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JAL-3438 spotless for 2.11.2.0
[jalview.git] / test / jalview / ext / pymol / PymolCommandsTest.java
diff --git a/test/jalview/ext/pymol/PymolCommandsTest.java b/test/jalview/ext/pymol/PymolCommandsTest.java
index 3eb05f5..168e707 100644 (file)
--- a/test/jalview/ext/pymol/PymolCommandsTest.java
+++ b/test/jalview/ext/pymol/PymolCommandsTest.java
@@ -36,12 +36,13 @@ import jalview.ext.rbvi.chimera.ChimeraCommands;
 import jalview.structure.AtomSpecModel;
 import jalview.structure.StructureCommand;
 import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
 
 public class PymolCommandsTest
 {
   private PymolCommands testee;
 
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public void setUp()
   {
     testee = new PymolCommands();
@@ -68,11 +69,9 @@ public class PymolCommandsTest
     assertEquals(commands.size(), 3);
     assertEquals(commands.get(0), new StructureCommand("color", "0x0000ff",
             "0//A/2-5+9-23/ 0//B/7/ 1//A/1/ 1//B/4-7/"));
-    assertEquals(commands.get(
-            1),
+    assertEquals(commands.get(1),
             new StructureCommand("color", "0xffff00", "1//A/3-5+8/"));
-    assertEquals(commands.get(
-            2),
+    assertEquals(commands.get(2),
             new StructureCommand("color", "0xff0000", "0//A/3-9/"));
   }
 
@@ -80,32 +79,36 @@ public class PymolCommandsTest
   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/ 1//B/5-7/");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+            "1//A/2-4+8/ 1//B/5-7/");
     model.addRange("1", 3, 5, "A");
-    assertEquals(testee.getAtomSpec(model, false), "1//A/2-5+8/ 1//B/5-7/");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+            "1//A/2-5+8/ 1//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/ 1//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/ 0//C/5-9/ 1//A/2-5+8/ 1//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/ 0//C/5-9/ 1//A/2-5+8/ 1//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/ 0//C/5-9/ 1//A/2-5+8/ 1//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/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/");
     model.addRange("5", 25, 35, " ");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/ 5///25-35/");
 
   }
@@ -122,18 +125,18 @@ public class PymolCommandsTest
     toAlign.addRange("2", 20, 21, "B");
     toAlign.addRange("2", 22, 22, "C");
     List<StructureCommandI> commands = testee.superposeStructures(ref,
-            toAlign);
-    assertEquals(commands.size(), 2);
-    String refSpecCA = "1//A/12-14/CA 1//B/18+22-23/CA";
-    String toAlignSpecCA = "2//B/15-17+20-21/CA 2//C/22/CA";
+            toAlign, AtomSpecType.ALPHA);
+    assertEquals(commands.size(), 4);
+    String refSpecCA = "(1//A/12-14/CA 1//B/18+22-23/CA";
+    String toAlignSpecCA = "(2//B/15-17+20-21/CA 2//C/22/CA";
     String refSpec = "1//A/12-14/ 1//B/18+22-23/";
     String toAlignSpec = "2//B/15-17+20-21/ 2//C/22/";
-
+    String altLoc = " and (altloc '' or altloc 'a'))";
     // super command: separate arguments for regions to align
-    assertEquals(commands.get(0),
-            new StructureCommand("super", refSpecCA, toAlignSpecCA));
+    assertEquals(commands.get(1), new StructureCommand("pair_fit",
+            toAlignSpecCA + altLoc, refSpecCA + altLoc));
     // show aligned regions: one argument for combined atom specs
-    assertEquals(commands.get(1), new StructureCommand("show", "cartoon",
+    assertEquals(commands.get(3), new StructureCommand("show", "cartoon",
             refSpec + " " + toAlignSpec));
   }
 
@@ -141,34 +144,36 @@ public class PymolCommandsTest
   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),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "1//A/2-4+8/CA 1//B/5-7/CA");
     model.addRange("1", 3, 5, "A");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "1//A/2-5+8/CA 1//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/CA 1//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/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//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/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//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/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//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/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA");
     model.addRange("5", 25, 35, " ");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA 5///25-35/CA");
   }
 
@@ -238,8 +243,7 @@ public class PymolCommandsTest
   @Test(groups = "Functional")
   public void testColourResidues()
   {
-    assertEquals(testee.colourResidues("something",
-            Color.MAGENTA),
+    assertEquals(testee.colourResidues("something", Color.MAGENTA),
             new StructureCommand("color", "0xff00ff", "something"));
   }
 
@@ -253,8 +257,7 @@ public class PymolCommandsTest
   @Test(groups = "Functional")
   public void testSetBackgroundColour()
   {
-    assertEquals(testee.setBackgroundColour(
-            Color.PINK),
+    assertEquals(testee.setBackgroundColour(Color.PINK),
             new StructureCommand("bg_color", "0xffafaf"));
   }
 
@@ -341,4 +344,10 @@ public class PymolCommandsTest
             "p.jv_side_chain_binding_='<html>metal <a href=\"http:a.b.c/x\"> &#39;ion!'");
     assertEquals(commands.get(0), expected3);
   }
+
+  @Test(groups = "Functional")
+  public void testCloseViewer()
+  {
+    assertEquals(testee.closeViewer(), new StructureCommand("quit"));
+  }
 }