assertEquals(commands.size(), 3);
assertEquals(commands.get(0), new StructureCommand("color", "0x0000ff",
"0//A/2-5+9-23/ 0//B/7/ 1//A/1/ 1//B/4-7/"));
assertEquals(commands.size(), 3);
assertEquals(commands.get(0), new StructureCommand("color", "0x0000ff",
"0//A/2-5+9-23/ 0//B/7/ 1//A/1/ 1//B/4-7/"));
AtomSpecModel model = new AtomSpecModel();
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
model.addRange("1", 2, 4, "A");
AtomSpecModel model = new AtomSpecModel();
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
model.addRange("1", 2, 4, "A");
model.addRange("1", 8, 8, "A");
model.addRange("1", 8, 8, "A");
model.addRange("1", 5, 7, "B");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4+8/ 1//B/5-7/");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "1//A/2-4+8/ 1//B/5-7/");
model.addRange("1", 3, 5, "A");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-5+8/ 1//B/5-7/");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "1//A/2-5+8/ 1//B/5-7/");
model.addRange("0", 1, 4, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 1//A/2-5+8/ 1//B/5-7/");
model.addRange("0", 1, 4, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 1//A/2-5+8/ 1//B/5-7/");
String toAlignSpecCA = "(2//B/15-17+20-21/CA 2//C/22/CA";
String refSpec = "1//A/12-14/ 1//B/18+22-23/";
String toAlignSpec = "2//B/15-17+20-21/ 2//C/22/";
String toAlignSpecCA = "(2//B/15-17+20-21/CA 2//C/22/CA";
String refSpec = "1//A/12-14/ 1//B/18+22-23/";
String toAlignSpec = "2//B/15-17+20-21/ 2//C/22/";
- assertEquals(commands.get(1),
- new StructureCommand("pair_fit", toAlignSpecCA+altLoc, refSpecCA+altLoc));
+ assertEquals(commands.get(1), new StructureCommand("pair_fit",
+ toAlignSpecCA + altLoc, refSpecCA + altLoc));
// show aligned regions: one argument for combined atom specs
assertEquals(commands.get(3), new StructureCommand("show", "cartoon",
refSpec + " " + toAlignSpec));
// show aligned regions: one argument for combined atom specs
assertEquals(commands.get(3), new StructureCommand("show", "cartoon",
refSpec + " " + toAlignSpec));
AtomSpecModel model = new AtomSpecModel();
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
model.addRange("1", 2, 4, "A");
AtomSpecModel model = new AtomSpecModel();
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
model.addRange("1", 2, 4, "A");
model.addRange("1", 8, 8, "A");
model.addRange("1", 8, 8, "A");
model.addRange("1", 5, 7, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"1//A/2-4+8/CA 1//B/5-7/CA");
model.addRange("1", 5, 7, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"1//A/2-4+8/CA 1//B/5-7/CA");