/*
* 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.
*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
import jalview.api.AlignViewportI;
import jalview.api.FinderI;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
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.HashMap;
import java.util.List;
import java.util.Map;
public class Finder extends Panel implements ActionListener
{
private AlignViewportI av;
private AlignmentPanel ap;
private TextField textfield = new TextField();
private Button findAll = new Button();
private Button findNext = new Button();
private Button createFeatures = new Button();
private Checkbox caseSensitive = new Checkbox();
private Checkbox searchDescription = new Checkbox();
private SearchResultsI searchResults;
/*
* Finder agent per viewport searched
*/
Map finders;
public Finder(final AlignmentPanel ap)
{
finders = new HashMap<>();
try
{
jbInit();
} catch (Exception e)
{
e.printStackTrace();
}
this.av = ap.av;
this.ap = ap;
Frame frame = new Frame();
frame.add(this);
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)
{
doSearch(false);
}
else if (evt.getSource() == findNext)
{
doSearch(false);
}
else if (evt.getSource() == findAll)
{
doSearch(true);
}
else if (evt.getSource() == createFeatures)
{
createFeatures_actionPerformed();
}
}
public void createFeatures_actionPerformed()
{
List seqs = new ArrayList<>();
List features = new ArrayList<>();
String searchString = textfield.getText().trim();
for (SearchResultMatchI match : searchResults.getResults())
{
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.setShowSequenceFeatures(true);
ap.highlightSearchResults(null);
}
}
void doSearch(boolean doFindAll)
{
if (ap.av.applet.currentAlignFrame != null)
{
ap = ap.av.applet.currentAlignFrame.alignPanel;
av = ap.av;
}
createFeatures.setEnabled(false);
FinderI finder = finders.get(av);
if (finder == null)
{
/*
* first time we searched this viewport
*/
finder = new jalview.analysis.Finder(av);
finders.put(av, finder);
}
String searchString = textfield.getText();
boolean isCaseSensitive = caseSensitive.getState();
boolean doSearchDescription = searchDescription.getState();
if (doFindAll)
{
finder.findAll(searchString, isCaseSensitive, doSearchDescription,
false);
}
else
{
finder.findNext(searchString, isCaseSensitive, doSearchDescription,
false);
}
searchResults = finder.getSearchResults();
List idMatches = finder.getIdMatches();
ap.idPanel.highlightSearchResults(idMatches);
if (searchResults.isEmpty())
{
searchResults = null;
}
else
{
createFeatures.setEnabled(true);
}
// 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 (idMatches.isEmpty() && searchResults == null)
{
ap.alignFrame.statusBar.setText(
MessageManager.getString("label.finished_searching"));
}
else
{
if (doFindAll)
{
String message = (idMatches.size() > 0)
? "" + idMatches.size() + " IDs"
: "";
if (idMatches.size() > 0 && searchResults != null
&& searchResults.getCount() > 0)
{
message += " and ";
}
if (searchResults != null)
{
message += searchResults.getCount() + " subsequence matches.";
}
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 }));
}
}
}
private void jbInit() throws Exception
{
Label jLabel1 = new Label(MessageManager.getString("action.find"));
jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
this.setLayout(null);
textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
textfield.setText("");
textfield.setBounds(new Rectangle(40, 17, 133, 21));
textfield.addKeyListener(new java.awt.event.KeyAdapter()
{
@Override
public void keyTyped(KeyEvent e)
{
textfield_keyTyped();
}
});
textfield.addActionListener(this);
findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
findAll.setLabel(MessageManager.getString("action.find_all"));
findAll.addActionListener(this);
findNext.setEnabled(false);
findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
findNext.setLabel(MessageManager.getString("action.find_next"));
findNext.addActionListener(this);
Panel actionsPanel = new Panel();
actionsPanel.setBounds(new Rectangle(195, 5, 141, 64));
GridLayout gridLayout1 = new GridLayout();
actionsPanel.setLayout(gridLayout1);
gridLayout1.setHgap(0);
gridLayout1.setRows(3);
gridLayout1.setVgap(2);
createFeatures.setEnabled(false);
createFeatures.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
createFeatures.setLabel(MessageManager.getString("label.new_feature"));
createFeatures.addActionListener(this);
caseSensitive.setLabel(MessageManager.getString("label.match_case"));
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(createFeatures, null);
this.add(caseSensitive);
this.add(textfield, null);
this.add(jLabel1, null);
this.add(actionsPanel, null);
this.add(searchDescription);
}
void textfield_keyTyped()
{
findNext.setEnabled(true);
}
}