*/
package jalview.appletgui;
-import jalview.bin.JalviewLite;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.DataSourceType;
-import jalview.io.FileParse;
-import jalview.io.StructureFile;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.UserColourScheme;
-import jalview.schemes.ZappoColourScheme;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.CheckboxMenuItem;
import java.awt.Color;
import java.util.List;
import java.util.Vector;
+import jalview.bin.JalviewLite;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.StructureFile;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+
public class AppletJmol extends EmbmenuFrame implements
// StructureListener,
KeyListener, ActionListener, ItemListener
}
FileParse fp = new FileParse(pdbentry.getFile(), protocol);
fp.mark();
- // reader = new MCview.PDBfile(fp);
+ // reader = new mc_view.PDBfile(fp);
// could set ID, etc.
// if (!reader.isValid())
// {
void centerViewer()
{
- Vector<String> toshow = new Vector<>();
+ Vector<String> toHide = new Vector<>();
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
{
CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
- if (item.getState())
+ if (!item.getState())
{
- toshow.addElement(item.getLabel());
+ toHide.addElement(item.getLabel());
}
}
}
- jmb.showChains(toshow);
+ jmb.setChainsToHide(toHide);
+ jmb.centerViewer();
}
void closeViewer()
{
- jmb.closeViewer();
+ jmb.closeViewer(true);
jmb = null;
this.setVisible(false);
}
else if (evt.getSource() == seqColour)
{
setEnabled(seqColour);
- jmb.colourBySequence(ap);
+ jmb.updateStructureColours(ap);
}
else if (!allChainsSelected)
{
public void updateColours(Object source)
{
AlignmentPanel panel = (AlignmentPanel) source;
- jmb.colourBySequence(panel);
+ jmb.updateStructureColours(panel);
}
public void updateTitleAndMenus()
return;
}
setChainMenuItems(jmb.getChainNames());
- jmb.colourBySequence(ap);
+ jmb.updateStructureColours(ap);
setTitle(jmb.getViewerTitle());
}