JAL-2189 apply license

[jalview.git] / test / jalview / datamodel / xdb / embl / EmblEntryTest.java

diff --git a/test/jalview/datamodel/xdb/embl/EmblEntryTest.java b/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
index f332fa6..8ed5cc4 100644 (file)
--- a/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
+++ b/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
@@ -1,7 +1,26 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel.xdb.embl;
 
 import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 
@@ -41,21 +60,20 @@ public class EmblEntryTest
     // not the whole sequence but enough for this test...
     List<SequenceI> peptides = new ArrayList<SequenceI>();
     SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
-    EmblEntry ef = EmblTestHelper.getEmblFile();
-    assertNotNull(ef);
-    // assertEquals(1, ef.getEntries().size());
-    // EmblEntry testee = ef.getEntries().get(0);
+    EmblFile ef = EmblTestHelper.getEmblFile();
+    assertEquals(1, ef.getEntries().size());
+    EmblEntry testee = ef.getEntries().get(0);
     String sourceDb = "EMBL";
-    SequenceI dna = ef.makeSequence(sourceDb);
+    SequenceI dna = testee.makeSequence(sourceDb);
 
     /*
      * parse three CDS features, with two/one/no Uniprot cross-refs
      */
-    for (EmblFeature feature : ef.getFeatures())
+    for (EmblFeature feature : ef.getEntries().get(0).getFeatures())
     {
       if ("CDS".equals(feature.getName()))
       {
-        ef.parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
+        testee.parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
       }
     }
 
@@ -218,8 +236,7 @@ public class EmblEntryTest
 
     // truncate last exon by 6bp
     int[] truncated = EmblEntry.adjustForProteinLength(4, exons);
-    assertEquals("[11, 15, 21, 25, 31, 32]",
-            Arrays.toString(truncated));
+    assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
 
     // remove last exon and truncate preceding by 1bp
     truncated = EmblEntry.adjustForProteinLength(3, exons);