/**
* bind an alignment view to an external Jmol instance.
+ *
* @author JimP
- *
+ *
*/
public class ExtJmol extends JalviewJmolBinding
{
private AlignmentPanel ap;
- protected ExtJmol(jalview.appletgui.AlignFrame alframe, PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
+ protected ExtJmol(jalview.appletgui.AlignFrame alframe,
+ PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
String protocol)
{
super(pdbentry, seq, chains, protocol);
public void updateColours(Object source)
{
-
+
// TODO Auto-generated method stub
}
Vector pdbe = new Vector();
Hashtable fileids = new Hashtable();
SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
- for (int s=0;s<sq.length;s++)
+ for (int s = 0; s < sq.length; s++)
{
Vector pdbids = sq[s].getPDBId();
- if (pdbids!=null)
+ if (pdbids != null)
{
- for (int pe=0,peSize=pdbids.size(); pe<peSize; pe++)
+ for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
{
PDBEntry pentry = (PDBEntry) pdbids.elementAt(pe);
- if (!fileids.containsKey(pentry.getId())) {
+ if (!fileids.containsKey(pentry.getId()))
+ {
pdbe.addElement(pentry);
}
}
}
}
pdbentry = new PDBEntry[pdbe.size()];
- for (int pe=0;pe<pdbe.size(); pe++)
+ for (int pe = 0; pe < pdbe.size(); pe++)
{
pdbentry[pe] = (PDBEntry) pdbe.elementAt(pe);
}
@Override
public void showConsole(boolean show)
{
- // This never gets called because we haven't overriden the associated Jmol's console
- System.err.println("WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="+show);
+ // This never gets called because we haven't overriden the associated Jmol's
+ // console
+ System.err
+ .println("WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
+ + show);
}
@Override
// TODO Auto-generated method stub
return null;
}
+
@Override
protected void releaseUIResources()
{
ap = null;
- if (console!=null) {
- try {
+ if (console != null)
+ {
+ try
+ {
console.setVisible(false);
- } catch (Error e) {} catch (Exception x) {};
- console=null;
+ } catch (Error e)
+ {
+ } catch (Exception x)
+ {
+ }
+ ;
+ console = null;
}
-
+
}
}