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 org.testng.annotations.Test;
+import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI;
+
public class ChimeraCommandsTest
{
@Test(groups = { "Functional" })
- public void testBuildColourCommands()
+ 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");
+ 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 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");
+ List<StructureCommandI> commands = new ChimeraCommands()
+ .colourBySequence(map);
+ assertEquals(commands.size(), 1);
+ assertEquals(commands.get(0).getCommand(),
+ "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" })
- public void testBuildSetAttributeCommands()
+ public void testSetAttributes()
{
/*
* make a map of { featureType, {featureValue, {residue range specification } } }
* start with just one feature/value...
*/
featuresMap.put("chain", featureValues);
- ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 8, 20, "A");
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
ChimeraCommands commandGenerator = new ChimeraCommands();
- List<String> commands = commandGenerator
- .buildSetAttributeCommands(featuresMap);
+ List<StructureCommandI> commands = commandGenerator
+ .setAttributes(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 res jv_chain 'X' #0:8-20.A");
+ assertEquals(commands.get(0).getCommand(),
+ "setattr res jv_chain 'X' #0:8-20.A");
// 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);
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A");
+ commands = commandGenerator.setAttributes(featuresMap);
assertEquals(1, commands.size());
- assertEquals(commands.get(0), "setattr res jv_chain 'X' #0:3-25.A");
+ assertEquals(commands.get(0).getCommand(),
+ "setattr res jv_chain 'X' #0:3-25.A");
// 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);
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A");
+ commands = commandGenerator.setAttributes(featuresMap);
assertEquals(1, commands.size());
- assertEquals(commands.get(0),
- "setattr res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A");
+ String expected1 = "setattr res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A";
+ 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 = commandGenerator.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 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"));
+ // 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 res jv_chain 'Y' #0:40-50.A";
+ 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,
+ "<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 res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' #0:7-15.A"));
+ commands = commandGenerator.setAttributes(featuresMap);
+ assertEquals(commands.size(), 1);
+ String expected3 = "setattr res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' #0:7-15.A";
+ assertTrue(commands.get(0).getCommand().equals(expected3));
}
/**
"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");
+ model.addRange("1", 2, 4, "A");
assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A");
- model.addRange(1, 8, 8, "A");
+ model.addRange("1", 8, 8, "A");
assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A");
- model.addRange(1, 5, 7, "B");
+ 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");
+ 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");
+ 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");
+ 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");
+ 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");
+ 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
+ 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
+ model.addRange("5", 25, 35, " ");
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 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");
+ List<StructureCommandI> command = testee.superposeStructures(ref,
+ toAlign);
+ // qualifier to restrict match to CA and no altlocs
+ String carbonAlphas = "@CA&~@.B-Z&~@.2-9";
+ String refSpec = "#1:12-14.A,18.B,22-23.B";
+ String toAlignSpec = "#2:15-17.B,20-21.B,22.C";
+ String expected = String.format(
+ "match %s%s %s%s; ribbon %s|%s; focus", toAlignSpec,
+ carbonAlphas, refSpec, carbonAlphas, toAlignSpec, refSpec);
+ assertEquals(command.get(0).getCommand(), expected);
+ }
+
@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");
+ model.addRange("1", 2, 4, "A");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#1:2-4.A@CA&~@.B-Z&~@.2-9");
+ model.addRange("1", 8, 8, "A");
assertEquals(testee.getAtomSpec(model, true),
- "#1:2-4.A,8.A,5-7.B@CA|P");
- model.addRange(1, 3, 5, "A");
+ "#1:2-4.A,8.A@CA&~@.B-Z&~@.2-9");
+ model.addRange("1", 5, 7, "B");
assertEquals(testee.getAtomSpec(model, true),
- "#1:2-5.A,8.A,5-7.B@CA|P");
- model.addRange(0, 1, 4, "B");
+ "#1:2-4.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
+ model.addRange("1", 3, 5, "A");
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");
+ "#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
+ model.addRange("0", 1, 4, "B");
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");
+ "#0:1-4.B@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
+ 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,5-10.B@CA|P");
- model.addRange(1, 8, 9, "B");
+ "#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
+ 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(0, 3, 10, "C"); // subsumes 5-9
+ "#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
+ model.addRange("1", 8, 9, "B");
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
+ "#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
+ 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|#5:25-35.@CA|P");
+ "#0:1-4.B,3-10.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
+ model.addRange("5", 25, 35, " "); // empty chain code
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0:1-4.B,3-10.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9|#5:25-35.@CA&~@.B-Z&~@.2-9");
}
- @Test(groups = { "Functional" })
- public void testSuperposeStructures()
+ @Test(groups = "Functional")
+ public void testGetModelStartNo()
{
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);
+ assertEquals(testee.getModelStartNo(), 0);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetResidueSpec()
+ {
+ ChimeraCommands testee = new ChimeraCommands();
+ assertEquals(testee.getResidueSpec("ALA"), "::ALA");
+ }
+
+ @Test(groups = "Functional")
+ public void testShowBackbone()
+ {
+ ChimeraCommands testee = new ChimeraCommands();
+ List<StructureCommandI> cmds = testee.showBackbone();
+ assertEquals(cmds.size(), 1);
+ assertEquals(cmds.get(0).getCommand(),
+ "~display all;~ribbon;chain @CA|P");
+ }
+
+ @Test(groups = "Functional")
+ public void testOpenCommandFile()
+ {
+ ChimeraCommands testee = new ChimeraCommands();
+ assertEquals(testee.openCommandFile("nowhere").getCommand(),
+ "open cmd:nowhere");
+ }
+
+ @Test(groups = "Functional")
+ public void testSaveSession()
+ {
+ ChimeraCommands testee = new ChimeraCommands();
+ assertEquals(testee.saveSession("somewhere").getCommand(),
+ "save somewhere");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetColourCommand()
+ {
+ ChimeraCommands testee = new ChimeraCommands();
+ assertEquals(testee.getColourCommand("something", Color.MAGENTA)
+ .getCommand(),
+ "color #ff00ff something");
+ }
+
+ @Test(groups = "Functional")
+ public void testSetAttribute()
+ {
+ ChimeraCommands testee = new ChimeraCommands();
+ 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("phi", "27.3", model).getCommand(),
+ "setattr res phi '27.3' #1:89-92.A|#2:8-9.B,12-20.B");
}
}
git://source.jalview.org / jalview.git / blobdiff