/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.rbvi.chimera;
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.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsI.AtomSpecType;
public class ChimeraCommandsTest
{
private ChimeraCommands testee;
@BeforeClass(alwaysRun = true)
public void setUp()
{
testee = new ChimeraCommands();
}
@Test(groups = { "Functional" })
public void testColourBySequence()
{
Map 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");
// 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
List 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" })
public void testSetAttributes()
{
/*
* make a map of { featureType, {featureValue, {residue range specification } } }
*/
Map> featuresMap = new LinkedHashMap<>();
Map featureValues = new HashMap<>();
/*
* start with just one feature/value...
*/
featuresMap.put("chain", featureValues);
ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
List 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.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");
// same feature value, contiguous range
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");
// same feature value and chain, different model
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.get(0).getCommand(), expected1);
// same feature, different value
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
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,
"metal '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 = testee.setAttributes(featuresMap);
assertEquals(commands.size(), 1);
String expected3 = "setattr res jv_side_chain_binding_ 'metal 'ion!' #0:7-15.A";
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 or PyMol
*/
@Test(groups = { "Functional" })
public void testMakeAttributeName()
{
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(testee.makeAttributeName("!this is-a_very*{odd(name"),
"jv__this_is_a_very__odd_name");
// name ending in color gets underscore appended
assertEquals(testee.makeAttributeName("helixColor"), "jv_helixColor_");
}
@Test(groups = "Functional")
public void testGetAtomSpec()
{
AtomSpecModel model = new AtomSpecModel();
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
model.addRange("1", 2, 4, "A");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#1:2-4.A");
model.addRange("1", 8, 8, "A");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#1:2-4.A,8.A");
model.addRange("1", 5, 7, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#1:2-4.A,8.A,5-7.B");
model.addRange("1", 3, 5, "A");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#1:2-5.A,8.A,5-7.B");
model.addRange("0", 1, 4, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B|#1:2-5.A,8.A,5-7.B");
model.addRange("0", 5, 9, "C");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-7.B");
model.addRange("1", 8, 10, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
model.addRange("1", 8, 9, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#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(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B");
model.addRange("5", 25, 35, " ");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#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()
{
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 command = testee.superposeStructures(ref,
toAlign, AtomSpecType.ALPHA);
// 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()
{
AtomSpecModel model = new AtomSpecModel();
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
model.addRange("1", 2, 4, "A");
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#1:2-4.A@CA&~@.B-Z&~@.2-9");
model.addRange("1", 8, 8, "A");
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#1:2-4.A,8.A@CA&~@.B-Z&~@.2-9");
model.addRange("1", 5, 7, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#1:2-4.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
model.addRange("1", 3, 5, "A");
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
model.addRange("0", 1, 4, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#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, AtomSpecType.ALPHA),
"#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, AtomSpecType.ALPHA),
"#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, AtomSpecType.ALPHA),
"#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, AtomSpecType.ALPHA),
"#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, AtomSpecType.ALPHA),
"#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 testGetModelStartNo()
{
assertEquals(testee.getModelStartNo(), 0);
}
@Test(groups = "Functional")
public void testGetResidueSpec()
{
assertEquals(testee.getResidueSpec("ALA"), "::ALA");
}
@Test(groups = "Functional")
public void testShowBackbone()
{
List cmds = testee.showBackbone();
assertEquals(cmds.size(), 1);
assertEquals(cmds.get(0).getCommand(),
"~display all;~ribbon;chain @CA|P");
}
@Test(groups = "Functional")
public void testOpenCommandFile()
{
assertEquals(testee.openCommandFile("nowhere").getCommand(),
"open cmd:nowhere");
}
@Test(groups = "Functional")
public void testSaveSession()
{
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 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()
{
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()
{
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("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 testCloseViewer()
{
assertEquals(testee.closeViewer(), new StructureCommand("stop really"));
}
@Test(groups = "Functional")
public void testGetSelectedResidues()
{
assertEquals(testee.getSelectedResidues(),
new StructureCommand("list selection level residue"));
}
@Test(groups = "Functional")
public void testListResidueAttributes()
{
assertEquals(testee.listResidueAttributes(),
new StructureCommand("list resattr"));
}
@Test(groups = "Functional")
public void testGetResidueAttributes()
{
assertEquals(testee.getResidueAttributes("binding site"),
new StructureCommand("list residues attr 'binding site'"));
}
@Test(groups = "Functional")
public void testStartNotifications()
{
List cmds = testee.startNotifications("to here");
assertEquals(cmds.size(), 2);
assertEquals(cmds.get(0),
new StructureCommand("listen start models url to here"));
assertEquals(cmds.get(1), new StructureCommand(
"listen start select prefix SelectionChanged url to here"));
}
@Test(groups = "Functional")
public void testStopNotifications()
{
List cmds = testee.stopNotifications();
assertEquals(cmds.size(), 2);
assertEquals(cmds.get(0), new StructureCommand("listen stop models"));
assertEquals(cmds.get(1),
new StructureCommand("listen stop selection"));
}
}