X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraXCommandsTest.java;fp=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraXCommandsTest.java;h=439401a86e7f83ae48216d312a129c6eb4f2438f;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=0000000000000000000000000000000000000000;hpb=cfb79b69d9fa44595560659bd95d1d1cd27677ad;p=jalview.git

diff --git a/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java
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+/*
+ * 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 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;
+
+public class ChimeraXCommandsTest
+{
+  private ChimeraXCommands testee;
+
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+    testee = new ChimeraXCommands();
+  }
+
+  @Test(groups = { "Functional" })
+  public void testColourByCharge()
+  {
+    List<StructureCommandI> cmd = testee.colourByCharge();
+    assertEquals(cmd.size(), 1);
+    assertEquals(cmd.get(0).getCommand(),
+            "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow");
+  }
+
+  @Test(groups = { "Functional" })
+  public void testColourByChain()
+  {
+    StructureCommandI cmd = testee.colourByChain();
+    assertEquals(cmd.getCommand(), "rainbow chain");
+  }
+
+  @Test(groups = { "Functional" })
+  public void testFocusView()
+  {
+    StructureCommandI cmd = testee.focusView();
+    assertEquals(cmd.getCommand(), "view");
+  }
+
+  @Test(groups = { "Functional" })
+  public void testSetBackgroundColour()
+  {
+    StructureCommandI cmd = testee.setBackgroundColour(Color.PINK);
+    assertEquals(cmd.getCommand(), "set bgColor #ffafaf");
+  }
+
+  @Test(groups = { "Functional" })
+  public void testOpenSession()
+  {
+    StructureCommandI cmd = testee.openSession("/some/filepath");
+    assertEquals(cmd.getCommand(), "open /some/filepath format session");
+  }
+
+  @Test(groups = { "Functional" })
+  public void testColourBySequence()
+  {
+    Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
+    ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 2, 5, "A");
+    ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 7, 7, "B");
+    ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 9, 23, "A");
+    ChimeraCommands.addAtomSpecRange(map, Color.blue, "2", 1, 1, "A");
+    ChimeraCommands.addAtomSpecRange(map, Color.blue, "2", 4, 7, "B");
+    ChimeraCommands.addAtomSpecRange(map, Color.yellow, "2", 8, 8, "A");
+    ChimeraCommands.addAtomSpecRange(map, Color.yellow, "2", 3, 5, "A");
+    ChimeraCommands.addAtomSpecRange(map, Color.red, "1", 3, 5, "A");
+    ChimeraCommands.addAtomSpecRange(map, Color.red, "1", 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<StructureCommandI> commands = testee.colourBySequence(map);
+    assertEquals(commands.size(), 1);
+    assertEquals(commands.get(0).getCommand(),
+            "color #1/A:2-5,9-23/B:7|#2/A:1/B:4-7 #0000ff;color #2/A:3-5,8 #ffff00;color #1/A:3-9 #ff0000");
+  }
+
+  @Test(groups = { "Functional" })
+  public void testSetAttributes()
+  {
+    /*
+     * 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");
+
+    List<StructureCommandI> commands = testee.setAttributes(featuresMap);
+    assertEquals(commands.size(), 1);
+
+    /*
+     * feature name gets a jv_ namespace prefix
+     * feature value is quoted in case it contains spaces
+     */
+    assertEquals(commands.get(0).getCommand(),
+            "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 = testee.setAttributes(featuresMap);
+    assertEquals(commands.size(), 1);
+    assertEquals(commands.get(0).getCommand(),
+            "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 = testee.setAttributes(featuresMap);
+    assertEquals(commands.size(), 1);
+    String expected1 = "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true";
+    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 #0/A:40-50 res jv_chain 'Y' create true";
+    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");
+    // 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 #0/A:7-15 res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> &#39;ion!' create true";
+    assertTrue(commands.get(0).getCommand().equals(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);
+    assertEquals(command.size(), 1);
+    String cmd = command.get(0).getCommand();
+    String refSpec = "#1/A:12-14/B:18,22-23";
+    String toAlignSpec = "#2/B:15-17,20-21/C:22";
+
+    /*
+     * superposition arguments include AlphaCarbon restriction,
+     * ribbon command does not
+     */
+    String expected = String.format(
+            "align %s@CA toAtoms %s@CA; ribbon %s|%s; view", toAlignSpec,
+            refSpec, toAlignSpec, refSpec);
+    assertEquals(cmd, expected);
+  }
+
+  @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), "#1/A:2-4");
+    model.addRange("1", 8, 8, "A");
+    assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8");
+    model.addRange("1", 5, 7, "B");
+    assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8/B:5-7");
+    model.addRange("1", 3, 5, "A");
+    assertEquals(testee.getAtomSpec(model, false), "#1/A:2-5,8/B:5-7");
+    model.addRange("0", 1, 4, "B");
