X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FGenBankFileTest.java;h=85547e2b6efa110f7b5caa1a032cfb8d5561fcd2;hb=2d44b9594da6c691eca72697060c166d0389affd;hp=d800b1d74dd4a636969083e7ffeb772dbae0f90a;hpb=da62703518a88707b9144bc51e50d6af7093a7c7;p=jalview.git

diff --git a/test/jalview/io/GenBankFileTest.java b/test/jalview/io/GenBankFileTest.java
index d800b1d..85547e2 100644
--- a/test/jalview/io/GenBankFileTest.java
+++ b/test/jalview/io/GenBankFileTest.java
@@ -1,3 +1,23 @@
+/*
+ * 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.io;
 
 import static org.testng.Assert.assertEquals;
@@ -7,14 +27,13 @@ import static org.testng.AssertJUnit.assertNull;
 import java.io.File;
 import java.io.IOException;
 import java.net.MalformedURLException;
-import java.util.Arrays;
 import java.util.List;
 import java.util.Set;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceFeature;
@@ -27,7 +46,7 @@ public class GenBankFileTest
   @BeforeClass(alwaysRun = true)
   public void setUp()
   {
-    Cache.initLogger();
+    Console.initLogger();
   }
 
   /**
@@ -43,8 +62,7 @@ public class GenBankFileTest
     File dataFile = new File("test/jalview/io/J03321.gb");
     FileParse fp = new FileParse(dataFile.getAbsolutePath(),
             DataSourceType.FILE);
-    FlatFile parser = new GenBankFile(fp, "GenBankTest");
-    parser.parse();
+    EMBLLikeFlatFile parser = new GenBankFile(fp, "GenBankTest");
     List<SequenceI> seqs = parser.getSeqs();
 
     assertEquals(seqs.size(), 1);
@@ -132,7 +150,7 @@ public class GenBankFileTest
      * xref to self : 1
      * protein products: 8
      */
-    List<DBRefEntry> dbrefs = Arrays.asList(seq.getDBRefs());
+    List<DBRefEntry> dbrefs = seq.getDBRefs();
 
     assertEquals(dbrefs.size(), 9);
     // xref to 'self':
@@ -185,7 +203,7 @@ public class GenBankFileTest
     assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
     assertEquals(dbref.getAccessionId(), "AAA91574.1");
     mapping = dbref.getMap();
-     mapTo = mapping.getTo();
+    mapTo = mapping.getTo();
     assertEquals(mapTo.getName(), "AAA91574.1");
     // the /product qualifier transfers to protein product description
     assertEquals(mapTo.getDescription(), "hypothetical protein");
@@ -195,7 +213,7 @@ public class GenBankFileTest
     assertTrue(seqString.endsWith("FKQKS"));
     map = mapping.getMap();
     assertEquals(map.getFromLowest(), 6045);
-    assertEquals(map.getFromHighest(), 6788);
+    assertEquals(map.getFromHighest(), 6785); // excludes stop at 6788
     assertEquals(map.getToLowest(), 1);
     assertEquals(map.getToHighest(), 247);
     assertEquals(map.getFromRatio(), 3);