From e1dbbc5edc07f65706eeb1dda9f4c9bcdee9d3a5 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 18 May 2020 11:01:29 +0100
Subject: [PATCH] JAL-3529 test updated for revised signature of getDBRefs()

---
 test/jalview/io/StockholmFileTest.java |   28 +++++++++++++++-------------
 1 file changed, 15 insertions(+), 13 deletions(-)

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 9fdd7b9..5b74306 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -26,17 +26,6 @@ import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.AssertJUnit.fail;
 
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.gui.JvOptionPane;
-import jalview.util.DBRefUtils;
-
 import java.io.File;
 import java.util.Arrays;
 import java.util.BitSet;
@@ -50,6 +39,17 @@ import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import jalview.util.DBRefUtils;
+
 public class StockholmFileTest
 {
 
@@ -125,10 +125,12 @@ public class StockholmFileTest
     AlignmentI fromStockholm = af.readFile(toStockholm,
             DataSourceType.PASTE, FileFormat.Stockholm);
     SequenceI importedSeq = fromStockholm.getSequenceAt(0);
-    assertTrue(importedSeq.getDBRefs().length == 1,
+    assertTrue(importedSeq.getDBRefs()
+            .size() == 1,
             "Expected just one database reference to be added to sequence.");
     assertTrue(
-            importedSeq.getDBRefs()[0].getAccessionId().indexOf(" ") == -1,
+            importedSeq.getDBRefs().get(0).getAccessionId().indexOf(
+                    " ") == -1,
             "Spaces were found in accession ID.");
     List<DBRefEntry> dbrefs = DBRefUtils.searchRefs(importedSeq.getDBRefs(),
             "P00224");
-- 
1.7.10.2