import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
+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.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.gui.SequenceRenderer;
import jalview.schemes.JalviewColourScheme;
import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsI;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
-import java.util.HashMap;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
public class JmolCommandsTest
{
}
@Test(groups = { "Functional" })
- public void testGetColourBySequenceCommand_noFeatures()
- {
- SequenceI seq1 = new Sequence("seq1", "MHRSQTRALK");
- SequenceI seq2 = new Sequence("seq2", "MRLEITQSGD");
- AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
- AlignFrame af = new AlignFrame(al, 800, 500);
- SequenceRenderer sr = new SequenceRenderer(af.getViewport());
- SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
- String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
- StructureSelectionManager ssm = new StructureSelectionManager();
-
- // need some mappings!
-
- String[] commands = new JmolCommands().colourBySequence(ssm, files,
- seqs, sr, af.alignPanel);
- assertEquals(commands.length, 0);
- }
-
- @Test(groups = { "Functional" })
public void testGetColourBySequenceCommands_hiddenColumns()
{
/*
StructureCommandsI testee = new JmolCommands();
AtomSpecModel model = new AtomSpecModel();
assertEquals(testee.getAtomSpec(model, false), "");
- model.addRange(1, 2, 4, "A");
+ model.addRange("1", 2, 4, "A");
assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1");
- model.addRange(1, 8, 8, "A");
+ model.addRange("1", 8, 8, "A");
assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1|8:A/1.1");
- model.addRange(1, 5, 7, "B");
+ model.addRange("1", 5, 7, "B");
assertEquals(testee.getAtomSpec(model, false),
"2-4:A/1.1|8:A/1.1|5-7:B/1.1");
- model.addRange(1, 3, 5, "A");
+ model.addRange("1", 3, 5, "A");
assertEquals(testee.getAtomSpec(model, false),
"2-5:A/1.1|8:A/1.1|5-7:B/1.1");
- model.addRange(2, 1, 4, "B");
+ model.addRange("2", 1, 4, "B");
assertEquals(testee.getAtomSpec(model, false),
"2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1");
- model.addRange(2, 5, 9, "C");
+ model.addRange("2", 5, 9, "C");
assertEquals(testee.getAtomSpec(model, false),
"2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1|5-9:C/2.1");
- model.addRange(1, 8, 10, "B");
+ model.addRange("1", 8, 10, "B");
assertEquals(testee.getAtomSpec(model, false),
"2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
- model.addRange(1, 8, 9, "B");
+ model.addRange("1", 8, 9, "B");
assertEquals(testee.getAtomSpec(model, false),
"2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
- model.addRange(2, 3, 10, "C"); // subsumes 5-9
+ model.addRange("2", 3, 10, "C"); // subsumes 5-9
assertEquals(testee.getAtomSpec(model, false),
"2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1");
- model.addRange(5, 25, 35, " ");
+ model.addRange("5", 25, 35, " ");
assertEquals(testee.getAtomSpec(model, false),
"2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1|25-35:/5.1");
}
@Test(groups = { "Functional" })
+ public void testColourBySequence()
+ {
+ Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
+ JmolCommands.addAtomSpecRange(map, Color.blue, "1", 2, 5, "A");
+ JmolCommands.addAtomSpecRange(map, Color.blue, "1", 7, 7, "B");
+ JmolCommands.addAtomSpecRange(map, Color.blue, "1", 9, 23, "A");
+ JmolCommands.addAtomSpecRange(map, Color.blue, "2", 1, 1, "A");
+ JmolCommands.addAtomSpecRange(map, Color.blue, "2", 4, 7, "B");
+ JmolCommands.addAtomSpecRange(map, Color.yellow, "2", 8, 8, "A");
+ JmolCommands.addAtomSpecRange(map, Color.yellow, "2", 3, 5, "A");
+ JmolCommands.addAtomSpecRange(map, Color.red, "1", 3, 5, "A");
+ JmolCommands.addAtomSpecRange(map, Color.red, "1", 6, 9, "A");
+
+ // Colours should appear in the Jmol command in the order in which
+ // they were added; within colour, by model, by chain, ranges in start order
+ List<StructureCommandI> commands = new JmolCommands()
+ .colourBySequence(map);
+ assertEquals(commands.size(), 1);
+ String expected1 = "select 2-5:A/1.1|9-23:A/1.1|7:B/1.1|1:A/2.1|4-7:B/2.1;color[0,0,255]";
+ String expected2 = "select 3-5:A/2.1|8:A/2.1;color[255,255,0]";
+ String expected3 = "select 3-9:A/1.1;color[255,0,0]";
+ assertEquals(commands.get(0).getCommand(),
+ expected1 + ";" + expected2 + ";" + expected3);
+ }
+
+ @Test(groups = { "Functional" })
public void testSuperposeStructures()
{
StructureCommandsI testee = new JmolCommands();
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 refSpec = "12-14:A/1.1|18:B/1.1|22-23:B/1.1";
String toAlignSpec = "15-17:B/2.1|20-21:B/2.1|22:C/2.1";
String expected = String.format(
"compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS {%s}{%s} ROTATE TRANSLATE ;select %s|%s;cartoons",
toAlignSpec, refSpec, toAlignSpec, refSpec);
- assertEquals(command, expected);
+ assertEquals(command.get(0).getCommand(), expected);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetModelStartNo()
+ {
+ StructureCommandsI testee = new JmolCommands();
+ assertEquals(testee.getModelStartNo(), 1);
}
}
git://source.jalview.org / jalview.git / blobdiff