import jalview.analysis.TreeBuilder;
import jalview.analysis.scoremodels.PIDModel;
import jalview.analysis.scoremodels.ScoreModels;
-import jalview.api.AlignFrameI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.IOException;
+import java.io.UnsupportedEncodingException;
import java.net.URL;
import java.net.URLEncoder;
import java.util.Arrays;
import org.jmol.viewer.Viewer;
-public class AlignFrame extends EmbmenuFrame implements AlignFrameI,
- ActionListener,
+public class AlignFrame extends EmbmenuFrame implements ActionListener,
ItemListener, KeyListener, AlignViewControllerGuiI
{
public AlignViewControllerI avc;
}
else if (source == autoCalculate)
{
- viewport.setAutoCalculateConsensusAndConservation(autoCalculate.getState());
+ viewport.autoCalculateConsensus = autoCalculate.getState();
}
else if (source == sortByTree)
{
try
{
new URL(url);
- url = URLEncoder.encode(url);
+ url = URLEncoder.encode(url, "UTF-8");
}
/*
* When we finally deprecate 1.1 compatibility, we can start to use
{
url = viewport.applet.getCodeBase() + url;
}
+ catch (UnsupportedEncodingException ex)
+ {
+ System.err.println(
+ "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
+ + url);
+ ex.printStackTrace();
+ }
return url;
}