X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSeqCigarTest.java;fp=test%2Fjalview%2Fdatamodel%2FSeqCigarTest.java;h=89169d6dbb10cc387f372442133b575e8fa5d580;hb=2dd39c36211f947fda099c550e711ef5905efefd;hp=ab25aa6b57625aef24a254bf17cf9a8ee030d663;hpb=4dd40d33a5becefd51c31a426f2501b21029f82c;p=jalview.git

diff --git a/test/jalview/datamodel/SeqCigarTest.java b/test/jalview/datamodel/SeqCigarTest.java
index ab25aa6..89169d6 100644
--- a/test/jalview/datamodel/SeqCigarTest.java
+++ b/test/jalview/datamodel/SeqCigarTest.java
@@ -121,7 +121,7 @@ public class SeqCigarTest
     /*
      * TODO: can we add assertions to the sysouts that follow?
      */
-    System.out.println("Original sequence align:\n" + sub_gapped_s
+    System.out.println("\nOriginal sequence align:\n" + sub_gapped_s
             + "\nReconstructed window from 8 to 48\n" + "XXXXXXXX"
             + sub_se_gp.getSequenceString('-') + "..." + "\nCigar String:"
             + sub_se_gp.getCigarstring() + "\n");
@@ -193,7 +193,8 @@ public class SeqCigarTest
     SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
     // assertEquals("Couldn't reconstruct sequence", s_gapped.getSequence(),
     // gen_sgapped_s);
-    if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
+    if (!gen_sgapped_s.getSequenceAsString().equals(
+            s_gapped.getSequenceAsString()))
     {
       // TODO: investigate errors reported here, to allow full conversion to
       // passing JUnit assertion form