From: Jim Procter <j.procter@dundee.ac.uk>
Date: Thu, 17 Feb 2022 17:28:24 +0000 (+0000)
Subject: Merge branch 'develop' into improvement/JAL-3830_install4j9_macos_setup_application
X-Git-Tag: Release_2_11_2_1~60^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=15cc6b7e4b9682e16b0b1c6d850858e5f9762c4e;hp=7ac3ec098a5f0ba4f120144c6e975f20466c8fc4;p=jalview.git

Merge branch 'develop' into improvement/JAL-3830_install4j9_macos_setup_application
---

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));
   }