/*
- * 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
- * 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.
- *
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import java.util.*;
-import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class Finder
- extends GFinder
+public class Finder extends GFinder
{
AlignViewport 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!
+ *
+ * @param av
+ * DOCUMENT ME!
+ * @param ap
+ * DOCUMENT ME!
+ * @param f
+ * DOCUMENT ME!
*/
public Finder()
{
+ this(null, null);
+ focusfixed = false;
+ }
+
+ public Finder(AlignViewport viewport, AlignmentPanel alignPanel)
+ {
+ av = viewport;
+ ap = alignPanel;
+ focusfixed = true;
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void findNext_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
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)
{
- av = ( (AlignFrame) frame).viewport;
- ap = ( (AlignFrame) frame).alignPanel;
- return true;
+ 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++)
+ {
+ 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)
{
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(textfield.getText().trim(),
- "Search Results", null,
- searchResults.getResultStart(i),
- searchResults.getResultEnd(i),
- "Search Results");
+ "Search Results", null, searchResults.getResultStart(i),
+ searchResults.getResultEnd(i), "Search Results");
}
- if (ap.seqPanel.seqCanvas.getFeatureRenderer()
- .createNewFeatures(seqs, features))
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ features, true, ap))
{
ap.alignFrame.showSeqFeatures.setSelected(true);
av.setShowSequenceFeatures(true);
}
/**
- * DOCUMENT ME!
- *
- * @param findAll DOCUMENT ME!
+ * incrementally search the alignment
+ *
+ * @param findAll
+ * true means find all results and raise a dialog box
*/
void doSearch(boolean findAll)
{
{
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);
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))
{
+ haveResults = true;
ap.idPanel.highlightSearchResults(idMatch);
}
-
- int resultSize = searchResults.getSize();
+ else
+ {
+ ap.idPanel.highlightSearchResults(null);
+ }
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;
+ null, JOptionPane.INFORMATION_MESSAGE);
+ resIndex = -1;
seqIndex = 0;
}
if (findAll)
{
- String message = resultSize + " matches 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);
+ JOptionPane.INFORMATION_MESSAGE);
+ resIndex = -1;
+ seqIndex = 0;
}
}
git://source.jalview.org / jalview.git / blobdiff