+    assertEquals(testee.getAtomSpec(model, false),
+            "#0/B:1-4|#1/A:2-5,8/B:5-7");
+    model.addRange("0", 5, 9, "C");
+    assertEquals(testee.getAtomSpec(model, false),
+            "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-7");
+    model.addRange("1", 8, 10, "B");
+    assertEquals(testee.getAtomSpec(model, false),
+            "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
+    model.addRange("1", 8, 9, "B");
+    assertEquals(testee.getAtomSpec(model, false),
+            "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
+    model.addRange("0", 3, 10, "C"); // subsumes 5-9
+    assertEquals(testee.getAtomSpec(model, false),
+            "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10");
+    model.addRange("5", 25, 35, " ");
+    assertEquals(testee.getAtomSpec(model, false),
+            "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10|#5/:25-35");
+  }
+
+  @Test(groups = "Functional")
+  public void testGetAtomSpec_alphaOnly()
+  {
+    AtomSpecModel model = new AtomSpecModel();
+    assertEquals(testee.getAtomSpec(model, true), "");
+    model.addRange("1", 2, 4, "A");
+    assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4@CA");
+    model.addRange("1", 8, 8, "A");
+    assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8@CA");
+    model.addRange("1", 5, 7, "B");
+    assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8/B:5-7@CA");
+    model.addRange("1", 3, 5, "A");
+    assertEquals(testee.getAtomSpec(model, true), "#1/A:2-5,8/B:5-7@CA");
+    model.addRange("0", 1, 4, "B");
+    assertEquals(testee.getAtomSpec(model, true),
+            "#0/B:1-4@CA|#1/A:2-5,8/B:5-7@CA");
+    model.addRange("0", 5, 9, "C");
+    assertEquals(testee.getAtomSpec(model, true),
+            "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-7@CA");
+    model.addRange("1", 8, 10, "B");
+    assertEquals(testee.getAtomSpec(model, true),
+            "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
+    model.addRange("1", 8, 9, "B");
+    assertEquals(testee.getAtomSpec(model, true),
+            "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
+    model.addRange("0", 3, 10, "C"); // subsumes 5-9
+    assertEquals(testee.getAtomSpec(model, true),
+            "#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA");
+    model.addRange("5", 25, 35, " "); // empty chain code
+    assertEquals(testee.getAtomSpec(model, true),
+            "#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA|#5/:25-35@CA");
+  }
+
+  @Test(groups = "Functional")
+  public void testGetModelStartNo()
+  {
+    assertEquals(testee.getModelStartNo(), 1);
+  }
+
+  @Test(groups = "Functional")
+  public void testGetResidueSpec()
+  {
+    assertEquals(testee.getResidueSpec("ALA"), ":ALA");
+  }
+
+  @Test(groups = "Functional")
+  public void testShowBackbone()
+  {
+    List<StructureCommandI> showBackbone = testee.showBackbone();
+    assertEquals(showBackbone.size(), 1);
+    assertEquals(showBackbone.get(0).getCommand(),
+            "~display all;~ribbon;show @CA|P atoms");
+  }
+
+  @Test(groups = "Functional")
+  public void testOpenCommandFile()
+  {
+    assertEquals(testee.openCommandFile("nowhere").getCommand(),
+            "open nowhere");
+  }
+
+  @Test(groups = "Functional")
+  public void testSaveSession()
+  {
+    assertEquals(testee.saveSession("somewhere").getCommand(),
+            "save somewhere format session");
+  }
+
+  @Test(groups = "Functional")
+  public void testGetColourCommand()
+  {
+    assertEquals(testee.colourResidues("something", Color.MAGENTA)
+            .getCommand(),
+            "color something #ff00ff");
+  }
+
+  @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 #1/A:89-92|#2/B:8-9,12-20 res jv_kd '27.3' create true");
+  }
+
+  @Test(groups = "Functional")
+  public void testCloseViewer()
+  {
+    assertEquals(testee.closeViewer(), new StructureCommand("exit"));
+  }
+
+  @Test(groups = "Functional")
+  public void testGetSelectedResidues()
+  {
+    assertEquals(testee.getSelectedResidues(),
+            new StructureCommand("info selection level residue"));
+  }
+
+  @Test(groups = "Functional")
+  public void testStartNotifications()
+  {
+    List<StructureCommandI> cmds = testee.startNotifications("to here");
+    assertEquals(cmds.size(), 2);
+    assertEquals(cmds.get(0), new StructureCommand("info notify start models jalview prefix ModelChanged url to here"));
+    assertEquals(cmds.get(1), new StructureCommand("info notify start selection jalview prefix SelectionChanged url to here"));
+  }
+
+  @Test(groups = "Functional")
+  public void testStopNotifications()
+  {
+    List<StructureCommandI> cmds = testee.stopNotifications();
+    assertEquals(cmds.size(), 2);
+    assertEquals(cmds.get(0), new StructureCommand("info notify stop models jalview"));
+    assertEquals(cmds.get(1), new StructureCommand("info notify stop selection jalview"));
+  }
+
+  @Test(groups = "Functional")
+  public void testListResidueAttributes()
+  {
+    assertEquals(testee.listResidueAttributes(),
+            new StructureCommand("info resattr"));
+  }
+}