Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[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 4b7a435..db02528 100644 (file)
--- a/test/jalview/datamodel/features/FeatureAttributesTest.java
+++ b/test/jalview/datamodel/features/FeatureAttributesTest.java
@@ -1,3 +1,23 @@
+/*
+ * 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.datamodel.features;
 
 import static org.testng.Assert.assertEquals;
@@ -12,6 +32,7 @@ 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;
@@ -20,9 +41,19 @@ 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
+  @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
     FeatureAttributes fa = FeatureAttributes.getInstance();
@@ -33,7 +64,7 @@ public class FeatureAttributesTest
    * 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();
@@ -41,22 +72,27 @@ 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", "a" }, new String[] { "csq" }) > 0);
 
-    assertTrue(comp.compare(new String[] { "CSQ" }, new String[] { "csq",
-        "b" }) < 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", "AF" }, new String[] { "csq", "ac" }) > 0);
 
-    assertTrue(comp.compare(new String[] { "CSQ", "ac" }, new String[] {
-        "csq", "AF" }) < 0);
+    assertTrue(
+            comp.compare(new String[]
+            { "CSQ", "ac" }, new String[] { "csq", "AF" }) < 0);
   }
 
-  @Test
+  @Test(groups = "Functional")
   public void testGetMinMax()
   {
     SequenceFeature sf = new SequenceFeature("Pfam", "desc", 10, 20,
@@ -65,12 +101,14 @@ public class FeatureAttributesTest
     assertNull(fa.getMinMax("Pfam", "kd"));
     sf.setValue("domain", "xyz");
     assertNull(fa.getMinMax("Pfam", "kd"));
-    sf.setValue("kd", "some text");
-    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);
@@ -88,7 +126,7 @@ public class FeatureAttributesTest
    * Test the method that returns an attribute description, provided it is
    * recorded and unique
    */
-  @Test
+  @Test(groups = "Functional")
   public void testGetDescription()
   {
     FeatureAttributes fa = FeatureAttributes.getInstance();
@@ -102,7 +140,7 @@ public class FeatureAttributesTest
     assertNull(fa.getDescription("Pfam", "kd"));
   }
 
-  @Test
+  @Test(groups = "Functional")
   public void testDatatype()
   {
     FeatureAttributes fa = FeatureAttributes.getInstance();
@@ -111,10 +149,13 @@ public class FeatureAttributesTest
             "group");
     sf.setValue("kd", "-1");
     sf.setValue("domain", "Metal");
+    sf.setValue("foo", " ");
     sf.setValue("phase", "1");
-    sf.setValue("phase", "reverse");
+    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
   }
 }