X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=03efec5dfeec0f609c3f4f6071ecd977ac3b0a7b;hb=e134764b7eec841cb56a417250f2dd898680f985;hp=93a51017a7071463bb7761cc04301ad5f08d9e78;hpb=6b13a606027284408286d1cd2833470d1f9b9bfe;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 93a5101..03efec5 100644
--- 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.
@@ -546,10 +550,12 @@ public interface AlignViewportI extends ViewStyleI
    * regions of the alignment
    * 
    * @param selectedRegionOnly
-   *                             if true, and the view has a selection region,
-   *                             then only the intersection of visible columns
-   *                             with the selection region is returned
+   *          if true, and the view has a selection region, then only the
+   *          intersection of visible columns with the selection region is
+   *          returned
    * @return
    */
   Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+
+  ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
 }