+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ext.jmol;
+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.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.SequenceRenderer;
-import jalview.structure.StructureMappingcommandSet;
+import jalview.schemes.JalviewColourScheme;
+import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommandI;
+import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
-import org.testng.annotations.Test;
-
public class JmolCommandsTest
{
+ private JmolCommands testee;
+
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ testee = new JmolCommands();
+ }
@Test(groups = { "Functional" })
- public void testGetColourBySequenceCommand_noFeatures()
+ public void testGetColourBySequenceCommands_hiddenColumns()
{
- SequenceI seq1 = new Sequence("seq1", "MHRSQTRALK");
- SequenceI seq2 = new Sequence("seq2", "MRLEITQSGD");
+ /*
+ * 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();
- // need some mappings!
+ /*
+ * 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 = testee.colourBySequence(ssm,
+ files,
+ seqs, sr, af.alignPanel);
+ assertEquals(commands.length, 2);
+
+ String chainACommand = commands[0];
+ // M colour is #82827d == (130, 130, 125) (see strand.html help page)
+ assertTrue(
+ chainACommand.contains("select 21:A/1.1;color[130,130,125]")); // first
+ // one
+ // H colour is #60609f == (96, 96, 159)
+ assertTrue(chainACommand.contains(";select 22:A/1.1;color[96,96,159]"));
+ // hidden columns are Gray (128, 128, 128)
+ assertTrue(chainACommand
+ .contains(";select 23-25:A/1.1;color[128,128,128]"));
+ // S and G are both coloured #4949b6 == (73, 73, 182)
+ assertTrue(
+ chainACommand.contains(";select 26-30:A/1.1;color[73,73,182]"));
+
+ String chainBCommand = commands[1];
+ // M colour is #82827d == (130, 130, 125)
+ assertTrue(
+ chainBCommand.contains("select 21:B/2.1;color[130,130,125]"));
+ // V colour is #ffff00 == (255, 255, 0)
+ assertTrue(chainBCommand.contains(";select 22:B/2.1;color[255,255,0]"));
+ // hidden columns are Gray (128, 128, 128)
+ assertTrue(chainBCommand
+ .contains(";select 23-25:B/2.1;color[128,128,128]"));
+ // S and G are both coloured #4949b6 == (73, 73, 182)
+ assertTrue(
+ chainBCommand.contains(";select 26-30:B/2.1;color[73,73,182]"));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetAtomSpec()
+ {
+ AtomSpecModel model = new AtomSpecModel();
+ assertEquals(testee.getAtomSpec(model, false), "");
+ model.addRange("1", 2, 4, "A");
+ assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1");
+ 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");
+ 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");
+ 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");
+ 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");
+ 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");
+ 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");
+ 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
+ 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, " ");
+ 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 = testee.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()
+ {
+ 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, false); // doesn't matter for Jmol whether nuc or protein
+ 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.get(0).getCommand(), expected);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetModelStartNo()
+ {
+ assertEquals(testee.getModelStartNo(), 1);
+ }
+
+ @Test(groups = "Functional")
+ public void testColourByChain()
+ {
+ StructureCommandI cmd = testee.colourByChain();
+ assertEquals(cmd.getCommand(), "select *;color chain");
+ }
+
+ @Test(groups = "Functional")
+ public void testColourByCharge()
+ {
+ List<StructureCommandI> cmds = testee.colourByCharge();
+ assertEquals(cmds.size(), 1);
+ assertEquals(cmds.get(0).getCommand(),
+ "select *;color white;select ASP,GLU;color red;"
+ + "select LYS,ARG;color blue;select CYS;color yellow");
+ }
+
+ @Test(groups = "Functional")
+ public void testSetBackgroundColour()
+ {
+ StructureCommandI cmd = testee.setBackgroundColour(Color.PINK);
+ assertEquals(cmd.getCommand(), "background [255,175,175]");
+ }
+
+ @Test(groups = "Functional")
+ public void testFocusView()
+ {
+ StructureCommandI cmd = testee.focusView();
+ assertEquals(cmd.getCommand(), "zoom 0");
+ }
+
+ @Test(groups = "Functional")
+ public void testSaveSession()
+ {
+ StructureCommandI cmd = testee.saveSession("/some/filepath");
+ assertEquals(cmd.getCommand(), "write STATE \"/some/filepath\"");
+ }
+
+ @Test(groups = "Functional")
+ public void testShowBackbone()
+ {
+ List<StructureCommandI> cmds = testee.showBackbone();
+ assertEquals(cmds.size(), 1);
+ assertEquals(cmds.get(0).getCommand(),
+ "select *; cartoons off; backbone");
+ }
+
+ @Test(groups = "Functional")
+ public void testLoadFile()
+ {
+ StructureCommandI cmd = testee.loadFile("/some/filepath");
+ assertEquals(cmd.getCommand(), "load FILES \"/some/filepath\"");
+
+ // single backslash gets escaped to double
+ cmd = testee.loadFile("\\some\\filepath");
+ assertEquals(cmd.getCommand(), "load FILES \"\\\\some\\\\filepath\"");
+ }
+
+ @Test(groups = "Functional")
+ public void testOpenSession()
+ {
+ StructureCommandI cmd = testee.openSession("/some/filepath");
+ assertEquals(cmd.getCommand(), "load FILES \"/some/filepath\"");
- StructureMappingcommandSet[] commands = JmolCommands
- .getColourBySequenceCommand(ssm, files, seqs, sr, null, al);
+ // single backslash gets escaped to double
+ cmd = testee.openSession("\\some\\filepath");
+ assertEquals(cmd.getCommand(), "load FILES \"\\\\some\\\\filepath\"");
}
}
git://source.jalview.org / jalview.git / blobdiff