import java.util.List;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandI;
-import jalview.structure.StructureCommandsI;
public class ChimeraXCommandsTest
{
+ private ChimeraXCommands testee;
+
+ @BeforeClass
+ public void setUp()
+ {
+ testee = new ChimeraXCommands();
+ }
+
@Test(groups = { "Functional" })
public void testColourByCharge()
{
- List<StructureCommandI> cmd = new ChimeraXCommands().colourByCharge();
+ List<StructureCommandI> cmd = testee.colourByCharge();
assertEquals(cmd.size(), 1);
assertEquals(cmd.get(0).getCommand(),
"color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow");
@Test(groups = { "Functional" })
public void testColourByChain()
{
- StructureCommandI cmd = new ChimeraXCommands().colourByChain();
+ StructureCommandI cmd = testee.colourByChain();
assertEquals(cmd.getCommand(), "rainbow chain");
}
@Test(groups = { "Functional" })
public void testFocusView()
{
- StructureCommandI cmd = new ChimeraXCommands().focusView();
+ StructureCommandI cmd = testee.focusView();
assertEquals(cmd.getCommand(), "view");
}
@Test(groups = { "Functional" })
+ public void testSetBackgroundColour()
+ {
+ StructureCommandI cmd = testee.setBackgroundColour(Color.PINK);
+ assertEquals(cmd.getCommand(), "set bgColor #ffafaf");
+ }
+
+ @Test(groups = { "Functional" })
+ public void testOpenSession()
+ {
+ StructureCommandI cmd = testee.openSession("/some/filepath");
+ assertEquals(cmd.getCommand(), "open /some/filepath format session");
+ }
+
+ @Test(groups = { "Functional" })
public void testColourBySequence()
{
Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
* Colours should appear in the Chimera command in the order in which
* they were added; within colour, by model, by chain, ranges in start order
*/
- List<StructureCommandI> commands = new ChimeraXCommands()
- .colourBySequence(map);
+ List<StructureCommandI> commands = testee.colourBySequence(map);
assertEquals(commands.size(), 1);
assertEquals(commands.get(0).getCommand(),
"color #1/A:2-5,9-23/B:7|#2/A:1/B:4-7 #0000ff;color #2/A:3-5,8 #ffff00;color #1/A:3-9 #ff0000");
*/
Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
Map<Object, AtomSpecModel> featureValues = new HashMap<>();
-
+
/*
* start with just one feature/value...
*/
featuresMap.put("chain", featureValues);
ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
-
- ChimeraXCommands commandGenerator = new ChimeraXCommands();
- List<StructureCommandI> commands = commandGenerator
- .setAttributes(featuresMap);
+
+ List<StructureCommandI> commands = testee.setAttributes(featuresMap);
assertEquals(commands.size(), 1);
/*
ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 3, 9, "A");
// same feature value, contiguous range
ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A");
- commands = commandGenerator.setAttributes(featuresMap);
+ commands = testee.setAttributes(featuresMap);
assertEquals(commands.size(), 1);
assertEquals(commands.get(0).getCommand(),
"setattr #0/A:3-25 res jv_chain 'X' create true");
ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "B");
// same feature value and chain, different model
ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A");
- commands = commandGenerator.setAttributes(featuresMap);
+ commands = testee.setAttributes(featuresMap);
assertEquals(commands.size(), 1);
String expected1 = "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true";
assertEquals(commands.get(0).getCommand(), expected1);
// same feature, different value
ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A");
- commands = commandGenerator.setAttributes(featuresMap);
+ commands = testee.setAttributes(featuresMap);
assertEquals(2, commands.size());
// commands are ordered by feature type but not by value
// so test for the expected command in either order
String cmd1 = commands.get(0).getCommand();
String cmd2 = commands.get(1).getCommand();
- assertTrue(
