Merge branch 'features/JAL-2295setChimeraAttributes' into

[jalview.git] / test / jalview / ext / rbvi / chimera / ChimeraCommandsTest.java

diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
index 3c6f830..fb442e3 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
+++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
@@ -20,21 +20,35 @@
  */
 package jalview.ext.rbvi.chimera;
 
-import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+
+import jalview.gui.JvOptionPane;
 
 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;
 
 public class ChimeraCommandsTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @Test(groups = { "Functional" })
   public void testBuildColourCommands()
   {
 
-    Map<Color, AtomSpecModel> map = new LinkedHashMap<Color, AtomSpecModel>();
+    Map<Object, AtomSpecModel> map = new LinkedHashMap<Object, AtomSpecModel>();
     ChimeraCommands.addColourRange(map, Color.blue, 0, 2, 5, "A");
     ChimeraCommands.addColourRange(map, Color.blue, 0, 7, 7, "B");
     ChimeraCommands.addColourRange(map, Color.blue, 0, 9, 23, "A");
@@ -49,7 +63,90 @@ public class ChimeraCommandsTest
     // they were added; within colour, by model, by chain, ranges in start order
     String command = ChimeraCommands.buildColourCommands(map).get(0);
     assertEquals(
-            "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",
-            command);
+            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<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
+    Map<Object, AtomSpecModel> featureValues = new HashMap<Object, AtomSpecModel>();
+    
+    /*
+     * start with just one feature/value...
+     */
+    featuresMap.put("chain", featureValues);
+    ChimeraCommands.addColourRange(featureValues, "X", 0, 8, 20, "A");
+  
+    List<String> commands = ChimeraCommands
+            .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 r jv_chain \"X\" #0:8-20.A");
+
+    // add same feature value, overlapping range
+    ChimeraCommands.addColourRange(featureValues, "X", 0, 3, 9, "A");
+    // same feature value, contiguous range
+    ChimeraCommands.addColourRange(featureValues, "X", 0, 21, 25, "A");
+    commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+    assertEquals(1, commands.size());
+    assertEquals(commands.get(0), "setattr r jv_chain \"X\" #0:3-25.A");
+
+    // same feature value and model, different chain
+    ChimeraCommands.addColourRange(featureValues, "X", 0, 21, 25, "B");
+    // same feature value and chain, different model
+    ChimeraCommands.addColourRange(featureValues, "X", 1, 26, 30, "A");
+    commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+    assertEquals(1, commands.size());
+    assertEquals(commands.get(0),
+            "setattr r jv_chain \"X\" #0:3-25.A,21-25.B|#1:26-30.A");
+
+    // same feature, different value
+    ChimeraCommands.addColourRange(featureValues, "Y", 0, 40, 50, "A");
+    commands = ChimeraCommands.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 r jv_chain \"X\" #0:3-25.A,21-25.B|#1:26-30.A"));
+    assertTrue(commands.contains("setattr r jv_chain \"Y\" #0:40-50.A"));
+
+    featuresMap.clear();
+    featureValues.clear();
+    featuresMap.put("side-chain binding!", featureValues);
+    ChimeraCommands.addColourRange(featureValues, "metal ion!", 0, 7, 15,
+            "A");
+    // feature names are sanitised to change space or hyphen to underscore
+    commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+    assertTrue(commands
+            .contains("setattr r 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_");
   }
 }