import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.gui.SequenceRenderer;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.JalviewColourScheme;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureMappingcommandSet;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+
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 junit.extensions.PA;
+
public class ChimeraCommandsTest
{
+
+ private SequenceRenderer sr;
+
+ private AAStructureBindingModel mockBinding = new AAStructureBindingModel(
+ null, null)
+ {
+ @Override
+ public void releaseReferences(Object svl)
+ {
+ }
+
+ @Override
+ public void highlightAtoms(List<AtomSpec> atoms)
+ {
+ }
+
+ @Override
+ public List<String> getChainNames()
+ {
+ return null;
+ }
+
+ @Override
+ public void setJalviewColourScheme(ColourSchemeI cs)
+ {
+ }
+
+ @Override
+ public String superposeStructures(AlignmentI[] alignments,
+ int[] structureIndices, HiddenColumns[] hiddenCols)
+ {
+ return null;
+ }
+
+ @Override
+ public void setBackgroundColour(Color col)
+ {
+ }
+
+ @Override
+ protected StructureMappingcommandSet[] getColourBySequenceCommands(
+ String[] files, AlignmentViewPanel avp)
+ {
+ return null;
+ }
+
+ @Override
+ public jalview.api.SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment)
+ {
+ return sr;
+ }
+
+ @Override
+ protected void colourBySequence(
+ StructureMappingcommandSet[] colourBySequenceCommands)
+ {
+ }
+
+ @Override
+ public void colourByChain()
+ {
+ }
+
+ @Override
+ public void colourByCharge()
+ {
+ }
+
+ @Override
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+ {
+ return null;
+ }
+
+ @Override
+ public String[] getStructureFiles()
+ {
+ return null;
+ }
+
+ @Override
+ public String getModelSpec(int model)
+ {
+ return "#" + String.valueOf(model);
+ }
+ };
+
+ @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.addColourRange(map, Color.blue, 0, 2, 5, "A");
+ ChimeraCommands.addColourRange(map, Color.blue, 0, 7, 7, "B");
+ ChimeraCommands.addColourRange(map, Color.blue, 0, 9, 23, "A");
+ ChimeraCommands.addColourRange(map, Color.blue, 1, 1, 1, "A");
+ ChimeraCommands.addColourRange(map, Color.blue, 1, 4, 7, "B");
+ ChimeraCommands.addColourRange(map, Color.yellow, 1, 8, 8, "A");
+ ChimeraCommands.addColourRange(map, Color.yellow, 1, 3, 5, "A");
+ ChimeraCommands.addColourRange(map, Color.red, 0, 3, 5, "A");
+ ChimeraCommands.addColourRange(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);
+ // all prefixed with #808080 to colour hidden regions (if shown) gray
+ String command = ChimeraCommands.buildColourCommands(map, mockBinding)
+ .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");
+ "color #808080; 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" })
/*
* 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.addColourRange(featureValues, "X", 0, 8, 20, "A");
List<String> commands = ChimeraCommands
- .buildSetAttributeCommands(featuresMap);
+ .buildSetAttributeCommands(featuresMap, mockBinding);
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 r jv_chain 'X' #0:8-20.A");
// add same feature value, overlapping range
- ChimeraCommands.addRange(featureValues, "X", 0, 3, 9, "A");
+ ChimeraCommands.addColourRange(featureValues, "X", 0, 3, 9, "A");
// same feature value, contiguous range
- ChimeraCommands.addRange(featureValues, "X", 0, 21, 25, "A");
- commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+ ChimeraCommands.addColourRange(featureValues, "X", 0, 21, 25, "A");
+ commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
+ mockBinding);
assertEquals(1, commands.size());
- assertEquals(commands.get(0), "setattr r jv_chain \"X\" #0:3-25.A");
+ assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:3-25.A");
// same feature value and model, different chain
- ChimeraCommands.addRange(featureValues, "X", 0, 21, 25, "B");
+ ChimeraCommands.addColourRange(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.addColourRange(featureValues, "X", 1, 26, 30, "A");
+ commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
+ mockBinding);
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 r 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.addColourRange(featureValues, "Y", 0, 40, 50, "A");
+ commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
+ mockBinding);
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 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"));
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.addColourRange(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 = ChimeraCommands.buildSetAttributeCommands(featuresMap,
+ mockBinding);
assertTrue(commands
- .contains("setattr r jv_side_chain_binding_ \"metal ion!\" #0:7-15.A"));
+ .contains("setattr r 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 testGetColourBySequenceCommands_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);
+ 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);
+
+ /*
+ * put data into the mock binding object
+ */
+ PA.setValue(mockBinding, "ssm", ssm);
+ PA.setValue(mockBinding, "sequence", seqs);
+
+ StructureMappingcommandSet[] commands = ChimeraCommands
+ .getColourBySequenceCommand(files, af.alignPanel, mockBinding);
+ assertEquals(1, commands.length);
+ assertEquals(1, commands[0].commands.length);
+ String theCommand = commands[0].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()
+ {
+ AtomSpecModel model = new AtomSpecModel();
+ assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding), "");
+ model.addRange(1, 2, 4, "A");
+ assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding),
+ "#1:2-4.A");
+ model.addRange(1, 8, 8, "A");
+ assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding),
+ "#1:2-4.A,8.A");
+ model.addRange(1, 5, 7, "B");
+ assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding),
+ "#1:2-4.A,8.A,5-7.B");
+ model.addRange(1, 3, 5, "A");
+ assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding),
+ "#1:2-5.A,8.A,5-7.B");
+ model.addRange(0, 1, 4, "B");
+ assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding),
+ "#0:1-4.B|#1:2-5.A,8.A,5-7.B");
+ model.addRange(0, 5, 9, "C");
+ assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding),
+ "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-7.B");
+ model.addRange(1, 8, 10, "B");
+ assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding),
+ "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
+ model.addRange(1, 8, 9, "B");
+ assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding),
+ "#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(ChimeraCommands.getAtomSpec(model, mockBinding),
+ "#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(ChimeraCommands.getAtomSpec(model, mockBinding),
+ "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B|#5:25-35.");
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff