X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fjmol%2FJmolCommandsTest.java;h=1ade00ee5be3cbaa240f044f00486a4e94446849;hb=c38d37887ae51d63942ac4321f6769308188ed6b;hp=d1a9df6ce5bb089c44411628084069bb6db8d9e5;hpb=fea6f8ed76719fd78b600adfea8891dafb8c9d12;p=jalview.git

diff --git a/test/jalview/ext/jmol/JmolCommandsTest.java b/test/jalview/ext/jmol/JmolCommandsTest.java
index d1a9df6..1ade00e 100644
--- a/test/jalview/ext/jmol/JmolCommandsTest.java
+++ b/test/jalview/ext/jmol/JmolCommandsTest.java
@@ -23,6 +23,15 @@ package jalview.ext.jmol;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertTrue;
 
+import java.awt.Color;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.List;
+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;
@@ -33,18 +42,11 @@ import jalview.gui.JvOptionPane;
 import jalview.gui.SequenceRenderer;
 import jalview.schemes.JalviewColourScheme;
 import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommandI;
 import jalview.structure.StructureCommandsI;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
 
-import java.awt.Color;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.Map;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 public class JmolCommandsTest
 {
 
@@ -131,32 +133,32 @@ public class JmolCommandsTest
     StructureCommandsI testee = new JmolCommands();
     AtomSpecModel model = new AtomSpecModel();
     assertEquals(testee.getAtomSpec(model, false), "");
-    model.addRange(1, 2, 4, "A");
+    model.addRange("1", 2, 4, "A");
     assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1");
-    model.addRange(1, 8, 8, "A");
+    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");
+    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");
+    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");
+    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");
+    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");
+    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");
+    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
+    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, " ");
+    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");
   
@@ -166,24 +168,26 @@ public class JmolCommandsTest
   public void testColourBySequence()
   {
     Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
-    JmolCommands.addAtomSpecRange(map, Color.blue, 1, 2, 5, "A");
-    JmolCommands.addAtomSpecRange(map, Color.blue, 1, 7, 7, "B");
-    JmolCommands.addAtomSpecRange(map, Color.blue, 1, 9, 23, "A");
-    JmolCommands.addAtomSpecRange(map, Color.blue, 2, 1, 1, "A");
-    JmolCommands.addAtomSpecRange(map, Color.blue, 2, 4, 7, "B");
-    JmolCommands.addAtomSpecRange(map, Color.yellow, 2, 8, 8, "A");
-    JmolCommands.addAtomSpecRange(map, Color.yellow, 2, 3, 5, "A");
-    JmolCommands.addAtomSpecRange(map, Color.red, 1, 3, 5, "A");
-    JmolCommands.addAtomSpecRange(map, Color.red, 1, 6, 9, "A");
+    JmolCommands.addAtomSpecRange(map, Color.blue, "1", 2, 5, "A");
+    JmolCommands.addAtomSpecRange(map, Color.blue, "1", 7, 7, "B");
+    JmolCommands.addAtomSpecRange(map, Color.blue, "1", 9, 23, "A");
+    JmolCommands.addAtomSpecRange(map, Color.blue, "2", 1, 1, "A");
+    JmolCommands.addAtomSpecRange(map, Color.blue, "2", 4, 7, "B");
+    JmolCommands.addAtomSpecRange(map, Color.yellow, "2", 8, 8, "A");
+    JmolCommands.addAtomSpecRange(map, Color.yellow, "2", 3, 5, "A");
+    JmolCommands.addAtomSpecRange(map, Color.red, "1", 3, 5, "A");
+    JmolCommands.addAtomSpecRange(map, Color.red, "1", 6, 9, "A");
 
     // Colours should appear in the Jmol command in the order in which
     // they were added; within colour, by model, by chain, ranges in start order
-    String[] commands = new JmolCommands().colourBySequence(map);
-    assertEquals(commands.length, 1);
-    String expected = "select 2-5:A/1.1|9-23:A/1.1|7:B/1.1|1:A/2.1|4-7:B/2.1;color[0,0,255]; "
-            + "select 3-5:A/2.1|8:A/2.1;color[255,255,0]; "
-            + "select 3-9:A/1.1;color[255,0,0]";
-    assertEquals(commands[0], expected);
+    List<StructureCommandI> commands = new JmolCommands()
+            .colourBySequence(map);
+    assertEquals(commands.size(), 1);
+    String expected1 = "select 2-5:A/1.1|9-23:A/1.1|7:B/1.1|1:A/2.1|4-7:B/2.1;color[0,0,255]";
+    String expected2 = "select 3-5:A/2.1|8:A/2.1;color[255,255,0]";
+    String expected3 = "select 3-9:A/1.1;color[255,0,0]";
+    assertEquals(commands.get(0).getCommand(),
+            expected1 + ";" + expected2 + ";" + expected3);
   }
 
   @Test(groups = { "Functional" })
@@ -191,20 +195,22 @@ public class JmolCommandsTest
   {
     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");
+    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);
+    toAlign.addRange("2", 15, 17, "B");
+    toAlign.addRange("2", 20, 21, "B");
+    toAlign.addRange("2", 22, 22, "C");
+    List<StructureCommandI> command = testee.superposeStructures(ref,
+            toAlign);
+    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";
     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);
+    assertEquals(command.get(0).getCommand(), expected);
   }
 
   @Test(groups = "Functional")