import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Iterator;
-import java.util.List;
import javax.swing.JInternalFrame;
{
if (!inSession())
{
- throw new Error(MessageManager.getString(
- "error.implementation_error_vamsas_operation_not_init"));
+ throw new Error(
+ "Implementation error! Vamsas Operations when client not initialised and connected");
}
addDocumentUpdateHandler();
addStoreDocumentHandler();
{
if (!inSession())
{
- throw new Error(MessageManager
- .getString("error.jalview_no_connected_vamsas_session"));
+ throw new Error("Jalview not connected to Vamsas session");
}
Cache.log.info("Jalview disconnecting from the Vamsas Session.");
try
errorsDuringUpdate = true;
Cache.log.error("Exception synchronizing " + af.getTitle()
+ " "
- + (af.getViewport().viewName == null ? ""
- : " view " + af.getViewport().viewName)
+ + (af.getViewport().getViewName() == null ? ""
+ : " view " + af.getViewport().getViewName())
+ " to document.", e);
stored = false;
}
public void disableGui(boolean b)
{
- Desktop.instance.setVamsasUpdate(b);
+ // JAL-3311 TODO: remove this class!
+ // Desktop.instance.setVamsasUpdate(b);
}
Hashtable _backup_vobj2jv;
return;
}
- throw new Error(MessageManager.getString(
- "error.implementation_error_cannot_recover_vamsas_object_mappings"));
+ throw new Error(
+ "IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made");
}
jv2vobj.clear();
Iterator el = _backup_jv2vobj.entrySet().iterator();
}
else
{
- // int[] intervals = colsel.getVisibleContigs(
- // seqsel.getStartRes(), seqsel.getEndRes() + 1);
- List<int[]> intervals = hidden.getVisibleContigs(
- seqsel.getStartRes(), seqsel.getEndRes() + 1);
- for (int[] region : intervals)
+ Iterator<int[]> intervals = hidden
+ .getVisContigsIterator(seqsel.getStartRes(),
+ seqsel.getEndRes() + 1, false);
+ while (intervals.hasNext())
{
+ int[] region = intervals.next();
Seg s = new Seg();
- s.setStart(region[0] + 1); // vamsas indices begin at
- // 1, not zero.
+ s.setStart(region[0] + 1); // vamsas indices begin at 1,
+ // not zero.
s.setEnd(region[1] + 1);
s.setInclusive(true);
range.addSeg(s);