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.SearchResults;
24 import jalview.datamodel.SequenceFeature;
25 import jalview.datamodel.SequenceI;
26 import jalview.jbgui.GFinder;
27 import jalview.util.MessageManager;
28 import jalview.viewmodel.AlignmentViewport;
30 import java.awt.event.ActionEvent;
31 import java.util.Vector;
32 import java.util.regex.Pattern;
33 import java.util.regex.PatternSyntaxException;
35 import javax.swing.JInternalFrame;
36 import javax.swing.JLayeredPane;
37 import javax.swing.JOptionPane;
40 * Performs the menu option for searching the alignment, for the next or all
41 * matches. If matches are found, they are highlighted, and the user has the
42 * option to create a new feature on the alignment for the matched positions.
44 * Searches can be for a simple base sequence, or may use a regular expression.
45 * Any gaps are ignored.
50 public class Finder extends GFinder
52 private static final int HEIGHT = 110;
54 private static final int WIDTH = 340;
66 SearchResults searchResults;
69 * Creates a new Finder object with no associated viewport or panel.
78 * Constructor given an associated viewport and alignment panel. Constructs
79 * and displays an internal frame where the user can enter a search string.
84 public Finder(AlignmentViewport viewport, AlignmentPanel alignPanel)
89 frame = new JInternalFrame();
90 frame.setContentPane(this);
91 frame.setLayer(JLayeredPane.PALETTE_LAYER);
92 Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
95 textfield.requestFocus();
99 * Performs the 'Find Next' action.
103 public void findNext_actionPerformed(ActionEvent e)
105 if (getFocusedViewport())
112 * Performs the 'Find All' action.
116 public void findAll_actionPerformed(ActionEvent e)
118 if (getFocusedViewport())
127 * do we only search a given alignment view ?
129 private boolean focusfixed;
132 * if !focusfixed and not in a desktop environment, checks that av and ap are
133 * valid. Otherwise, gets the topmost alignment window and sets av and ap
136 * @return false if no alignment window was found
138 boolean getFocusedViewport()
140 if (focusfixed || Desktop.desktop == null)
142 if (ap != null && av != null)
146 // we aren't in a desktop environment, so give up now.
149 // now checks further down the window stack to fix bug
150 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
151 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
152 for (int f = 0; f < frames.length; f++)
154 JInternalFrame frame = frames[f];
155 if (frame != null && frame instanceof AlignFrame)
157 av = ((AlignFrame) frame).viewport;
158 ap = ((AlignFrame) frame).alignPanel;
171 public void createNewGroup_actionPerformed(ActionEvent e)
173 SequenceI[] seqs = new SequenceI[searchResults.getSize()];
174 SequenceFeature[] features = new SequenceFeature[searchResults
177 for (int i = 0; i < searchResults.getSize(); i++)
179 seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();
181 features[i] = new SequenceFeature(textfield.getText().trim(),
182 "Search Results", null, searchResults.getResultStart(i),
183 searchResults.getResultEnd(i), "Search Results");
186 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
189 ap.alignFrame.showSeqFeatures.setSelected(true);
190 av.setShowSequenceFeatures(true);
191 ap.highlightSearchResults(null);
196 * Search the alignment for the next or all matches. If 'all matches', a
197 * dialog is shown with the number of sequence ids and subsequences matched.
201 void doSearch(boolean findAll)
203 createNewGroup.setEnabled(false);
205 String searchString = textfield.getText().trim();
207 if (isInvalidSearchString(searchString))
211 // TODO: extend finder to match descriptions, features and annotation, and
213 // TODO: add switches to control what is searched - sequences, IDS,
214 // descriptions, features
215 jalview.analysis.Finder finder = new jalview.analysis.Finder(
216 av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
217 finder.setCaseSensitive(caseSensitive.isSelected());
218 finder.setIncludeDescription(searchDescription.isSelected());
220 finder.setFindAll(findAll);
222 finder.find(searchString); // returns true if anything was actually found
224 seqIndex = finder.getSeqIndex();
225 resIndex = finder.getResIndex();
227 searchResults = finder.getSearchResults(); // find(regex,
228 // caseSensitive.isSelected(), )
229 Vector idMatch = finder.getIdMatch();
230 boolean haveResults = false;
231 // set or reset the GUI
232 if ((idMatch.size() > 0))
235 ap.getIdPanel().highlightSearchResults(idMatch);
239 ap.getIdPanel().highlightSearchResults(null);
242 if (searchResults.getSize() > 0)
245 createNewGroup.setEnabled(true);
249 searchResults = null;
252 // if allResults is null, this effectively switches displaySearch flag in
254 ap.highlightSearchResults(searchResults);
255 // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
256 // 'SelectRegion' selection
259 JOptionPane.showInternalMessageDialog(this,
260 MessageManager.getString("label.finished_searching"), null,
261 JOptionPane.INFORMATION_MESSAGE);
269 // then we report the matches that were found
270 String message = (idMatch.size() > 0) ? "" + idMatch.size()
272 if (searchResults != null)
274 if (idMatch.size() > 0 && searchResults.getSize() > 0)
278 message += searchResults.getSize()
279 + " subsequence matches found.";
281 JOptionPane.showInternalMessageDialog(this, message, null,
282 JOptionPane.INFORMATION_MESSAGE);
291 * Displays an error dialog, and answers false, if the search string is
292 * invalid, else answers true.
294 * @param searchString
297 protected boolean isInvalidSearchString(String searchString)
299 String error = getSearchValidationError(searchString);
304 JOptionPane.showInternalMessageDialog(this, error,
305 MessageManager.getString("label.invalid_search"), // $NON-NLS-1$
306 JOptionPane.ERROR_MESSAGE);
311 * Returns an error message string if the search string is invalid, else
314 * Currently validation is limited to checking the string is not empty, and is
315 * a valid regular expression (simple searches for base sub-sequences will
316 * pass this test). Additional validations may be added in future if the
317 * search syntax is expanded.
319 * @param searchString
322 protected String getSearchValidationError(String searchString)
325 if (searchString == null || searchString.length() == 0)
327 error = MessageManager.getString("label.invalid_search");
331 Pattern.compile(searchString);
332 } catch (PatternSyntaxException e)
334 error = MessageManager.getString("error.invalid_regex") + ": "
335 + e.getDescription();