Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[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 366d208..88e5833 100644 (file)
--- a/test/jalview/ext/jmol/JmolCommandsTest.java
+++ b/test/jalview/ext/jmol/JmolCommandsTest.java
@@ -31,6 +31,7 @@ import java.util.Map;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
+
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
@@ -41,10 +42,10 @@ import jalview.gui.SequenceRenderer;
 import jalview.schemes.JalviewColourScheme;
 import jalview.structure.AtomSpecModel;
 import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
 
-
 public class JmolCommandsTest
 {
   private JmolCommands testee;
@@ -76,7 +77,8 @@ public class JmolCommandsTest
     SequenceRenderer sr = new SequenceRenderer(af.getViewport());
     SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
     String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
-    StructureSelectionManager ssm = new StructureSelectionManager();
+    StructureSelectionManager ssm = StructureSelectionManager.getStructureSelectionManager(null);
+
     /*
      * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
      */
@@ -91,11 +93,11 @@ public class JmolCommandsTest
     StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
             "B", map, null);
     ssm.addStructureMapping(sm2);
-    String[] commands = testee.colourBySequence(ssm,
-            files,
-            seqs, sr, af.alignPanel);
+
+    // TODO - comments in testee suggest this tests an obsolete method!
+    String[] commands = testee.colourBySequence(ssm, files, seqs, sr,
+            af.alignPanel);
     assertEquals(commands.length, 2);
-    assertEquals(commands[0].commands.length, 1); // from 2.12 merge from 2.11.2
 
     String chainACommand = commands[0];
     // M colour is #82827d == (130, 130, 125) (see strand.html help page)
@@ -129,34 +131,36 @@ public class JmolCommandsTest
   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), "2-4:A/1.1");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+            "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");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+            "2-4:A/1.1|8:A/1.1");
     model.addRange("1", 5, 7, "B");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "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),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "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),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "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),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "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),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "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),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "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),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "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),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "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");
 
   }
@@ -198,7 +202,8 @@ public class JmolCommandsTest
     toAlign.addRange("2", 20, 21, "B");
     toAlign.addRange("2", 22, 22, "C");
     List<StructureCommandI> command = testee.superposeStructures(ref,
-            toAlign);
+            toAlign, AtomSpecType.ALPHA); // doesn't matter for Jmol whether nuc
+                                          // or protein
     assertEquals(command.size(), 1);
     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";