JAL-3446 post-merge unit test fixes, formatting

[jalview.git] / test / jalview / datamodel / features / FeatureAttributesTest.java

diff --git a/test/jalview/datamodel/features/FeatureAttributesTest.java b/test/jalview/datamodel/features/FeatureAttributesTest.java
index e464326..d9efa23 100644 (file)
--- a/test/jalview/datamodel/features/FeatureAttributesTest.java
+++ b/test/jalview/datamodel/features/FeatureAttributesTest.java
@@ -1,22 +1,50 @@
 package jalview.datamodel.features;
 
 import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertTrue;
 
-import java.util.Comparator;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.features.FeatureAttributes.Datatype;
 
-import junit.extensions.PA;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.Map;
 
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 public class FeatureAttributesTest
 {
 
   /**
+   * clear down attributes map before tests
+   */
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+    FeatureAttributes fa = FeatureAttributes.getInstance();
+    ((Map<?, ?>) PA.getValue(fa, "attributes")).clear();
+  }
+
+  /**
+   * clear down attributes map after tests
+   */
+  @AfterMethod(alwaysRun = true)
+  public void tearDown()
+  {
+    FeatureAttributes fa = FeatureAttributes.getInstance();
+    ((Map<?, ?>) PA.getValue(fa, "attributes")).clear();
+  }
+
+  /**
    * Test the method that keeps attribute names in non-case-sensitive order,
    * including handling of 'compound' names
    */
-  @Test(groups="Functional")
+  @Test(groups = "Functional")
   public void testAttributeNameComparator()
   {
     FeatureAttributes fa = FeatureAttributes.getInstance();
@@ -24,18 +52,90 @@ public class FeatureAttributesTest
             "comparator");
 
     assertEquals(
-            comp.compare(new String[] { "CSQ" }, new String[] { "csq" }), 0);
+            comp.compare(new String[]
+            { "CSQ" }, new String[] { "csq" }), 0);
+
+    assertTrue(
+            comp.compare(new String[]
+            { "CSQ", "a" }, new String[] { "csq" }) > 0);
+
+    assertTrue(
+            comp.compare(new String[]
+            { "CSQ" }, new String[] { "csq", "b" }) < 0);
+
+    assertTrue(
+            comp.compare(new String[]
+            { "CSQ", "AF" }, new String[] { "csq", "ac" }) > 0);
 
-    assertTrue(comp.compare(new String[] { "CSQ", "a" },
-            new String[] { "csq" }) > 0);
+    assertTrue(
+            comp.compare(new String[]
+            { "CSQ", "ac" }, new String[] { "csq", "AF" }) < 0);
+  }
+
+  @Test(groups = "Functional")
+  public void testGetMinMax()
+  {
+    SequenceFeature sf = new SequenceFeature("Pfam", "desc", 10, 20,
+            "group");
+    FeatureAttributes fa = FeatureAttributes.getInstance();
+    assertNull(fa.getMinMax("Pfam", "kd"));
+    sf.setValue("domain", "xyz");
+    assertNull(fa.getMinMax("Pfam", "kd"));
+    sf.setValue("kd", "1.3");
+    assertEquals(fa.getMinMax("Pfam", "kd"), new float[] { 1.3f, 1.3f });
+    sf.setValue("kd", "-2.6");
+    assertEquals(fa.getMinMax("Pfam", "kd"), new float[] { -2.6f, 1.3f });
+    // setting 'mixed' character and numeric values wipes the min/max value
+    sf.setValue("kd", "some text");
+    assertNull(fa.getMinMax("Pfam", "kd"));
 
-    assertTrue(comp.compare(new String[] { "CSQ" }, new String[] { "csq",
-        "b" }) < 0);
+    Map<String, String> csq = new HashMap<>();
+    csq.put("AF", "-3");
+    sf.setValue("CSQ", csq);
+    assertEquals(fa.getMinMax("Pfam", "CSQ", "AF"),
+            new float[]
+            { -3f, -3f });
+    csq.put("AF", "4");
+    sf.setValue("CSQ", csq);
+    assertEquals(fa.getMinMax("Pfam", "CSQ", "AF"),
+            new float[]
+            { -3f, 4f });
+  }
 
-    assertTrue(comp.compare(new String[] { "CSQ", "AF" }, new String[] {
-        "csq", "ac" }) > 0);
+  /**
+   * Test the method that returns an attribute description, provided it is
+   * recorded and unique
+   */
+  @Test(groups = "Functional")
+  public void testGetDescription()
+  {
+    FeatureAttributes fa = FeatureAttributes.getInstance();
+    // with no description returns null
+    assertNull(fa.getDescription("Pfam", "kd"));
+    // with a unique description, returns that value
+    fa.addDescription("Pfam", "desc1", "kd");
+    assertEquals(fa.getDescription("Pfam", "kd"), "desc1");
+    // with ambiguous description, returns null
+    fa.addDescription("Pfam", "desc2", "kd");
+    assertNull(fa.getDescription("Pfam", "kd"));
+  }
 
-    assertTrue(comp.compare(new String[] { "CSQ", "ac" }, new String[] {
-        "csq", "AF" }) < 0);
+  @Test(groups = "Functional")
+  public void testDatatype()
+  {
+    FeatureAttributes fa = FeatureAttributes.getInstance();
+    assertNull(fa.getDatatype("Pfam", "kd"));
+    SequenceFeature sf = new SequenceFeature("Pfam", "desc", 10, 20,
+            "group");
+    sf.setValue("kd", "-1");
+    sf.setValue("domain", "Metal");
+    sf.setValue("foo", " ");
+    sf.setValue("phase", "1");
+    sf.setValue("phase", "1reverse");
+    assertEquals(fa.getDatatype("Pfam", "kd"), Datatype.Number);
+    assertEquals(fa.getDatatype("Pfam", "domain"), Datatype.Character);
+    assertEquals(fa.getDatatype("Pfam", "phase"), Datatype.Mixed);
+    assertNull(fa.getDatatype("Pfam", "unobserved"));
+    assertNull(fa.getDatatype("Pfam", "foo"));// empty values are ignored
   }
 }