JAL-845 implement alignment of protein to match cDNA alignment

[jalview.git] / src / jalview / io / vamsas / Rangetype.java

diff --git a/src/jalview/io/vamsas/Rangetype.java b/src/jalview/io/vamsas/Rangetype.java
index 3cc977f..49227fd 100644 (file)
--- a/src/jalview/io/vamsas/Rangetype.java
+++ b/src/jalview/io/vamsas/Rangetype.java
@@ -20,6 +20,10 @@
  */
 package jalview.io.vamsas;
 
+import jalview.io.VamsasAppDatastore;
+import jalview.util.MessageManager;
+
+import java.util.List;
 import java.util.Vector;
 
 import uk.ac.vamsas.client.Vobject;
@@ -28,8 +32,6 @@ import uk.ac.vamsas.objects.core.MapType;
 import uk.ac.vamsas.objects.core.Mapped;
 import uk.ac.vamsas.objects.core.RangeType;
 import uk.ac.vamsas.objects.core.Seg;
-import jalview.io.VamsasAppDatastore;
-import jalview.util.MessageManager;
 
 /**
  * Enhances DatastoreItem objects with additional functions to do with RangeType
@@ -221,15 +223,15 @@ public abstract class Rangetype extends DatastoreItem
    * initialise a range type object from a set of start/end inclusive intervals
    * 
    * @param mrt
-   * @param range
+   * @param ranges
    */
-  protected void initRangeType(RangeType mrt, int[] range)
+  protected void initRangeType(RangeType mrt, List<int[]> ranges)
   {
-    for (int i = 0; i < range.length; i += 2)
+    for (int[] range : ranges)
     {
       Seg vSeg = new Seg();
-      vSeg.setStart(range[i]);
-      vSeg.setEnd(range[i + 1]);
+      vSeg.setStart(range[0]);
+      vSeg.setEnd(range[1]);
       vSeg.setInclusive(true);
       mrt.addSeg(vSeg);
     }