Program: 12626
Project: 12626
Buggy source:
@Test public void test_ComponentDefinitionOutput() throws Exception {
  String prURI="String_Node_Str";
  String prPrefix="String_Node_Str";
  SBOLDocument document=new SBOLDocument();
  document.setTypesInURIs(true);
  document.addNamespace(URI.create(prURI),prPrefix);
  document.setDefaultURIprefix(prURI);
  Sequence seqpTetR=document.createSequence("String_Node_Str","String_Node_Str","String_Node_Str",URI.create("String_Node_Str"));
  Sequence seqRbs=document.createSequence("String_Node_Str","String_Node_Str","String_Node_Str",URI.create("String_Node_Str"));
  Sequence seqCds=document.createSequence("String_Node_Str","String_Node_Str","String_Node_Str",URI.create("String_Node_Str"));
  Sequence seqTer=document.createSequence("String_Node_Str","String_Node_Str","String_Node_Str",URI.create("String_Node_Str"));
  Sequence seqPluxR=document.createSequence("String_Node_Str","String_Node_Str","String_Node_Str",URI.create("String_Node_Str"));
  ComponentDefinition pTetR=document.createComponentDefinition("String_Node_Str","String_Node_Str",new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
  pTetR.addRole(SequenceOntology.PROMOTER);
  pTetR.setName("String_Node_Str");
  pTetR.setDescription("String_Node_Str");
  pTetR.addSequence(seqpTetR.getIdentity());
  ComponentDefinition rbs=document.createComponentDefinition("String_Node_Str","String_Node_Str",new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
  rbs.addRole(SequenceOntology.RIBOSOME_ENTRY_SITE);
  rbs.setName("String_Node_Str");
  rbs.setDescription("String_Node_Str");
  rbs.addSequence(seqRbs.getIdentity());
  ComponentDefinition cds=document.createComponentDefinition("String_Node_Str","String_Node_Str",new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
  cds.addRole(SequenceOntology.CDS);
  cds.setName("String_Node_Str");
  cds.setDescription("String_Node_Str");
  cds.addSequence(seqCds.getIdentity());
  ComponentDefinition ter=document.createComponentDefinition("String_Node_Str","String_Node_Str",new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
  ter.addRole(URI.create("String_Node_Str"));
  ter.setName("String_Node_Str");
  ter.setDescription("String_Node_Str");
  ter.addSequence(seqTer.getIdentity());
  ComponentDefinition pluxR=document.createComponentDefinition("String_Node_Str","String_Node_Str",new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
  pluxR.addRole(SequenceOntology.PROMOTER);
  pluxR.setName("String_Node_Str");
  pluxR.setDescription("String_Node_Str");
  pluxR.addSequence(seqPluxR.getIdentity());
  ComponentDefinition device=document.createComponentDefinition("String_Node_Str","String_Node_Str",new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
  device.addRole(URI.create("String_Node_Str"));
  device.setName("String_Node_Str");
  device.setDescription("String_Node_Str");
  Component comPtetR=device.createComponent("String_Node_Str",AccessType.PUBLIC,pTetR.getIdentity());
  Component comRbs=device.createComponent("String_Node_Str",AccessType.PUBLIC,cds.getIdentity());
  Component comCds=device.createComponent("String_Node_Str",AccessType.PUBLIC,rbs.getIdentity());
  Component comTer=device.createComponent("String_Node_Str",AccessType.PUBLIC,ter.getIdentity());
  Component comPluxR=device.createComponent("String_Node_Str",AccessType.PUBLIC,pluxR.getIdentity());
  int start=1;
  int end=seqPluxR.getElements().length();
  SequenceAnnotation anno=device.createSequenceAnnotation("String_Node_Str","String_Node_Str",start,end,OrientationType.INLINE);
  anno.setComponent(comPtetR.getIdentity());
  start=end + 1;
  end=seqRbs.getElements().length() + end + 1;
  SequenceAnnotation anno2=device.createSequenceAnnotation("String_Node_Str","String_Node_Str",start,end,OrientationType.INLINE);
  anno2.setComponent(comRbs.getIdentity());
  start=end + 1;
  end=seqCds.getElements().length() + end + 1;
  SequenceAnnotation anno3=device.createSequenceAnnotation("String_Node_Str","String_Node_Str",start,end,OrientationType.INLINE);
  anno3.setComponent(comCds.getIdentity());
  start=end + 1;
  end=seqTer.getElements().length() + end + 1;
  SequenceAnnotation anno4=device.createSequenceAnnotation("String_Node_Str","String_Node_Str",start,end,OrientationType.INLINE);
  anno4.setComponent(comTer.getIdentity());
  start=end + 1;
  end=seqPluxR.getElements().length() + end + 1;
  SequenceAnnotation anno5=device.createSequenceAnnotation("String_Node_Str","String_Node_Str",start,end,OrientationType.INLINE);
  anno5.setComponent(comPluxR.getIdentity());
