*/
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
MessageManager.getString("label.colourScheme_hydrophobic"));
MenuItem helix = new MenuItem(
- MessageManager.getString("label.colourScheme_helix_propensity"));
+ MessageManager.getString("label.colourScheme_helixpropensity"));
MenuItem strand = new MenuItem(
- MessageManager.getString("label.colourScheme_strand_propensity"));
+ MessageManager.getString("label.colourScheme_strandpropensity"));
MenuItem turn = new MenuItem(
- MessageManager.getString("label.colourScheme_turn_propensity"));
+ MessageManager.getString("label.colourScheme_turnpropensity"));
MenuItem buried = new MenuItem(
- MessageManager.getString("label.colourScheme_buried_index"));
+ MessageManager.getString("label.colourScheme_buriedindex"));
MenuItem purinepyrimidine = new MenuItem(
MessageManager.getString("label.colourScheme_purine/pyrimidine"));
AlignmentPanel ap;
List<AlignmentPanel> _aps = new ArrayList<>(); // remove? never
- // added to
+ // added to
String fileLoadingError;
}
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())
// {
}
}
}
- jmb.centerViewer(toshow);
+ jmb.showChains(toshow);
}
void closeViewer()
{
- jmb.closeViewer();
+ jmb.closeViewer(true);
jmb = null;
this.setVisible(false);
}
else if (evt.getSource() == zappo)
{
setEnabled(zappo);
- jmb.setJalviewColourScheme(new ZappoColourScheme());
+ jmb.colourByJalviewColourScheme(new ZappoColourScheme());
}
else if (evt.getSource() == taylor)
{
setEnabled(taylor);
- jmb.setJalviewColourScheme(new TaylorColourScheme());
+ jmb.colourByJalviewColourScheme(new TaylorColourScheme());
}
else if (evt.getSource() == hydro)
{
setEnabled(hydro);
- jmb.setJalviewColourScheme(new HydrophobicColourScheme());
+ jmb.colourByJalviewColourScheme(new HydrophobicColourScheme());
}
else if (evt.getSource() == helix)
{
setEnabled(helix);
- jmb.setJalviewColourScheme(new HelixColourScheme());
+ jmb.colourByJalviewColourScheme(new HelixColourScheme());
}
else if (evt.getSource() == strand)
{
setEnabled(strand);
- jmb.setJalviewColourScheme(new StrandColourScheme());
+ jmb.colourByJalviewColourScheme(new StrandColourScheme());
}
else if (evt.getSource() == turn)
{
setEnabled(turn);
- jmb.setJalviewColourScheme(new TurnColourScheme());
+ jmb.colourByJalviewColourScheme(new TurnColourScheme());
}
else if (evt.getSource() == buried)
{
setEnabled(buried);
- jmb.setJalviewColourScheme(new BuriedColourScheme());
+ jmb.colourByJalviewColourScheme(new BuriedColourScheme());
}
else if (evt.getSource() == purinepyrimidine)
{
- jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme());
+ jmb.colourByJalviewColourScheme(new PurinePyrimidineColourScheme());
}
else if (evt.getSource() == user)
{
*
* }
*/
- public void setJalviewColourScheme(UserColourScheme ucs)
+ public void colourByJalviewColourScheme(UserColourScheme ucs)
{
- jmb.setJalviewColourScheme(ucs);
+ jmb.colourByJalviewColourScheme(ucs);
}
public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)