JAL-3567 report mapped location for virtual features in tooltip etc

[jalview.git] / test / jalview / datamodel / SequenceFeatureTest.java

diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java
index d105cc5..673ea29 100644 (file)
--- a/test/jalview/datamodel/SequenceFeatureTest.java
+++ b/test/jalview/datamodel/SequenceFeatureTest.java
@@ -26,11 +26,11 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.gui.JvOptionPane;
-
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.gui.JvOptionPane;
+
 public class SequenceFeatureTest
 {
 
@@ -42,13 +42,13 @@ public class SequenceFeatureTest
   }
 
   @Test(groups = { "Functional" })
-  public void testCopyConstructor()
+  public void testCopyConstructors()
   {
     SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
             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);
@@ -56,10 +56,41 @@ public class SequenceFeatureTest
     assertEquals("desc", sf2.getDescription());
     assertEquals(22, sf2.getBegin());
     assertEquals(33, sf2.getEnd());
+    assertEquals(12.5f, sf2.getScore());
     assertEquals("+", sf2.getValue("STRAND"));
     assertEquals("Testing", sf2.getValue("Note"));
     // shallow clone of otherDetails map - contains the same object values!
     assertSame(count, sf2.getValue("Count"));
+
+    /*
+     * copy constructor modifying begin/end/group/score
+     */
+    SequenceFeature sf3 = new SequenceFeature(sf1, 11, 14, "group2", 17.4f);
+    assertEquals("type", sf3.getType());
+    assertEquals("desc", sf3.getDescription());
+    assertEquals(11, sf3.getBegin());
+    assertEquals(14, sf3.getEnd());
+    assertEquals(17.4f, sf3.getScore());
+    assertEquals("+", sf3.getValue("STRAND"));
+    assertEquals("Testing", sf3.getValue("Note"));
+    // shallow clone of otherDetails map - contains the same object values!
+    assertSame(count, sf3.getValue("Count"));
+
+    /*
+     * copy constructor modifying type/begin/end/group/score
+     */
+    SequenceFeature sf4 = new SequenceFeature(sf1, "Disulfide bond", 12,
+            15, "group3", -9.1f);
+    assertEquals("Disulfide bond", sf4.getType());
+    assertTrue(sf4.isContactFeature());
+    assertEquals("desc", sf4.getDescription());
+    assertEquals(12, sf4.getBegin());
+    assertEquals(15, sf4.getEnd());
+    assertEquals(-9.1f, sf4.getScore());
+    assertEquals("+", sf4.getValue("STRAND"));
+    assertEquals("Testing", sf4.getValue("Note"));
+    // shallow clone of otherDetails map - contains the same object values!
+    assertSame(count, sf4.getValue("Count"));
   }
 
   /**
@@ -75,7 +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));
   }
 
@@ -242,4 +273,50 @@ public class SequenceFeatureTest
             "group");
     assertTrue(sf.isContactFeature());
   }
+
+  @Test(groups = { "Functional" })
+  public void testGetDetailsReport()
+  {
+    SequenceI seq = new Sequence("TestSeq", "PLRFQMD");
+    String seqName = seq.getName();
+
+    // single locus, no group, no score
+    SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22, null);
+    String expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22</td></tr>"
+            + "<tr><td>Type</td><td>variant</td><td></td></tr>"
+            + "<tr><td>Description</td><td>G,C</td><td></td></tr></table>";
+    assertEquals(expected, sf.getDetailsReport(seqName, null));
+
+    // contact feature
+    sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31,
+            null);
+    expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>28:31</td></tr>"
+            + "<tr><td>Type</td><td>Disulphide Bond</td><td></td></tr>"
+            + "<tr><td>Description</td><td>a description</td><td></td></tr></table>";
+    assertEquals(expected, sf.getDetailsReport(seqName, null));
+
+    sf = new SequenceFeature("variant", "G,C", 22, 33,
+            12.5f, "group");
+    sf.setValue("Parent", "ENSG001");
+    sf.setValue("Child", "ENSP002");
+    expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22-33</td></tr>"
+            + "<tr><td>Type</td><td>variant</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(seqName, null));
+
+    /*
+     * 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>Location</td><td>TestSeq</td><td>8-83</td></tr>"
+            + "<tr><td>Type</td><td>Pfam</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(seqName, null));
+  }
 }