/*
- * 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
- * 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)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
*/
package jalview.gui;
-import jalview.datamodel.*;
-
-import jalview.jbgui.*;
+import java.util.*;
import java.awt.*;
import java.awt.event.*;
-
-import java.util.*;
-
import javax.swing.*;
-import javax.swing.event.*;
+import jalview.datamodel.*;
+import jalview.jbgui.*;
/**
* DOCUMENT ME!
- *
+ *
* @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()
+ AlignViewport av;
+
+ AlignmentPanel ap;
+
+ JInternalFrame frame;
+
+ int seqIndex = 0;
+
+ int resIndex = -1;
+
+ SearchResults searchResults;
+
+ /**
+ * Creates a new Finder object.
+ *
+ * @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);
+ Desktop.addInternalFrame(frame, "Find", 340, 110);
+
+ textfield.requestFocus();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void findNext_actionPerformed(ActionEvent e)
+ {
+ if (getFocusedViewport())
{
- frame = new JInternalFrame();
- frame.setContentPane(this);
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, "Find", 340, 110);
-
- textfield.requestFocus();
+ doSearch(false);
}
-
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void findNext_actionPerformed(ActionEvent e)
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void findAll_actionPerformed(ActionEvent e)
+ {
+ if (getFocusedViewport())
{
- if (getFocusedViewport())
- doSearch(false);
+ resIndex = -1;
+ seqIndex = 0;
+ doSearch(true);
}
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void findAll_actionPerformed(ActionEvent e)
+ }
+
+ /**
+ * 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()
+ {
+ if (focusfixed || Desktop.desktop == null)
{
- if(getFocusedViewport())
+ if (ap != null && av != null)
{
- resIndex = 0;
- seqIndex = 0;
- doSearch(true);
+ return true;
}
+ // we aren't in a desktop environment, so give up now.
+ return false;
}
-
- boolean getFocusedViewport()
+ // 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 = Desktop.desktop.getAllFrames()[1];
-
- if(frame!=null && frame instanceof AlignFrame)
+ JInternalFrame frame = frames[f];
+ if (frame != null && frame instanceof AlignFrame)
{
- av = ((AlignFrame)frame).viewport;
- ap = ((AlignFrame)frame).alignPanel;
+ av = ((AlignFrame) frame).viewport;
+ ap = ((AlignFrame) frame).alignPanel;
return true;
}
- return false;
}
-
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void createNewGroup_actionPerformed(ActionEvent e)
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void createNewGroup_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] seqs = new SequenceI[searchResults.getSize()];
+ SequenceFeature[] features = new SequenceFeature[searchResults
+ .getSize()];
+
+ for (int i = 0; i < searchResults.getSize(); i++)
{
- 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);
-
+ seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();
- SequenceI [] seqs = new SequenceI[searchResults.getSize()];
- SequenceFeature [] features = new SequenceFeature[searchResults.getSize()];
+ features[i] = new SequenceFeature(textfield.getText().trim(),
+ "Search Results", null, searchResults.getResultStart(i),
+ searchResults.getResultEnd(i), "Search Results");
+ }
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ features, true, ap))
+ {
+ ap.alignFrame.showSeqFeatures.setSelected(true);
+ av.setShowSequenceFeatures(true);
+ ap.highlightSearchResults(null);
+ }
+ }
- for (int i = 0; i < searchResults.getSize(); i ++ )
- {
- seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();
+ /**
+ * incrementally search the alignment
+ *
+ * @param findAll
+ * true means find all results and raise a dialog box
+ */
+ void doSearch(boolean findAll)
+ {
+ createNewGroup.setEnabled(false);
- features[i] = new SequenceFeature(textinput.getText(),
- "Search Results", null,
- searchResults.getResultStart(i),
- searchResults.getResultEnd(i),
- "Search Results");
- }
+ String searchString = textfield.getText().trim();
- if( ap.seqPanel.seqCanvas.getFeatureRenderer()
- .createNewFeatures(seqs, features))
- {
- ap.alignFrame.showSeqFeatures.setSelected(true);
- av.setShowSequenceFeatures(true);
- ap.highlightSearchResults(null);
- }
+ if (searchString.length() < 1)
+ {
+ return;
}
-
- /**
- * DOCUMENT ME!
- *
- * @param findAll DOCUMENT ME!
- */
- void doSearch(boolean findAll)
+ // 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.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();
+ boolean haveResults = false;
+ // set or reset the GUI
+ if ((idMatch.size() > 0))
{
- 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);
- }
-
-
- int resultSize = searchResults.getSize();
+ haveResults = true;
+ ap.idPanel.highlightSearchResults(idMatch);
+ }
+ else
+ {
+ ap.idPanel.highlightSearchResults(null);
+ }
- if (searchResults.getSize() > 0)
- createNewGroup.setEnabled(true);
- else
- searchResults = null;
+ if (searchResults.getSize() > 0)
+ {
+ haveResults = true;
+ createNewGroup.setEnabled(true);
+ }
+ else
+ {
+ searchResults = null;
+ }
- // 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)
- {
- JOptionPane.showInternalMessageDialog(this, "Finished searching",
- null, JOptionPane.INFORMATION_MESSAGE);
- resIndex = 0;
- seqIndex = 0;
- }
+ // 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 (!haveResults)
+ {
+ JOptionPane.showInternalMessageDialog(this, "Finished searching",
+ null, JOptionPane.INFORMATION_MESSAGE);
+ resIndex = -1;
+ seqIndex = 0;
+ }
- if (findAll)
+ if (findAll)
+ {
+ String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
+ : "";
+ if (searchResults != null)
+ {
+ if (idMatch.size() > 0 && searchResults.getSize() > 0)
{
- String message = resultSize + " matches found.";
- JOptionPane.showInternalMessageDialog(this, message, null,
- JOptionPane.INFORMATION_MESSAGE);
+ message += " and ";
}
-
+ message += searchResults.getSize() + " subsequence matches found.";
+ }
+ JOptionPane.showInternalMessageDialog(this, message, null,
+ JOptionPane.INFORMATION_MESSAGE);
+ resIndex = -1;
+ seqIndex = 0;
}
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff