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 java.awt.Dimension;
24 import java.awt.event.ActionEvent;
25 import java.awt.event.FocusAdapter;
26 import java.awt.event.FocusEvent;
27 import java.awt.event.KeyEvent;
28 import java.util.ArrayList;
29 import java.util.HashMap;
30 import java.util.List;
31 import java.util.Locale;
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.KeyStroke;
41 import javax.swing.event.InternalFrameAdapter;
42 import javax.swing.event.InternalFrameEvent;
44 import jalview.api.AlignViewportI;
45 import jalview.api.FinderI;
46 import jalview.datamodel.SearchResultMatchI;
47 import jalview.datamodel.SearchResultsI;
48 import jalview.datamodel.SequenceFeature;
49 import jalview.datamodel.SequenceI;
50 import jalview.jbgui.GFinder;
51 import jalview.util.MessageManager;
54 * Performs the menu option for searching the alignment, for the next or all
55 * matches. If matches are found, they are highlighted, and the user has the
56 * option to create a new feature on the alignment for the matched positions.
58 * Searches can be for a simple base sequence, or may use a regular expression.
59 * Any gaps are ignored.
64 public class Finder extends GFinder
66 private static final int MIN_WIDTH = 350;
68 private static final int MIN_HEIGHT = 120;
70 private static final int MY_HEIGHT = 150;
72 private static final int MY_WIDTH = 400;
74 private AlignViewportI av;
76 private AlignmentPanel ap;
78 private JInternalFrame frame;
81 * Finder agent per viewport searched
83 private Map<AlignViewportI, FinderI> finders;
85 private SearchResultsI searchResults;
88 * true if Finder always acts on the same alignment,
89 * false if it acts on the alignment with focus
91 private boolean focusFixed;
94 * Constructor given an associated alignment panel. Constructs and displays an
95 * internal frame where the user can enter a search string. The Finder may
96 * have 'fixed focus' (always act the panel for which it is constructed), or
97 * not (acts on the alignment that has focus). An optional 'scope' may be
98 * added to be shown in the title of the Finder frame.
104 public Finder(AlignmentPanel alignPanel, boolean fixedFocus, String scope)
106 av = alignPanel.getAlignViewport();
108 focusFixed = fixedFocus;
109 finders = new HashMap<>();
110 frame = new JInternalFrame();
111 frame.setContentPane(this);
112 frame.setLayer(JLayeredPane.PALETTE_LAYER);
113 frame.addInternalFrameListener(new InternalFrameAdapter()
116 public void internalFrameClosing(InternalFrameEvent e)
121 frame.addFocusListener(new FocusAdapter()
124 public void focusGained(FocusEvent e)
127 * ensure 'ignore hidden columns' is only enabled
128 * if the alignment with focus has hidden columns
130 getFocusedViewport();
136 String title = MessageManager.getString("label.find");
139 title += " " + scope;
141 Desktop.addInternalFrame(frame, title, MY_WIDTH, MY_HEIGHT);
142 frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
143 searchBox.getComponent().requestFocus();
147 * Add a handler for the Escape key when the window has focus
149 private void addEscapeHandler()
151 getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
152 .put(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel");
153 getRootPane().getActionMap().put("Cancel", new AbstractAction()
156 public void actionPerformed(ActionEvent e)
164 * Performs the 'Find Next' action on the alignment panel with focus
167 public void findNext_actionPerformed()
169 if (getFocusedViewport())
176 * Performs the 'Find All' action on the alignment panel with focus
179 public void findAll_actionPerformed()
181 if (getFocusedViewport())
188 * if !focusfixed and not in a desktop environment, checks that av and ap are
189 * valid. Otherwise, gets the topmost alignment window and sets av and ap
190 * accordingly. Also sets the 'ignore hidden' checkbox disabled if the
191 * viewport has no hidden columns.
193 * @return false if no alignment window was found
195 boolean getFocusedViewport()
197 if (focusFixed || Desktop.desktop == null)
199 if (ap != null && av != null)
201 ignoreHidden.setEnabled(av.hasHiddenColumns());
204 // we aren't in a desktop environment, so give up now.
