/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import jalview.datamodel.*;
-
-import jalview.jbgui.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import java.util.*;
-
-import javax.swing.*;
-import javax.swing.event.*;
-
+import java.util.Locale;
+
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.KeyEvent;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.regex.Pattern;
+import java.util.regex.PatternSyntaxException;
+
+import javax.swing.AbstractAction;
+import javax.swing.JComponent;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.KeyStroke;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
+import jalview.api.AlignViewportI;
+import jalview.api.FinderI;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GFinder;
+import jalview.util.MessageManager;
/**
- * DOCUMENT ME!
- *
+ * Performs the menu option for searching the alignment, for the next or all
+ * matches. If matches are found, they are highlighted, and the user has the
+ * option to create a new feature on the alignment for the matched positions.
+ *
+ * Searches can be for a simple base sequence, or may use a regular expression.
+ * Any gaps are ignored.
+ *
* @author $author$
* @version $Revision$
*/
public class Finder extends GFinder
{
- AlignViewport av;
- AlignmentPanel ap;
- JInternalFrame frame;
- int seqIndex = 0;
- int resIndex = 0;
-
- SearchResults searchResults;
-
- /**
- * Creates a new Finder object.
- *
- * @param av DOCUMENT ME!
- * @param ap DOCUMENT ME!
- * @param f DOCUMENT ME!
- */
- public Finder()
+ private static final int MIN_WIDTH = 350;
+
+ private static final int MIN_HEIGHT = 120;
+
+ private static final int MY_HEIGHT = 150;
+
+ private static final int MY_WIDTH = 400;
+
+ private AlignViewportI av;
+
+ private AlignmentPanel ap;
+
+ private JInternalFrame frame;
+
+ /*
+ * Finder agent per viewport searched
+ */
+ private Map<AlignViewportI, FinderI> finders;
+
+ private SearchResultsI searchResults;
+
+ /*
+ * true if Finder always acts on the same alignment,
+ * false if it acts on the alignment with focus
+ */
+ private boolean focusFixed;
+
+ /**
+ * Constructor given an associated alignment panel. Constructs and displays an
+ * internal frame where the user can enter a search string. The Finder may
+ * have 'fixed focus' (always act the panel for which it is constructed), or
+ * not (acts on the alignment that has focus). An optional 'scope' may be
+ * added to be shown in the title of the Finder frame.
+ *
+ * @param alignPanel
+ * @param fixedFocus
+ * @param scope
+ */
+ public Finder(AlignmentPanel alignPanel, boolean fixedFocus, String scope)
+ {
+ av = alignPanel.getAlignViewport();
+ ap = alignPanel;
+ focusFixed = fixedFocus;
+ finders = new HashMap<>();
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ frame.addInternalFrameListener(new InternalFrameAdapter()
{
- frame = new JInternalFrame();
- frame.setContentPane(this);
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, "Find", 340, 110);
-
- textfield.requestFocus();
- }
+ @Override
+ public void internalFrameClosing(InternalFrameEvent e)
+ {
+ closeAction();
+ }
+ });
+ frame.addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusGained(FocusEvent e)
+ {
+ /*
+ * ensure 'ignore hidden columns' is only enabled
+ * if the alignment with focus has hidden columns
+ */
+ getFocusedViewport();
+ }
+ });
+ addEscapeHandler();
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void findNext_actionPerformed(ActionEvent e)
+ String title = MessageManager.getString("label.find");
+ if (scope != null)
{
- if (getFocusedViewport())
- doSearch(false);
+ title += " " + scope;
}
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void findAll_actionPerformed(ActionEvent e)
+ Desktop.addInternalFrame(frame, title, Desktop.FRAME_MAKE_VISIBLE, MY_WIDTH, MY_HEIGHT, Desktop.FRAME_ALLOW_RESIZE, Desktop.FRAME_ALLOW_ANY_SIZE);
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+ searchBox.getComponent().requestFocus();
+ }
+
+ /**
+ * Add a handler for the Escape key when the window has focus
+ */
+ private void addEscapeHandler()
+ {
+ getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
+ .put(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel");
+ getRootPane().getActionMap().put("Cancel", new AbstractAction()
{
- if(getFocusedViewport())
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- resIndex = 0;
- seqIndex = 0;
- doSearch(true);
+ closeAction();
}
+ });
+ }
+
+ /**
+ * Performs the 'Find Next' action on the alignment panel with focus
+ */
+ @Override
+ public void findNext_actionPerformed()
+ {
+ if (getFocusedViewport())
+ {
+ doSearch(false);
}
-
- boolean getFocusedViewport()
+ }
+
+ /**
+ * Performs the 'Find All' action on the alignment panel with focus
+ */
+ @Override
+ public void findAll_actionPerformed()
+ {
+ if (getFocusedViewport())
{
- JInternalFrame frame = Desktop.desktop.getAllFrames()[1];
-
- if(frame!=null && frame instanceof AlignFrame)
+ doSearch(true);
+ }
+ }
+
+ /**
+ * if !focusfixed and not in a desktop environment, checks that av and ap are
+ * valid. Otherwise, gets the topmost alignment window and sets av and ap
+ * accordingly. Also sets the 'ignore hidden' checkbox disabled if the
+ * viewport has no hidden columns.
