JAL-3130 Lots of deprecation fixes. See utils/deprecation_auto_fixes.sh for commands...

[jalview.git] / test / jalview / datamodel / SequenceFeatureTest.java
diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java

index fbeb365..9111e5a 100644 (file)
--- a/test/jalview/datamodel/SequenceFeatureTest.java
+++ b/test/jalview/datamodel/SequenceFeatureTest.java
@@ -48,7 +48,7 @@ public class SequenceFeatureTest
              12.5f, "group");
      sf1.setValue("STRAND", "+");
      sf1.setValue("Note", "Testing");
-    Integer count = new Integer(7);
+    Integer count = Integer.valueOf(7);
      sf1.setValue("Count", count);
  
      SequenceFeature sf2 = new SequenceFeature(sf1);
@@ -106,7 +106,7 @@ public class SequenceFeatureTest
      assertEquals("+", sf1.getValue("STRAND"));
      assertNull(sf1.getValue("strand")); // case-sensitive
      assertEquals(".", sf1.getValue("unknown", "."));
-    Integer i = new Integer(27);
+    Integer i = Integer.valueOf(27);
      assertSame(i, sf1.getValue("Unknown", i));
    }
  
@@ -273,4 +273,47 @@ public class SequenceFeatureTest
              "group");
      assertTrue(sf.isContactFeature());
    }
+
+  @Test(groups = { "Functional" })
+  public void testGetDetailsReport()
+  {
+    // single locus, no group, no score
+    SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22, null);
+    String expected = "<br><table><tr><td>Type</td><td>variant</td><td></td></tr>"
+            + "<tr><td>Start/end</td><td>22</td><td></td></tr>"
+            + "<tr><td>Description</td><td>G,C</td><td></td></tr></table>";
+    assertEquals(expected, sf.getDetailsReport());
+
+    // contact feature
+    sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31,
+            null);
+    expected = "<br><table><tr><td>Type</td><td>Disulphide Bond</td><td></td></tr>"
+            + "<tr><td>Start/end</td><td>28:31</td><td></td></tr>"
+            + "<tr><td>Description</td><td>a description</td><td></td></tr></table>";
+    assertEquals(expected, sf.getDetailsReport());
+
+    sf = new SequenceFeature("variant", "G,C", 22, 33,
+            12.5f, "group");
+    sf.setValue("Parent", "ENSG001");
+    sf.setValue("Child", "ENSP002");
+    expected = "<br><table><tr><td>Type</td><td>variant</td><td></td></tr>"
+            + "<tr><td>Start/end</td><td>22-33</td><td></td></tr>"
+            + "<tr><td>Description</td><td>G,C</td><td></td></tr>"
+            + "<tr><td>Score</td><td>12.5</td><td></td></tr>"
+            + "<tr><td>Group</td><td>group</td><td></td></tr>"
+            + "<tr><td>Child</td><td></td><td>ENSP002</td></tr>"
+            + "<tr><td>Parent</td><td></td><td>ENSG001</td></tr></table>";
+    assertEquals(expected, sf.getDetailsReport());
+
+    /*
+     * feature with embedded html link in description
+     */
+    String desc = "<html>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></html>";
+    sf = new SequenceFeature("Pfam", desc, 8, 83, "Uniprot");
+    expected = "<br><table><tr><td>Type</td><td>Pfam</td><td></td></tr>"
+            + "<tr><td>Start/end</td><td>8-83</td><td></td></tr>"
+            + "<tr><td>Description</td><td>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></td><td></td></tr>"
+            + "<tr><td>Group</td><td>Uniprot</td><td></td></tr></table>";
+    assertEquals(expected, sf.getDetailsReport());
+  }
  }