X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=244e6df22223488500709993974b0fedafcfadc0;hb=2cc0663ace7adaa36478db77ca96daa736993890;hp=5668b42312a9e64c0b75ec0ffbc0fe9afed0c93f;hpb=cbfa4d2bc1282662ad88756f1b0b2d8b3b82bd11;p=jalview.git
diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 5668b42..244e6df 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,71 +1,145 @@
/*
- * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.*;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
+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.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.KeyEvent;
+import java.util.ArrayList;
+import java.util.List;
+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.KeyStroke;
+import javax.swing.event.InternalFrameEvent;
/**
- * 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 MY_HEIGHT = 120;
+
+ private static final int MY_WIDTH = 400;
+
+ AlignmentViewport av;
+
AlignmentPanel ap;
+
+ private static final int MIN_WIDTH = 350;
+
+ private static final int MIN_HEIGHT = 120;
+
JInternalFrame frame;
+
int seqIndex = 0;
- int resIndex = 0;
- SearchResults searchResults;
+ int resIndex = -1;
+
+ SearchResultsI 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);
+ frame.addInternalFrameListener(
+ new javax.swing.event.InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosing(InternalFrameEvent e)
+ {
+ closeAction();
+ }
+ });
+ addEscapeHandler();
+ Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
+ MY_WIDTH, MY_HEIGHT);
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+ searchBox.requestFocus();
+ }
- textfield.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()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ closeAction();
+ }
+ });
}
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * Performs the 'Find Next' action.
+ *
+ * @param e
*/
+ @Override
public void findNext_actionPerformed(ActionEvent e)
{
if (getFocusedViewport())
@@ -75,127 +149,254 @@ public class Finder
}
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * Performs the 'Find All' action.
+ *
+ * @param e
*/
+ @Override
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 alignFrame = frames[f];
+ if (alignFrame != null && alignFrame instanceof AlignFrame)
+ {
+ av = ((AlignFrame) alignFrame).viewport;
+ ap = ((AlignFrame) alignFrame).alignPanel;
+ return true;
+ }
}
return false;
}
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * Opens a dialog that allows the user to create sequence features for the
+ * find match results.
*/
- public void createNewGroup_actionPerformed(ActionEvent e)
+ @Override
+ public void createFeatures_actionPerformed()
{
- SequenceI[] seqs = new SequenceI[searchResults.getSize()];
- SequenceFeature[] features = new SequenceFeature[searchResults.getSize()];
+ List seqs = new ArrayList();
+ List features = new ArrayList();
- for (int i = 0; i < searchResults.getSize(); i++)
- {
- seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();
+ String searchString = searchBox.getEditor().getItem().toString().trim();
+ String desc = "Search Results";
- features[i] = new SequenceFeature(textfield.getText().trim(),
- "Search Results", null,
- searchResults.getResultStart(i),
- searchResults.getResultEnd(i),
- "Search Results");
+ /*
+ * assemble dataset sequences, and template new sequence features,
+ * for the amend features dialog
+ */
+ for (SearchResultMatchI match : searchResults.getResults())
+ {
+ seqs.add(match.getSequence().getDatasetSequence());
+ features.add(new SequenceFeature(searchString, desc, match.getStart(),
+ match.getEnd(), desc));
}
- if (ap.seqPanel.seqCanvas.getFeatureRenderer()
- .amendFeatures(seqs, features, true, ap))
+ new FeatureEditor(ap).amendFeatures(seqs, features, true, new Runnable()
{
- ap.alignFrame.showSeqFeatures.setSelected(true);
- av.setShowSequenceFeatures(true);
- ap.highlightSearchResults(null);
- }
+ @Override
+ public void run()
+ {
+
+ /*
+ * ensure feature display is turned on to show the new features,
+ * and remove them as highlighted regions
+ */
+ ap.alignFrame.showSeqFeatures.setSelected(true);
+ av.setShowSequenceFeatures(true);
+ ap.highlightSearchResults(null);
+ }
+ });
}
/**
- * 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 doFindAll
*/
- void doSearch(boolean findAll)
+ void doSearch(boolean doFindAll)
{
- createNewGroup.setEnabled(false);
+ createFeatures.setEnabled(false);
- String searchString = textfield.getText().trim();
+ String searchString = searchBox.getUserInput().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.setFindAll(findAll);
+ finder.setIncludeDescription(searchDescription.isSelected());
+
+ finder.setFindAll(doFindAll);
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();
+ 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)
{
- createNewGroup.setEnabled(true);
+ haveResults = true;
+ createFeatures.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;
+ JvOptionPane.showInternalMessageDialog(this,
+ MessageManager.getString("label.finished_searching"), null,
+ JvOptionPane.INFORMATION_MESSAGE);
+ resIndex = -1;
seqIndex = 0;
}
+ else
+ {
+ if (doFindAll)
+ {
+ // 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.";
+ }
+ JvOptionPane.showInternalMessageDialog(this, message, null,
+ JvOptionPane.INFORMATION_MESSAGE);
+ resIndex = -1;
+ seqIndex = 0;
+ }
+ }
+ searchBox.updateCache();
+ }
+
+ /**
+ * 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;
+ }
- if (findAll)
+ /**
+ * 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)
{
- String message = resultSize + " matches found.";
- JOptionPane.showInternalMessageDialog(this, message, null,
- JOptionPane.INFORMATION_MESSAGE);
+ 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();
+ }
}
}