--- /dev/null
+/*
+ * 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.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.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 ChimeraXCommandsTest
+{
+
+ @Test(groups = { "Functional" })
+ public void testBuildColourCommands()
+ {
+
+ 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");
+
+ // 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 ChimeraXCommands().buildColourCommands(map).get(0);
+ assertEquals(
+ command,
+ "color #0/A:2-5,9-23/B:7|#1/A:1/B:4-7 #0000ff; color #1/A:3-5,8 #ffff00; color #0/A:3-9 #ff0000");
+ }
+
+ @Test(groups = { "Functional" })
+ public void testBuildSetAttributeCommands()
+ {
+ /*
+ * make a map of { featureType, {featureValue, {residue range specification } } }
+ */
+ 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");
+
+ ChimeraXCommands commandGenerator = new ChimeraXCommands();
+ List<String> 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 #0/A:8-20 res jv_chain 'X' create true");
+
+ // 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 #0/A:3-25 res jv_chain 'X' create true");
+
+ // 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 #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true");
+
+ // 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 #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true"));
+ assertTrue(commands
+ .contains("setattr #0/A:40-50 res jv_chain 'Y' create true"));
+
+ 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");
+ // 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 #0/A:7-15 res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' create true"));
+ }
+
+ @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 ChimeraXCommands()
+ .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 #0/A:21|#1/B:21 #82827d"));// #0:21.A|#1:21.B"));
+ // H colour is #60609f
+ assertTrue(theCommand.contains("color #0/A:22 #60609f"));
+ // V colour is #ffff00
+ assertTrue(theCommand.contains("color #1/B:22 #ffff00"));
+ // hidden columns are Gray (128, 128, 128)
+ assertTrue(theCommand.contains("color #0/A:23-25|#1/B:23-25"));
+ // S and G are both coloured #4949b6
+ assertTrue(theCommand.contains("color #0/A:26-30|#1/B:26-30"));
+ }
+}
git://source.jalview.org / jalview.git / blobdiff