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;
32 import java.awt.Dimension;
33 import java.awt.Graphics;
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 = 150;
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 * Constructor given an associated alignment panel. Constructs and displays an
87 * internal frame where the user can enter a search string.
91 public Finder(AlignmentPanel alignPanel)
93 av = alignPanel.getAlignViewport();
95 finders = new HashMap<>();
96 frame = new JInternalFrame();
97 frame.setContentPane(this);
98 frame.setLayer(JLayeredPane.PALETTE_LAYER);
99 frame.addInternalFrameListener(
100 new InternalFrameAdapter()
103 public void internalFrameClosing(InternalFrameEvent e)
110 Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
111 MY_WIDTH, MY_HEIGHT);
112 frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
113 searchBox.requestFocus();
117 * Add a handler for the Escape key when the window has focus
119 private void addEscapeHandler()
121 getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
122 .put(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel");
123 getRootPane().getActionMap().put("Cancel", new AbstractAction()
126 public void actionPerformed(ActionEvent e)
134 * Performs the 'Find Next' action on the alignment panel with focus
137 public void findNext_actionPerformed()
139 if (getFocusedViewport())
146 * Performs the 'Find All' action on the alignment panel with focus
149 public void findAll_actionPerformed()
151 if (getFocusedViewport())
158 * if !focusfixed and not in a desktop environment, checks that av and ap are
159 * valid. Otherwise, gets the topmost alignment window and sets av and ap
160 * accordingly. Also sets the 'ignore hidden' checkbox disabled if the viewport
161 * has no hidden columns.
163 * @return false if no alignment window was found
165 boolean getFocusedViewport()
167 if (Desktop.desktop == null)
169 if (ap != null && av != null)
173 // we aren't in a desktop environment, so give up now.
176 // now checks further down the window stack to fix bug
177 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
178 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
179 for (int f = 0; f < frames.length; f++)
181 JInternalFrame alignFrame = frames[f];
182 if (alignFrame != null && alignFrame instanceof AlignFrame
183 && !alignFrame.isIcon())
185 av = ((AlignFrame) alignFrame).viewport;
186 ap = ((AlignFrame) alignFrame).alignPanel;
187 ignoreHidden.setEnabled(av.hasHiddenColumns());
195 * Opens a dialog that allows the user to create sequence features for the
196 * find match results.
199 public void createFeatures_actionPerformed()
201 List<SequenceI> seqs = new ArrayList<>();
202 List<SequenceFeature> features = new ArrayList<>();
204 String searchString = searchBox.getEditor().getItem().toString().trim();
205 String desc = "Search Results";
208 * assemble dataset sequences, and template new sequence features,
209 * for the amend features dialog
211 for (SearchResultMatchI match : searchResults.getResults())
213 seqs.add(match.getSequence().getDatasetSequence());
214 features.add(new SequenceFeature(searchString, desc,
216 .getStart(), match.getEnd(), desc));
219 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
223 * ensure feature display is turned on to show the new features,
224 * and remove them as highlighted regions
226 ap.alignFrame.showSeqFeatures.setSelected(true);
227 av.setShowSequenceFeatures(true);
228 ap.highlightSearchResults(null);
233 * Search the alignment for the next or all matches. If 'all matches', a
234 * dialog is shown with the number of sequence ids and subsequences matched.
238 void doSearch(boolean doFindAll)
240 createFeatures.setEnabled(false);
242 String searchString = searchBox.getUserInput().trim();
244 if (isInvalidSearchString(searchString))
248 // TODO: extend finder to match descriptions, features and annotation, and
250 // TODO: add switches to control what is searched - sequences, IDS,
251 // descriptions, features
252 FinderI finder = finders.get(av);
256 * first time we've searched this viewport
258 finder = new jalview.analysis.Finder(av);
259 finders.put(av, finder);
262 boolean isCaseSensitive = caseSensitive.isSelected();
263 boolean doSearchDescription = searchDescription.isSelected();
264 boolean skipHidden = ignoreHidden.isSelected();
267 finder.findAll(searchString, isCaseSensitive, doSearchDescription,
272 finder.findNext(searchString, isCaseSensitive, doSearchDescription,
276 searchResults = finder.getSearchResults();
277 List<SequenceI> idMatch = finder.getIdMatches();
278 ap.getIdPanel().highlightSearchResults(idMatch);
280 if (searchResults.isEmpty())
282 searchResults = null;
286 createFeatures.setEnabled(true);
289 ap.highlightSearchResults(searchResults);
290 // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
291 // 'SelectRegion' selection
292 if (idMatch.isEmpty() && searchResults == null)
294 JvOptionPane.showInternalMessageDialog(this,
295 MessageManager.getString("label.finished_searching"), null,
296 JvOptionPane.INFORMATION_MESSAGE);
302 // then we report the matches that were found
303 String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
305 if (searchResults != null)
307 if (idMatch.size() > 0 && searchResults.getCount() > 0)
311 message += searchResults.getCount()
312 + " subsequence matches found.";
314 JvOptionPane.showInternalMessageDialog(this, message, null,
315 JvOptionPane.INFORMATION_MESSAGE);
318 searchBox.updateCache();
322 * Displays an error dialog, and answers false, if the search string is
323 * invalid, else answers true.
325 * @param searchString
328 protected boolean isInvalidSearchString(String searchString)
330 String error = getSearchValidationError(searchString);
335 JvOptionPane.showInternalMessageDialog(this, error,
336 MessageManager.getString("label.invalid_search"), // $NON-NLS-1$
337 JvOptionPane.ERROR_MESSAGE);
342 * Returns an error message string if the search string is invalid, else
345 * Currently validation is limited to checking the string is not empty, and is
346 * a valid regular expression (simple searches for base sub-sequences will
347 * pass this test). Additional validations may be added in future if the
348 * search syntax is expanded.
350 * @param searchString
353 protected String getSearchValidationError(String searchString)
356 if (searchString == null || searchString.length() == 0)
358 error = MessageManager.getString("label.invalid_search");
362 Pattern.compile(searchString);
363 } catch (PatternSyntaxException e)
365 error = MessageManager.getString("error.invalid_regex") + ": "
366 + e.getDescription();
371 protected void closeAction()
373 frame.setVisible(false);
375 searchBox.persistCache();
376 if (getFocusedViewport())
378 ap.alignFrame.requestFocus();
383 protected void paintComponent(Graphics g)
386 * enable 'hidden regions' option only if
387 * 'top' viewport has hidden columns
389 getFocusedViewport();
390 super.paintComponent(g);