*/
package jalview.gui;
+import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
-import java.util.Vector;
-import javax.swing.JCheckBoxMenuItem;
import javax.swing.JPanel;
import javax.swing.JSplitPane;
import javax.swing.SwingUtilities;
@Override
void showSelectedChains()
{
- Vector<String> toshow = new Vector<>();
- for (int i = 0; i < chainMenu.getItemCount(); i++)
- {
- if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
- {
- JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
- if (item.isSelected())
- {
- toshow.addElement(item.getText());
- }
- }
- }
- jmb.centerViewer(toshow);
+ setSelectedChains();
+ jmb.centerViewer();
}
@Override
for (String s : files)
{
fileList.append(SPACE).append(QUOTE)
- .append(Platform.escapeString(s)).append(QUOTE);
+ .append(Platform.escapeBackslashes(s)).append(QUOTE);
}
String filesString = fileList.toString();
}
// refresh the sequence colours for the new structure(s)
- for (AlignmentPanel ap : _colourwith)
+ for (AlignmentViewPanel avp : _colourwith)
{
- jmb.updateColours(ap);
+ jmb.updateColours(avp);
}
// do superposition if asked to
if (alignAddedStructures)
addingStructures = true; // already files loaded.
for (int c = 0; c < filesInViewer.length; c++)
{
- if (filesInViewer[c].equals(file))
+ if (Platform.pathEquals(filesInViewer[c], file))
{
file = null;
break;