From eccc204bba7aab9101c16df03cc5f740241d9184 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 9 Dec 2019 14:31:37 +0000
Subject: [PATCH] JAL-3490 pull up getViewAsVisibleContigs to base class and
 interface

---
 src/jalview/api/AlignViewportI.java          |   13 +++++++++++++
 src/jalview/gui/AlignViewport.java           |   26 --------------------------
 src/jalview/viewmodel/AlignmentViewport.java |   18 ++++++++++++++++++
 3 files changed, 31 insertions(+), 26 deletions(-)

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);
 }
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 61b0d1b..34146dd 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -59,7 +59,6 @@ import java.awt.FontMetrics;
 import java.awt.Rectangle;
 import java.util.ArrayList;
 import java.util.Hashtable;
-import java.util.Iterator;
 import java.util.List;
 
 import javax.swing.JInternalFrame;
@@ -446,31 +445,6 @@ public class AlignViewport extends AlignmentViewport
   }
 
   /**
-   * returns the visible column regions of the alignment
-   * 
-   * @param selectedRegionOnly
-   *          true to just return the contigs intersecting with the selected
-   *          area
-   * @return
-   */
-  public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
-  {
-    int start = 0;
-    int end = 0;
-    if (selectedRegionOnly && selectionGroup != null)
-    {
-      start = selectionGroup.getStartRes();
-      end = selectionGroup.getEndRes() + 1;
-    }
-    else
-    {
-      end = alignment.getWidth();
-    }
-    return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
-            false));
-  }
-
-  /**
    * get hash of undo and redo list for the alignment
    * 
    * @return long[] { historyList.hashCode, redoList.hashCode };
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 8dcd1b3..2c430db 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -3044,4 +3044,22 @@ public abstract class AlignmentViewport
       codingComplement.setUpdateStructures(needToUpdateStructureViews);
     }
   }
+
+  @Override
+  public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
+  {
+    int start = 0;
+    int end = 0;
+    if (selectedRegionOnly && selectionGroup != null)
+    {
+      start = selectionGroup.getStartRes();
+      end = selectionGroup.getEndRes() + 1;
+    }
+    else
+    {
+      end = alignment.getWidth();
+    }
+    return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+            false));
+  }
 }
-- 
1.7.10.2