/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ * 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/>.
+ * 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 java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Button;
+import java.awt.Checkbox;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.GridLayout;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.Rectangle;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Vector;
public class Finder extends Panel implements ActionListener
{
- AlignViewport av;
+ AlignmentViewport av;
AlignmentPanel ap;
Frame frame;
- SearchResults searchResults;
+ SearchResultsI searchResults;
int seqIndex = 0;
this.ap = ap;
frame = new Frame();
frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.find"), 340, 120);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("action.find"), 340, 120);
frame.repaint();
frame.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent evt)
{
ap.highlightSearchResults(null);
textfield.requestFocus();
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == textfield)
public void createNewGroup_actionPerformed()
{
- SequenceI[] seqs = new SequenceI[searchResults.getSize()];
- SequenceFeature[] features = new SequenceFeature[searchResults
- .getSize()];
+ List<SequenceI> seqs = new ArrayList<SequenceI>();
+ List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+ String searchString = textfield.getText().trim();
- for (int i = 0; i < searchResults.getSize(); i++)
+ for (SearchResultMatchI match : searchResults.getResults())
{
- seqs[i] = searchResults.getResultSequence(i);
-
- features[i] = new SequenceFeature(textfield.getText().trim(),
- "Search Results", null, searchResults.getResultStart(i),
- searchResults.getResultEnd(i), "Search Results");
+ seqs.add(match.getSequence().getDatasetSequence());
+ features.add(new SequenceFeature(searchString, "Search Results",
+ match.getStart(), match.getEnd(), "Search Results"));
}
if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
features, true, ap))
{
ap.alignFrame.sequenceFeatures.setState(true);
- av.showSequenceFeatures(true);
+ av.setShowSequenceFeatures(true);
ap.highlightSearchResults(null);
}
}
jalview.analysis.Finder finder = new jalview.analysis.Finder(
av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
finder.setCaseSensitive(caseSensitive.getState());
+ finder.setIncludeDescription(searchDescription.getState());
finder.setFindAll(findAll);
String searchString = textfield.getText();
seqIndex = finder.getSeqIndex();
resIndex = finder.getResIndex();
searchResults = finder.getSearchResults();
- Vector idMatch = finder.getIdMatch();
+ Vector<SequenceI> idMatch = finder.getIdMatch();
boolean haveResults = false;
// set or reset the GUI
if ((idMatch.size() > 0))
// 'SelectRegion' selection
if (!haveResults)
{
- ap.alignFrame.statusBar.setText(MessageManager.getString("label.finished_searching"));
+ ap.alignFrame.statusBar.setText(
+ MessageManager.getString("label.finished_searching"));
resIndex = -1;
seqIndex = 0;
}
{
if (findAll)
{
- String message = (idMatch.size() > 0) ? "" + idMatch.size()
- + " IDs" : "";
+ String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
+ : "";
if (idMatch.size() > 0 && searchResults != null
&& searchResults.getSize() > 0)
{
{
message += searchResults.getSize() + " subsequence matches.";
}
- ap.alignFrame.statusBar.setText(MessageManager.formatMessage("label.search_results", new String[] {searchString, message}));
+ ap.alignFrame.statusBar.setText(MessageManager
+ .formatMessage("label.search_results", new String[]
+ { searchString, message }));
}
else
{
// TODO: indicate sequence and matching position in status bar
- ap.alignFrame.statusBar.setText(MessageManager.formatMessage("label.found_match_for", new String[]{searchString}));
+ ap.alignFrame.statusBar.setText(MessageManager
+ .formatMessage("label.found_match_for", new String[]
+ { searchString }));
}
}
}
protected Button findNext = new Button();
- Panel jPanel1 = new Panel();
+ Panel actionsPanel = new Panel();
GridLayout gridLayout1 = new GridLayout();
Checkbox caseSensitive = new Checkbox();
+ Checkbox searchDescription = new Checkbox();
+
private void jbInit() throws Exception
{
jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
this.setLayout(null);
textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
textfield.setText("");
- textfield.setBounds(new Rectangle(40, 27, 133, 21));
+ textfield.setBounds(new Rectangle(40, 17, 133, 21));
textfield.addKeyListener(new java.awt.event.KeyAdapter()
{
+ @Override
public void keyTyped(KeyEvent e)
{
textfield_keyTyped(e);
findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
findNext.setLabel(MessageManager.getString("action.find_next"));
findNext.addActionListener(this);
- jPanel1.setBounds(new Rectangle(180, 5, 141, 64));
- jPanel1.setLayout(gridLayout1);
+ actionsPanel.setBounds(new Rectangle(195, 5, 141, 64));
+ actionsPanel.setLayout(gridLayout1);
gridLayout1.setHgap(0);
gridLayout1.setRows(3);
gridLayout1.setVgap(2);
createNewGroup.setLabel(MessageManager.getString("label.new_feature"));
createNewGroup.addActionListener(this);
caseSensitive.setLabel(MessageManager.getString("label.match_case"));
- caseSensitive.setBounds(new Rectangle(40, 49, 126, 23));
- jPanel1.add(findNext, null);
- jPanel1.add(findAll, null);
- jPanel1.add(createNewGroup, null);
+ caseSensitive.setBounds(new Rectangle(30, 39, 126, 23));
+
+ searchDescription.setLabel(
+ MessageManager.getString("label.include_description"));
+ searchDescription.setBounds(new Rectangle(30, 59, 170, 23));
+ actionsPanel.add(findNext, null);
+ actionsPanel.add(findAll, null);
+ actionsPanel.add(createNewGroup, null);
this.add(caseSensitive);
this.add(textfield, null);
this.add(jLabel1, null);
- this.add(jPanel1, null);
+ this.add(actionsPanel, null);
+ this.add(searchDescription);
}
void textfield_keyTyped(KeyEvent e)
git://source.jalview.org / jalview.git / blobdiff