import org.testng.annotations.Test;
import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
public class ChimeraCommandsTest
{
assertEquals(testee.makeAttributeName(null), "jv_");
assertEquals(testee.makeAttributeName(""), "jv_");
assertEquals(testee.makeAttributeName("helix"), "jv_helix");
- assertEquals(testee.makeAttributeName(
- "Hello World 24"),
+ assertEquals(testee.makeAttributeName("Hello World 24"),
"jv_Hello_World_24");
- assertEquals(testee.makeAttributeName(
- "!this is-a_very*{odd(name"),
+ assertEquals(testee.makeAttributeName("!this is-a_very*{odd(name"),
"jv__this_is_a_very__odd_name");
// name ending in color gets underscore appended
assertEquals(testee.makeAttributeName("helixColor"), "jv_helixColor_");
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), "#1:2-4.A");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "#1:2-4.A");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "#1:2-4.A,8.A");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A,5-7.B");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "#1:2-4.A,8.A,5-7.B");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1:2-5.A,8.A,5-7.B");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "#1:2-5.A,8.A,5-7.B");
model.addRange("0", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B|#1:2-5.A,8.A,5-7.B");
model.addRange("0", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-7.B");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B");
model.addRange("5", 25, 35, " ");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B|#5:25-35.");
}
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
- toAlign);
+ toAlign, AtomSpecType.ALPHA);
// 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";
public void testGetAtomSpec_alphaOnly()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, true), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#1:2-4.A@CA&~@.B-Z&~@.2-9");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#1:2-4.A,8.A@CA&~@.B-Z&~@.2-9");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#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),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#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),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#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),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#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),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#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),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#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),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#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),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#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");
}
{
List<StructureCommandI> cmds = testee.colourByCharge();
assertEquals(cmds.size(), 1);
- assertEquals(cmds.get(0)
- .getCommand(),
+ assertEquals(cmds.get(0).getCommand(),
"color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS");
}
@Test(groups = "Functional")
public void testGetColourCommand()
{
- assertEquals(testee.colourResidues("something", Color.MAGENTA)
- .getCommand(),
+ assertEquals(
+ testee.colourResidues("something", Color.MAGENTA).getCommand(),
"color #ff00ff something");
}
assertEquals(testee.setAttribute("jv_kd", "27.3", model).getCommand(),
"setattr res jv_kd '27.3' #1:89-92.A|#2:8-9.B,12-20.B");
}
+
+ @Test(groups = "Functional")
+ public void testCloseViewer()
+ {
+ assertEquals(testee.closeViewer(), new StructureCommand("stop really"));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetSelectedResidues()
+ {
+ assertEquals(testee.getSelectedResidues(),
+ new StructureCommand("list selection level residue"));
+ }
+
+ @Test(groups = "Functional")
+ public void testListResidueAttributes()
+ {
+ assertEquals(testee.listResidueAttributes(),
+ new StructureCommand("list resattr"));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetResidueAttributes()
+ {
+ assertEquals(testee.getResidueAttributes("binding site"),
+ new StructureCommand("list residues attr 'binding site'"));
+ }
+
+ @Test(groups = "Functional")
+ public void testStartNotifications()
+ {
+ List<StructureCommandI> cmds = testee.startNotifications("to here");
+ assertEquals(cmds.size(), 2);
+ assertEquals(cmds.get(0),
+ new StructureCommand("listen start models url to here"));
+ assertEquals(cmds.get(1), new StructureCommand(
+ "listen start select prefix SelectionChanged url to here"));
+ }
+
+ @Test(groups = "Functional")
+ public void testStopNotifications()
+ {
+ List<StructureCommandI> cmds = testee.stopNotifications();
+ assertEquals(cmds.size(), 2);
+ assertEquals(cmds.get(0), new StructureCommand("listen stop models"));
+ assertEquals(cmds.get(1),
+ new StructureCommand("listen stop selection"));
+ }
}