JAL-3806 JAL-3725 update tests since CDS mappings now exclude the stop codon

[jalview.git] / test / jalview / io / GenBankFileTest.java

diff --git a/test/jalview/io/GenBankFileTest.java b/test/jalview/io/GenBankFileTest.java
index d800b1d..20d458f 100644 (file)
--- a/test/jalview/io/GenBankFileTest.java
+++ b/test/jalview/io/GenBankFileTest.java
@@ -7,7 +7,6 @@ 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;
 
@@ -43,8 +42,7 @@ 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 +130,7 @@ 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 +183,7 @@ 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 +193,7 @@ 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);