import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
private String getStage(Stage stg)
{
if (stg == Stage.SUBMIT)
+ {
return "submitting ";
+ }
if (stg == Stage.POLL)
+ {
return "checking status of ";
+ }
return (" being confused about ");
}
// total number of distinct alignment sets generated by job set.
int numAlSets = 0, als = 0;
List<AlignmentI> destAls = new ArrayList<AlignmentI>();
- List<jalview.datamodel.ColumnSelection> destColsel = new ArrayList<jalview.datamodel.ColumnSelection>();
+ List<jalview.datamodel.HiddenColumns> destColsel = new ArrayList<jalview.datamodel.HiddenColumns>();
List<List<NewickFile>> trees = new ArrayList<List<NewickFile>>();
do
RestJob rj = (RestJob) jobs[nrj];
int contigs[] = input.getVisibleContigs();
AlignmentI destAl = null;
- jalview.datamodel.ColumnSelection destCs = null;
+ jalview.datamodel.HiddenColumns destHCs = null;
// Resolve destAl for this data.
if (als == 0 && rj.isInputContextModified())
{
if (!restClient.isAlignmentModified() && merge)
{
destAl = restClient.av.getAlignment();
- destCs = restClient.av.getColumnSelection();
+ destHCs = restClient.av.getAlignment().getHiddenColumns();
resultDest
.add(restClient.isShowResultsInNewView() ? AddDataTo.newView
: AddDataTo.currentView);
newAlignment = true;
// recreate the input alignment data
Object[] idat = input
- .getAlignmentAndColumnSelection(gapCharacter);
+ .getAlignmentAndHiddenColumns(gapCharacter);
destAl = new Alignment((SequenceI[]) idat[0]);
- destCs = (ColumnSelection) idat[1];
+ destHCs = (HiddenColumns) idat[1];
resultDest.add(AddDataTo.newAlignment);
// but do not add to the alignment panel list - since we need to
// create a whole new alignFrame set.
}
destAls.add(destAl);
- destColsel.add(destCs);
+ destColsel.add(destHCs);
}
}
else
// recover reference to last alignment created for this rest frame
// ready for extension
destAl = destAls.get(als);
- destCs = destColsel.get(als);
+ destHCs = destColsel.get(als);
}
else
{
newview = input.getUpdatedView(rseqs, orders, gapCharacter);
}
destAl = new Alignment((SequenceI[]) newview[0]);
- destCs = (ColumnSelection) newview[1];
+ destHCs = (HiddenColumns) newview[1];
newAlignment = true;
// TODO create alignment from result data with propagated
// references.
destAls.add(destAl);
- destColsel.add(destCs);
+ destColsel.add(destHCs);
resultDest.add(AddDataTo.newAlignment);
throw new Error(
MessageManager
for (AddDataTo action : resultDest)
{
AlignmentI destal;
- ColumnSelection destcs;
+ HiddenColumns destcs;
String alTitle = MessageManager.formatMessage(
"label.webservice_job_title_on", new String[] {
restClient.service.details.Action,