Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 5715a95..ba3ed75 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -34,6 +34,8 @@ 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;
@@ -477,6 +479,17 @@ 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);
+
+  /**
    * Updates view settings with the given font. You may need to call
    * AlignmentPanel.fontChanged to update the layout geometry.
    * 
@@ -555,4 +568,6 @@ public interface AlignViewportI extends ViewStyleI
   Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
 
   IdColumns getIdColumns();
+
+  ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
 }