/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * 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 java.awt.event.*;
+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 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 jalview.util.MessageManager;
+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
{
- AlignViewport av;
+ private static final int HEIGHT = 110;
+
+ private static final int WIDTH = 340;
+
+ AlignmentViewport av;
AlignmentPanel ap;
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()
{
focusfixed = false;
}
- public Finder(AlignViewport viewport, AlignmentPanel alignPanel)
+ /**
+ * 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;
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!
+ * 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
- * DOCUMENT ME!
*/
public void findNext_actionPerformed(ActionEvent e)
{
}
/**
- * DOCUMENT ME!
+ * Performs the 'Find All' action.
*
* @param e
- * DOCUMENT ME!
*/
public void findAll_actionPerformed(ActionEvent e)
{
searchResults.getResultEnd(i), "Search Results");
}
- if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
features, true, ap))
{
ap.alignFrame.showSeqFeatures.setSelected(true);
}
/**
- * incrementally search the alignment
+ * 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
- * true means find all results and raise a dialog box
*/
void doSearch(boolean findAll)
{
String searchString = textfield.getText().trim();
- if (searchString.length() < 1)
+ if (isInvalidSearchString(searchString))
{
return;
}
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
if ((idMatch.size() > 0))
{
haveResults = true;
- ap.idPanel.highlightSearchResults(idMatch);
+ ap.getIdPanel().highlightSearchResults(idMatch);
}
else
{
- ap.idPanel.highlightSearchResults(null);
+ ap.getIdPanel().highlightSearchResults(null);
}
if (searchResults.getSize() > 0)
// 'SelectRegion' selection
if (!haveResults)
{
- JOptionPane.showInternalMessageDialog(this, MessageManager.getString("label.finished_searching"),
- null, JOptionPane.INFORMATION_MESSAGE);
+ JOptionPane.showInternalMessageDialog(this,
+ MessageManager.getString("label.finished_searching"), null,
+ JOptionPane.INFORMATION_MESSAGE);
resIndex = -1;
seqIndex = 0;
}
-
- if (findAll)
+ else
{
- String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
- : "";
- if (searchResults != null)
+ if (findAll)
{
- if (idMatch.size() > 0 && searchResults.getSize() > 0)
+ // then we report the matches that were found
+ String message = (idMatch.size() > 0) ? "" + idMatch.size()
+ + " IDs" : "";
+ if (searchResults != null)
{
- message += " and ";
+ if (idMatch.size() > 0 && searchResults.getSize() > 0)
+ {
+ message += " and ";
+ }
+ message += searchResults.getSize()
+ + " subsequence matches found.";
}
- message += searchResults.getSize() + " subsequence matches found.";
+ JOptionPane.showInternalMessageDialog(this, message, null,
+ JOptionPane.INFORMATION_MESSAGE);
+ resIndex = -1;
+ seqIndex = 0;
}
- JOptionPane.showInternalMessageDialog(this, message, null,
- JOptionPane.INFORMATION_MESSAGE);
- resIndex = -1;
- seqIndex = 0;
}
}
+
+ /**
+ * 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;
+ }
+ 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