Merge branch 'bug/JAL-2541cutWithFeatures' into features/JAL-2446NCList

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

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 739ef5d..ebf4857 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -41,6 +41,8 @@ import java.util.Vector;
 
 import junit.extensions.PA;
 
+import junit.extensions.PA;
+
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
@@ -453,7 +455,7 @@ public class SequenceTest
     /*
      * SequenceFeature on sequence
      */
-    SequenceFeature sf = new SequenceFeature();
+    SequenceFeature sf = new SequenceFeature("Cath", "desc", 2, 4, 2f, null);
     sq.addSequenceFeature(sf);
     SequenceFeature[] sfs = sq.getSequenceFeatures();
     assertEquals(1, sfs.length);
@@ -548,11 +550,26 @@ public class SequenceTest
   public void testCreateDatasetSequence()
   {
     SequenceI sq = new Sequence("my", "ASDASD");
+    sq.addSequenceFeature(new SequenceFeature("type", "desc", 1, 10, 1f,
+            "group"));
+    sq.addDBRef(new DBRefEntry("source", "version", "accession"));
     assertNull(sq.getDatasetSequence());
+    assertNotNull(PA.getValue(sq, "sequenceFeatures")); // to be removed!
+    assertNotNull(PA.getValue(sq, "sequenceFeatureStore"));
+    assertNotNull(PA.getValue(sq, "dbrefs"));
+
     SequenceI rds = sq.createDatasetSequence();
     assertNotNull(rds);
     assertNull(rds.getDatasetSequence());
-    assertEquals(sq.getDatasetSequence(), rds);
+    assertSame(sq.getDatasetSequence(), rds);
+
+    // sequence features and dbrefs transferred to dataset sequence
+    assertNull(PA.getValue(sq, "sequenceFeatures"));
+    assertNull(PA.getValue(sq, "sequenceFeatureStore"));
+    assertNull(PA.getValue(sq, "dbrefs"));
+    assertNotNull(PA.getValue(rds, "sequenceFeatures"));
+    assertNotNull(PA.getValue(rds, "sequenceFeatureStore"));
+    assertNotNull(PA.getValue(rds, "dbrefs"));
   }
 
   /**
@@ -824,6 +841,36 @@ public class SequenceTest
     assertEquals(' ', sq.getCharAt(-1));
   }
 
+  @Test(groups = { "Functional" })
+  public void testAddSequenceFeatures()
+  {
+    SequenceI sq = new Sequence("", "abcde");
+    // type may not be null
+    assertFalse(sq.addSequenceFeature(new SequenceFeature(null, "desc", 4,
+            8, 0f, null)));
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
+            8, 0f, null)));
+    // can't add a duplicate feature
+    assertFalse(sq.addSequenceFeature(new SequenceFeature("Cath", "desc",
+            4, 8, 0f, null)));
+    // can add a different feature
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Scop", "desc", 4,
+            8, 0f, null))); // different type
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath",
+            "description", 4, 8, 0f, null)));// different description
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 3,
+            8, 0f, null))); // different start position
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
+            9, 0f, null))); // different end position
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
+            8, 1f, null))); // different score
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
+            8, Float.NaN, null))); // score NaN
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
+            8, 0f, "Metal"))); // different group
+    assertEquals(8, sq.getFeatures().getAllFeatures().size());
+  }
+
   /**
    * Tests for adding (or updating) dbrefs
    *