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 true, MY_WIDTH, MY_HEIGHT, true, true);
112 searchBox.getComponent().requestFocus();
116 * Add a handler for the Escape key when the window has focus
118 private void addEscapeHandler()
120 getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
121 .put(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel");
122 getRootPane().getActionMap().put("Cancel", new AbstractAction()
125 public void actionPerformed(ActionEvent e)
133 * Performs the 'Find Next' action on the alignment panel with focus
136 public void findNext_actionPerformed()
138 if (getFocusedViewport())
145 * Performs the 'Find All' action on the alignment panel with focus
148 public void findAll_actionPerformed()
150 if (getFocusedViewport())
157 * if !focusfixed and not in a desktop environment, checks that av and ap are
158 * valid. Otherwise, gets the topmost alignment window and sets av and ap
159 * accordingly. Also sets the 'ignore hidden' checkbox disabled if the viewport
160 * has no hidden columns.
162 * @return false if no alignment window was found
164 boolean getFocusedViewport()
166 if (Desktop.desktop == null)
168 if (ap != null && av != null)
172 // we aren't in a desktop environment, so give up now.
175 // now checks further down the window stack to fix bug
176 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
177 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
178 for (int f = 0; f < frames.length; f++)
180 JInternalFrame alignFrame = frames[f];
181 if (alignFrame != null && alignFrame instanceof AlignFrame
182 && !alignFrame.isIcon())
184 av = ((AlignFrame) alignFrame).viewport;
185 ap = ((AlignFrame) alignFrame).alignPanel;
186 ignoreHidden.setEnabled(av.hasHiddenColumns());
194 * Opens a dialog that allows the user to create sequence features for the
198 public void createFeatures_actionPerformed()
200 if (searchResults.isEmpty())
202 return; // shouldn't happen
204 List<SequenceI> seqs = new ArrayList<>();
205 List<SequenceFeature> features = new ArrayList<>();
207 String searchString = searchBox.getUserInput();
208 String desc = "Search Results";
211 * assemble dataset sequences, and template new sequence features,
212 * for the amend features dialog
214 for (SearchResultMatchI match : searchResults.getResults())
216 seqs.add(match.getSequence().getDatasetSequence());
217 features.add(new SequenceFeature(searchString, desc, match.getStart(),
218 match.getEnd(), desc));
221 new FeatureEditor(ap, seqs, features, true).showDialog();
225 * Search the alignment for the next or all matches. If 'all matches', a
226 * dialog is shown with the number of sequence ids and subsequences matched.
230 void doSearch(boolean doFindAll)
232 createFeatures.setEnabled(false);
234 String searchString = searchBox.getUserInput();
236 if (isInvalidSearchString(searchString))
240 // TODO: extend finder to match descriptions, features and annotation, and
242 // TODO: add switches to control what is searched - sequences, IDS,
243 // descriptions, features
244 FinderI finder = finders.get(av);
248 * first time we've searched this viewport
250 finder = new jalview.analysis.Finder(av);
251 finders.put(av, finder);
254 boolean isCaseSensitive = caseSensitive.isSelected();
255 boolean doSearchDescription = searchDescription.isSelected();
256 boolean skipHidden = ignoreHidden.isSelected();
259 finder.findAll(searchString, isCaseSensitive, doSearchDescription,
264 finder.findNext(searchString, isCaseSensitive, doSearchDescription,
268 searchResults = finder.getSearchResults();
269 List<SequenceI> idMatch = finder.getIdMatches();
270 ap.getIdPanel().highlightSearchResults(idMatch);
272 if (searchResults.isEmpty())
274 searchResults = null;
278 createFeatures.setEnabled(true);
281 searchBox.updateCache();
283 ap.highlightSearchResults(searchResults);
284 // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
285 // 'SelectRegion' selection
286 if (idMatch.isEmpty() && searchResults == null)
288 JvOptionPane.showInternalMessageDialog(this,
289 MessageManager.getString("label.finished_searching"), null,
290 JvOptionPane.PLAIN_MESSAGE);
296 // then we report the matches that were found
297 String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
299 if (searchResults != null)
301 if (idMatch.size() > 0 && searchResults.getCount() > 0)
305 message += searchResults.getCount()
306 + " subsequence matches found.";
308 JvOptionPane.showInternalMessageDialog(this, message, null,
309 JvOptionPane.PLAIN_MESSAGE);
315 * Displays an error dialog, and answers false, if the search string is
316 * invalid, else answers true.
318 * @param searchString
321 protected boolean isInvalidSearchString(String searchString)
323 String error = getSearchValidationError(searchString);
328 JvOptionPane.showInternalMessageDialog(this, error,
329 MessageManager.getString("label.invalid_search"), // $NON-NLS-1$
330 JvOptionPane.ERROR_MESSAGE);
335 * Returns an error message string if the search string is invalid, else
338 * Currently validation is limited to checking the string is not empty, and is
339 * a valid regular expression (simple searches for base sub-sequences will
340 * pass this test). Additional validations may be added in future if the
341 * search syntax is expanded.
343 * @param searchString
346 protected String getSearchValidationError(String searchString)
349 if (searchString == null || searchString.length() == 0)
351 error = MessageManager.getString("label.invalid_search");
355 Pattern.compile(searchString);
356 } catch (PatternSyntaxException e)
358 error = MessageManager.getString("error.invalid_regex") + ": "
359 + e.getDescription();
364 protected void closeAction()
366 frame.setVisible(false);
368 searchBox.persistCache();
369 if (getFocusedViewport())
371 ap.alignFrame.requestFocus();
376 protected void paintComponent(Graphics g)
379 * enable 'hidden regions' option only if
380 * 'top' viewport has hidden columns
382 getFocusedViewport();
383 super.paintComponent(g);