/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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
/**
* 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;
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()
{
/**
* 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 (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!
+ *
+ * @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.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ features, true, ap))
{
ap.alignFrame.showSeqFeatures.setSelected(true);
av.setShowSequenceFeatures(true);
/**
* DOCUMENT ME!
- *
- * @param findAll DOCUMENT ME!
+ *
+ * @param findAll
+ * DOCUMENT ME!
*/
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.alignment, 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();
// set or reset the GUI
- if ( (searchResults.getSize() == 0) && (idMatch.size() > 0))
+ if ((searchResults.getSize() == 0) && (idMatch.size() > 0))
{
ap.idPanel.highlightSearchResults(idMatch);
}
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
+ // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
+ // 'SelectRegion' selection
if (!findAll && resultSize == 0)
{
JOptionPane.showInternalMessageDialog(this, "Finished searching",
- null,
- JOptionPane.INFORMATION_MESSAGE);
+ null, JOptionPane.INFORMATION_MESSAGE);
resIndex = 0;
seqIndex = 0;
}
{
String message = resultSize + " matches found.";
JOptionPane.showInternalMessageDialog(this, message, null,
- JOptionPane.INFORMATION_MESSAGE);
+ JOptionPane.INFORMATION_MESSAGE);
}
}