+ *
+ * @return false if no alignment window was found
+ */
+ boolean getFocusedViewport()
+ {
+ if (focusFixed || Desktop.getDesktopPane() == null)
+ {
+ if (ap != null && av != null)
{
- av = ((AlignFrame)frame).viewport;
- ap = ((AlignFrame)frame).alignPanel;
+ ignoreHidden.setEnabled(av.hasHiddenColumns());
return true;
}
+ // we aren't in a desktop environment, so give up now.
return false;
}
+ // now checks further down the window stack to fix bug
+ // https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
+ for (int f = 0; f < frames.length; f++)
+ {
+ JInternalFrame alignFrame = frames[f];
+ if (alignFrame != null && alignFrame instanceof AlignFrame
+ && !alignFrame.isIcon())
+ {
+ av = ((AlignFrame) alignFrame).viewport;
+ ap = ((AlignFrame) alignFrame).alignPanel;
+ ignoreHidden.setEnabled(av.hasHiddenColumns());
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Opens a dialog that allows the user to create sequence features for the
+ * find match results
+ */
+ @Override
+ public void createFeatures_actionPerformed()
+ {
+ if (searchResults.isEmpty())
+ {
+ return; // shouldn't happen
+ }
+ List<SequenceI> seqs = new ArrayList<>();
+ List<SequenceFeature> features = new ArrayList<>();
+ String searchString = searchBox.getUserInput();
+ String desc = "Search Results";
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ /*
+ * assemble dataset sequences, and template new sequence features,
+ * for the amend features dialog
*/
- public void createNewGroup_actionPerformed(ActionEvent e)
+ for (SearchResultMatchI match : searchResults.getResults())
{
- JLabel label = new JLabel("Enter name of new sequence feature");
- JTextField textinput = new JTextField(textfield.getText());
- JPanel panel = new JPanel(new BorderLayout());
- panel.add(label, BorderLayout.NORTH);
- panel.add(textinput, BorderLayout.SOUTH);
-
-
- SequenceI [] seqs = new SequenceI[searchResults.getSize()];
- SequenceFeature [] features = new SequenceFeature[searchResults.getSize()];
+ seqs.add(match.getSequence().getDatasetSequence());
+ features.add(new SequenceFeature(searchString, desc, match.getStart(),
+ match.getEnd(), desc));
+ }
+ new FeatureEditor(ap, seqs, features, true).showDialog();
+ }
- for (int i = 0; i < searchResults.getSize(); i ++ )
- {
- seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();
+ /**
+ * Search the alignment for the next or all matches. If 'all matches', a
+ * dialog is shown with the number of sequence ids and subsequences matched.
+ *
+ * @param doFindAll
+ */
+ void doSearch(boolean doFindAll)
+ {
+ createFeatures.setEnabled(false);
- features[i] = new SequenceFeature(textinput.getText(),
- "Search Results", null,
- searchResults.getResultStart(i),
- searchResults.getResultEnd(i),
- "Search Results");
- }
+ String searchString = searchBox.getUserInput();
- if( ap.seqPanel.seqCanvas.getFeatureRenderer()
- .createNewFeatures(seqs, features))
- {
- ap.alignFrame.showSeqFeatures.setSelected(true);
- av.setShowSequenceFeatures(true);
- ap.highlightSearchResults(null);
- }
+ if (isInvalidSearchString(searchString))
+ {
+ return;
+ }
+ // TODO: extend finder to match descriptions, features and annotation, and
+ // other stuff
+ // TODO: add switches to control what is searched - sequences, IDS,
+ // descriptions, features
+ FinderI finder = finders.get(av);
+ if (finder == null)
+ {
+ /*
+ * first time we've searched this viewport
+ */
+ finder = new jalview.analysis.Finder(av);
+ finders.put(av, finder);
}
- /**
- * DOCUMENT ME!
- *
- * @param findAll DOCUMENT ME!
