import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
private ClientHandle getJalviewHandle()
{
return new ClientHandle("jalview.bin.Jalview",
private ClientHandle getJalviewHandle()
{
return new ClientHandle("jalview.bin.Jalview",
boolean ourprompt = this.promptUser;
this.promptUser = promptUser;
vclient.finalizeClient();
boolean ourprompt = this.promptUser;
this.promptUser = promptUser;
vclient.finalizeClient();
ensureJvVamsas();
VamsasAppDatastore vds = new VamsasAppDatastore(cdoc, vobj2jv, jv2vobj,
baseProvEntry(), alRedoState);
ensureJvVamsas();
VamsasAppDatastore vds = new VamsasAppDatastore(cdoc, vobj2jv, jv2vobj,
baseProvEntry(), alRedoState);
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
if (fromJalview)
{
storedviews += updateVamsasDocument(cdoc);
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
if (fromJalview)
{
storedviews += updateVamsasDocument(cdoc);
"Time taken to update Vamsas Document from jalview\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
cdoc.setVamsasRoots(cdoc.getVamsasRoots());
"Time taken to update Vamsas Document from jalview\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
cdoc.setVamsasRoots(cdoc.getVamsasRoots());
"Time taken to update Jalview from vamsas document Roots\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
"Time taken to update Jalview from vamsas document Roots\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
"Asking user if the vamsas session should be stored.");
int reply = JvOptionPane.showInternalConfirmDialog(
Desktop.desktop,
"Asking user if the vamsas session should be stored.");
int reply = JvOptionPane.showInternalConfirmDialog(
Desktop.desktop,
// bound to "+jvobj+" at "+mm.getPosition());
// position is character position in aligned sequence
ssm.mouseOverVamsasSequence((SequenceI) jvobj,
// bound to "+jvobj+" at "+mm.getPosition());
// position is character position in aligned sequence
ssm.mouseOverVamsasSequence((SequenceI) jvobj,