JAL-2446 merged to spike branch

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

diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java
index 2ec824d..d105cc5 100644 (file)
--- a/test/jalview/datamodel/SequenceFeatureTest.java
+++ b/test/jalview/datamodel/SequenceFeatureTest.java
@@ -26,10 +26,21 @@ 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;
 
 public class SequenceFeatureTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @Test(groups = { "Functional" })
   public void testCopyConstructor()
   {
@@ -112,56 +123,93 @@ public class SequenceFeatureTest
     assertEquals(sf1.hashCode(), sf2.hashCode());
 
     // changing type breaks equals:
-    sf2.setType("Type");
-    assertFalse(sf1.equals(sf2));
+    SequenceFeature sf3 = new SequenceFeature("type", "desc", 22, 33,
+            12.5f, "group");
+    SequenceFeature sf4 = new SequenceFeature("Type", "desc", 22, 33,
+            12.5f, "group");
+    assertFalse(sf3.equals(sf4));
 
     // changing description breaks equals:
-    sf2.setType("type");
+    String restores = sf2.getDescription();
     sf2.setDescription("Desc");
     assertFalse(sf1.equals(sf2));
+    sf2.setDescription(restores);
+
+    // changing score breaks equals:
+    float restoref = sf2.getScore();
+    sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
+            sf2.getFeatureGroup(), 10f);
+    assertFalse(sf1.equals(sf2));
+    sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
+            sf2.getFeatureGroup(), restoref);
+
+    // NaN doesn't match a number
+    restoref = sf2.getScore();
+    sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
+            sf2.getFeatureGroup(), Float.NaN);
+    assertFalse(sf1.equals(sf2));
+
+    // NaN matches NaN
+    sf1 = new SequenceFeature(sf1, sf1.getBegin(), sf1.getEnd(),
+            sf1.getFeatureGroup(), Float.NaN);
+    assertTrue(sf1.equals(sf2));
+    sf1 = new SequenceFeature(sf1, sf1.getBegin(), sf1.getEnd(),
+            sf1.getFeatureGroup(), restoref);
+    sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
+            sf2.getFeatureGroup(), restoref);
 
     // changing start position breaks equals:
-    sf2.setDescription("desc");
-    sf2.setBegin(21);
+    int restorei = sf2.getBegin();
+    sf2 = new SequenceFeature(sf2, 21, sf2.getEnd(), sf2.getFeatureGroup(), sf2.getScore());
     assertFalse(sf1.equals(sf2));
+    sf2 = new SequenceFeature(sf2, restorei, sf2.getEnd(),
+            sf2.getFeatureGroup(), sf2.getScore());
 
     // changing end position breaks equals:
-    sf2.setBegin(22);
-    sf2.setEnd(32);
+    restorei = sf2.getEnd();
+    sf2 = new SequenceFeature(sf2, sf2.getBegin(), 32,
+            sf2.getFeatureGroup(), sf2.getScore());
     assertFalse(sf1.equals(sf2));
+    sf2 = new SequenceFeature(sf2, sf2.getBegin(), restorei,
+            sf2.getFeatureGroup(), sf2.getScore());
 
     // changing feature group breaks equals:
-    sf2.setEnd(33);
-    sf2.setFeatureGroup("Group");
+    restores = sf2.getFeatureGroup();
+    sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), "Group", sf2.getScore());
     assertFalse(sf1.equals(sf2));
+    sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), restores, sf2.getScore());
 
     // changing ID breaks equals:
-    sf2.setFeatureGroup("group");
+    restores = (String) sf2.getValue("ID");
     sf2.setValue("ID", "id2");
     assertFalse(sf1.equals(sf2));
+    sf2.setValue("ID", restores);
 
     // changing Name breaks equals:
-    sf2.setValue("ID", "id");
+    restores = (String) sf2.getValue("Name");
     sf2.setValue("Name", "Name");
     assertFalse(sf1.equals(sf2));
+    sf2.setValue("Name", restores);
 
     // changing Parent breaks equals:
-    sf2.setValue("Name", "name");
+    restores = (String) sf1.getValue("Parent");
     sf1.setValue("Parent", "Parent");
     assertFalse(sf1.equals(sf2));
+    sf1.setValue("Parent", restores);
 
     // changing strand breaks equals:
-    sf1.setValue("Parent", "parent");
+    restorei = sf2.getStrand();
     sf2.setStrand("-");
     assertFalse(sf1.equals(sf2));
+    sf2.setStrand(restorei == 1 ? "+" : "-");
 
     // changing phase breaks equals:
-    sf2.setStrand("+");
+    restores = sf1.getPhase();
     sf1.setPhase("2");
     assertFalse(sf1.equals(sf2));
+    sf1.setPhase(restores);
 
     // restore equality as sanity check:
-    sf1.setPhase("1");
     assertTrue(sf1.equals(sf2));
     assertTrue(sf2.equals(sf1));
     assertEquals(sf1.hashCode(), sf2.hashCode());
@@ -170,4 +218,28 @@ public class SequenceFeatureTest
     sf1.setStatus("new");
     assertTrue(sf1.equals(sf2));
   }
+
+  @Test(groups = { "Functional" })
+  public void testIsContactFeature()
+  {
+    SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
+            "group");
+    assertFalse(sf.isContactFeature());
+    sf = new SequenceFeature("", "desc", 22, 33, 12.5f, "group");
+    assertFalse(sf.isContactFeature());
+    sf = new SequenceFeature(null, "desc", 22, 33, 12.5f, "group");
+    assertFalse(sf.isContactFeature());
+    sf = new SequenceFeature("Disulfide Bond", "desc", 22, 33, 12.5f,
+            "group");
+    assertTrue(sf.isContactFeature());
+    sf = new SequenceFeature("disulfide bond", "desc", 22, 33, 12.5f,
+            "group");
+    assertTrue(sf.isContactFeature());
+    sf = new SequenceFeature("Disulphide Bond", "desc", 22, 33, 12.5f,
+            "group");
+    assertTrue(sf.isContactFeature());
+    sf = new SequenceFeature("disulphide bond", "desc", 22, 33, 12.5f,
+            "group");
+    assertTrue(sf.isContactFeature());
+  }
 }