X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=0cfd03df961163dfe01bce3530716c8921c83319;hb=e5d038fc1bfc07d3879ef57f7726c60617988965;hp=065be7516ae95a898793f1994f80646216b89b01;hpb=17e4ea278bc9a5fb280db1252ce78b7a295215f5;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 065be75..0cfd03d 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;
@@ -39,6 +41,7 @@ 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;
 
@@ -475,6 +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.
    * 
@@ -539,4 +553,18 @@ public interface AlignViewportI extends ViewStyleI
    *          - a group defined on sequences in the alignment held by the view
    */
   void addSequenceGroup(SequenceGroup sequenceGroup);
+
+  /**
+   * Returns an interator over the [start, end] column positions of the visible
+   * 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
+   * @return
+   */
+  Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+
+  ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
 }