import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
-import jalview.gui.JvOptionPane;
+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.List;
import java.util.Map;
-import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ChimeraCommandsTest
{
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
@Test(groups = { "Functional" })
public void testBuildColourCommands()
{
- Map<Object, AtomSpecModel> map = new LinkedHashMap<Object, AtomSpecModel>();
- ChimeraCommands.addRange(map, Color.blue, 0, 2, 5, "A");
- ChimeraCommands.addRange(map, Color.blue, 0, 7, 7, "B");
- ChimeraCommands.addRange(map, Color.blue, 0, 9, 23, "A");
- ChimeraCommands.addRange(map, Color.blue, 1, 1, 1, "A");
- ChimeraCommands.addRange(map, Color.blue, 1, 4, 7, "B");
- ChimeraCommands.addRange(map, Color.yellow, 1, 8, 8, "A");
- ChimeraCommands.addRange(map, Color.yellow, 1, 3, 5, "A");
- ChimeraCommands.addRange(map, Color.red, 0, 3, 5, "A");
- ChimeraCommands.addRange(map, Color.red, 0, 6, 9, "A");
+ 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 = ChimeraCommands.buildColourCommands(map).get(0);
+ String command = new ChimeraCommands().buildColourCommands(map).get(0);
assertEquals(
command,
"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");
/*
* make a map of { featureType, {featureValue, {residue range specification } } }
*/
- Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
- Map<Object, AtomSpecModel> featureValues = new HashMap<Object, AtomSpecModel>();
+ 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.addRange(featureValues, "X", 0, 8, 20, "A");
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 8, 20, "A");
- List<String> commands = ChimeraCommands
+ ChimeraCommands commandGenerator = new ChimeraCommands();
+ List<String> commands = commandGenerator
.buildSetAttributeCommands(featuresMap);
assertEquals(1, commands.size());
* feature name gets a jv_ namespace prefix
* feature value is quoted in case it contains spaces
*/
- assertEquals(commands.get(0), "setattr r jv_chain \"X\" #0:8-20.A");
+ assertEquals(commands.get(0), "setattr res jv_chain 'X' #0:8-20.A");
// add same feature value, overlapping range
- ChimeraCommands.addRange(featureValues, "X", 0, 3, 9, "A");
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 3, 9, "A");
// same feature value, contiguous range
- ChimeraCommands.addRange(featureValues, "X", 0, 21, 25, "A");
- commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "A");
+ commands = commandGenerator.buildSetAttributeCommands(featuresMap);
assertEquals(1, commands.size());
- assertEquals(commands.get(0), "setattr r jv_chain \"X\" #0:3-25.A");
+ assertEquals(commands.get(0), "setattr res jv_chain 'X' #0:3-25.A");
// same feature value and model, different chain
- ChimeraCommands.addRange(featureValues, "X", 0, 21, 25, "B");
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "B");
// same feature value and chain, different model
- ChimeraCommands.addRange(featureValues, "X", 1, 26, 30, "A");
- commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", 1, 26, 30, "A");
+ commands = commandGenerator.buildSetAttributeCommands(featuresMap);
assertEquals(1, commands.size());
assertEquals(commands.get(0),
- "setattr r jv_chain \"X\" #0:3-25.A,21-25.B|#1:26-30.A");
+ "setattr res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A");
// same feature, different value
- ChimeraCommands.addRange(featureValues, "Y", 0, 40, 50, "A");
- commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+ ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A");
+ commands = commandGenerator.buildSetAttributeCommands(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 r jv_chain \"X\" #0:3-25.A,21-25.B|#1:26-30.A"));
- assertTrue(commands.contains("setattr r jv_chain \"Y\" #0:40-50.A"));
+ .contains(
+ "setattr res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A"));
+ assertTrue(commands.contains("setattr res jv_chain 'Y' #0:40-50.A"));
featuresMap.clear();
featureValues.clear();
featuresMap.put("side-chain binding!", featureValues);
- ChimeraCommands.addRange(featureValues, "metal ion!", 0, 7, 15, "A");
- // feature names are sanitised to change space or hyphen to underscore
- commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+ ChimeraCommands.addAtomSpecRange(featureValues,
+ "<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 r jv_side_chain_binding_ \"metal ion!\" #0:7-15.A"));
+ .contains(
+ "setattr res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' #0:7-15.A"));
}
/**
assertEquals(ChimeraCommands.makeAttributeName("helixColor"),
"jv_helixColor_");
}
+
+ @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 ChimeraCommands()
+ .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 #82827d #0:21.A|#1:21.B"));
+ // H colour is #60609f
+ assertTrue(theCommand.contains("color #60609f #0:22.A"));
+ // V colour is #ffff00
+ assertTrue(theCommand.contains("color #ffff00 #1:22.B"));
+ // hidden columns are Gray (128, 128, 128)
+ assertTrue(theCommand.contains("color #808080 #0:23-25.A|#1:23-25.B"));
+ // S and G are both coloured #4949b6
+ assertTrue(theCommand.contains("color #4949b6 #0:26-30.A|#1:26-30.B"));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetAtomSpec()
+ {
+ StructureCommandsI testee = new ChimeraCommands();
+ AtomSpecModel model = new AtomSpecModel();
+ assertEquals(testee.getAtomSpec(model, false), "");
+ model.addRange(1, 2, 4, "A");
+ assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A");
+ model.addRange(1, 8, 8, "A");
+ assertEquals(testee.getAtomSpec(model, false), "#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");
+ model.addRange(1, 3, 5, "A");
+ assertEquals(testee.getAtomSpec(model, false), "#1:2-5.A,8.A,5-7.B");
+ model.addRange(0, 1, 4, "B");
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0:1-4.B|#1:2-5.A,8.A,5-7.B");
+ model.addRange(0, 5, 9, "C");
+ assertEquals(testee.getAtomSpec(model, false),
+ "#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),
+ "#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),
+ "#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),
+ "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B");
+ model.addRange(5, 25, 35, " "); // empty chain code - e.g. from homology
+ // modelling
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B|#5:25-35.");
+
+ }
+
+ @Test(groups = "Functional")
+ public void testGetAtomSpec_alphaOnly()
+ {
+ StructureCommandsI testee = new ChimeraCommands();
+ AtomSpecModel model = new AtomSpecModel();
+ assertEquals(testee.getAtomSpec(model, true), "");
+ model.addRange(1, 2, 4, "A");
+ assertEquals(testee.getAtomSpec(model, true), "#1:2-4.A@CA|P");
+ model.addRange(1, 8, 8, "A");
+ assertEquals(testee.getAtomSpec(model, true), "#1:2-4.A,8.A@CA|P");
+ model.addRange(1, 5, 7, "B");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#1:2-4.A,8.A,5-7.B@CA|P");
+ model.addRange(1, 3, 5, "A");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#1:2-5.A,8.A,5-7.B@CA|P");
+ model.addRange(0, 1, 4, "B");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0:1-4.B@CA|P|#1:2-5.A,8.A,5-7.B@CA|P");
+ model.addRange(0, 5, 9, "C");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0:1-4.B,5-9.C@CA|P|#1:2-5.A,8.A,5-7.B@CA|P");
+ model.addRange(1, 8, 10, "B");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0:1-4.B,5-9.C@CA|P|#1:2-5.A,8.A,5-10.B@CA|P");
+ model.addRange(1, 8, 9, "B");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0:1-4.B,5-9.C@CA|P|#1:2-5.A,8.A,5-10.B@CA|P");
+ model.addRange(0, 3, 10, "C"); // subsumes 5-9
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0:1-4.B,3-10.C@CA|P|#1:2-5.A,8.A,5-10.B@CA|P");
+ model.addRange(5, 25, 35, " "); // empty chain code
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0:1-4.B,3-10.C@CA|P|#1:2-5.A,8.A,5-10.B@CA|P|#5:25-35.@CA|P");
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void testSuperposeStructures()
+ {
+ StructureCommandsI testee = new ChimeraCommands();
+ AtomSpecModel ref = new AtomSpecModel();
+ 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);
+ 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";
+ String expected = String.format(
+ "match %s %s;~display all; chain @CA|P; ribbon %s|%s; focus",
+ refSpec, toAlignSpec, refSpec, toAlignSpec);
+ assertEquals(command, expected);
+ }
}
git://source.jalview.org / jalview.git / blobdiff