Merge branch 'develop' into merged_2_11_2_0_to_2_12

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

diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
index 821ebde..d71b5fd 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
+++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
@@ -23,7 +23,6 @@ package jalview.ext.rbvi.chimera;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertTrue;
 
-
 import java.awt.Color;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
@@ -36,6 +35,8 @@ 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
 {
   private ChimeraCommands testee;
@@ -77,6 +78,7 @@ public class ChimeraCommandsTest
      */
     Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
     Map<Object, AtomSpecModel> featureValues = new HashMap<>();
+
     /*
      * start with just one feature/value...
      */
@@ -146,11 +148,9 @@ public class ChimeraCommandsTest
     assertEquals(testee.makeAttributeName(null), "jv_");
     assertEquals(testee.makeAttributeName(""), "jv_");
     assertEquals(testee.makeAttributeName("helix"), "jv_helix");
-    assertEquals(testee.makeAttributeName(
-            "Hello World 24"),
+    assertEquals(testee.makeAttributeName("Hello World 24"),
             "jv_Hello_World_24");
-    assertEquals(testee.makeAttributeName(
-            "!this is-a_very*{odd(name"),
+    assertEquals(testee.makeAttributeName("!this is-a_very*{odd(name"),
             "jv__this_is_a_very__odd_name");
     // name ending in color gets underscore appended
     assertEquals(testee.makeAttributeName("helixColor"), "jv_helixColor_");
@@ -160,33 +160,38 @@ 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.");
+
   }
 
   @Test(groups = { "Functional" })
@@ -201,7 +206,7 @@ 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";
@@ -216,36 +221,36 @@ 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");
 
   }
@@ -317,16 +322,15 @@ public class ChimeraCommandsTest
   {
     List<StructureCommandI> cmds = testee.colourByCharge();
     assertEquals(cmds.size(), 1);
-    assertEquals(cmds.get(0)
-            .getCommand(),
+    assertEquals(cmds.get(0).getCommand(),
             "color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS");
   }
 
   @Test(groups = "Functional")
   public void testGetColourCommand()
   {
-    assertEquals(testee.colourResidues("something", Color.MAGENTA)
-            .getCommand(),
+    assertEquals(
+            testee.colourResidues("something", Color.MAGENTA).getCommand(),
             "color #ff00ff something");
   }
 
@@ -379,8 +383,10 @@ public class ChimeraCommandsTest
   {
     List<StructureCommandI> cmds = testee.startNotifications("to here");
     assertEquals(cmds.size(), 2);
-    assertEquals(cmds.get(0), new StructureCommand("listen start models url to here"));
-    assertEquals(cmds.get(1), new StructureCommand("listen start select prefix SelectionChanged url to here"));
+    assertEquals(cmds.get(0),
+            new StructureCommand("listen start models url to here"));
+    assertEquals(cmds.get(1), new StructureCommand(
+            "listen start select prefix SelectionChanged url to here"));
   }
 
   @Test(groups = "Functional")
@@ -389,6 +395,7 @@ public class ChimeraCommandsTest
     List<StructureCommandI> cmds = testee.stopNotifications();
     assertEquals(cmds.size(), 2);
     assertEquals(cmds.get(0), new StructureCommand("listen stop models"));
-    assertEquals(cmds.get(1), new StructureCommand("listen stop selection"));
+    assertEquals(cmds.get(1),
+            new StructureCommand("listen stop selection"));
   }
 }