}
} catch (InvalidSessionDocumentException e)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString(
"label.vamsas_doc_couldnt_be_opened_as_new_session"),
{
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
VamsasAppDatastore vds = new VamsasAppDatastore(doc, vobj2jv, jv2vobj,
baseProvEntry(), alRedoState);
// wander through frames
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
if (frames == null)
{
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;
}
Cache.log.debug(
"Asking user if the vamsas session should be stored.");
int reply = JvOptionPane.showInternalConfirmDialog(
- Desktop.desktop,
+ Desktop.getDesktopPane(),
"The current VAMSAS session has unsaved data - do you want to save it ?",
"VAMSAS Session Shutdown",
JvOptionPane.YES_NO_OPTION,
if (reply == JvOptionPane.YES_OPTION)
{
Cache.log.debug("Prompting for vamsas store filename.");
- Desktop.instance.vamsasSave_actionPerformed(null);
+ Desktop.getInstance().vamsasSave_actionPerformed(null);
Cache.log
.debug("Finished attempt at storing document.");
}
public void disableGui(boolean b)
{
- Desktop.instance.setVamsasUpdate(b);
+ // JAL-3311 TODO: remove this class!
+ // Desktop.getInstance().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();
{
final IPickManager pm = vclient.getPickManager();
final StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
final VamsasApplication me = this;
pm.registerMessageHandler(new IMessageHandler()
{
}
else
{
- // int[] intervals = colsel.getVisibleContigs(
- // seqsel.getStartRes(), seqsel.getEndRes() + 1);
- int[] intervals = hidden.getVisibleContigs(
- seqsel.getStartRes(), seqsel.getEndRes() + 1);
- for (int iv = 0; iv < intervals.length; iv += 2)
+ Iterator<int[]> intervals = hidden
+ .getVisContigsIterator(seqsel.getStartRes(),
+ seqsel.getEndRes() + 1, false);
+ while (intervals.hasNext())
{
+ int[] region = intervals.next();
Seg s = new Seg();
- s.setStart(intervals[iv] + 1); // vamsas indices begin at
- // 1, not zero.
- s.setEnd(intervals[iv + 1] + 1);
+ s.setStart(region[0] + 1); // vamsas indices begin at 1,
+ // not zero.
+ s.setEnd(region[1] + 1);
s.setInclusive(true);
range.addSeg(s);
}