selected region output also supports generation of annotations

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 2068b0b..01a0907 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1302,16 +1302,22 @@ public class PopupMenu
 
     String[] omitHidden = null;
 
-    if (ap.av.hasHiddenColumns)
-    {
-      System.out.println("PROMPT USER HERE");
-      omitHidden = ap.av.getViewAsString(true);
+    System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens or we simply trust the user wants wysiwig behaviour
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
+    omitHidden = ap.av.getViewAsString(true);
+    Alignment oal = new Alignment(ap.av.getSequenceSelection());
+    AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
+    for (int i=0; i<nala.length; i++)
+    {
+      AlignmentAnnotation na =nala[i];
+      oal.addAnnotation(na);
     }
-
     cap.setText(new FormatAdapter().formatSequences(
-        e.getActionCommand(),
-        ap.av.getSelectionAsNewSequence(),
-        omitHidden));
+            e.getActionCommand(),
+            oal,
+            omitHidden, csel, sg));
+    oal=null;
   }
 
   public void pdbFromFile_actionPerformed()