X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fpymol%2FPymolCommandsTest.java;h=d5dbc8604270d24afaca49236601300b73ab7b3b;hb=f1fa440f885429399436bb09ef6d0639c8acd991;hp=7759724698004fdaf3587bb1cc36bd9d9a9d75a7;hpb=f9062df1303c1ff071075256cf4b7ad7c9db9658;p=jalview.git

diff --git a/test/jalview/ext/pymol/PymolCommandsTest.java b/test/jalview/ext/pymol/PymolCommandsTest.java
index 7759724..d5dbc86 100644
--- a/test/jalview/ext/pymol/PymolCommandsTest.java
+++ b/test/jalview/ext/pymol/PymolCommandsTest.java
@@ -124,17 +124,17 @@ public class PymolCommandsTest
     toAlign.addRange("2", 22, 22, "C");
     List<StructureCommandI> commands = testee.superposeStructures(ref,
             toAlign, AtomSpecType.ALPHA);
-    assertEquals(commands.size(), 2);
+    assertEquals(commands.size(), 4);
     String refSpecCA = "(1//A/12-14/CA 1//B/18+22-23/CA";
     String toAlignSpecCA = "(2//B/15-17+20-21/CA 2//C/22/CA";
     String refSpec = "1//A/12-14/ 1//B/18+22-23/";
     String toAlignSpec = "2//B/15-17+20-21/ 2//C/22/";
     String altLoc =  " and (altloc '' or altloc 'a'))";
     // super command: separate arguments for regions to align
-    assertEquals(commands.get(0),
+    assertEquals(commands.get(1),
             new StructureCommand("pair_fit", toAlignSpecCA+altLoc, refSpecCA+altLoc));
     // show aligned regions: one argument for combined atom specs
-    assertEquals(commands.get(1), new StructureCommand("show", "cartoon",
+    assertEquals(commands.get(3), new StructureCommand("show", "cartoon",
             refSpec + " " + toAlignSpec));
   }