import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.SequenceRenderer;
-import jalview.schemes.JalviewColourScheme;
-import jalview.structure.AtomSpecModel;
-import jalview.structure.StructureCommandsI;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-
import java.awt.Color;
import java.util.HashMap;
import java.util.LinkedHashMap;
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.StructureCommand;
+import jalview.structure.StructureCommandI;
+
public class ChimeraXCommandsTest
{
+ private ChimeraXCommands testee;
+
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ testee = new ChimeraXCommands();
+ }
+
+ @Test(groups = { "Functional" })
+ public void testColourByCharge()
+ {
+ 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 testBuildColourCommands()
+ public void testColourByChain()
{
+ StructureCommandI cmd = testee.colourByChain();
+ assertEquals(cmd.getCommand(), "rainbow chain");
+ }
+
+ @Test(groups = { "Functional" })
+ public void testFocusView()
+ {
+ 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<>();
- ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 2, 5, "A");
- ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 7, 7, "B");
- ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 9, 23, "A");
- ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 1, 1, "A");
- ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 4, 7, "B");
- ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 8, 8, "A");
- ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 3, 5, "A");
- ChimeraCommands.addAtomSpecRange(map, Color.red, 0, 3, 5, "A");
- ChimeraCommands.addAtomSpecRange(map, Color.red, 0, 6, 9, "A");
-
- // 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
- String command = new ChimeraXCommands().buildColourCommands(map).get(0);
- assertEquals(
- command,
- "color #0/A:2-5,9-23/B:7|#1/A:1/B:4-7 #0000ff; color #1/A:3-5,8 #ffff00; color #0/A:3-9 #ff0000");
+ ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 2, 5, "A");
+ ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 7, 7, "B");
+ ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 9, 23, "A");
+ ChimeraCommands.addAtomSpecRange(map, Color.blue, "2", 1, 1, "A");
+ ChimeraCommands.addAtomSpecRange(map, Color.blue, "2", 4, 7, "B");
+ ChimeraCommands.addAtomSpecRange(map, Color.yellow, "2", 8, 8, "A");
+ ChimeraCommands.addAtomSpecRange(map, Color.yellow, "2", 3, 5, "A");
+ ChimeraCommands.addAtomSpecRange(map, Color.red, "1", 3, 5, "A");
+ ChimeraCommands.addAtomSpecRange(map, Color.red, "1", 6, 9, "A");
+
+ /*
+ * 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 = 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");
}
@Test(groups = { "Functional" })
- public void testBuildSetAttributeCommands()
+ public void testSetAttributes()
{
/*
* make a map of { featureType, {featureValue, {residue range specification } } }
*/
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<String> commands = commandGenerator
- .buildSetAttributeCommands(featuresMap);
- assertEquals(1, commands.size());
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
+
+ List<StructureCommandI> commands = testee.setAttributes(featuresMap);
+ assertEquals(commands.size(), 1);
/*
* feature name gets a jv_ namespace prefix
* feature value is quoted in case it contains spaces
*/
- assertEquals(commands.get(0),
+ assertEquals(commands.get(0).getCommand(),
"setattr #0/A:8-20 res jv_chain 'X' create true");
// add same feature value, overlapping range
- ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 3, 9, "A");
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 3, 9, "A");
// same feature value, contiguous range
- ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "A");
- commands = commandGenerator.buildSetAttributeCommands(featuresMap);
- assertEquals(1, commands.size());
- assertEquals(commands.get(0),
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A");
+ commands = testee.setAttributes(featuresMap);
+ assertEquals(commands.size(), 1);
+ assertEquals(commands.get(0).getCommand(),
"setattr #0/A:3-25 res jv_chain 'X' create true");
// same feature value and model, different chain
- ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "B");
+ 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.buildSetAttributeCommands(featuresMap);
- assertEquals(1, commands.size());
- assertEquals(commands.get(0),
- "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true");
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A");
