/*
- * 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 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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.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();
}
ap.highlightSearchResults(null);
}
});
+ textfield.requestFocus();
}
public void actionPerformed(ActionEvent evt)
else if (evt.getSource() == findAll)
{
- resIndex = 0;
+ resIndex = -1;
seqIndex = 0;
doSearch(true);
}
public void createNewGroup_actionPerformed()
{
-
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, null);
- cap.accept.setLabel("Accept");
- Dialog dialog = new Dialog(ap.alignFrame, "Enter New Feature Name", true);
- dialog.add(cap);
-
- cap.setText(textfield.getText());
-
- dialog.setBounds(frame.getLocation().x + frame.getSize().width + 5,
- frame.getLocation().y + 20, 300, 100);
- dialog.show();
-
- String featureName = cap.getText().trim();
- if (featureName.length() < 1)
- {
- return;
- }
+ SequenceI[] seqs = new SequenceI[searchResults.getSize()];
+ SequenceFeature[] features = new SequenceFeature[searchResults
+ .getSize()];
for (int i = 0; i < searchResults.getSize(); i++)
{
- SequenceI seq = searchResults.getResultSequence(i);
+ seqs[i] = searchResults.getResultSequence(i);
- SequenceFeature sf = new SequenceFeature(featureName,
- null, null,
- searchResults.getResultStart(i),
- searchResults.getResultEnd(i),
- "Search Results");
-
- ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
- featureName, new Color(60, 160, 115));
- seq.addSequenceFeature(sf);
+ features[i] = new SequenceFeature(textfield.getText().trim(),
+ "Search Results", null, searchResults.getResultStart(i),
+ searchResults.getResultEnd(i), "Search Results");
}
- ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();
- ap.alignFrame.sequenceFeatures.setState(true);
- av.showSequenceFeatures(true);
- ap.highlightSearchResults(null);
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ features, true, ap))
+ {
+ ap.alignFrame.sequenceFeatures.setState(true);
+ av.showSequenceFeatures(true);
+ ap.highlightSearchResults(null);
+ }
}
void doSearch(boolean findAll)
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);
-
+ // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
+ // 'SelectRegion' selection
+ if (!haveResults)
+ {
+ ap.alignFrame.statusBar.setText("Finished searching.");
+ resIndex = -1;
+ seqIndex = 0;
+ }
if (findAll)
{
- String message = (searchResults == null ? 0 : searchResults.getSize()) +
- " matches found.";
- ap.alignFrame.statusBar.setText("Search results: " + searchString + " : " +
- message);
+ 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);
+
}
}
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