X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=2a82a32d0c4e81cf5a6116b92f79e4d3251e4ba7;hb=5c1262f120d4fca072bc8fd9800a1a856cc46843;hp=56d25d5b9c013e7d3c204028864fd8620264c9ad;hpb=eccc204bba7aab9101c16df03cc5f740241d9184;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 56d25d5..2a82a32 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -268,6 +268,15 @@ public interface AlignViewportI extends ViewStyleI
   AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups);
 
   /**
+   * @return an alignment view, optionally without a complement view
+   * @param selectedOnly
+   * @param markGroups
+   * @param withComplement - false if no complement view required
+   */
+  AlignmentView getAlignmentViewWithComplement(boolean selectedOnly,
+          boolean markGroups, boolean withComplement);
+
+  /**
    * This method returns the visible alignment as text, as seen on the GUI, ie
    * if columns are hidden they will not be returned in the result. Use this for
    * calculating trees, PCA, redundancy etc on views which contain hidden