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

[jalview.git] / test / jalview / ext / rbvi / chimera / ChimeraXCommandsTest.java

diff --git a/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java
index 80bf042..143a5d8 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java
+++ b/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java
@@ -35,6 +35,7 @@ import org.testng.annotations.Test;
 import jalview.structure.AtomSpecModel;
 import jalview.structure.StructureCommand;
 import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
 
 public class ChimeraXCommandsTest
 {
@@ -187,7 +188,7 @@ public class ChimeraXCommandsTest
     toAlign.addRange("2", 20, 21, "B");
     toAlign.addRange("2", 22, 22, "C");
     List<StructureCommandI> command = testee.superposeStructures(ref,
-            toAlign,false);
+            toAlign,AtomSpecType.ALPHA);
     assertEquals(command.size(), 1);
     String cmd = command.get(0).getCommand();
     String refSpec = "#1/A:12-14/B:18,22-23";
@@ -207,32 +208,33 @@ public class ChimeraXCommandsTest
   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), "#1/A:2-4");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-4");
     model.addRange("1", 8, 8, "A");
-    assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-4,8");
     model.addRange("1", 5, 7, "B");
-    assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8/B:5-7");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-4,8/B:5-7");
     model.addRange("1", 3, 5, "A");
-    assertEquals(testee.getAtomSpec(model, false), "#1/A:2-5,8/B:5-7");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-5,8/B:5-7");
     model.addRange("0", 1, 4, "B");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "#0/B:1-4|#1/A:2-5,8/B:5-7");
     model.addRange("0", 5, 9, "C");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-7");
     model.addRange("1", 8, 10, "B");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
     model.addRange("1", 8, 9, "B");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
     model.addRange("0", 3, 10, "C"); // subsumes 5-9
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10");
     model.addRange("5", 25, 35, " ");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10|#5/:25-35");
   }
 
@@ -240,32 +242,32 @@ public class ChimeraXCommandsTest
   public void testGetAtomSpec_alphaOnly()
   {
     AtomSpecModel model = new AtomSpecModel();
-    assertEquals(testee.getAtomSpec(model, true), "");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
     model.addRange("1", 2, 4, "A");
-    assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4@CA");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-4@CA");
     model.addRange("1", 8, 8, "A");
-    assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8@CA");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-4,8@CA");
     model.addRange("1", 5, 7, "B");
-    assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8/B:5-7@CA");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-4,8/B:5-7@CA");
     model.addRange("1", 3, 5, "A");
-    assertEquals(testee.getAtomSpec(model, true), "#1/A:2-5,8/B:5-7@CA");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-5,8/B:5-7@CA");
     model.addRange("0", 1, 4, "B");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "#0/B:1-4@CA|#1/A:2-5,8/B:5-7@CA");
     model.addRange("0", 5, 9, "C");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-7@CA");
     model.addRange("1", 8, 10, "B");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
     model.addRange("1", 8, 9, "B");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
     model.addRange("0", 3, 10, "C"); // subsumes 5-9
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA");
     model.addRange("5", 25, 35, " "); // empty chain code
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA|#5/:25-35@CA");
   }