+ 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.buildSetAttributeCommands(featuresMap);
+ ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A");
+ commands = testee.setAttributes(featuresMap);
assertEquals(2, commands.size());
// commands are ordered by feature type but not by value
- // so use contains to test for the expected command:
- assertTrue(commands
- .contains(
- "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true"));
- assertTrue(commands
- .contains("setattr #0/A:40-50 res jv_chain 'Y' create true"));
+ // 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));
+ String expected2 = "setattr #0/A:40-50 res jv_chain 'Y' create true";
+ 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.buildSetAttributeCommands(featuresMap);
- assertTrue(commands.contains(
- "setattr #0/A:7-15 res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' create true"));
- }
-
- @Test(groups = { "Functional" })
- public void testColourBySequence_hiddenColumns()
- {
- /*
- * load these sequences, coloured by Strand propensity,
- * with columns 2-4 hidden
- */
- SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
- SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS");
- AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
- AlignFrame af = new AlignFrame(al, 800, 500);
- af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
- ColumnSelection cs = new ColumnSelection();
- cs.addElement(2);
- cs.addElement(3);
- cs.addElement(4);
- af.getViewport().setColumnSelection(cs);
- af.hideSelColumns_actionPerformed(null);
- SequenceRenderer sr = new SequenceRenderer(af.getViewport());
- SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
- String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
- StructureSelectionManager ssm = new StructureSelectionManager();
-
- /*
- * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
- */
- HashMap<Integer, int[]> map = new HashMap<>();
- for (int pos = 1; pos <= seq1.getLength(); pos++)
- {
- map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
- }
- StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
- "A", map, null);
- ssm.addStructureMapping(sm1);
- StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
- "B", map, null);
- ssm.addStructureMapping(sm2);
-
- String[] commands = new ChimeraXCommands()
- .colourBySequence(ssm, files, seqs, sr, af.alignPanel);
- assertEquals(1, commands.length);
- String theCommand = commands[0];
- // M colour is #82827d (see strand.html help page)
- assertTrue(theCommand.contains("color #0/A:21|#1/B:21 #82827d"));// #0:21.A|#1:21.B"));
- // H colour is #60609f
- assertTrue(theCommand.contains("color #0/A:22 #60609f"));
- // V colour is #ffff00
- assertTrue(theCommand.contains("color #1/B:22 #ffff00"));
- // hidden columns are Gray (128, 128, 128)
- assertTrue(theCommand.contains("color #0/A:23-25|#1/B:23-25"));
- // S and G are both coloured #4949b6
- assertTrue(theCommand.contains("color #0/A:26-30|#1/B:26-30"));
+ 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");
- ref.addRange(1, 22, 23, "B");
+ ref.addRange("1", 12, 14, "A");
+ ref.addRange("1", 18, 18, "B");
+ ref.addRange("1", 22, 23, "B");
AtomSpecModel toAlign = new AtomSpecModel();
- toAlign.addRange(2, 15, 17, "B");
- toAlign.addRange(2, 20, 21, "B");
- toAlign.addRange(2, 22, 22, "C");
- String command = testee.superposeStructures(ref, toAlign);
+ toAlign.addRange("2", 15, 17, "B");
+ toAlign.addRange("2", 20, 21, "B");
+ toAlign.addRange("2", 22, 22, "C");
+ List<StructureCommandI> command = testee.superposeStructures(ref,
+ toAlign);
+ assertEquals(command.size(), 1);
+ String cmd = command.get(0).getCommand();
String refSpec = "#1/A:12-14/B:18,22-23";
String toAlignSpec = "#2/B:15-17,20-21/C:22";
+
+ /*
+ * superposition arguments include AlphaCarbon restriction,
+ * ribbon command does not
+ */
String expected = String.format(
- "align %s %s;~display all; chain @CA|P; ribbon %s|%s; focus",
- refSpec, toAlignSpec, refSpec, toAlignSpec);
- assertEquals(command, expected);
+ "align %s@CA toAtoms %s@CA; ribbon %s|%s; view", toAlignSpec,
+ refSpec, toAlignSpec, refSpec);
+ assertEquals(cmd, expected);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetAtomSpec()
+ {
+ AtomSpecModel model = new AtomSpecModel();
+ assertEquals(testee.getAtomSpec(model, false), "");
+ model.addRange("1", 2, 4, "A");
+ assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4");
+ model.addRange("1", 8, 8, "A");
+ assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8");
+ model.addRange("1", 5, 7, "B");
+ assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8/B:5-7");
+ model.addRange("1", 3, 5, "A");
+ assertEquals(testee.getAtomSpec(model, false), "#1/A:2-5,8/B:5-7");
+ model.addRange("0", 1, 4, "B");
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0/B:1-4|#1/A:2-5,8/B:5-7");
+ model.addRange("0", 5, 9, "C");
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-7");
+ model.addRange("1", 8, 10, "B");
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
+ model.addRange("1", 8, 9, "B");
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
+ model.addRange("0", 3, 10, "C"); // subsumes 5-9
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10");
+ model.addRange("5", 25, 35, " ");
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10|#5/:25-35");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetAtomSpec_alphaOnly()
+ {
+ AtomSpecModel model = new AtomSpecModel();
+ assertEquals(testee.getAtomSpec(model, true), "");
+ model.addRange("1", 2, 4, "A");
+ assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4@CA");
+ model.addRange("1", 8, 8, "A");
+ assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8@CA");
+ model.addRange("1", 5, 7, "B");
+ assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8/B:5-7@CA");
+ model.addRange("1", 3, 5, "A");
+ assertEquals(testee.getAtomSpec(model, true), "#1/A:2-5,8/B:5-7@CA");
+ model.addRange("0", 1, 4, "B");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0/B:1-4@CA|#1/A:2-5,8/B:5-7@CA");
+ model.addRange("0", 5, 9, "C");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-7@CA");
+ model.addRange("1", 8, 10, "B");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
+ model.addRange("1", 8, 9, "B");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
+ model.addRange("0", 3, 10, "C"); // subsumes 5-9
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA");
+ model.addRange("5", 25, 35, " "); // empty chain code
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA|#5/:25-35@CA");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetModelStartNo()
+ {
+ assertEquals(testee.getModelStartNo(), 1);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetResidueSpec()
+ {
+ assertEquals(testee.getResidueSpec("ALA"), ":ALA");
+ }
+
+ @Test(groups = "Functional")
+ public void testShowBackbone()
+ {
+ List<StructureCommandI> showBackbone = testee.showBackbone();
+ assertEquals(showBackbone.size(), 1);
+ assertEquals(showBackbone.get(0).getCommand(),
+ "~display all;~ribbon;show @CA|P atoms");
+ }
+
+ @Test(groups = "Functional")
+ public void testOpenCommandFile()
+ {
+ assertEquals(testee.openCommandFile("nowhere").getCommand(),
+ "open nowhere");
+ }
+
+ @Test(groups = "Functional")
+ public void testSaveSession()
+ {
+ assertEquals(testee.saveSession("somewhere").getCommand(),
+ "save somewhere format session");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetColourCommand()
+ {
+ assertEquals(testee.colourResidues("something", Color.MAGENTA)
+ .getCommand(),
+ "color something #ff00ff");
+ }
+
+ @Test(groups = "Functional")
+ public void testSetAttribute()
+ {
+ 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("jv_kd", "27.3", model)
+ .getCommand(),
+ "setattr #1/A:89-92|#2/B:8-9,12-20 res jv_kd '27.3' create true");
+ }
+
+ @Test(groups = "Functional")
+ public void testCloseViewer()
+ {
+ assertEquals(testee.closeViewer(), new StructureCommand("exit"));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetSelectedResidues()
+ {
+ assertEquals(testee.getSelectedResidues(),
+ new StructureCommand("info selection level residue"));
+ }
+
+ @Test(groups = "Functional")
+ public void testStartNotifications()
+ {
+ List<StructureCommandI> cmds = testee.startNotifications("to here");
+ assertEquals(cmds.size(), 2);
+ assertEquals(cmds.get(0), new StructureCommand("info notify start models jalview prefix ModelChanged url to here"));
+ assertEquals(cmds.get(1), new StructureCommand("info notify start selection jalview 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("info notify stop models jalview"));
+ assertEquals(cmds.get(1), new StructureCommand("info notify stop selection jalview"));
+ }
+
+ @Test(groups = "Functional")
+ public void testListResidueAttributes()
+ {
+ assertEquals(testee.listResidueAttributes(),
+ new StructureCommand("info resattr"));
}
}
git://source.jalview.org / jalview.git / blobdiff