JAL-244 Fix mismatched vertical positioning of sequences and their labels in wrap...

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

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index b09538e..0cfd03d 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -28,6 +28,7 @@ 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;
@@ -476,6 +477,15 @@ public interface AlignViewportI extends ViewStyleI
    */
   SearchResultsI getSearchResults();
 
+  /**
+   * Retrieve a ContactListI corresponding to column in an annotation row in an
+   * alignment.
+   * 
+   * @param _aa
+   *          - annotation with associated matrix data
+   * @param column
+   *          - column in alignment where _aa is associated
+   */
   ContactListI getContactList(AlignmentAnnotation _aa, int column);
 
   /**
@@ -555,4 +565,6 @@ public interface AlignViewportI extends ViewStyleI
    * @return
    */
   Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+
+  ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
 }