import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
-import jalview.structure.AtomSpecModel;
-import jalview.structure.StructureCommandsI;
-
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.structure.AtomSpecModel;
+import jalview.structure.StructureCommandI;
+
public class ChimeraCommandsTest
{
+ private ChimeraCommands testee;
+
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ testee = new ChimeraCommands();
+ }
@Test(groups = { "Functional" })
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[] commands = new ChimeraCommands().colourBySequence(map);
- assertEquals(commands.length, 1);
- assertEquals(
- commands[0],
- "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 = testee.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" })
*/
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.addAtomSpecRange(featureValues, "X", 0, 8, 20, "A");
-
- ChimeraCommands commandGenerator = new ChimeraCommands();
- String[] commands = commandGenerator.setAttributes(featuresMap);
- assertEquals(1, commands.length);
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
+
+ List<StructureCommandI> commands = testee.setAttributes(featuresMap);
+ assertEquals(1, commands.size());
/*
* feature name gets a jv_ namespace prefix
* feature value is quoted in case it contains spaces
*/
- assertEquals(commands[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.setAttributes(featuresMap);
- assertEquals(1, commands.length);
- assertEquals(commands[0], "setattr res jv_chain 'X' #0:3-25.A");
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A");
+ commands = testee.setAttributes(featuresMap);
+ assertEquals(1, commands.size());
+ 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.setAttributes(featuresMap);
- assertEquals(1, commands.length);
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A");
+ commands = testee.setAttributes(featuresMap);
+ assertEquals(1, commands.size());
String expected1 = "setattr res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A";
- assertEquals(commands[0],
- expected1);
+ assertEquals(commands.get(0).getCommand(), expected1);
// same feature, different value
- ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A");
- commands = commandGenerator.setAttributes(featuresMap);
- assertEquals(2, commands.length);
+ ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A");
+ commands = testee.setAttributes(featuresMap);
+ assertEquals(2, commands.size());
// commands are ordered by feature type but not by value
// so test for the expected command in either order
- assertTrue(
- commands[0].equals(expected1) || commands[1].equals(expected1));
+ 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(
- commands[0].equals(expected2) || commands[1].equals(expected2));
+ 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,
- "A");
+ "<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.setAttributes(featuresMap);
+ commands = testee.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[0].equals(expected3) || commands[1].equals(expected3));
+ assertTrue(commands.get(0).getCommand().equals(expected3));
}
/**
* Tests for the method that prefixes and sanitises a feature name so it can
- * be used as a valid, namespaced attribute name in Chimera
+ * be used as a valid, namespaced attribute name in Chimera or PyMol
*/
@Test(groups = { "Functional" })
public void testMakeAttributeName()
{
- assertEquals(ChimeraCommands.makeAttributeName(null), "jv_");
- assertEquals(ChimeraCommands.makeAttributeName(""), "jv_");
- assertEquals(ChimeraCommands.makeAttributeName("helix"), "jv_helix");
- assertEquals(ChimeraCommands.makeAttributeName("Hello World 24"),
+ assertEquals(testee.makeAttributeName(null), "jv_");
+ assertEquals(testee.makeAttributeName(""), "jv_");
+ assertEquals(testee.makeAttributeName("helix"), "jv_helix");
+ assertEquals(testee.makeAttributeName(
+ "Hello World 24"),
"jv_Hello_World_24");
- assertEquals(
- ChimeraCommands.makeAttributeName("!this is-a_very*{odd(name"),
+ assertEquals(testee.makeAttributeName(
+ "!this is-a_very*{odd(name"),
"jv__this_is_a_very__odd_name");
// name ending in color gets underscore appended
- assertEquals(ChimeraCommands.makeAttributeName("helixColor"),
- "jv_helixColor_");
+ assertEquals(testee.makeAttributeName("helixColor"), "jv_helixColor_");
}
@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");
+ 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);
+ 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");
+ model.addRange("1", 2, 4, "A");
assertEquals(testee.getAtomSpec(model, true),
- "#1:2-4.A@CA|P&~@.B-Z&~@.2-9");
- model.addRange(1, 8, 8, "A");
+ "#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@CA|P&~@.B-Z&~@.2-9");
- model.addRange(1, 5, 7, "B");
+ "#1:2-4.A,8.A@CA&~@.B-Z&~@.2-9");
+ model.addRange("1", 5, 7, "B");
assertEquals(testee.getAtomSpec(model, true),
- "#1:2-4.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
- model.addRange(1, 3, 5, "A");