207 // now checks further down the window stack to fix bug
208 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
209 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
210 for (int f = 0; f < frames.length; f++)
212 JInternalFrame alignFrame = frames[f];
213 if (alignFrame != null && alignFrame instanceof AlignFrame
214 && !alignFrame.isIcon())
216 av = ((AlignFrame) alignFrame).viewport;
217 ap = ((AlignFrame) alignFrame).alignPanel;
218 ignoreHidden.setEnabled(av.hasHiddenColumns());
226 * Opens a dialog that allows the user to create sequence features for the
230 public void createFeatures_actionPerformed()
232 if (searchResults.isEmpty())
234 return; // shouldn't happen
236 List<SequenceI> seqs = new ArrayList<>();
237 List<SequenceFeature> features = new ArrayList<>();
239 String searchString = searchBox.getUserInput();
240 String desc = "Search Results";
243 * assemble dataset sequences, and template new sequence features,
244 * for the amend features dialog
246 for (SearchResultMatchI match : searchResults.getResults())
248 seqs.add(match.getSequence().getDatasetSequence());
249 features.add(new SequenceFeature(searchString, desc, match.getStart(),
250 match.getEnd(), desc));
253 new FeatureEditor(ap, seqs, features, true).showDialog();
257 protected void copyToClipboard_actionPerformed()
259 if (searchResults.isEmpty())
261 return; // shouldn't happen
263 // assume viewport controller has same searchResults as we do...
264 ap.alignFrame.avc.copyHighlightedRegionsToClipboard();
268 * Search the alignment for the next or all matches. If 'all matches', a
269 * dialog is shown with the number of sequence ids and subsequences matched.
273 void doSearch(boolean doFindAll)
275 createFeatures.setEnabled(false);
276 copyToClipboard.setEnabled(false);
278 String searchString = searchBox.getUserInput();
280 if (isInvalidSearchString(searchString))
284 // TODO: extend finder to match descriptions, features and annotation, and
286 // TODO: add switches to control what is searched - sequences, IDS,
287 // descriptions, features
288 FinderI finder = finders.get(av);
292 * first time we've searched this viewport
294 finder = new jalview.analysis.Finder(av);
295 finders.put(av, finder);
297 finder.setFeatureRenderer(ap.getFeatureRenderer());
299 boolean isCaseSensitive = caseSensitive.isSelected();
300 boolean doSearchDescription = searchDescription.isSelected();
301 boolean doSearchfeatures = searchFeatures.isSelected();
302 boolean skipHidden = ignoreHidden.isSelected();
305 finder.findAll(searchString, isCaseSensitive, doSearchDescription,
306 doSearchfeatures, skipHidden);
310 finder.findNext(searchString, isCaseSensitive, doSearchDescription,
311 doSearchfeatures, skipHidden);
314 searchResults = finder.getSearchResults();
315 List<SequenceI> idMatch = finder.getIdMatches();
316 ap.getIdPanel().highlightSearchResults(idMatch);
318 if (searchResults.isEmpty())
320 searchResults = null;
324 createFeatures.setEnabled(true);
325 copyToClipboard.setEnabled(true);
328 searchBox.updateCache();
330 ap.highlightSearchResults(searchResults);
331 // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
332 // 'SelectRegion' selection
333 if (idMatch.isEmpty() && searchResults == null)
335 JvOptionPane.showInternalMessageDialog(this,
336 MessageManager.getString("label.finished_searching"), null,
337 JvOptionPane.PLAIN_MESSAGE);
343 // then we report the matches that were found
344 StringBuilder message = new StringBuilder();
345 if (idMatch.size() > 0)
347 message.append(idMatch.size()).append(" IDs");
349 if (searchResults != null)
351 if (idMatch.size() > 0 && searchResults.getCount() > 0)
353 message.append(" ").append(MessageManager.getString("label.and")
354 .toLowerCase(Locale.ROOT)).append(" ");
356 message.append(MessageManager.formatMessage(
357 "label.subsequence_matches_found",
358 searchResults.getCount()));
360 JvOptionPane.showInternalMessageDialog(this, message.toString(),
361 null, JvOptionPane.INFORMATION_MESSAGE);
367 * Displays an error dialog, and answers false, if the search string is
368 * invalid, else answers true.
370 * @param searchString
373 protected boolean isInvalidSearchString(String searchString)
375 String error = getSearchValidationError(searchString);
380 JvOptionPane.showInternalMessageDialog(this, error,
381 MessageManager.getString("label.invalid_search"), // $NON-NLS-1$
382 JvOptionPane.ERROR_MESSAGE);
387 * Returns an error message string if the search string is invalid, else
390 * Currently validation is limited to checking the string is not empty, and is
391 * a valid regular expression (simple searches for base sub-sequences will
392 * pass this test). Additional validations may be added in future if the
393 * search syntax is expanded.
395 * @param searchString
398 protected String getSearchValidationError(String searchString)
401 if (searchString == null || searchString.length() == 0)
403 error = MessageManager.getString("label.invalid_search");
407 Pattern.compile(searchString);
408 } catch (PatternSyntaxException e)
410 error = MessageManager.getString("error.invalid_regex") + ": "
411 + e.getDescription();
416 protected void closeAction()
418 frame.setVisible(false);
420 searchBox.persistCache();
421 if (getFocusedViewport())
423 ap.alignFrame.requestFocus();