X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSeqCigarTest.java;h=2eec987a69ef024db3f7cf112cbb97a85e2d9494;hb=a5928e2c1b9e2cea8d9c43f3d03f9cce2604f3b2;hp=761835d3ddb928aa00338d99639f67e7827cc34c;hpb=73d0b3417c14be3e826826cd7848fc2923332e0e;p=jalview.git

diff --git a/test/jalview/datamodel/SeqCigarTest.java b/test/jalview/datamodel/SeqCigarTest.java
index 761835d..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;
 
@@ -67,29 +66,6 @@ public class SeqCigarTest
     }
   }
 
-  @Test(groups= {"Functional"})
-  public void testReconstructSeq()
-  {
-    String o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt";
-    SequenceI s = new Sequence("MySeq", o_seq, 39, 80);
-    String orig_gapped = "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt";
-    // name of sequence in a particular alignment should be recovered
-    SequenceI s_gapped = new Sequence("MySeqAlign", orig_gapped, 39, 80);
-    s_gapped.setDatasetSequence(s);
-    SeqCigar cg_sgapped = new SeqCigar(s_gapped);
-    assertTrue(testSeqRecovery(cg_sgapped,s_gapped,true));
-    SequenceI subseq_gapped = s_gapped.getSubSequence(44, 60);
-    SeqCigar subseq_cg_range=new SeqCigar(s_gapped,44,59);
-    assertTrue(testSeqRecovery(subseq_cg_range, subseq_gapped, true),"SeqCigar created on range of sequence failed");
-
-    // test another way of reconstructing a sequence from seqCigar
-    SequenceI[] sqs=SeqCigar.createAlignmentSequences(new SeqCigar[] {subseq_cg_range}, '-', new HiddenColumns(), null);
-    assertTrue(testSeqRecovery(subseq_cg_range, sqs[0], true),"createAlignmentSequences didn't reconstruct same sequence as for SeqCigar created on range of sequence failed (used by AlignmentView for selections)");
-
-    subseq_gapped.setName("SubSeqMySeqAlign"); // name of sequence in a particular alignment should be recovered
-    SeqCigar subseq_cg = new SeqCigar(subseq_gapped);
-    assertTrue(testSeqRecovery(subseq_cg,subseq_gapped,true));
-  }
   /*
    * refactored 'as is' from main method
    * 
@@ -118,13 +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
@@ -211,28 +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;
   }
 
 }