*/
package jalview.ext.rbvi.chimera;
-import static org.testng.AssertJUnit.assertEquals;
+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.Test;
// 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.addRange(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.addRange(featureValues, "X", 0, 3, 9, "A");
+ // same feature value, contiguous range
+ ChimeraCommands.addRange(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.addRange(featureValues, "X", 0, 21, 25, "B");
+ // same feature value and chain, different model
+ ChimeraCommands.addRange(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.addRange(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.addRange(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_");
}
}