X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarArray.java;fp=src%2Fjalview%2Fdatamodel%2FCigarArray.java;h=1723f1d45d148bd082b5d9c17ff0661df2e2216d;hb=0efc6021e63ff62bb2e275501586c1900561b303;hp=b6224c2d803579c04b8e6b8edc8769581acae8d4;hpb=771d1758a42abc6e3e330dd6c5117734acf0067f;p=jalview.git

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index b6224c2..1723f1d 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -170,32 +170,30 @@ public class CigarArray extends CigarBase
         hideStart = region[0];
         hideEnd = region[1];
         // edit hidden regions to selection range
-        if (hideStart < last)
+
+        // just move on if hideEnd is before last
+        if (hideEnd < last)
         {
-          if (hideEnd > last)
-          {
-            hideStart = last;
-          }
-          else
-          {
-            continue;
-          }
+          continue;
         }
-
+        // exit if next region is after end
         if (hideStart > end)
         {
           break;
         }
 
-        if (hideEnd > end)
+        // truncate region at start if last falls in region
+        if ((hideStart < last) && (hideEnd >= last))
         {
-          hideEnd = end;
+          hideStart = last;
         }
 
-        if (hideStart > hideEnd)
+        // truncate region at end if end falls in region
+        if (hideEnd > end) // already checked that hideStart<=end
         {
-          break;
+          hideEnd = end;
         }
+
         /**
          * form operations...
          */
@@ -207,7 +205,7 @@ public class CigarArray extends CigarBase
         last = hideEnd + 1;
       }
       // Final match if necessary.
-      if (last < end)
+      if (last <= end)
       {
         addOperation(CigarArray.M, end - last + 1);
       }