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;
45 import javax.swing.event.InternalFrameEvent;
48 * Performs the menu option for searching the alignment, for the next or all
49 * matches. If matches are found, they are highlighted, and the user has the
50 * option to create a new feature on the alignment for the matched positions.
52 * Searches can be for a simple base sequence, or may use a regular expression.
53 * Any gaps are ignored.
58 public class Finder extends GFinder
60 private static final int MY_HEIGHT = 120;
62 private static final int MY_WIDTH = 400;
68 private static final int MIN_WIDTH = 350;
70 private static final int MIN_HEIGHT = 120;
78 SearchResultsI searchResults;
81 * Creates a new Finder object with no associated viewport or panel.
90 * Constructor given an associated viewport and alignment panel. Constructs
91 * and displays an internal frame where the user can enter a search string.
96 public Finder(AlignmentViewport viewport, AlignmentPanel alignPanel)
101 frame = new JInternalFrame();
102 frame.setContentPane(this);
103 frame.setLayer(JLayeredPane.PALETTE_LAYER);
104 frame.addInternalFrameListener(
105 new javax.swing.event.InternalFrameAdapter()
108 public void internalFrameClosing(InternalFrameEvent e)
114 Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
115 MY_WIDTH, MY_HEIGHT);
116 frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
117 searchBox.requestFocus();
121 * Add a handler for the Escape key when the window has focus
123 private void addEscapeHandler()
125 getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
126 .put(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel");
127 getRootPane().getActionMap().put("Cancel", new AbstractAction()
130 public void actionPerformed(ActionEvent e)
138 * Performs the 'Find Next' action.
143 public void findNext_actionPerformed(ActionEvent e)
145 if (getFocusedViewport())
152 * Performs the 'Find All' action.
157 public void findAll_actionPerformed(ActionEvent e)
159 if (getFocusedViewport())
168 * do we only search a given alignment view ?
170 private boolean focusfixed;
173 * if !focusfixed and not in a desktop environment, checks that av and ap are
174 * valid. Otherwise, gets the topmost alignment window and sets av and ap
177 * @return false if no alignment window was found
179 boolean getFocusedViewport()
181 if (focusfixed || Desktop.desktop == null)
183 if (ap != null && av != null)
187 // we aren't in a desktop environment, so give up now.
190 // now checks further down the window stack to fix bug
191 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
192 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
193 for (int f = 0; f < frames.length; f++)
195 JInternalFrame alignFrame = frames[f];
196 if (alignFrame != null && alignFrame instanceof AlignFrame)
198 av = ((AlignFrame) alignFrame).viewport;
199 ap = ((AlignFrame) alignFrame).alignPanel;
207 * Opens a dialog that allows the user to create sequence features for the
208 * find match results.
211 public void createFeatures_actionPerformed()
213 List<SequenceI> seqs = new ArrayList<SequenceI>();
214 List<SequenceFeature> features = new ArrayList<SequenceFeature>();
216 String searchString = searchBox.getEditor().getItem().toString().trim();
217 String desc = "Search Results";
220 * assemble dataset sequences, and template new sequence features,
221 * for the amend features dialog
223 for (SearchResultMatchI match : searchResults.getResults())
225 seqs.add(match.getSequence().getDatasetSequence());
226 features.add(new SequenceFeature(searchString, desc, match.getStart(),
227 match.getEnd(), desc));
230 ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
231 features, true, ap, new Runnable()
238 * ensure feature display is turned on to show the new features,
239 * and remove them as highlighted regions
241 ap.alignFrame.showSeqFeatures.setSelected(true);
242 av.setShowSequenceFeatures(true);
243 ap.highlightSearchResults(null);
249 * Search the alignment for the next or all matches. If 'all matches', a
250 * dialog is shown with the number of sequence ids and subsequences matched.
254 void doSearch(boolean doFindAll)
256 createFeatures.setEnabled(false);
258 String searchString = searchBox.getUserInput().trim();
260 if (isInvalidSearchString(searchString))
264 // TODO: extend finder to match descriptions, features and annotation, and
266 // TODO: add switches to control what is searched - sequences, IDS,
267 // descriptions, features
268 jalview.analysis.Finder finder = new jalview.analysis.Finder(
269 av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
270 finder.setCaseSensitive(caseSensitive.isSelected());
271 finder.setIncludeDescription(searchDescription.isSelected());
273 finder.setFindAll(doFindAll);
275 finder.find(searchString); // returns true if anything was actually found
277 seqIndex = finder.getSeqIndex();
278 resIndex = finder.getResIndex();
280 searchResults = finder.getSearchResults(); // find(regex,
281 // caseSensitive.isSelected(), )
282 Vector<SequenceI> idMatch = finder.getIdMatch();
283 boolean haveResults = false;
284 // set or reset the GUI
285 if ((idMatch.size() > 0))
288 ap.getIdPanel().highlightSearchResults(idMatch);
292 ap.getIdPanel().highlightSearchResults(null);
295 if (searchResults.getSize() > 0)
298 createFeatures.setEnabled(true);
302 searchResults = null;
305 // if allResults is null, this effectively switches displaySearch flag in
307 ap.highlightSearchResults(searchResults);
308 // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
309 // 'SelectRegion' selection
312 JvOptionPane.showInternalMessageDialog(this,
313 MessageManager.getString("label.finished_searching"), null,
314 JvOptionPane.INFORMATION_MESSAGE);
322 // then we report the matches that were found
323 String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
325 if (searchResults != null)
327 if (idMatch.size() > 0 && searchResults.getSize() > 0)
331 message += searchResults.getSize()
332 + " subsequence matches found.";
334 JvOptionPane.showInternalMessageDialog(this, message, null,
335 JvOptionPane.INFORMATION_MESSAGE);
340 searchBox.updateCache();
344 * Displays an error dialog, and answers false, if the search string is
345 * invalid, else answers true.
347 * @param searchString
350 protected boolean isInvalidSearchString(String searchString)
352 String error = getSearchValidationError(searchString);
357 JvOptionPane.showInternalMessageDialog(this, error,
358 MessageManager.getString("label.invalid_search"), // $NON-NLS-1$
359 JvOptionPane.ERROR_MESSAGE);
364 * Returns an error message string if the search string is invalid, else
367 * Currently validation is limited to checking the string is not empty, and is
368 * a valid regular expression (simple searches for base sub-sequences will
369 * pass this test). Additional validations may be added in future if the
370 * search syntax is expanded.
372 * @param searchString
375 protected String getSearchValidationError(String searchString)
378 if (searchString == null || searchString.length() == 0)
380 error = MessageManager.getString("label.invalid_search");
384 Pattern.compile(searchString);
385 } catch (PatternSyntaxException e)
387 error = MessageManager.getString("error.invalid_regex") + ": "
388 + e.getDescription();
393 protected void closeAction()
395 frame.setVisible(false);
397 searchBox.persistCache();
398 if (getFocusedViewport())
400 ap.alignFrame.requestFocus();