JAL-1565 automatically mark query sequence as the sequence reference and hide any...

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index dab649e..e022c73 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -2024,6 +2024,12 @@ public class JalviewLite extends Applet implements
                     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