, and the user has the
54 * option to create a new feature on the alignment for the matched positions.
56 * Searches can be for a simple base sequence, or may use a regular expression.
57 * Any gaps are ignored.
62 public class Finder extends GFinder
64 private static final int MIN_WIDTH = 350;
66 private static final int MIN_HEIGHT = 120;
68 private static final int MY_HEIGHT = 120;
70 private static final int MY_WIDTH = 400;
72 private AlignViewportI av;
74 private AlignmentPanel ap;
76 private JInternalFrame frame;
79 * Finder agent per viewport searched
81 private Map<AlignViewportI, FinderI> finders;
83 private SearchResultsI searchResults;
86 * true if we only search a given alignment view
88 private boolean focusfixed;
91 * Creates a new Finder object with no associated viewport or panel. Each Find
92 * or Find Next action will act on whichever viewport has focus at the time.
100 * Constructor given an associated viewport and alignment panel. Constructs
101 * and displays an internal frame where the user can enter a search string.
106 public Finder(AlignmentViewport viewport, AlignmentPanel alignPanel)
110 finders = new HashMap<>();
111 focusfixed = viewport != null;
112 frame = new JInternalFrame();
113 frame.setContentPane(this);
114 frame.setLayer(JLayeredPane.PALETTE_LAYER);
115 frame.addInternalFrameListener(
116 new InternalFrameAdapter()
119 public void internalFrameClosing(InternalFrameEvent e)
125 Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
126 MY_WIDTH, MY_HEIGHT);
127 frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
128 searchBox.requestFocus();
132 * Add a handler for the Escape key when the window has focus
134 private void addEscapeHandler()
136 getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
137 .put(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel");
138 getRootPane().getActionMap().put("Cancel", new AbstractAction()
141 public void actionPerformed(ActionEvent e)
149 * Performs the 'Find Next' action on the alignment panel with focus
152 public void findNext_actionPerformed()
154 if (getFocusedViewport())
161 * Performs the 'Find All' action on the alignment panel with focus
164 public void findAll_actionPerformed()
166 if (getFocusedViewport())
173 * if !focusfixed and not in a desktop environment, checks that av and ap are
174 * valid. Otherwise, gets the topmost alignment window and sets av and ap
177 * @return false if no alignment window was found
179 boolean getFocusedViewport()
181 if (focusfixed || Desktop.desktop == null)
183 if (ap != null && av != null)
187 // we aren't in a desktop environment, so give up now.
190 // now checks further down the window stack to fix bug
191 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
192 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
193 for (int f = 0; f < frames.length; f++)
195 JInternalFrame alignFrame = frames[f];
196 if (alignFrame != null && alignFrame instanceof AlignFrame
197 && !alignFrame.isIcon())
199 av = ((AlignFrame) alignFrame).viewport;
200 ap = ((AlignFrame) alignFrame).alignPanel;
208 * Opens a dialog that allows the user to create sequence features for the
209 * find match results.
212 public void createFeatures_actionPerformed()
214 List<SequenceI> seqs = new ArrayList<>();
215 List<SequenceFeature> features = new ArrayList<>();
217 String searchString = searchBox.getEditor().getItem().toString().trim();
218 String desc = "Search Results";
221 * assemble dataset sequences, and template new sequence features,
222 * for the amend features dialog
224 for (SearchResultMatchI match : searchResults.getResults())
226 seqs.add(match.getSequence().getDatasetSequence());
227 features.add(new SequenceFeature(searchString, desc,
229 .getStart(), match.getEnd(), desc));
232 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
236 * ensure feature display is turned on to show the new features,
237 * and remove them as highlighted regions
239 ap.alignFrame.showSeqFeatures.setSelected(true);
240 av.setShowSequenceFeatures(true);
241 ap.highlightSearchResults(null);
246 * Search the alignment for the next or all matches. If 'all matches', a
247 * dialog is shown with the number of sequence ids and subsequences matched.
251 void doSearch(boolean doFindAll)
253 createFeatures.setEnabled(false);
255 String searchString = searchBox.getUserInput().trim();
257 if (isInvalidSearchString(searchString))
261 // TODO: extend finder to match descriptions, features and annotation, and
263 // TODO: add switches to control what is searched - sequences, IDS,
264 // descriptions, features
265 FinderI finder = finders.get(av);
269 * first time we've searched this viewport
271 finder = new jalview.analysis.Finder(av);
272 finders.put(av, finder);
275 boolean isCaseSensitive = caseSensitive.isSelected();
276 boolean doSearchDescription = searchDescription.isSelected();
279 finder.findAll(searchString, isCaseSensitive, doSearchDescription);
283 finder.findNext(searchString, isCaseSensitive, doSearchDescription);
286 searchResults = finder.getSearchResults();
287 List<SequenceI> idMatch = finder.getIdMatches();
288 ap.getIdPanel().highlightSearchResults(idMatch);
290 if (searchResults.isEmpty())
292 searchResults = null;
296 createFeatures.setEnabled(true);
299 ap.highlightSearchResults(searchResults);
300 // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
301 // 'SelectRegion' selection
302 if (idMatch.isEmpty() && searchResults == null)
304 JvOptionPane.showInternalMessageDialog(this,
305 MessageManager.getString("label.finished_searching"), null,
306 JvOptionPane.INFORMATION_MESSAGE);
312 // then we report the matches that were found
313 String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
315 if (searchResults != null)
317 if (idMatch.size() > 0 && searchResults.getSize() > 0)
321 message += searchResults.getSize()
322 + " subsequence matches found.";
324 JvOptionPane.showInternalMessageDialog(this, message, null,
325 JvOptionPane.INFORMATION_MESSAGE);
328 searchBox.updateCache();
332 * Displays an error dialog, and answers false, if the search string is
333 * invalid, else answers true.
335 * @param searchString
338 protected boolean isInvalidSearchString(String searchString)
340 String error = getSearchValidationError(searchString);
345 JvOptionPane.showInternalMessageDialog(this, error,
346 MessageManager.getString("label.invalid_search"), // $NON-NLS-1$
347 JvOptionPane.ERROR_MESSAGE);
352 * Returns an error message string if the search string is invalid, else
355 * Currently validation is limited to checking the string is not empty, and is
356 * a valid regular expression (simple searches for base sub-sequences will
357 * pass this test). Additional validations may be added in future if the
358 * search syntax is expanded.
360 * @param searchString
363 protected String getSearchValidationError(String searchString)
366 if (searchString == null || searchString.length() == 0)
368 error = MessageManager.getString("label.invalid_search");
372 Pattern.compile(searchString);
373 } catch (PatternSyntaxException e)
375 error = MessageManager.getString("error.invalid_regex") + ": "
376 + e.getDescription();
381 protected void closeAction()
383 frame.setVisible(false);
385 searchBox.persistCache();
386 if (getFocusedViewport())
388 ap.alignFrame.requestFocus();