X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;fp=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=295a9c43cd52113f8bf9f076b99494b59a9cdec3;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=2f992a6f499fac16a4edc0d3f55fa943f967085f;hpb=cfb79b69d9fa44595560659bd95d1d1cd27677ad;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 2f992a6..295a9c4 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -39,6 +39,7 @@ 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;
 
@@ -561,4 +562,16 @@ 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);
 }