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.ArrayList;
34 import java.util.List;
35 import java.util.Vector;
36 import java.util.regex.Pattern;
37 import java.util.regex.PatternSyntaxException;
39 import javax.swing.AbstractAction;
40 import javax.swing.JComponent;
41 import javax.swing.JInternalFrame;
42 import javax.swing.JLayeredPane;
43 import javax.swing.KeyStroke;
44 import javax.swing.event.InternalFrameEvent;
47 * Performs the menu option for searching the alignment, for the next or all
48 * matches. If matches are found, they are highlighted, and the user has the
49 * option to create a new feature on the alignment for the matched positions.
51 * Searches can be for a simple base sequence, or may use a regular expression.
52 * Any gaps are ignored.
57 public class Finder extends GFinder
59 private static final int MY_HEIGHT = 120;
61 private static final int MY_WIDTH = 400;
67 private static final int MIN_WIDTH = 350;
69 private static final int MIN_HEIGHT = 120;
77 SearchResultsI searchResults;
80 * Creates a new Finder object with no associated viewport or panel.
89 * Constructor given an associated viewport and alignment panel. Constructs
90 * and displays an internal frame where the user can enter a search string.
95 public Finder(AlignmentViewport viewport, AlignmentPanel alignPanel)
100 frame = new JInternalFrame();
101 frame.setContentPane(this);
102 frame.setLayer(JLayeredPane.PALETTE_LAYER);
103 frame.addInternalFrameListener(
104 new javax.swing.event.InternalFrameAdapter()
107 public void internalFrameClosing(InternalFrameEvent e)
113 Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
114 true, MY_WIDTH, MY_HEIGHT, true, true);
115 searchBox.getComponent().requestFocus();
119 * Add a handler for the Escape key when the window has focus
121 private void addEscapeHandler()
123 getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
124 .put(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel");
125 getRootPane().getActionMap().put("Cancel", new AbstractAction()
128 public void actionPerformed(ActionEvent e)
136 * Performs the 'Find Next' action.
141 public void findNext_actionPerformed(ActionEvent e)
143 if (getFocusedViewport())
150 * Performs the 'Find All' action.
155 public void findAll_actionPerformed(ActionEvent e)
157 if (getFocusedViewport())
166 * do we only search a given alignment view ?
168 private boolean focusfixed;
171 * if !focusfixed and not in a desktop environment, checks that av and ap are
172 * valid. Otherwise, gets the topmost alignment window and sets av and ap
175 * @return false if no alignment window was found
177 boolean getFocusedViewport()
179 if (focusfixed || Desktop.desktop == null)
181 if (ap != null && av != null)
185 // we aren't in a desktop environment, so give up now.
188 // now checks further down the window stack to fix bug
189 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
190 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
191 for (int f = 0; f < frames.length; f++)
193 JInternalFrame alignFrame = frames[f];
194 if (alignFrame != null && alignFrame instanceof AlignFrame)
196 av = ((AlignFrame) alignFrame).viewport;
197 ap = ((AlignFrame) alignFrame).alignPanel;
205 * Opens a dialog that allows the user to create sequence features for the
209 public void createFeatures_actionPerformed()
211 if (searchResults.isEmpty())
213 return; // shouldn't happen
215 List<SequenceI> seqs = new ArrayList<SequenceI>();
216 List<SequenceFeature> features = new ArrayList<SequenceFeature>();
218 String searchString = searchBox.getUserInput();
219 String desc = "Search Results";
222 * assemble dataset sequences, and template new sequence features,
223 * for the amend features dialog
225 for (SearchResultMatchI match : searchResults.getResults())
227 seqs.add(match.getSequence().getDatasetSequence());
228 features.add(new SequenceFeature(searchString, desc, match.getStart(),
229 match.getEnd(), desc));
232 new FeatureEditor(ap, seqs, features, true).showDialog();
236 * Search the alignment for the next or all matches. If 'all matches', a
237 * dialog is shown with the number of sequence ids and subsequences matched.
241 void doSearch(boolean doFindAll)
243 createFeatures.setEnabled(false);
245 String searchString = searchBox.getUserInput();
247 if (isInvalidSearchString(searchString))
251 // TODO: extend finder to match descriptions, features and annotation, and
253 // TODO: add switches to control what is searched - sequences, IDS,
254 // descriptions, features
255 jalview.analysis.Finder finder = new jalview.analysis.Finder(
256 av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
257 finder.setCaseSensitive(caseSensitive.isSelected());
258 finder.setIncludeDescription(searchDescription.isSelected());
260 finder.setFindAll(doFindAll);
262 finder.find(searchString); // returns true if anything was actually found
264 seqIndex = finder.getSeqIndex();
265 resIndex = finder.getResIndex();
267 searchResults = finder.getSearchResults(); // find(regex,
268 // caseSensitive.isSelected(), )
269 Vector<SequenceI> idMatch = finder.getIdMatch();
270 boolean haveResults = false;
271 // set or reset the GUI
272 if ((idMatch.size() > 0))
275 ap.getIdPanel().highlightSearchResults(idMatch);
279 ap.getIdPanel().highlightSearchResults(null);
282 if (searchResults.getSize() > 0)
285 createFeatures.setEnabled(true);
289 searchResults = null;
292 searchBox.updateCache();
294 // if allResults is null, this effectively switches displaySearch flag in
296 ap.highlightSearchResults(searchResults);
297 // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
298 // 'SelectRegion' selection
303 JvOptionPane.showInternalMessageDialog(this,
304 MessageManager.getString("label.finished_searching"), null,
305 JvOptionPane.PLAIN_MESSAGE);
311 // then we report the matches that were found
312 String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
314 if (searchResults != null)
316 if (idMatch.size() > 0 && searchResults.getSize() > 0)
320 message += searchResults.getSize()
321 + " subsequence matches found.";
325 JvOptionPane.showInternalMessageDialog(this, message, null,
326 JvOptionPane.PLAIN_MESSAGE);
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();