JAL-2422 JAL-3551 unit tests updated for code changes

[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 3bd64d7..044a1d9 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java
+++ b/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java
@@ -23,10 +23,6 @@ package jalview.ext.rbvi.chimera;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertTrue;
 
-import jalview.structure.AtomSpecModel;
-import jalview.structure.StructureCommandI;
-import jalview.structure.StructureCommandsI;
-
 import java.awt.Color;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
@@ -35,6 +31,10 @@ import java.util.Map;
 
 import org.testng.annotations.Test;
 
+import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI;
+
 public class ChimeraXCommandsTest
 {
   @Test(groups = { "Functional" })
@@ -80,11 +80,9 @@ public class ChimeraXCommandsTest
      */
     List<StructureCommandI> commands = new ChimeraXCommands()
             .colourBySequence(map);
-    assertEquals(commands.size(), 3);
+    assertEquals(commands.size(), 1);
     assertEquals(commands.get(0).getCommand(),
-            "color #1/A:2-5,9-23/B:7|#2/A:1/B:4-7 #0000ff");
-    assertEquals(commands.get(1).getCommand(), "color #2/A:3-5,8 #ffff00");
-    assertEquals(commands.get(2).getCommand(), "color #1/A:3-9 #ff0000");
+            "color #1/A:2-5,9-23/B:7|#2/A:1/B:4-7 #0000ff;color #2/A:3-5,8 #ffff00;color #1/A:3-9 #ff0000");
   }
 
   @Test(groups = { "Functional" })
@@ -184,8 +182,8 @@ public class ChimeraXCommandsTest
      * ribbon command does not
      */
     String expected = String.format(
-            "align %s@CA|P toAtoms %s@CA|P; ribbon %s|%s; view",
-            refSpec, toAlignSpec, refSpec, toAlignSpec);
+            "align %s@CA toAtoms %s@CA; ribbon %s|%s; view",
+            toAlignSpec, refSpec, toAlignSpec, refSpec);
     assertEquals(cmd, expected);
   }
 
@@ -230,31 +228,31 @@ public class ChimeraXCommandsTest
     AtomSpecModel model = new AtomSpecModel();
     assertEquals(testee.getAtomSpec(model, true), "");
     model.addRange("1", 2, 4, "A");
-    assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4@CA|P");
+    assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4@CA");
     model.addRange("1", 8, 8, "A");
-    assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8@CA|P");
+    assertEquals(testee.getAtomSpec(model, true), "#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|P");
+    assertEquals(testee.getAtomSpec(model, true), "#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|P");
+    assertEquals(testee.getAtomSpec(model, true), "#1/A:2-5,8/B:5-7@CA");
     model.addRange("0", 1, 4, "B");
     assertEquals(testee.getAtomSpec(model, true),
-            "#0/B:1-4@CA|P|#1/A:2-5,8/B:5-7@CA|P");
+            "#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),
-            "#0/B:1-4/C:5-9@CA|P|#1/A:2-5,8/B:5-7@CA|P");
+            "#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),
-            "#0/B:1-4/C:5-9@CA|P|#1/A:2-5,8/B:5-10@CA|P");
+            "#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),
-            "#0/B:1-4/C:5-9@CA|P|#1/A:2-5,8/B:5-10@CA|P");
+            "#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),
-            "#0/B:1-4/C:3-10@CA|P|#1/A:2-5,8/B:5-10@CA|P");
+            "#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),
-            "#0/B:1-4/C:3-10@CA|P|#1/A:2-5,8/B:5-10@CA|P|#5/:25-35@CA|P");
+            "#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA|#5/:25-35@CA");
   }
 
   @Test(groups = "Functional")
@@ -278,7 +276,7 @@ public class ChimeraXCommandsTest
     List<StructureCommandI> showBackbone = testee.showBackbone();
     assertEquals(showBackbone.size(), 1);
     assertEquals(showBackbone.get(0).getCommand(),
-            "~display all;show @CA|P pbonds");
+            "~display all;~ribbon;show @CA|P atoms");
   }
 
   @Test(groups = "Functional")