param, protocol);
JnetAnnotationMaker.add_annotation(predictions,
newAlignFrame.viewport.getAlignment(), 0, false); // false==do
+ SequenceI repseq = newAlignFrame.viewport.getAlignment()
+ .getSequenceAt(0);
+ newAlignFrame.viewport.getAlignment().setSeqrep(repseq);
+ ColumnSelection cs = new ColumnSelection();
+ cs.hideInsertionsFor(repseq);
+ newAlignFrame.viewport.setColumnSelection(cs);
// not
// add
// sequence