JAL-845 implement alignment of protein to match cDNA alignment

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 8342151..f01e775 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1787,20 +1787,20 @@ public class Jalview2XML
       mp = new Mapping();
 
       jalview.util.MapList mlst = jmp.getMap();
-      int r[] = mlst.getFromRanges();
-      for (int s = 0; s < r.length; s += 2)
+      List<int[]> r = mlst.getFromRanges();
+      for (int[] range : r)
       {
         MapListFrom mfrom = new MapListFrom();
-        mfrom.setStart(r[s]);
-        mfrom.setEnd(r[s + 1]);
+        mfrom.setStart(range[0]);
+        mfrom.setEnd(range[1]);
         mp.addMapListFrom(mfrom);
       }
       r = mlst.getToRanges();
-      for (int s = 0; s < r.length; s += 2)
+      for (int[] range : r)
       {
         MapListTo mto = new MapListTo();
-        mto.setStart(r[s]);
-        mto.setEnd(r[s + 1]);
+        mto.setStart(range[0]);
+        mto.setEnd(range[1]);
         mp.addMapListTo(mto);
       }
       mp.setMapFromUnit(mlst.getFromRatio());