"B", map, null);
ssm.addStructureMapping(sm2);
- String[] commands = testee.colourBySequence(ssm,
- files,
- seqs, sr, af.alignPanel);
+ String[] commands = testee.colourBySequence(ssm, files, seqs, sr,
+ af.alignPanel);
assertEquals(commands.length, 2);
String chainACommand = commands[0];
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");
+ 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");
+ 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");
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
+ 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";