JAL-629 Better formatting of Arg.Opt options in usage statement

[jalview.git] / src / jalview / api / AlignViewportI.java

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index d15c5fb..03efec5 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -27,6 +27,8 @@ import jalview.datamodel.AlignmentExportData;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceCollectionI;
@@ -475,6 +477,8 @@ public interface AlignViewportI extends ViewStyleI
    */
   SearchResultsI getSearchResults();
 
+  ContactListI getContactList(AlignmentAnnotation _aa, int column);
+
   /**
    * Updates view settings with the given font. You may need to call
    * AlignmentPanel.fontChanged to update the layout geometry.
@@ -552,4 +556,6 @@ public interface AlignViewportI extends ViewStyleI
    * @return
    */
   Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+
+  ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
 }