From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 28 Sep 2016 14:26:52 +0000 (+0100)
Subject: JAL-2235 patch tests where self-reference was used for dataset sequence ref
X-Git-Tag: Release_2_10_0~20^2~27
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1986948868e6643ea811a70cd0018c8103a7b3f0;p=jalview.git

JAL-2235 patch tests where self-reference was used for dataset sequence ref
---

diff --git a/test/jalview/commands/EditCommandTest.java b/test/jalview/commands/EditCommandTest.java
index 9afae37..7fb80fb 100644
--- a/test/jalview/commands/EditCommandTest.java
+++ b/test/jalview/commands/EditCommandTest.java
@@ -239,7 +239,7 @@ public class EditCommandTest
   public void testReplace()
   {
     // seem to need a dataset sequence on the edited sequence here
-    seqs[1].setDatasetSequence(seqs[1]);
+    seqs[1].createDatasetSequence();
     new EditCommand("", Action.REPLACE, "ZXY", new SequenceI[] { seqs[1] },
             4, 8, al);
     assertEquals("abcdefghjk", seqs[0].getSequenceAsString());
diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index bad536b..16dfa6b 100644
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -44,7 +44,7 @@ public class StructureChooserTest
   {
     seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
             26);
-    seq.setDatasetSequence(seq);
+    seq.createDatasetSequence();
     for (int x = 1; x < 5; x++)
     {
       DBRefEntry dbRef = new DBRefEntry();
diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index 625244d..c9b5f4a 100644
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -75,8 +75,7 @@ public class AnnotationFileIOTest
       // make sure dataset is initialised ? not sure about this
       for (int i = 0; i < al.getSequencesArray().length; ++i)
       {
-        al.getSequenceAt(i).setDatasetSequence(
-                al.getSequenceAt(i).createDatasetSequence());
+        al.getSequenceAt(i).createDatasetSequence();
       }
       assertNotNull("Couldn't read supplied alignment data.", al);
       return al;
diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java
index 93fb12b..f75f433 100644
--- a/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@ -114,7 +114,7 @@ public class JSONFileTest
 
     for (Sequence seq : seqs)
     {
-      seq.setDatasetSequence(seq);
+      seq.createDatasetSequence();
       expectedSeqs.put(seq.getName(), seq);
     }
 
diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 0e2b630..b635aa3 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -103,7 +103,7 @@ public class StockholmFileTest
       // make sure dataset is initialised ? not sure about this
       for (int i = 0; i < al.getSequencesArray().length; ++i)
       {
-        al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i));
+        al.getSequenceAt(i).createDatasetSequence();
       }
       String outputfile = rf.formatSequences(ioformat, al, true);
       System.out.println("Output file in '" + ioformat + "':\n"