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.Vector;
35 import java.util.regex.Pattern;
36 import java.util.regex.PatternSyntaxException;
38 import javax.swing.AbstractAction;
39 import javax.swing.JComponent;
40 import javax.swing.JInternalFrame;
41 import javax.swing.JLayeredPane;
42 import javax.swing.KeyStroke;
45 * Performs the menu option for searching the alignment, for the next or all
46 * matches. If matches are found, they are highlighted, and the user has the
47 * option to create a new feature on the alignment for the matched positions.
49 * Searches can be for a simple base sequence, or may use a regular expression.
50 * Any gaps are ignored.
55 public class Finder extends GFinder
57 private static final int HEIGHT = 120;
59 private static final int WIDTH = 400;
65 private static final int MIN_WIDTH = 350;
67 private static final int MIN_HEIGHT = 120;
75 SearchResultsI searchResults;
78 * Creates a new Finder object with no associated viewport or panel.
87 * Constructor given an associated viewport and alignment panel. Constructs
88 * and displays an internal frame where the user can enter a search string.
93 public Finder(AlignmentViewport viewport, AlignmentPanel alignPanel)
98 frame = new JInternalFrame();
99 frame.setContentPane(this);
100 frame.setLayer(JLayeredPane.PALETTE_LAYER);
102 Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
104 frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
105 textfield.requestFocus();
109 * Add a handler for the Escape key when the window has focus
111 private void addEscapeHandler()
113 getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
114 KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel");
115 getRootPane().getActionMap().put("Cancel", new AbstractAction()
118 public void actionPerformed(ActionEvent e)
120 escapeActionPerformed();
126 * Close the panel on Escape key press
128 protected void escapeActionPerformed()
135 * Performs the 'Find Next' action.
140 public void findNext_actionPerformed(ActionEvent e)
142 if (getFocusedViewport())
149 * Performs the 'Find All' action.
154 public void findAll_actionPerformed(ActionEvent e)
156 if (getFocusedViewport())
165 * do we only search a given alignment view ?
167 private boolean focusfixed;
170 * if !focusfixed and not in a desktop environment, checks that av and ap are
171 * valid. Otherwise, gets the topmost alignment window and sets av and ap
174 * @return false if no alignment window was found
176 boolean getFocusedViewport()
178 if (focusfixed || Desktop.desktop == null)
180 if (ap != null && av != null)
184 // we aren't in a desktop environment, so give up now.
187 // now checks further down the window stack to fix bug
188 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
189 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
190 for (int f = 0; f < frames.length; f++)
192 JInternalFrame frame = frames[f];
193 if (frame != null && frame instanceof AlignFrame)
195 av = ((AlignFrame) frame).viewport;
196 ap = ((AlignFrame) frame).alignPanel;
210 public void createNewGroup_actionPerformed(ActionEvent e)
212 SequenceI[] seqs = new SequenceI[searchResults.getSize()];
213 SequenceFeature[] features = new SequenceFeature[searchResults
217 for (SearchResultMatchI match : searchResults.getResults())
219 seqs[i] = match.getSequence().getDatasetSequence();
221 features[i] = new SequenceFeature(textfield.getText().trim(),
222 "Search Results", null, match.getStart(), match.getEnd(),
227 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
230 ap.alignFrame.showSeqFeatures.setSelected(true);
231 av.setShowSequenceFeatures(true);
232 ap.highlightSearchResults(null);
237 * Search the alignment for the next or all matches. If 'all matches', a
238 * dialog is shown with the number of sequence ids and subsequences matched.
242 void doSearch(boolean findAll)
244 createNewGroup.setEnabled(false);
246 String searchString = textfield.getText().trim();
248 if (isInvalidSearchString(searchString))
252 // TODO: extend finder to match descriptions, features and annotation, and
254 // TODO: add switches to control what is searched - sequences, IDS,
255 // descriptions, features
256 jalview.analysis.Finder finder = new jalview.analysis.Finder(
257 av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
258 finder.setCaseSensitive(caseSensitive.isSelected());
259 finder.setIncludeDescription(searchDescription.isSelected());
261 finder.setFindAll(findAll);
263 finder.find(searchString); // returns true if anything was actually found
265 seqIndex = finder.getSeqIndex();
266 resIndex = finder.getResIndex();
268 searchResults = finder.getSearchResults(); // find(regex,
269 // caseSensitive.isSelected(), )
270 Vector<SequenceI> idMatch = finder.getIdMatch();
271 boolean haveResults = false;
272 // set or reset the GUI
273 if ((idMatch.size() > 0))
276 ap.getIdPanel().highlightSearchResults(idMatch);
280 ap.getIdPanel().highlightSearchResults(null);
283 if (searchResults.getSize() > 0)
286 createNewGroup.setEnabled(true);
290 searchResults = null;
293 // if allResults is null, this effectively switches displaySearch flag in
295 ap.highlightSearchResults(searchResults);
296 // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
297 // 'SelectRegion' selection
300 JvOptionPane.showInternalMessageDialog(this,
301 MessageManager.getString("label.finished_searching"), null,
302 JvOptionPane.INFORMATION_MESSAGE);
310 // then we report the matches that were found
311 String message = (idMatch.size() > 0) ? "" + idMatch.size()
313 if (searchResults != null)
315 if (idMatch.size() > 0 && searchResults.getSize() > 0)
319 message += searchResults.getSize()
320 + " subsequence matches found.";
322 JvOptionPane.showInternalMessageDialog(this, message, null,
323 JvOptionPane.INFORMATION_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();