/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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 java.util.*;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GFinder;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.KeyEvent;
+import java.util.Vector;
+import java.util.regex.Pattern;
+import java.util.regex.PatternSyntaxException;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
+import javax.swing.AbstractAction;
+import javax.swing.JComponent;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JOptionPane;
+import javax.swing.KeyStroke;
/**
- * 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
+public class Finder extends GFinder
{
- AlignViewport av;
+ private static final int HEIGHT = 110;
+
+ private static final int WIDTH = 340;
+
+ AlignmentViewport av;
+
AlignmentPanel ap;
+
JInternalFrame frame;
+
int seqIndex = 0;
- int resIndex = 0;
+
+ int resIndex = -1;
SearchResults searchResults;
/**
- * Creates a new Finder object.
- *
- * @param av DOCUMENT ME!
- * @param ap DOCUMENT ME!
- * @param f DOCUMENT ME!
+ * Creates a new Finder object with no associated viewport or panel.
*/
public Finder()
{
+ this(null, null);
+ focusfixed = false;
+ }
+
+ /**
+ * Constructor given an associated viewport and alignment panel. Constructs
+ * and displays an internal frame where the user can enter a search string.
+ *
+ * @param viewport
+ * @param alignPanel
+ */
+ public Finder(AlignmentViewport viewport, AlignmentPanel alignPanel)
+ {
+ av = viewport;
+ ap = alignPanel;
+ focusfixed = true;
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, "Find", 340, 110);
+ addEscapeHandler();
+ Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
+ WIDTH, HEIGHT);
textfield.requestFocus();
}
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * 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()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ escapeActionPerformed();
+ }
+ });
+ }
+
+ /**
+ * Close the panel on Escape key press
+ */
+ protected void escapeActionPerformed()
+ {
+ setVisible(false);
+ frame.dispose();
+ }
+
+ /**
+ * Performs the 'Find Next' action.
+ *
+ * @param e
*/
public void findNext_actionPerformed(ActionEvent e)
{
}
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * Performs the 'Find All' action.
+ *
+ * @param e
*/
public void findAll_actionPerformed(ActionEvent e)
{
if (getFocusedViewport())
{
- resIndex = 0;
+ resIndex = -1;
seqIndex = 0;
doSearch(true);
}
}
+ /**
+ * do we only search a given alignment view ?
+ */
+ private boolean focusfixed;
+
+ /**
+ * 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
+ *
+ * @return false if no alignment window was found
+ */
boolean getFocusedViewport()
{
- JInternalFrame frame = Desktop.desktop.getAllFrames()[1];
-
- if (frame != null && frame instanceof AlignFrame)
+ if (focusfixed || Desktop.desktop == null)
+ {
+ if (ap != null && av != null)
+ {
+ 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.desktop.getAllFrames();
+ for (int f = 0; f < frames.length; f++)
{
- av = ( (AlignFrame) frame).viewport;
- ap = ( (AlignFrame) frame).alignPanel;
- return true;
+ JInternalFrame frame = frames[f];
+ if (frame != null && frame instanceof AlignFrame)
+ {
+ av = ((AlignFrame) frame).viewport;
+ ap = ((AlignFrame) frame).alignPanel;
+ return true;
+ }
}
return false;
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void createNewGroup_actionPerformed(ActionEvent e)
{
- 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()];
+ SequenceFeature[] features = new SequenceFeature[searchResults
+ .getSize()];
for (int i = 0; i < searchResults.getSize(); i++)
{
seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();
- features[i] = new SequenceFeature(textinput.getText(),
- "Search Results", null,
- searchResults.getResultStart(i),
- searchResults.getResultEnd(i),
- "Search Results");
+ features[i] = new SequenceFeature(textfield.getText().trim(),
+ "Search Results", null, searchResults.getResultStart(i),
+ searchResults.getResultEnd(i), "Search Results");
}
- if (ap.seqPanel.seqCanvas.getFeatureRenderer()
- .createNewFeatures(seqs, features))
+ if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ features, true, ap))
{
ap.alignFrame.showSeqFeatures.setSelected(true);
av.setShowSequenceFeatures(true);
}
/**
- * DOCUMENT ME!
- *
- * @param findAll DOCUMENT ME!
+ * 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 findAll
*/
void doSearch(boolean findAll)
{
String searchString = textfield.getText().trim();
- if (searchString.length() < 1)
+ 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
- jalview.analysis.Finder finder = new jalview.analysis.Finder(av.alignment,
- av.getSelectionGroup(), seqIndex, resIndex);
+ // 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.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
finder.setCaseSensitive(caseSensitive.isSelected());
+ finder.setIncludeDescription(searchDescription.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(), )
+ searchResults = finder.getSearchResults(); // find(regex,
+ // caseSensitive.isSelected(), )
Vector idMatch = finder.getIdMatch();
+ boolean haveResults = false;
// set or reset the GUI
- if ( (searchResults.getSize() == 0) && (idMatch.size() > 0))
+ if ((idMatch.size() > 0))
{
- ap.idPanel.highlightSearchResults(idMatch);
+ haveResults = true;
+ ap.getIdPanel().highlightSearchResults(idMatch);
+ }
+ else
+ {
+ ap.getIdPanel().highlightSearchResults(null);
}
-
- int resultSize = searchResults.getSize();
if (searchResults.getSize() > 0)
{
+ haveResults = true;
createNewGroup.setEnabled(true);
}
else
searchResults = null;
}
- // if allResults is null, this effectively switches displaySearch flag in seqCanvas
+ // 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)
+ // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
+ // 'SelectRegion' selection
+ if (!haveResults)
{
- JOptionPane.showInternalMessageDialog(this, "Finished searching",
- null,
- JOptionPane.INFORMATION_MESSAGE);
- resIndex = 0;
+ JOptionPane.showInternalMessageDialog(this,
+ MessageManager.getString("label.finished_searching"), null,
+ JOptionPane.INFORMATION_MESSAGE);
+ resIndex = -1;
seqIndex = 0;
}
+ else
+ {
+ if (findAll)
+ {
+ // then we report the matches that were found
+ String message = (idMatch.size() > 0) ? "" + idMatch.size()
+ + " IDs" : "";
+ if (searchResults != null)
+ {
+ if (idMatch.size() > 0 && searchResults.getSize() > 0)
+ {
+ message += " and ";
+ }
+ message += searchResults.getSize()
+ + " subsequence matches found.";
+ }
+ JOptionPane.showInternalMessageDialog(this, message, null,
+ JOptionPane.INFORMATION_MESSAGE);
+ resIndex = -1;
+ seqIndex = 0;
+ }
+ }
- if (findAll)
+ }
+
+ /**
+ * 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)
{
- String message = resultSize + " matches found.";
- JOptionPane.showInternalMessageDialog(this, message, null,
- JOptionPane.INFORMATION_MESSAGE);
+ return false;
}
+ JOptionPane.showInternalMessageDialog(this, error,
+ MessageManager.getString("label.invalid_search"), // $NON-NLS-1$
+ JOptionPane.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;
}
}
git://source.jalview.org / jalview.git / blobdiff