X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignmentUtilsTests.java;h=0426091236e3ff1273aa7b9dabf64acf8c4b74fa;hb=dbcbbb61457cb60da170cf99defec797941015b9;hp=1df7fd93963352ccbc3b13f57de37837d9335393;hpb=af2dbf10bbcc54d9b9e4d398e9283b3c4a758e06;p=jalview.git

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 1df7fd9..0426091 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -1059,6 +1059,7 @@ public class AlignmentUtilsTests
      * verify peptide has added a dbref with reverse mapping to CDS
      */
     assertNotNull(pep1.getDBRefs());
+    // FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ?
     assertEquals(2, pep1.getDBRefs().length);
     dbref = pep1.getDBRefs()[1];
     assertEquals("ENSEMBL", dbref.getSource());
@@ -2451,8 +2452,9 @@ public class AlignmentUtilsTests
   {
     SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
     SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
-    SequenceI as1 = dna1.deriveSequence(), as2 = dna1.deriveSequence()
-            .getSubSequence(3, 7), as3 = dna2.deriveSequence();
+    SequenceI as1 = dna1.deriveSequence();
+    SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7);
+    SequenceI as3 = dna2.deriveSequence();
     as1.insertCharAt(6, 5, '-');
     String s_as1 = as1.getSequenceAsString();
     as2.insertCharAt(6, 5, '-');
@@ -2463,8 +2465,9 @@ public class AlignmentUtilsTests
 
     // why do we need to cast this still ?
     ((Alignment) aligned).createDatasetAlignment();
-    SequenceI uas1 = dna1.deriveSequence(), uas2 = dna1.deriveSequence()
-            .getSubSequence(3, 7), uas3 = dna2.deriveSequence();
+    SequenceI uas1 = dna1.deriveSequence();
+    SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7);
+    SequenceI uas3 = dna2.deriveSequence();
     AlignmentI tobealigned = new Alignment(new SequenceI[] { uas1, uas2,
         uas3 });
     ((Alignment) tobealigned).createDatasetAlignment();