JAL-2647 more iterators

[jalview.git] / src / jalview / gui / VamsasApplication.java

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index d2086e0..3bf7c24 100644 (file)
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -42,6 +42,7 @@ import java.io.IOException;
 import java.util.Hashtable;
 import java.util.IdentityHashMap;
 import java.util.Iterator;
+import java.util.List;
 
 import javax.swing.JInternalFrame;
 
@@ -1076,14 +1077,14 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                   {
                     // int[] intervals = colsel.getVisibleContigs(
                     // seqsel.getStartRes(), seqsel.getEndRes() + 1);
-                    int[] intervals = hidden.getVisibleContigs(
+                    List<int[]> intervals = hidden.getVisibleContigs(
                             seqsel.getStartRes(), seqsel.getEndRes() + 1);
-                    for (int iv = 0; iv < intervals.length; iv += 2)
+                    for (int[] region : intervals)
                     {
                       Seg s = new Seg();
-                      s.setStart(intervals[iv] + 1); // vamsas indices begin at
+                      s.setStart(region[0] + 1); // vamsas indices begin at
                       // 1, not zero.
-                      s.setEnd(intervals[iv + 1] + 1);
+                      s.setEnd(region[1] + 1);
                       s.setInclusive(true);
                       range.addSeg(s);
                     }