X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommandsTest.java;fp=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommandsTest.java;h=23e42ca8415111d50ab4ecba7259d0b14c55e6c2;hb=3efc24bc7b7855ff135fa96e35ab1004eaeb4f5e;hp=6880985151f79529a199ebc6dd482e46ccf56aef;hpb=dae56c38c3f14e96308540c30f35ca8f1d917edf;p=jalview.git

diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
index 6880985..23e42ca 100644
--- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
+++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.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 ChimeraCommandsTest
 {
@@ -161,32 +162,32 @@ public class ChimeraCommandsTest
   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), "#1:2-4.A");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-4.A");
     model.addRange("1", 8, 8, "A");
-    assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-4.A,8.A");
     model.addRange("1", 5, 7, "B");
-    assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A,5-7.B");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-4.A,8.A,5-7.B");
     model.addRange("1", 3, 5, "A");
-    assertEquals(testee.getAtomSpec(model, false), "#1:2-5.A,8.A,5-7.B");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-5.A,8.A,5-7.B");
     model.addRange("0", 1, 4, "B");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "#0:1-4.B|#1:2-5.A,8.A,5-7.B");
     model.addRange("0", 5, 9, "C");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-7.B");
     model.addRange("1", 8, 10, "B");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
     model.addRange("1", 8, 9, "B");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
     model.addRange("0", 3, 10, "C"); // subsumes 5-9
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B");
     model.addRange("5", 25, 35, " ");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B|#5:25-35.");
 
   }
@@ -203,7 +204,7 @@ public class ChimeraCommandsTest
     toAlign.addRange("2", 20, 21, "B");
     toAlign.addRange("2", 22, 22, "C");
     List<StructureCommandI> command = testee.superposeStructures(ref,
-            toAlign);
+            toAlign, AtomSpecType.ALPHA);
     // qualifier to restrict match to CA and no altlocs
     String carbonAlphas = "@CA&~@.B-Z&~@.2-9";
     String refSpec = "#1:12-14.A,18.B,22-23.B";
@@ -218,36 +219,36 @@ public class ChimeraCommandsTest
   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),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "#1:2-4.A@CA&~@.B-Z&~@.2-9");
     model.addRange("1", 8, 8, "A");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "#1:2-4.A,8.A@CA&~@.B-Z&~@.2-9");
     model.addRange("1", 5, 7, "B");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "#1:2-4.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
     model.addRange("1", 3, 5, "A");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
     model.addRange("0", 1, 4, "B");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "#0:1-4.B@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
     model.addRange("0", 5, 9, "C");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
     model.addRange("1", 8, 10, "B");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
     model.addRange("1", 8, 9, "B");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
     model.addRange("0", 3, 10, "C"); // subsumes 5-9
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "#0:1-4.B,3-10.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
     model.addRange("5", 25, 35, " "); // empty chain code
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "#0:1-4.B,3-10.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9|#5:25-35.@CA&~@.B-Z&~@.2-9");
 
   }