From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 3 Aug 2020 11:06:42 +0000 (+0100)
Subject: JAL-3692 fix up test for 2.11.1 series datamodel API
X-Git-Tag: Release_2_11_1_1~13^2~24^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=84478e43fc8694f4c0c4c16515faf813744194da;p=jalview.git

JAL-3692 fix up test for 2.11.1 series datamodel API
---

diff --git a/test/jalview/io/EmblFlatFileTest.java b/test/jalview/io/EmblFlatFileTest.java
index 4ca826c..35b378b 100644
--- a/test/jalview/io/EmblFlatFileTest.java
+++ b/test/jalview/io/EmblFlatFileTest.java
@@ -18,7 +18,6 @@ import org.testng.annotations.Test;
 
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.Mapping;
-import jalview.datamodel.Sequence.DBModList;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.features.SequenceFeatures;
@@ -37,7 +36,7 @@ public class EmblFlatFileTest
   public void testParse() throws MalformedURLException, IOException
   {
     File dataFile = new File("test/jalview/io/J03321.embl.txt");
-    FileParse fp = new FileParse(dataFile, DataSourceType.FILE);
+    FileParse fp = new FileParse(dataFile.getAbsolutePath(), DataSourceType.FILE);
     EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
     parser.parse();
     List<SequenceI> seqs = parser.getSeqs();
@@ -127,7 +126,8 @@ public class EmblFlatFileTest
      * (some e.g. INTERPRO are duplicates). Jalview adds a dbref to 'self'.
      * Sample a few here. Note DBRefEntry constructor capitalises source.
      */
-    List<DBRefEntry> dbrefs = seq.getDBRefs();
+    List<DBRefEntry> dbrefs = Arrays.asList(seq.getDBRefs());
+
     assertEquals(dbrefs.size(), 32);
     // xref to 'self':
     DBRefEntry selfRef = new DBRefEntry("EMBLTEST", "1", "J03321");
@@ -256,7 +256,7 @@ public class EmblFlatFileTest
     List<SequenceI> seqs = parser.getSeqs();
     assertEquals(seqs.size(), 1);
     SequenceI seq = seqs.get(0);
-    DBModList<DBRefEntry> dbrefs = seq.getDBRefs();
+    List<DBRefEntry> dbrefs = Arrays.asList(seq.getDBRefs());
 
     /*
      * dna should have dbref to itself, and to inferred EMBLCDSPROTEIN:QHD43415.1