X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=56d25d5b9c013e7d3c204028864fd8620264c9ad;hb=eccc204bba7aab9101c16df03cc5f740241d9184;hp=785dd1416dc594198eb16b84cd878fc78ee573da;hpb=319d88f9dc025099158ac9193f5af7d827ea474b;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 785dd14..56d25d5 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -38,6 +38,7 @@ 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;
 
@@ -528,4 +529,16 @@ 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);
 }