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Merge branch 'develop' into trialMerge
[jalview.git]
/
src
/
jalview
/
appletgui
/
AppletJmol.java
diff --git
a/src/jalview/appletgui/AppletJmol.java
b/src/jalview/appletgui/AppletJmol.java
index
18e7d1a
..
9d4779c
100644
(file)
--- a/
src/jalview/appletgui/AppletJmol.java
+++ b/
src/jalview/appletgui/AppletJmol.java
@@
-61,7
+61,6
@@
import java.awt.event.KeyListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.util.ArrayList;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.util.ArrayList;
-import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
import java.util.List;
import java.util.Vector;
@@
-182,7
+181,7
@@
public class AppletJmol extends EmbmenuFrame implements
this.ap = ap;
jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
this.ap = ap;
jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
- new String[][] { chains }, protocol);
+ protocol);
jmb.setColourBySequence(true);
if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
{
jmb.setColourBySequence(true);
if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
{
@@
-291,12
+290,9
@@
public class AppletJmol extends EmbmenuFrame implements
closeViewer();
}
});
closeViewer();
}
});
- if (pdbentry.getProperty() == null)
- {
- pdbentry.setProperty(new Hashtable<String, String>());
- pdbentry.getProperty().put("protocol", protocol.toString());
- }
+ pdbentry.setProperty("protocol", protocol);
if (pdbentry.getFile() != null)
if (pdbentry.getFile() != null)
+
{
// import structure data from pdbentry.getFile based on given protocol
if (protocol == DataSourceType.PASTE)
{
// import structure data from pdbentry.getFile based on given protocol
if (protocol == DataSourceType.PASTE)
@@
-374,7
+370,7
@@
public class AppletJmol extends EmbmenuFrame implements
jmb.loadInline(string);
}
jmb.loadInline(string);
}
- void setChainMenuItems(Vector<String> chains)
+ void setChainMenuItems(List<String> chains)
{
chainMenu.removeAll();
{
chainMenu.removeAll();
@@
-593,7
+589,7
@@
public class AppletJmol extends EmbmenuFrame implements
repaint();
return;
}
repaint();
return;
}
- setChainMenuItems(jmb.chainNames);
+ setChainMenuItems(jmb.getChainNames());
jmb.colourBySequence(ap);
setTitle(jmb.getViewerTitle());
jmb.colourBySequence(ap);
setTitle(jmb.getViewerTitle());