- cmd1.equals(expected1) || cmd2.equals(expected1));
+ assertTrue(cmd1.equals(expected1) || cmd2.equals(expected1));
String expected2 = "setattr #0/A:40-50 res jv_chain 'Y' create true";
- assertTrue(
- cmd1.equals(expected2) || cmd2.equals(expected2));
+ assertTrue(cmd1.equals(expected2) || cmd2.equals(expected2));
featuresMap.clear();
featureValues.clear();
featuresMap.put("side-chain binding!", featureValues);
ChimeraCommands.addAtomSpecRange(featureValues,
- "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", "0", 7, 15,
- "A");
+ "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", "0", 7, 15, "A");
// feature names are sanitised to change non-alphanumeric to underscore
// feature values are sanitised to encode single quote characters
- commands = commandGenerator.setAttributes(featuresMap);
+ commands = testee.setAttributes(featuresMap);
assertEquals(commands.size(), 1);
String expected3 = "setattr #0/A:7-15 res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' create true";
assertTrue(commands.get(0).getCommand().equals(expected3));
@Test(groups = { "Functional" })
public void testSuperposeStructures()
{
- StructureCommandsI testee = new ChimeraXCommands();
AtomSpecModel ref = new AtomSpecModel();
ref.addRange("1", 12, 14, "A");
ref.addRange("1", 18, 18, "B");
* ribbon command does not
*/
String expected = String.format(
- "align %s@CA toAtoms %s@CA; ribbon %s|%s; view",
- toAlignSpec, refSpec, toAlignSpec, refSpec);
+ "align %s@CA toAtoms %s@CA; ribbon %s|%s; view", toAlignSpec,
+ refSpec, toAlignSpec, refSpec);
assertEquals(cmd, expected);
}
@Test(groups = "Functional")
public void testGetAtomSpec()
{
- StructureCommandsI testee = new ChimeraXCommands();
AtomSpecModel model = new AtomSpecModel();
assertEquals(testee.getAtomSpec(model, false), "");
model.addRange("1", 2, 4, "A");
@Test(groups = "Functional")
public void testGetAtomSpec_alphaOnly()
{
- StructureCommandsI testee = new ChimeraXCommands();
AtomSpecModel model = new AtomSpecModel();
assertEquals(testee.getAtomSpec(model, true), "");
model.addRange("1", 2, 4, "A");
@Test(groups = "Functional")
public void testGetModelStartNo()
{
- StructureCommandsI testee = new ChimeraXCommands();
assertEquals(testee.getModelStartNo(), 1);
}
@Test(groups = "Functional")
public void testGetResidueSpec()
{
- ChimeraCommands testee = new ChimeraXCommands();
assertEquals(testee.getResidueSpec("ALA"), ":ALA");
}
@Test(groups = "Functional")
public void testShowBackbone()
{
- ChimeraCommands testee = new ChimeraXCommands();
List<StructureCommandI> showBackbone = testee.showBackbone();
assertEquals(showBackbone.size(), 1);
assertEquals(showBackbone.get(0).getCommand(),
@Test(groups = "Functional")
public void testOpenCommandFile()
{
- ChimeraCommands testee = new ChimeraXCommands();
assertEquals(testee.openCommandFile("nowhere").getCommand(),
"open nowhere");
}
@Test(groups = "Functional")
public void testSaveSession()
{
- ChimeraCommands testee = new ChimeraXCommands();
assertEquals(testee.saveSession("somewhere").getCommand(),
"save somewhere format session");
}
@Test(groups = "Functional")
public void testGetColourCommand()
{
- ChimeraCommands testee = new ChimeraXCommands();
assertEquals(testee.colourResidues("something", Color.MAGENTA)
.getCommand(),
"color something #ff00ff");
@Test(groups = "Functional")
public void testSetAttribute()
{
- ChimeraCommands testee = new ChimeraXCommands();
AtomSpecModel model = new AtomSpecModel();
model.addRange("1", 89, 92, "A");
model.addRange("2", 12, 20, "B");
model.addRange("2", 8, 9, "B");
- assertEquals(testee.setAttribute("phi", "27.3", model).getCommand(),
- "setattr #1/A:89-92|#2/B:8-9,12-20 res phi '27.3' create true");
+ assertEquals(testee.setAttribute("jv_kd", "27.3", model)
+ .getCommand(),
+ "setattr #1/A:89-92|#2/B:8-9,12-20 res jv_kd '27.3' create true");
}
}
git://source.jalview.org / jalview.git / blobdiff