JAL-1761 backbone type parameter for configuring which atoms are used for superpositi...

[jalview.git] / test / jalview / ext / jmol / JmolCommandsTest.java

diff --git a/test/jalview/ext/jmol/JmolCommandsTest.java b/test/jalview/ext/jmol/JmolCommandsTest.java
index 64899d3..6265c05 100644 (file)
--- a/test/jalview/ext/jmol/JmolCommandsTest.java
+++ b/test/jalview/ext/jmol/JmolCommandsTest.java
@@ -42,6 +42,7 @@ import jalview.gui.SequenceRenderer;
 import jalview.schemes.JalviewColourScheme;
 import jalview.structure.AtomSpecModel;
 import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
 
@@ -130,34 +131,34 @@ public class JmolCommandsTest
   public void testGetAtomSpec()
   {
     AtomSpecModel model = new AtomSpecModel();
-    assertEquals(testee.getAtomSpec(model, false), "");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
     model.addRange("1", 2, 4, "A");
-    assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "2-4:A/1.1");
     model.addRange("1", 8, 8, "A");
-    assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1|8:A/1.1");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "2-4:A/1.1|8:A/1.1");
     model.addRange("1", 5, 7, "B");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "2-4:A/1.1|8:A/1.1|5-7:B/1.1");
     model.addRange("1", 3, 5, "A");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "2-5:A/1.1|8:A/1.1|5-7:B/1.1");
     model.addRange("2", 1, 4, "B");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1");
     model.addRange("2", 5, 9, "C");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1|5-9:C/2.1");
     model.addRange("1", 8, 10, "B");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
     model.addRange("1", 8, 9, "B");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
     model.addRange("2", 3, 10, "C"); // subsumes 5-9
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1");
     model.addRange("5", 25, 35, " ");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1|25-35:/5.1");
 
   }
@@ -199,7 +200,7 @@ public class JmolCommandsTest
     toAlign.addRange("2", 20, 21, "B");
     toAlign.addRange("2", 22, 22, "C");
     List<StructureCommandI> command = testee.superposeStructures(ref,
-            toAlign, false); // doesn't matter for Jmol whether nuc or protein
+            toAlign, AtomSpecType.ALPHA); // doesn't matter for Jmol whether nuc or protein
     assertEquals(command.size(), 1);
     String refSpec = "12-14:A/1.1|18:B/1.1|22-23:B/1.1";
     String toAlignSpec = "15-17:B/2.1|20-21:B/2.1|22:C/2.1";