JAL-3518 basic refactoring / pull up of superposeStructures; to tidy!

[jalview.git] / test / jalview / ext / jmol / JmolCommandsTest.java

diff --git a/test/jalview/ext/jmol/JmolCommandsTest.java b/test/jalview/ext/jmol/JmolCommandsTest.java
index 5846b33..c3ece9d 100644 (file)
--- a/test/jalview/ext/jmol/JmolCommandsTest.java
+++ b/test/jalview/ext/jmol/JmolCommandsTest.java
@@ -32,6 +32,8 @@ import jalview.gui.AlignFrame;
 import jalview.gui.JvOptionPane;
 import jalview.gui.SequenceRenderer;
 import jalview.schemes.JalviewColourScheme;
+import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommandsI;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
 
@@ -138,4 +140,62 @@ public class JmolCommandsTest
     assertTrue(
             chainBCommand.contains(";select 26-30:B/2.1;color[73,73,182]"));
   }
+
+  @Test(groups = "Functional")
+  public void testGetAtomSpec()
+  {
+    StructureCommandsI testee = new JmolCommands();
+    AtomSpecModel model = new AtomSpecModel();
+    assertEquals(testee.getAtomSpec(model, false), "");
+    model.addRange(1, 2, 4, "A");
+    assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1");
+    model.addRange(1, 8, 8, "A");
+    assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1|8:A/1.1");
+    model.addRange(1, 5, 7, "B");
+    assertEquals(testee.getAtomSpec(model, false),
+            "2-4:A/1.1|8:A/1.1|5-7:B/1.1");
+    model.addRange(1, 3, 5, "A");
+    assertEquals(testee.getAtomSpec(model, false),
+            "2-5:A/1.1|8:A/1.1|5-7:B/1.1");
+    model.addRange(2, 1, 4, "B");
+    assertEquals(testee.getAtomSpec(model, false),
+            "2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1");
+    model.addRange(2, 5, 9, "C");
+    assertEquals(testee.getAtomSpec(model, false),
+            "2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1|5-9:C/2.1");
+    model.addRange(1, 8, 10, "B");
+    assertEquals(testee.getAtomSpec(model, false),
+            "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
+    model.addRange(1, 8, 9, "B");
+    assertEquals(testee.getAtomSpec(model, false),
+            "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
+    model.addRange(2, 3, 10, "C"); // subsumes 5-9
+    assertEquals(testee.getAtomSpec(model, false),
+            "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1");
+    model.addRange(5, 25, 35, " ");
+    assertEquals(testee.getAtomSpec(model, false),
+            "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1|25-35:/5.1");
+  
+  }
+
+  @Test(groups = { "Functional" })
+  public void testSuperposeStructures()
+  {
+    StructureCommandsI testee = new JmolCommands();
+    AtomSpecModel ref = new AtomSpecModel();
+    ref.addRange(1, 12, 14, "A");
+    ref.addRange(1, 18, 18, "B");
+    ref.addRange(1, 22, 23, "B");
+    AtomSpecModel toAlign = new AtomSpecModel();
+    toAlign.addRange(2, 15, 17, "B");
+    toAlign.addRange(2, 20, 21, "B");
+    toAlign.addRange(2, 22, 22, "C");
+    String command = testee.superposeStructures(ref, toAlign);
+    String refSpec = "12-14:A/1.1|18:B/1.1|22-23:B/1.1";
+    String toAlignSpec = "15-17:B/2.1|20-21:B/2.1|22:C/2.1";
+    String expected = String.format(
+            "compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS {%s}{%s} ROTATE TRANSLATE ;select %s|%s;cartoons",
+            toAlignSpec, refSpec, toAlignSpec, refSpec);
+    assertEquals(command, expected);
+  }
 }