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 org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class ChimeraCommandsTest
{
+ private SequenceRenderer sr;
+
+ private String[] files;
+
+ 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 String[] getColourBySequenceCommands(String[] files,
+ AlignmentViewPanel avp)
+ {
+ return null;
+ }
+
+ @Override
+ public jalview.api.SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment)
+ {
+ return sr;
+ }
+
+ @Override
+ protected void colourBySequence(String[] colourBySequenceCommands)
+ {
+ }
+
+ @Override
+ public void colourByChain()
+ {
+ }
+
+ @Override
+ public void colourByCharge()
+ {
+ }
+
+ @Override
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+ {
+ return null;
+ }
+
+ @Override
+ public String[] getStructureFiles()
+ {
+ return files;
+ }
+
+ @Override
+ public String getModelSpec(int model)
+ {
+ return "#" + String.valueOf(model);
+ }
+ };
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
@Test(groups = { "Functional" })
public void testBuildColourCommands()
{
-
- Map<Object, AtomSpecModel> map = new LinkedHashMap<Object, AtomSpecModel>();
+ 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");
// 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...
ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 8, 20, "A");
List<String> commands = ChimeraCommands
- .buildSetAttributeCommands(featuresMap);
+ .buildSetAttributeCommands(featuresMap, mockBinding);
assertEquals(1, commands.size());
/*
ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 3, 9, "A");
// same feature value, contiguous range
ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "A");
- commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+ commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
+ mockBinding);
assertEquals(1, commands.size());
assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:3-25.A");
ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "B");
// same feature value and chain, different model
ChimeraCommands.addAtomSpecRange(featureValues, "X", 1, 26, 30, "A");
- commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+ 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");
// same feature, different value
ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A");
- commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+ 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:
"A");
// feature names are sanitised to change non-alphanumeric to underscore
// feature values are sanitised to encode single quote characters
- commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+ commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
+ mockBinding);
assertTrue(commands
.contains("setattr r jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' #0:7-15.A"));
}
cs.addElement(4);
af.getViewport().setColumnSelection(cs);
af.hideSelColumns_actionPerformed(null);
- SequenceRenderer sr = new SequenceRenderer(af.getViewport());
+ sr = new SequenceRenderer(af.getViewport());
SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
- String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
+ 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<Integer, int[]>();
+ HashMap<Integer, int[]> map = new HashMap<>();
for (int pos = 1; pos <= seq1.getLength(); pos++)
{
map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
"B", map, null);
ssm.addStructureMapping(sm2);
- StructureMappingcommandSet[] commands = ChimeraCommands
- .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
+ /*
+ * put data into the mock binding object
+ */
+ PA.setValue(mockBinding, "ssm", ssm);
+ PA.setValue(mockBinding, "sequence", seqs);
+
+ Map<Object, AtomSpecModel> colourMap = mockBinding
+ .buildColoursMap(af.alignPanel);
+ String[] commands = ChimeraCommands
+ .getColourBySequenceCommand(colourMap, mockBinding);
assertEquals(1, commands.length);
- assertEquals(1, commands[0].commands.length);
- String theCommand = commands[0].commands[0];
+ 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
// 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