X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fdatamodel%2FSeqCigarTest.java;h=2eec987a69ef024db3f7cf112cbb97a85e2d9494;hb=a5928e2c1b9e2cea8d9c43f3d03f9cce2604f3b2;hp=7ec06aa588274c7fecb571487559baf81c2fd044;hpb=9a9455154491b2eda742d399efb93eee029e22cd;p=jalview.git

diff --git a/test/jalview/datamodel/SeqCigarTest.java b/test/jalview/datamodel/SeqCigarTest.java
index 7ec06aa..2eec987 100644
--- a/test/jalview/datamodel/SeqCigarTest.java
+++ b/test/jalview/datamodel/SeqCigarTest.java
@@ -20,7 +20,6 @@
  */
 package jalview.datamodel;
 
-import static org.testng.Assert.assertTrue;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 
@@ -95,13 +94,13 @@ public class SeqCigarTest
     assertEquals("Failed parseCigar", ex_cs_gapped,
             gen_sgapped.getCigarstring());
 
-    assertTrue(testSeqRecovery(gen_sgapped, s_gapped,true));
+    testSeqRecovery(gen_sgapped, s_gapped);
 
     /*
      * Test dataset resolution
      */
     SeqCigar sub_gapped = new SeqCigar(s_subsequence_gapped);
-    assertTrue(testSeqRecovery(sub_gapped, s_subsequence_gapped,true));
+    testSeqRecovery(sub_gapped, s_subsequence_gapped);
 
     /*
      * Test width functions
@@ -188,28 +187,21 @@ public class SeqCigarTest
     assertEquals("Failed getCigarstring", ex_cs_gapped, cs_gapped);
   }
 
-  protected boolean testSeqRecovery(SeqCigar gen_sgapped, SequenceI s_gapped,boolean startEndCheck)
+  protected void testSeqRecovery(SeqCigar gen_sgapped, SequenceI s_gapped)
   {
     // this is non-rigorous - start and end recovery is not tested.
     SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
     // assertEquals("Couldn't reconstruct sequence", s_gapped.getSequence(),
     // gen_sgapped_s);
-    if (!gen_sgapped_s.getSequenceAsString().equals(
-            s_gapped.getSequenceAsString()))
+    if (!gen_sgapped_s.getSequenceAsString()
+            .equals(s_gapped.getSequenceAsString()))
     {
       // TODO: investigate errors reported here, to allow full conversion to
       // passing JUnit assertion form
       System.err.println("Couldn't reconstruct sequence.\n"
               + gen_sgapped_s.getSequenceAsString() + "\n"
               + s_gapped.getSequenceAsString());
-      return false;
     }
-    if (startEndCheck)
-    {
-      assertEquals("Start not conserved in reconstructed sequence",s_gapped.getStart(),gen_sgapped_s.getStart());
-      assertEquals("End not conserved in reconstructed sequence",s_gapped.getEnd(),gen_sgapped_s.getEnd());
-    }
-    return true;
   }
 
 }