JAL-3210 Barebones gradle/buildship/eclipse. See README

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

diff --git a/test/jalview/datamodel/features/FeatureAttributesTest.java b/test/jalview/datamodel/features/FeatureAttributesTest.java
deleted file mode 100644 (file)
index 0846ec2..0000000
--- a/test/jalview/datamodel/features/FeatureAttributesTest.java
+++ /dev/null
@@ -1,133 +0,0 @@
-package jalview.datamodel.features;
-
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertNull;
-import static org.testng.Assert.assertTrue;
-
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.features.FeatureAttributes.Datatype;
-
-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")
-  public void testAttributeNameComparator()
-  {
-    FeatureAttributes fa = FeatureAttributes.getInstance();
-    Comparator<String[]> comp = (Comparator<String[]>) PA.getValue(fa,
-            "comparator");
-
-    assertEquals(
-            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", "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"));
-
-    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 });
-  }
-
-  /**
-   * 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"));
-  }
-
-  @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("phase", "1");
-    sf.setValue("phase", "reverse");
-    assertEquals(fa.getDatatype("Pfam", "kd"), Datatype.Number);
-    assertEquals(fa.getDatatype("Pfam", "domain"), Datatype.Character);
-    assertEquals(fa.getDatatype("Pfam", "phase"), Datatype.Mixed);
-  }
-}