+ "#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),
- "#1:2-5.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
- model.addRange(0, 1, 4, "B");
+ "#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@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
- model.addRange(0, 5, 9, "C");
+ "#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&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
- model.addRange(1, 8, 10, "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&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9");
- model.addRange(1, 8, 9, "B");
+ "#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
+ model.addRange("1", 8, 9, "B");
assertEquals(testee.getAtomSpec(model, true),
- "#0:1-4.B,5-9.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9");
- 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("0", 3, 10, "C"); // subsumes 5-9
assertEquals(testee.getAtomSpec(model, true),
- "#0:1-4.B,3-10.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9");
- model.addRange(5, 25, 35, " "); // empty chain code
+ "#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|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9|#5:25-35.@CA|P&~@.B-Z&~@.2-9");
-
- }
-
- @Test(groups = "Functional")
- public void testGetModelStartNo()
- {
- StructureCommandsI testee = new ChimeraCommands();
- assertEquals(testee.getModelStartNo(), 0);
+ "#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 testGetResidueSpec()
{
- ChimeraCommands testee = new ChimeraCommands();
assertEquals(testee.getResidueSpec("ALA"), "::ALA");
}
@Test(groups = "Functional")
public void testShowBackbone()
{
- ChimeraCommands testee = new ChimeraCommands();
- assertEquals(testee.showBackbone(), "~display all;chain @CA|P");
+ 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"), "open cmd:nowhere");
+ assertEquals(testee.openCommandFile("nowhere").getCommand(),
+ "open cmd:nowhere");
}
@Test(groups = "Functional")
public void testSaveSession()
{
- ChimeraCommands testee = new ChimeraCommands();
- assertEquals(testee.saveSession("somewhere"), "save somewhere");
+ assertEquals(testee.saveSession("somewhere").getCommand(),
+ "save somewhere");
+ }
+
+ @Test(groups = "Functional")
+ public void testColourByChain()
+ {
+ assertEquals(testee.colourByChain().getCommand(), "rainbow chain");
+ }
+
+ @Test(groups = { "Functional" })
+ public void testSetBackgroundColour()
+ {
+ StructureCommandI cmd = testee.setBackgroundColour(Color.PINK);
+ assertEquals(cmd.getCommand(), "set bgColor #ffafaf");
+ }
+
+ @Test(groups = { "Functional" })
+ public void testLoadFile()
+ {
+ StructureCommandI cmd = testee.loadFile("/some/filepath");
+ assertEquals(cmd.getCommand(), "open /some/filepath");
+ }
+
+ @Test(groups = { "Functional" })
+ public void testOpenSession()
+ {
+ StructureCommandI cmd = testee.openSession("/some/filepath");
+ assertEquals(cmd.getCommand(), "open chimera:/some/filepath");
+ }
+
+ @Test(groups = "Functional")
+ public void testColourByCharge()
+ {
+ List<StructureCommandI> cmds = testee.colourByCharge();
+ assertEquals(cmds.size(), 1);
+ assertEquals(cmds.get(0)
+ .getCommand(),
+ "color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS");
}
@Test(groups = "Functional")
public void testGetColourCommand()
{
- ChimeraCommands testee = new ChimeraCommands();
- assertEquals(testee.getColourCommand("something", Color.MAGENTA),
+ assertEquals(testee.colourResidues("something", Color.MAGENTA)
+ .getCommand(),
"color #ff00ff something");
}
@Test(groups = "Functional")
+ public void testFocusView()
+ {
+ assertEquals(testee.focusView().getCommand(), "focus");
+ }
+
+ @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),
- "setattr res phi '27.3' #1:89-92.A|#2:8-9.B,12-20.B");
+ model.addRange("1", 89, 92, "A");
+ model.addRange("2", 12, 20, "B");
+ model.addRange("2", 8, 9, "B");
+ assertEquals(testee.setAttribute("jv_kd", "27.3", model).getCommand(),
+ "setattr res jv_kd '27.3' #1:89-92.A|#2:8-9.B,12-20.B");
+ }
+
+ @Test(groups = "Functional")
+ public void testHideAll()
+ {
+ StructureCommandI cmd = testee.hideAll();
+ assertEquals(cmd.getCommand(), "~display all; ~ribbon");
+ }
+
+ @Test(groups = "Functional")
+ public void testHideChain()
+ {
+ StructureCommandI cmd = testee.hideChain("1.1", "B");
+ assertEquals(cmd.getCommand(), "~ribbon #1.1:.B");
+ }
+
+ @Test(groups = "Functional")
+ public void testShowStructures()
+ {
+ /*
+ * with nothing excluded
+ */
+ StructureCommandI cmd = testee.showStructures(null);
+ assertEquals(cmd.getCommand(), "ribbon");
+
+ /*
+ * restricted to specified positions
+ */
+ AtomSpecModel restrictTo = new AtomSpecModel();
+ restrictTo.addRange("1.1", 12, 20, "A");
+ restrictTo.addRange("1.1", 30, 35, "A");
+ restrictTo.addRange("2.1", 11, 30, "B");
+ cmd = testee.showStructures(restrictTo);
+ assertEquals(cmd.getCommand(),
+ "ribbon #1.1:12-20.A,30-35.A|#2.1:11-30.B");
}
}
git://source.jalview.org / jalview.git / blobdiff