*/
package jalview.datamodel;
-import static org.testng.Assert.assertTrue;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
}
}
- @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
*
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
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;
}
}