import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
-import jalview.structure.AtomSpecModel;
-import jalview.structure.StructureCommandI;
-import jalview.structure.StructureCommandsI;
-
import java.awt.Color;
import java.util.HashMap;
import java.util.LinkedHashMap;
import org.testng.annotations.Test;
+import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI;
+
public class ChimeraCommandsTest
{
// they were added; within colour, by model, by chain, ranges in start order
List<StructureCommandI> commands = new ChimeraCommands()
.colourBySequence(map);
- assertEquals(commands.size(), 3);
+ assertEquals(commands.size(), 1);
assertEquals(commands.get(0).getCommand(),
- "color #0000ff #0:2-5.A,9-23.A,7.B|#1:1.A,4-7.B");
- assertEquals(commands.get(1).getCommand(),
- "color #ffff00 #1:3-5.A,8.A");
- assertEquals(commands.get(2).getCommand(), "color #ff0000 #0:3-9.A");
+ "color #0000ff #0:2-5.A,9-23.A,7.B|#1:1.A,4-7.B;color #ffff00 #1:3-5.A,8.A;color #ff0000 #0:3-9.A");
}
@Test(groups = { "Functional" })
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
toAlign);
- String refSpec = "#1:12-14.A,18.B,22-23.B@CA|P&~@.B-Z&~@.2-9";
- String toAlignSpec = "#2:15-17.B,20-21.B,22.C@CA|P&~@.B-Z&~@.2-9";
+ // qualifier to restrict match to CA and no altlocs
+ String carbonAlphas = "@CA&~@.B-Z&~@.2-9";
+ String refSpec = "#1:12-14.A,18.B,22-23.B";
+ String toAlignSpec = "#2:15-17.B,20-21.B,22.C";
String expected = String.format(
- "match %s %s; ribbon %s|%s; focus",
- refSpec, toAlignSpec, refSpec, toAlignSpec);
+ "match %s%s %s%s; ribbon %s|%s; focus", toAlignSpec,
+ carbonAlphas, refSpec, carbonAlphas, toAlignSpec, refSpec);
assertEquals(command.get(0).getCommand(), expected);
}
assertEquals(testee.getAtomSpec(model, true), "");
model.addRange("1", 2, 4, "A");
assertEquals(testee.getAtomSpec(model, true),
- "#1:2-4.A@CA|P&~@.B-Z&~@.2-9");
+ "#1:2-4.A@CA&~@.B-Z&~@.2-9");
model.addRange("1", 8, 8, "A");
assertEquals(testee.getAtomSpec(model, true),
- "#1:2-4.A,8.A@CA|P&~@.B-Z&~@.2-9");
+ "#1:2-4.A,8.A@CA&~@.B-Z&~@.2-9");
model.addRange("1", 5, 7, "B");
assertEquals(testee.getAtomSpec(model, true),
- "#1:2-4.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
+ "#1:2-4.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
model.addRange("1", 3, 5, "A");
assertEquals(testee.getAtomSpec(model, true),
- "#1:2-5.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
+ "#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
model.addRange("0", 1, 4, "B");
assertEquals(testee.getAtomSpec(model, true),
- "#0:1-4.B@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
+ "#0:1-4.B@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
model.addRange("0", 5, 9, "C");
assertEquals(testee.getAtomSpec(model, true),
- "#0:1-4.B,5-9.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
+ "#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
model.addRange("1", 8, 10, "B");
assertEquals(testee.getAtomSpec(model, true),
- "#0:1-4.B,5-9.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9");
+ "#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
model.addRange("1", 8, 9, "B");
assertEquals(testee.getAtomSpec(model, true),
- "#0:1-4.B,5-9.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9");
+ "#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
assertEquals(testee.getAtomSpec(model, true),
- "#0:1-4.B,3-10.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9");
+ "#0:1-4.B,3-10.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
model.addRange("5", 25, 35, " "); // empty chain code
assertEquals(testee.getAtomSpec(model, true),
- "#0:1-4.B,3-10.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9|#5:25-35.@CA|P&~@.B-Z&~@.2-9");
+ "#0:1-4.B,3-10.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9|#5:25-35.@CA&~@.B-Z&~@.2-9");
}
ChimeraCommands testee = new ChimeraCommands();
List<StructureCommandI> cmds = testee.showBackbone();
assertEquals(cmds.size(), 1);
- assertEquals(cmds.get(0).getCommand(), "~display all;chain @CA|P");
+ assertEquals(cmds.get(0).getCommand(),
+ "~display all;~ribbon;chain @CA|P");
}
@Test(groups = "Functional")