/*
- * 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.appletgui;
import java.util.*;
import jalview.datamodel.*;
-public class Finder
- extends Panel implements ActionListener
+public class Finder extends Panel implements ActionListener
{
AlignViewport av;
+
AlignmentPanel ap;
+
Frame frame;
SearchResults searchResults;
int seqIndex = 0;
- int resIndex = 0;
+
+ int resIndex = -1;
+
public Finder(final AlignmentPanel ap)
{
try
{
jbInit();
- }
- catch (Exception e)
+ } catch (Exception e)
{
e.printStackTrace();
}
else if (evt.getSource() == findAll)
{
- resIndex = 0;
+ resIndex = -1;
seqIndex = 0;
doSearch(true);
}
public void createNewGroup_actionPerformed()
{
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);
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, ap))
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ features, true, ap))
{
ap.alignFrame.sequenceFeatures.setState(true);
av.showSequenceFeatures(true);
void doSearch(boolean findAll)
{
- if (jalview.bin.JalviewLite.currentAlignFrame != null)
+ if (ap.av.applet.currentAlignFrame != null)
{
- ap = jalview.bin.JalviewLite.currentAlignFrame.alignPanel;
+ ap = ap.av.applet.currentAlignFrame.alignPanel;
av = ap.av;
}
createNewGroup.setEnabled(false);
- jalview.analysis.Finder finder = new jalview.analysis.Finder(av.
- getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
+ jalview.analysis.Finder finder = new jalview.analysis.Finder(
+ av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
finder.setCaseSensitive(caseSensitive.getState());
finder.setFindAll(findAll);
resIndex = finder.getResIndex();
searchResults = finder.getSearchResults();
Vector idMatch = finder.getIdMatch();
-
- if (searchResults.getSize() == 0 && idMatch.size() > 0)
+ boolean haveResults = false;
+ // set or reset the GUI
+ if ((idMatch.size() > 0))
{
+ haveResults = true;
ap.idPanel.highlightSearchResults(idMatch);
}
+ else
+ {
+ ap.idPanel.highlightSearchResults(null);
+ }
if (searchResults.getSize() > 0)
{
+ haveResults = true;
createNewGroup.setEnabled(true);
}
else
{
searchResults = null;
- resIndex = 0;
- seqIndex = 0;
}
- // 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);
-
- if (findAll)
+ // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
+ // 'SelectRegion' selection
+ if (!haveResults)
{
- String message = (searchResults == null ? 0 : searchResults.getSize()) +
- " matches found.";
- ap.alignFrame.statusBar.setText("Search results: " + searchString + " : " +
- message);
+ ap.alignFrame.statusBar.setText("Finished searching.");
+ resIndex = -1;
+ seqIndex = 0;
}
+ else
+ {
+ if (findAll)
+ {
+ String message = (idMatch.size() > 0) ? "" + idMatch.size()
+ + " IDs" : "";
+ if (idMatch.size() > 0 && searchResults != null
+ && searchResults.getSize() > 0)
+ {
+ message += " and ";
+ }
+ if (searchResults != null)
+ {
+ message += searchResults.getSize() + " subsequence matches.";
+ }
+ ap.alignFrame.statusBar.setText("Search results: " + searchString
+ + " : " + message);
+ }
+ else
+ {
+ // TODO: indicate sequence and matching position in status bar
+ ap.alignFrame.statusBar.setText("Found match for " + searchString);
+ }
+ }
}
Label jLabel1 = new Label();
+
protected TextField textfield = new TextField();
+
protected Button findAll = new Button();
+
protected Button findNext = new Button();
+
Panel jPanel1 = new Panel();
+
GridLayout gridLayout1 = new GridLayout();
+
protected Button createNewGroup = new Button();
+
Checkbox caseSensitive = new Checkbox();
- private void jbInit()
- throws Exception
+ private void jbInit() throws Exception
{
jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
jLabel1.setText("Find");
git://source.jalview.org / jalview.git / blobdiff