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;
"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];
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");
}
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
- toAlign, false); // 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";