  runTest("String_Node_Str",document,"String_Node_Str");
}

Fixed version (ground truth):
@Test public void test_ComponentDefinitionOutput() throws Exception {
  String prURI="String_Node_Str";
  String prPrefix="String_Node_Str";
  SBOLDocument document=new SBOLDocument();
  document.setTypesInURIs(true);
  document.addNamespace(URI.create(prURI),prPrefix);
  document.setDefaultURIprefix(prURI);
  Sequence seqpTetR=document.createSequence("String_Node_Str","String_Node_Str","String_Node_Str",Sequence.IUPAC_DNA);
  Sequence seqRbs=document.createSequence("String_Node_Str","String_Node_Str","String_Node_Str",Sequence.IUPAC_DNA);
  Sequence seqCds=document.createSequence("String_Node_Str","String_Node_Str","String_Node_Str",Sequence.IUPAC_DNA);
  Sequence seqTer=document.createSequence("String_Node_Str","String_Node_Str","String_Node_Str",Sequence.IUPAC_DNA);
  Sequence seqPluxR=document.createSequence("String_Node_Str","String_Node_Str","String_Node_Str",Sequence.IUPAC_DNA);
  ComponentDefinition pTetR=document.createComponentDefinition("String_Node_Str","String_Node_Str",new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
  pTetR.addRole(SequenceOntology.PROMOTER);
  pTetR.setName("String_Node_Str");
  pTetR.setDescription("String_Node_Str");
  pTetR.addSequence(seqpTetR.getIdentity());
  ComponentDefinition rbs=document.createComponentDefinition("String_Node_Str","String_Node_Str",new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
  rbs.addRole(SequenceOntology.RIBOSOME_ENTRY_SITE);
  rbs.setName("String_Node_Str");
  rbs.setDescription("String_Node_Str");
  rbs.addSequence(seqRbs.getIdentity());
  ComponentDefinition cds=document.createComponentDefinition("String_Node_Str","String_Node_Str",new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
  cds.addRole(SequenceOntology.CDS);
  cds.setName("String_Node_Str");
  cds.setDescription("String_Node_Str");
  cds.addSequence(seqCds.getIdentity());
  ComponentDefinition ter=document.createComponentDefinition("String_Node_Str","String_Node_Str",new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
  ter.addRole(URI.create("String_Node_Str"));
  ter.setName("String_Node_Str");
  ter.setDescription("String_Node_Str");
  ter.addSequence(seqTer.getIdentity());
  ComponentDefinition pluxR=document.createComponentDefinition("String_Node_Str","String_Node_Str",new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
  pluxR.addRole(SequenceOntology.PROMOTER);
  pluxR.setName("String_Node_Str");
  pluxR.setDescription("String_Node_Str");
  pluxR.addSequence(seqPluxR.getIdentity());
  ComponentDefinition device=document.createComponentDefinition("String_Node_Str","String_Node_Str",new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
  device.addRole(URI.create("String_Node_Str"));
  device.setName("String_Node_Str");
  device.setDescription("String_Node_Str");
  Component comPtetR=device.createComponent("String_Node_Str",AccessType.PUBLIC,pTetR.getIdentity());
  Component comRbs=device.createComponent("String_Node_Str",AccessType.PUBLIC,cds.getIdentity());
  Component comCds=device.createComponent("String_Node_Str",AccessType.PUBLIC,rbs.getIdentity());
  Component comTer=device.createComponent("String_Node_Str",AccessType.PUBLIC,ter.getIdentity());
  Component comPluxR=device.createComponent("String_Node_Str",AccessType.PUBLIC,pluxR.getIdentity());
  int start=1;
  int end=seqPluxR.getElements().length();
  SequenceAnnotation anno=device.createSequenceAnnotation("String_Node_Str","String_Node_Str",start,end,OrientationType.INLINE);
  anno.setComponent(comPtetR.getIdentity());
  start=end + 1;
  end=seqRbs.getElements().length() + end + 1;
  SequenceAnnotation anno2=device.createSequenceAnnotation("String_Node_Str","String_Node_Str",start,end,OrientationType.INLINE);
  anno2.setComponent(comRbs.getIdentity());
  start=end + 1;
  end=seqCds.getElements().length() + end + 1;
  SequenceAnnotation anno3=device.createSequenceAnnotation("String_Node_Str","String_Node_Str",start,end,OrientationType.INLINE);
  anno3.setComponent(comCds.getIdentity());
  start=end + 1;
  end=seqTer.getElements().length() + end + 1;
  SequenceAnnotation anno4=device.createSequenceAnnotation("String_Node_Str","String_Node_Str",start,end,OrientationType.INLINE);
  anno4.setComponent(comTer.getIdentity());
  start=end + 1;
  end=seqPluxR.getElements().length() + end + 1;
  SequenceAnnotation anno5=device.createSequenceAnnotation("String_Node_Str","String_Node_Str",start,end,OrientationType.INLINE);
  anno5.setComponent(comPluxR.getIdentity());
  runTest("String_Node_Str",document,"String_Node_Str");
}