- */
- void doSearch(boolean findAll)
- {
- createNewGroup.setEnabled(false);
-
- String searchString = textfield.getText().trim();
-
- if(searchString.length()<1)
- return;
- // TODO: extend finder to match descriptions, features and annotation, and other stuff
- // TODO: add switches to control what is searched - sequences, IDS, descriptions, features
- jalview.analysis.Finder finder=new jalview.analysis.Finder(av.alignment, av.getSelectionGroup(), seqIndex, resIndex);
- finder.setCaseSensitive(caseSensitive.isSelected());
- finder.setFindAll(findAll);
-
- finder.find(searchString); // returns true if anything was actually found
-
- seqIndex=finder.getSeqIndex();
- resIndex=finder.getResIndex();
-
- searchResults = finder.getSearchResults(); // find(regex, caseSensitive.isSelected(), )
- Vector idMatch = finder.getIdMatch();
- // set or reset the GUI
- if ((searchResults.getSize() == 0) && (idMatch.size() > 0))
- {
- ap.idPanel.highlightSearchResults(idMatch);
- }
+ boolean isCaseSensitive = caseSensitive.isSelected();
+ boolean doSearchDescription = searchDescription.isSelected();
+ boolean skipHidden = ignoreHidden.isSelected();
+ if (doFindAll)
+ {
+ finder.findAll(searchString, isCaseSensitive, doSearchDescription,
+ skipHidden);
+ }
+ else
+ {
+ finder.findNext(searchString, isCaseSensitive, doSearchDescription,
+ skipHidden);
+ }
+ searchResults = finder.getSearchResults();
+ List<SequenceI> idMatch = finder.getIdMatches();
+ ap.getIdPanel().highlightSearchResults(idMatch);
- int resultSize = searchResults.getSize();
+ if (searchResults.isEmpty())
+ {
+ searchResults = null;
+ }
+ else
+ {
+ createFeatures.setEnabled(true);
+ }
- if (searchResults.getSize() > 0)
- createNewGroup.setEnabled(true);
- else
- searchResults = null;
+ searchBox.updateCache();
- // if allResults is null, this effectively switches displaySearch flag in seqCanvas
- ap.highlightSearchResults(searchResults);
- // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or 'SelectRegion' selection
- if(!findAll && resultSize==0)
+ ap.highlightSearchResults(searchResults);
+ // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
+ // 'SelectRegion' selection
+ if (idMatch.isEmpty() && searchResults == null)
+ {
+ JvOptionPane.showInternalMessageDialog(this,
+ MessageManager.getString("label.finished_searching"), null,
+ JvOptionPane.PLAIN_MESSAGE);
+ }
+ else
+ {
+ if (doFindAll)
+ {
+ // then we report the matches that were found
+ StringBuilder message = new StringBuilder();
+ if (idMatch.size() > 0)
{
- JOptionPane.showInternalMessageDialog(this, "Finished searching",
- null, JOptionPane.INFORMATION_MESSAGE);
- resIndex = 0;
- seqIndex = 0;
+ message.append(idMatch.size()).append(" IDs");
}
-
- if (findAll)
+ if (searchResults != null)
{
- String message = resultSize + " matches found.";
- JOptionPane.showInternalMessageDialog(this, message, null,
- JOptionPane.INFORMATION_MESSAGE);
+ if (idMatch.size() > 0 && searchResults.getCount() > 0)
+ {
+ message.append(" ").append(MessageManager.getString("label.and")
+ .toLowerCase(Locale.ROOT)).append(" ");
+ }
+ message.append(MessageManager.formatMessage(
+ "label.subsequence_matches_found",
+ searchResults.getCount()));
}
-
+ JvOptionPane.showInternalMessageDialog(this, message.toString(),
+ null, JvOptionPane.INFORMATION_MESSAGE);
+ }
+ }
+ }
+
+ /**
+ * Displays an error dialog, and answers false, if the search string is
+ * invalid, else answers true.
+ *
+ * @param searchString
+ * @return
+ */
+ protected boolean isInvalidSearchString(String searchString)
+ {
+ String error = getSearchValidationError(searchString);
+ if (error == null)
+ {
+ return false;
+ }
+ JvOptionPane.showInternalMessageDialog(this, error,
+ MessageManager.getString("label.invalid_search"), // $NON-NLS-1$
+ JvOptionPane.ERROR_MESSAGE);
+ return true;
+ }
+
+ /**
+ * Returns an error message string if the search string is invalid, else
+ * returns null.
+ *
+ * Currently validation is limited to checking the string is not empty, and is
+ * a valid regular expression (simple searches for base sub-sequences will
+ * pass this test). Additional validations may be added in future if the
+ * search syntax is expanded.
+ *
+ * @param searchString
+ * @return
+ */
+ protected String getSearchValidationError(String searchString)
+ {
+ String error = null;
+ if (searchString == null || searchString.length() == 0)
+ {
+ error = MessageManager.getString("label.invalid_search");
+ }
+ try
+ {
+ Pattern.compile(searchString);
+ } catch (PatternSyntaxException e)
+ {
+ error = MessageManager.getString("error.invalid_regex") + ": "
+ + e.getDescription();
+ }
+ return error;
+ }
+
+ protected void closeAction()
+ {
+ frame.setVisible(false);
+ frame.dispose();
+ searchBox.persistCache();
+ if (getFocusedViewport())
+ {
+ ap.alignFrame.requestFocus();
}
+ }
}
git://source.jalview.org / jalview.git / blobdiff