+ assertTrue(
+ chainBCommand.contains(";select 26-30:B/2.1;color[73,73,182]"));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetAtomSpec()
+ {
+ AtomSpecModel model = new AtomSpecModel();
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
+ model.addRange("1", 2, 4, "A");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "2-4:A/1.1");
+ model.addRange("1", 8, 8, "A");
+ 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, 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, 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, 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, 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, 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, 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, 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, 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");
+
+ }
+
+ @Test(groups = { "Functional" })
+ 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");
+
+ // 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
+ List<StructureCommandI> commands = testee.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" })
+ public void testSuperposeStructures()
+ {
+ 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");
+ List<StructureCommandI> command = testee.superposeStructures(ref,
+ 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";
+ 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.get(0).getCommand(), expected);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetModelStartNo()
+ {
+ assertEquals(testee.getModelStartNo(), 1);
+ }
+
+ @Test(groups = "Functional")
+ public void testColourByChain()
+ {
+ StructureCommandI cmd = testee.colourByChain();
+ assertEquals(cmd.getCommand(), "select *;color chain");
+ }
+
+ @Test(groups = "Functional")
+ public void testColourByCharge()
+ {
+ List<StructureCommandI> cmds = testee.colourByCharge();
+ assertEquals(cmds.size(), 1);
+ assertEquals(cmds.get(0).getCommand(),
+ "select *;color white;select ASP,GLU;color red;"
+ + "select LYS,ARG;color blue;select CYS;color yellow");
+ }
+
+ @Test(groups = "Functional")
+ public void testSetBackgroundColour()
+ {
+ StructureCommandI cmd = testee.setBackgroundColour(Color.PINK);
+ assertEquals(cmd.getCommand(), "background [255,175,175]");
+ }
+
+ @Test(groups = "Functional")
+ public void testFocusView()
+ {
+ StructureCommandI cmd = testee.focusView();
+ assertEquals(cmd.getCommand(), "zoom 0");
+ }
+
+ @Test(groups = "Functional")
+ public void testSaveSession()
+ {
+ StructureCommandI cmd = testee.saveSession("/some/filepath");
+ assertEquals(cmd.getCommand(), "write STATE \"/some/filepath\"");
+ }
+
+ @Test(groups = "Functional")
+ public void testShowBackbone()
+ {
+ List<StructureCommandI> cmds = testee.showBackbone();
+ assertEquals(cmds.size(), 1);
+ assertEquals(cmds.get(0).getCommand(),
+ "select *; cartoons off; backbone");
+ }
+
+ @Test(groups = "Functional")
+ public void testLoadFile()
+ {
+ StructureCommandI cmd = testee.loadFile("/some/filepath");
+ assertEquals(cmd.getCommand(), "load FILES \"/some/filepath\"");
+
+ // single backslash gets escaped to double
+ cmd = testee.loadFile("\\some\\filepath");
+ assertEquals(cmd.getCommand(), "load FILES \"\\\\some\\\\filepath\"");
+ }
+
+ @Test(groups = "Functional")
+ public void testOpenSession()
+ {
+ StructureCommandI cmd = testee.openSession("/some/filepath");
+ assertEquals(cmd.getCommand(), "load FILES \"/some/filepath\"");
+
+ // single backslash gets escaped to double
+ cmd = testee.openSession("\\some\\filepath");
+ assertEquals(cmd.getCommand(), "load FILES \"\\\\some\\\\filepath\"");