JAL-3551 patch test for altloc handling atom spec in superposition code

diff --git a/test/jalview/ext/pymol/PymolCommandsTest.java b/test/jalview/ext/pymol/PymolCommandsTest.java
index f6bad92..bc12542 100644 (file)
--- a/test/jalview/ext/pymol/PymolCommandsTest.java
+++ b/test/jalview/ext/pymol/PymolCommandsTest.java
@@ -122,16 +122,16 @@ public class PymolCommandsTest
     toAlign.addRange("2", 20, 21, "B");
     toAlign.addRange("2", 22, 22, "C");
     List<StructureCommandI> commands = testee.superposeStructures(ref,
-            toAlign);
+            toAlign, false);
     assertEquals(commands.size(), 2);
-    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 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),
-            new StructureCommand("super", refSpecCA, toAlignSpecCA));
+            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",
             refSpec + " " + toAlignSpec));