{
if (sess != null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_cannot_import_vamsas_doc"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_cannot_import_vamsas_doc"));
}
try
{
}
} catch (InvalidSessionDocumentException e)
{
- JvOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager
- .getString("label.vamsas_doc_couldnt_be_opened_as_new_session"),
- MessageManager
- .getString("label.vamsas_document_import_failed"),
- JvOptionPane.ERROR_MESSAGE);
+ MessageManager.getString(
+ "label.vamsas_doc_couldnt_be_opened_as_new_session"),
+ MessageManager
+ .getString("label.vamsas_document_import_failed"),
+ JvOptionPane.ERROR_MESSAGE);
}
}
} catch (Exception e)
{
- jalview.bin.Cache.log
- .error("Couldn't instantiate vamsas client !", e);
+ jalview.bin.Cache.log.error("Couldn't instantiate vamsas client !",
+ e);
return false;
}
return true;
}
} catch (Error e)
{
- Cache.log
- .warn("Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",
- e);
+ Cache.log.warn(
+ "Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",
+ e);
} catch (Exception e)
{
- Cache.log
- .warn("Probable VAMSAS client incompatibility - carrying on regardless",
- e);
+ Cache.log.warn(
+ "Probable VAMSAS client incompatibility - carrying on regardless",
+ e);
}
}
if (!inSession())
{
throw new Error(
- MessageManager
- .getString("error.implementation_error_vamsas_operation_not_init"));
+ "Implementation error! Vamsas Operations when client not initialised and connected");
}
addDocumentUpdateHandler();
addStoreDocumentHandler();
startSession();
inInitialUpdate = true;
- Cache.log
- .debug("Jalview loading the Vamsas Session for the first time.");
+ Cache.log.debug(
+ "Jalview loading the Vamsas Session for the first time.");
dealWithDocumentUpdate(false); // we don't push an update out to the
inInitialUpdate = false;
// document yet.
}
} catch (Exception e)
{
- Cache.log
- .warn("Exception whilst refreshing jalview windows after a vamsas document update.",
- e);
+ Cache.log.warn(
+ "Exception whilst refreshing jalview windows after a vamsas document update.",
+ e);
}
}
{
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
}
else
{
- Cache.log
- .warn("JV Client leaving a session that's its not joined yet.");
+ Cache.log.warn(
+ "JV Client leaving a session that's its not joined yet.");
}
joinedSession = false;
vclient = null;
} catch (Exception e)
{
errorsDuringUpdate = true;
- Cache.log.error("Exception synchronizing "
- + af.getTitle()
+ 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;
}
storedviews += updateVamsasDocument(cdoc);
if (Cache.log.isDebugEnabled())
{
- Cache.log
- .debug("Time taken to update Vamsas Document from jalview\t= "
+ Cache.log.debug(
+ "Time taken to update Vamsas Document from jalview\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
updateJalview(cdoc);
if (Cache.log.isDebugEnabled())
{
- Cache.log
- .debug("Time taken to update Jalview from vamsas document Roots\t= "
+ Cache.log.debug(
+ "Time taken to update Jalview from vamsas document Roots\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
{
if (client.promptUser)
{
- Cache.log
- .debug("Asking user if the vamsas session should be stored.");
- int reply = JvOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- "The current VAMSAS session has unsaved data - do you want to save it ?",
- "VAMSAS Session Shutdown",
- JvOptionPane.YES_NO_OPTION,
- JvOptionPane.QUESTION_MESSAGE);
+ Cache.log.debug(
+ "Asking user if the vamsas session should be stored.");
+ int reply = JvOptionPane.showInternalConfirmDialog(
+ Desktop.desktop,
+ "The current VAMSAS session has unsaved data - do you want to save it ?",
+ "VAMSAS Session Shutdown",
+ JvOptionPane.YES_NO_OPTION,
+ JvOptionPane.QUESTION_MESSAGE);
if (reply == JvOptionPane.YES_OPTION)
{
Cache.log
.debug("Finished attempt at storing document.");
}
- Cache.log
- .debug("finished dealing with REQUESTTOCLOSE event.");
+ Cache.log.debug(
+ "finished dealing with REQUESTTOCLOSE event.");
}
else
{
- Cache.log
- .debug("Ignoring store document request (promptUser==false)");
+ Cache.log.debug(
+ "Ignoring store document request (promptUser==false)");
}
}
});
public void disableGui(boolean b)
{
- Desktop.instance.setVamsasUpdate(b);
+ // JAL-3311 TODO: remove this class!
+ // Desktop.instance.setVamsasUpdate(b);
}
Hashtable _backup_vobj2jv;
}
throw new Error(
- MessageManager
- .getString("error.implementation_error_cannot_recover_vamsas_object_mappings"));
+ "IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made");
}
jv2vobj.clear();
Iterator el = _backup_jv2vobj.entrySet().iterator();
{
jselection.setStartRes(prange[p + l] - 1);
}
- if (jselection.getEndRes() <= maxWidth
- && prange[p + u] == (jselection.getEndRes() + 2))
+ if (jselection.getEndRes() <= maxWidth && prange[p
+ + u] == (jselection.getEndRes() + 2))
{
jselection.setEndRes(prange[p + u] - 1);
}
{
if (vobj2jv == null)
{
- Cache.log
- .warn("Selection listener still active for dead session.");
+ Cache.log.warn(
+ "Selection listener still active for dead session.");
// not in a session.
return;
}
}
SelectionMessage sm = null;
if ((seqsel == null || seqsel.getSize() == 0)
- && (colsel == null || colsel.getSelected() == null || colsel
- .getSelected().size() == 0))
+ && (colsel == null || colsel.getSelected() == null
+ || colsel.getSelected().size() == 0))
{
if (source instanceof AlignViewport)
{
// the empty selection.
sm = new SelectionMessage("jalview",
- new String[] { ((AlignmentViewport) source)
- .getSequenceSetId() }, null, true);
+ new String[]
+ { ((AlignmentViewport) source)
+ .getSequenceSetId() },
+ null, true);
}
else
{
}
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);
}