public void AddDefaultOntologyHeader(string defaultOnt)
{
Frame hf = OWLAPIPreconditions.VerifyNotNull(HeaderFrame);
Clause?ontClause = hf.GetClause(OboFormatTag.TAG_ONTOLOGY);
if (ontClause == null)
{
ontClause = new Clause(OboFormatTag.TAG_ONTOLOGY, defaultOnt);
hf.AddClause(ontClause);
}
}
public void FreezeFrames()
{
OWLAPIPreconditions.VerifyNotNull(HeaderFrame,
"headerFrame cannot be null at this stage. Setting the headr frame has been skipped")
.Freeze();
FreezeFrameMap(termFrameMap);
FreezeFrameMap(typedefFrameMap);
FreezeFrameMap(instanceFrameMap);
foreach (Frame frame in annotationFrames)
{
frame.Freeze();
}
}
public XrefExpander(OBODoc src)
{
sourceOBODoc = src;
Frame shf = OWLAPIPreconditions.CheckNotNull(src.HeaderFrame);
string?ontId = shf.GetTagValue <string>(OboFormatTag.TAG_ONTOLOGY);
string tgtOntId = ontId + "/xref_expansions";
targetOBODoc = new OBODoc();
Frame thf = new Frame(FrameType.HEADER);
thf.AddClause(new Clause(OboFormatTag.TAG_ONTOLOGY, tgtOntId));
targetOBODoc.HeaderFrame = thf;
sourceOBODoc.AddImportedOBODoc(targetOBODoc);
SetUp();
}
public void Check()
{
OWLAPIPreconditions.VerifyNotNull(HeaderFrame).Check();
foreach (Frame f in GetTermFrames())
{
f.Check();
}
foreach (Frame f in GetTypedefFrames())
{
f.Check();
}
foreach (Frame f in GetInstanceFrames())
{
f.Check();
}
}
public void ExpandXrefs()
{
foreach (Frame f in sourceOBODoc.GetTermFrames())
{
string id = OWLAPIPreconditions.CheckNotNull(f.GetTagValue <string>(OboFormatTag.TAG_ID));
ICollection <Clause> clauses = f.GetClauses(OboFormatTag.TAG_XREF);
foreach (Clause c in clauses)
{
Xref? x = c.Value <Xref>();
string xid = x.Idref;
string s = GetIDSpace(xid);
if (treatMap.ContainsKey(s))
{
treatMap[s].Expand(this, f, id, xid);
}
}
}
}
protected Frame GetTargetFrame(XrefExpander expander, string id)
{
OBODoc targetDoc = expander.GetTargetDoc(OWLAPIPreconditions.VerifyNotNull(IdSpace, "idSpace not set yet"));
Frame? f = targetDoc.GetTermFrame(id);
if (f == null)
{
f = new Frame
{
Id = id
};
try
{
targetDoc.AddTermFrame(f);
}
catch (FrameMergeException e)
{
// this should be impossible
LOGGER.Error("Frame merge exceptions should not be possible", e);
}
}
return(f);
}