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[jalview.git]
/
src
/
jalview
/
appletgui
/
ExtJmol.java
diff --git
a/src/jalview/appletgui/ExtJmol.java
b/src/jalview/appletgui/ExtJmol.java
index
929a871
..
7a48770
100644
(file)
--- a/
src/jalview/appletgui/ExtJmol.java
+++ b/
src/jalview/appletgui/ExtJmol.java
@@
-26,6
+26,8
@@
import jalview.api.SequenceRenderer;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.gui.IProgressIndicator;
+import jalview.io.DataSourceType;
import java.awt.Container;
import java.util.ArrayList;
import java.awt.Container;
import java.util.ArrayList;
@@
-48,12
+50,12
@@
public class ExtJmol extends JalviewJmolBinding
private AlignmentPanel ap;
private AlignmentPanel ap;
- protected ExtJmol(jalview.appletgui.AlignFrame alframe,
- PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
- String protocol)
+ protected ExtJmol(AlignFrame alframe,
+ PDBEntry[] pdbentry, SequenceI[][] seq,
+ DataSourceType protocol)
{
super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
{
super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
- chains, protocol);
+ protocol);
}
public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,
}
public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,
@@
-64,6
+66,14
@@
public class ExtJmol extends JalviewJmolBinding
notifyFileLoaded(null, null, null, null, 0);
}
notifyFileLoaded(null, null, null, null, 0);
}
+ @Override
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ // no progress indicators on applet (could access javascript for this)
+ return null;
+ }
+
+ @Override
public void updateColours(Object source)
{
public void updateColours(Object source)
{
@@
-71,6
+81,7
@@
public class ExtJmol extends JalviewJmolBinding
}
}
+ @Override
public void showUrl(String arg0)
{
showUrl(arg0, "jmol");
public void showUrl(String arg0)
{
showUrl(arg0, "jmol");
@@
-79,10
+90,10
@@
public class ExtJmol extends JalviewJmolBinding
@Override
public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
@Override
public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
- AlignmentPanel ap = (AlignmentPanel) alignment;
- if (ap.av.isShowSequenceFeatures())
+ AlignmentPanel alignPanel = (AlignmentPanel) alignment;
+ if (alignPanel.av.isShowSequenceFeatures())
{
{
- return ap.getFeatureRenderer();
+ return alignPanel.getFeatureRenderer();
}
else
{
}
else
{
@@
-90,6
+101,7
@@
public class ExtJmol extends JalviewJmolBinding
}
}
}
}
+
@Override
public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
@Override
public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
@@
-126,6
+138,7
@@
public class ExtJmol extends JalviewJmolBinding
// ignore
}
// ignore
}
+ @Override
public void selectionChanged(BS arg0)
{
System.out.println(arg0);
public void selectionChanged(BS arg0)
{
System.out.println(arg0);