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.Dimension;
32 import java.awt.event.ActionEvent;
33 import java.awt.event.KeyEvent;
34 import java.util.ArrayList;
35 import java.util.List;
36 import java.util.Vector;
37 import java.util.regex.Pattern;
38 import java.util.regex.PatternSyntaxException;
40 import javax.swing.AbstractAction;
41 import javax.swing.JComponent;
42 import javax.swing.JInternalFrame;
43 import javax.swing.JLayeredPane;
44 import javax.swing.KeyStroke;
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);
104 Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
105 MY_WIDTH, MY_HEIGHT);
106 frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
107 textfield.requestFocus();
111 * Add a handler for the Escape key when the window has focus
113 private void addEscapeHandler()
115 getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
116 KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel");
117 getRootPane().getActionMap().put("Cancel", new AbstractAction()
120 public void actionPerformed(ActionEvent e)
122 escapeActionPerformed();
128 * Close the panel on Escape key press
130 protected void escapeActionPerformed()
137 * Performs the 'Find Next' action.
142 public void findNext_actionPerformed(ActionEvent e)
144 if (getFocusedViewport())
151 * Performs the 'Find All' action.
156 public void findAll_actionPerformed(ActionEvent e)
158 if (getFocusedViewport())
167 * do we only search a given alignment view ?
169 private boolean focusfixed;
172 * if !focusfixed and not in a desktop environment, checks that av and ap are
173 * valid. Otherwise, gets the topmost alignment window and sets av and ap
176 * @return false if no alignment window was found
178 boolean getFocusedViewport()
180 if (focusfixed || Desktop.desktop == null)
182 if (ap != null && av != null)
186 // we aren't in a desktop environment, so give up now.
189 // now checks further down the window stack to fix bug
190 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
191 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
192 for (int f = 0; f < frames.length; f++)
194 JInternalFrame alignFrame = frames[f];
195 if (alignFrame != null && alignFrame instanceof AlignFrame)
197 av = ((AlignFrame) alignFrame).viewport;
198 ap = ((AlignFrame) alignFrame).alignPanel;
206 * Opens a dialog that allows the user to create sequence features for the
207 * find match results.
210 public void createFeatures_actionPerformed()
212 List<SequenceI> seqs = new ArrayList<SequenceI>();
213 List<SequenceFeature> features = new ArrayList<SequenceFeature>();
215 String searchString = textfield.getText().trim();
216 String desc = "Search Results";
219 * assemble dataset sequences, and template new sequence features,
220 * for the amend features dialog
222 for (SearchResultMatchI match : searchResults.getResults())
224 seqs.add(match.getSequence().getDatasetSequence());
225 features.add(new SequenceFeature(searchString, desc, null, match
226 .getStart(), match.getEnd(), desc));
229 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
230 features, true, ap, searchString))
233 * ensure feature display is turned on to show the new features,
234 * and remove them as highlighted regions
236 ap.alignFrame.showSeqFeatures.setSelected(true);
237 av.setShowSequenceFeatures(true);
238 ap.highlightSearchResults(null);
243 * Search the alignment for the next or all matches. If 'all matches', a
244 * dialog is shown with the number of sequence ids and subsequences matched.
248 void doSearch(boolean doFindAll)
250 createFeatures.setEnabled(false);
252 String searchString = textfield.getText().trim();
254 if (isInvalidSearchString(searchString))
258 // TODO: extend finder to match descriptions, features and annotation, and
260 // TODO: add switches to control what is searched - sequences, IDS,
261 // descriptions, features
262 jalview.analysis.Finder finder = new jalview.analysis.Finder(
263 av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
264 finder.setCaseSensitive(caseSensitive.isSelected());
265 finder.setIncludeDescription(searchDescription.isSelected());
267 finder.setFindAll(doFindAll);
269 finder.find(searchString); // returns true if anything was actually found
271 seqIndex = finder.getSeqIndex();
272 resIndex = finder.getResIndex();
274 searchResults = finder.getSearchResults(); // find(regex,
275 // caseSensitive.isSelected(), )
276 Vector<SequenceI> idMatch = finder.getIdMatch();
277 boolean haveResults = false;
278 // set or reset the GUI
279 if ((idMatch.size() > 0))
282 ap.getIdPanel().highlightSearchResults(idMatch);
286 ap.getIdPanel().highlightSearchResults(null);
289 if (searchResults.getSize() > 0)
292 createFeatures.setEnabled(true);
296 searchResults = null;
299 // if allResults is null, this effectively switches displaySearch flag in
301 ap.highlightSearchResults(searchResults);
302 // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
303 // 'SelectRegion' selection
306 JvOptionPane.showInternalMessageDialog(this,
307 MessageManager.getString("label.finished_searching"), null,
308 JvOptionPane.INFORMATION_MESSAGE);
316 // then we report the matches that were found
317 String message = (idMatch.size() > 0) ? "" + idMatch.size()
319 if (searchResults != null)
321 if (idMatch.size() > 0 && searchResults.getSize() > 0)
325 message += searchResults.getSize()
326 + " subsequence matches found.";
328 JvOptionPane.showInternalMessageDialog(this, message, null,
329 JvOptionPane.INFORMATION_MESSAGE);
338 * Displays an error dialog, and answers false, if the search string is
339 * invalid, else answers true.
341 * @param searchString
344 protected boolean isInvalidSearchString(String searchString)
346 String error = getSearchValidationError(searchString);
351 JvOptionPane.showInternalMessageDialog(this, error,
352 MessageManager.getString("label.invalid_search"), // $NON-NLS-1$
353 JvOptionPane.ERROR_MESSAGE);
358 * Returns an error message string if the search string is invalid, else
361 * Currently validation is limited to checking the string is not empty, and is
362 * a valid regular expression (simple searches for base sub-sequences will
363 * pass this test). Additional validations may be added in future if the
364 * search syntax is expanded.
366 * @param searchString
369 protected String getSearchValidationError(String searchString)
372 if (searchString == null || searchString.length() == 0)
374 error = MessageManager.getString("label.invalid_search");
378 Pattern.compile(searchString);
379 } catch (PatternSyntaxException e)
381 error = MessageManager.getString("error.invalid_regex") + ": "
382 + e.getDescription();