/*
* 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 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 java.util.List;
import java.util.Map;
import org.testng.annotations.Test;
public class ChimeraCommandsTest
{
@Test(groups = { "Functional" })
public void testBuildColourCommands()
{
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
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");
}
@Test(groups = { "Functional" })
public void testBuildSetAttributeCommands()
{
/*
* 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");
ChimeraCommands commandGenerator = new ChimeraCommands();
List commands = commandGenerator
.buildSetAttributeCommands(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");
// 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 = commandGenerator.buildSetAttributeCommands(featuresMap);
assertEquals(1, commands.size());
assertEquals(commands.get(0), "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 = commandGenerator.buildSetAttributeCommands(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");
// same feature, different value
ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A");
commands = commandGenerator.buildSetAttributeCommands(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"));
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 = commandGenerator.buildSetAttributeCommands(featuresMap);
assertTrue(commands
.contains(
"setattr res jv_side_chain_binding_ 'metal 'ion!' #0:7-15.A"));
}
/**
* Tests for the method that prefixes and sanitises a feature name so it can
* be used as a valid, namespaced attribute name in Chimera
*/
@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"),
"jv_Hello_World_24");
assertEquals(
ChimeraCommands.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_");
}
@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 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");
assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A");
model.addRange(1, 8, 8, "A");
assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A");
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");
assertEquals(testee.getAtomSpec(model, false), "#1:2-5.A,8.A,5-7.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");
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");
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");
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
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
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 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");
assertEquals(testee.getAtomSpec(model, true),
"#1:2-4.A,8.A,5-7.B@CA|P");
model.addRange(1, 3, 5, "A");
assertEquals(testee.getAtomSpec(model, true),
"#1:2-5.A,8.A,5-7.B@CA|P");
model.addRange(0, 1, 4, "B");
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");
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");
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");
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
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
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");
}
@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");
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);
}
}