JAL-2480 always include all non-positional features in getAllFeatures()

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

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index e55e507..586cc5d 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -29,6 +29,7 @@ import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
 import jalview.datamodel.PDBEntry.Type;
+import jalview.gui.JvOptionPane;
 import jalview.util.MapList;
 
 import java.io.File;
@@ -37,12 +38,23 @@ import java.util.Arrays;
 import java.util.List;
 import java.util.Vector;
 
+import junit.extensions.PA;
+
 import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 public class SequenceTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   Sequence seq;
 
   @BeforeMethod(alwaysRun = true)
@@ -330,7 +342,7 @@ 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);
@@ -425,11 +437,26 @@ 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"));
   }
 
   /**
@@ -701,6 +728,36 @@ 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
    *