X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=e7afee0b9bd8ea2f9323171549e0d296d9c96f46;hb=c8d80485038ab96fb06bd0885c323803646d8e57;hp=d15c5fb21a9a23e67d7b8c2b707dae5f77db0e63;hpb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index d15c5fb..e7afee0 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -20,6 +20,13 @@
  */
 package jalview.api;
 
+import java.awt.Color;
+import java.awt.Font;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
 import jalview.analysis.Conservation;
 import jalview.analysis.TreeModel;
 import jalview.datamodel.AlignmentAnnotation;
@@ -27,6 +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;
@@ -36,13 +45,6 @@ import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
 import jalview.viewmodel.ViewportRanges;
 
-import java.awt.Color;
-import java.awt.Font;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
 /**
  * @author jimp
  * 
@@ -476,6 +478,17 @@ 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.
    * 
@@ -552,4 +565,16 @@ public interface AlignViewportI extends ViewStyleI
    * @return
    */
   Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+  /**
+   * notify all concerned that the alignment data has changed and derived data
+   * needs to be recalculated
+   */
+  public void notifyAlignmentChanged();
+
+  /**
+   * retrieve a matrix associated with the view's alignment's annotation 
+   * @param alignmentAnnotation
+   * @return contact matrix or NULL
+   */
+  ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
 }