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

[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 0679098..d0e6155 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
+++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
@@ -31,6 +31,8 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.SequenceRenderer;
 import jalview.schemes.JalviewColourScheme;
+import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommandsI;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
 
@@ -209,4 +211,98 @@ public class ChimeraCommandsTest
     // S and G are both coloured #4949b6
     assertTrue(theCommand.contains("color #4949b6 #0:26-30.A|#1:26-30.B"));
   }
+
+  @Test(groups = "Functional")
+  public void testGetAtomSpec()
+  {
+    StructureCommandsI testee = new ChimeraCommands();
+    AtomSpecModel model = new AtomSpecModel();
+    assertEquals(testee.getAtomSpec(model, false), "");
+    model.addRange(1, 2, 4, "A");
+    assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A");
+    model.addRange(1, 8, 8, "A");
+    assertEquals(testee.getAtomSpec(model, false), "#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");
+    model.addRange(1, 3, 5, "A");
+    assertEquals(testee.getAtomSpec(model, false), "#1:2-5.A,8.A,5-7.B");
+    model.addRange(0, 1, 4, "B");
+    assertEquals(testee.getAtomSpec(model, false),
+            "#0:1-4.B|#1:2-5.A,8.A,5-7.B");
+    model.addRange(0, 5, 9, "C");
+    assertEquals(testee.getAtomSpec(model, false),
+            "#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),
+            "#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),
+            "#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),
+            "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B");
+    model.addRange(5, 25, 35, " "); // empty chain code - e.g. from homology
+                                    // modelling
+    assertEquals(testee.getAtomSpec(model, false),
+            "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B|#5:25-35.");
+
+  }
+
+  @Test(groups = "Functional")
+  public void testGetAtomSpec_alphaOnly()
+  {
+    StructureCommandsI testee = new ChimeraCommands();
+    AtomSpecModel model = new AtomSpecModel();
+    assertEquals(testee.getAtomSpec(model, true), "");
+    model.addRange(1, 2, 4, "A");
+    assertEquals(testee.getAtomSpec(model, true), "#1:2-4.A@CA|P");
+    model.addRange(1, 8, 8, "A");
+    assertEquals(testee.getAtomSpec(model, true), "#1:2-4.A,8.A@CA|P");
+    model.addRange(1, 5, 7, "B");
+    assertEquals(testee.getAtomSpec(model, true),
+            "#1:2-4.A,8.A,5-7.B@CA|P");
+    model.addRange(1, 3, 5, "A");
+    assertEquals(testee.getAtomSpec(model, true),
+            "#1:2-5.A,8.A,5-7.B@CA|P");
+    model.addRange(0, 1, 4, "B");
+    assertEquals(testee.getAtomSpec(model, true),
+            "#0:1-4.B@CA|P|#1:2-5.A,8.A,5-7.B@CA|P");
+    model.addRange(0, 5, 9, "C");
+    assertEquals(testee.getAtomSpec(model, true),
+            "#0:1-4.B,5-9.C@CA|P|#1:2-5.A,8.A,5-7.B@CA|P");
+    model.addRange(1, 8, 10, "B");
+    assertEquals(testee.getAtomSpec(model, true),
+            "#0:1-4.B,5-9.C@CA|P|#1:2-5.A,8.A,5-10.B@CA|P");
+    model.addRange(1, 8, 9, "B");
+    assertEquals(testee.getAtomSpec(model, true),
+            "#0:1-4.B,5-9.C@CA|P|#1:2-5.A,8.A,5-10.B@CA|P");
+    model.addRange(0, 3, 10, "C"); // subsumes 5-9
+    assertEquals(testee.getAtomSpec(model, true),
+            "#0:1-4.B,3-10.C@CA|P|#1:2-5.A,8.A,5-10.B@CA|P");
+    model.addRange(5, 25, 35, " "); // empty chain code
+    assertEquals(testee.getAtomSpec(model, true),
+            "#0:1-4.B,3-10.C@CA|P|#1:2-5.A,8.A,5-10.B@CA|P|#5:25-35.@CA|P");
+  
+  }
+
+  @Test(groups = { "Functional" })
+  public void testSuperposeStructures()
+  {
+    StructureCommandsI testee = new ChimeraCommands();
+    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 = "#1:12-14.A,18.B,22-23.B@CA|P&~@.B-Z&~@.2-9";
+    String toAlignSpec = "#2:15-17.B,20-21.B,22.C@CA|P&~@.B-Z&~@.2-9";
+    String expected = String.format(
+            "match %s %s;~display all; chain @CA|P; ribbon %s|%s; focus",
+            refSpec, toAlignSpec, refSpec, toAlignSpec);
+    assertEquals(command, expected);
+  }
 }