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();
}
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);
}
public void SetUp()
{
// required for translation of IDs
IDictionary <string, string> relationsUseByIdSpace = new Dictionary <string, string>();
Frame?headerFrame = sourceOBODoc.HeaderFrame;
if (headerFrame != null)
{
foreach (Clause c in headerFrame.GetClauses())
{
string[] parts;
string v = c.Value().ToString();
parts = v.Split("\\s");
string?relation = null;
string idSpace = parts[0];
string?tag = c.Tag;
if (tag == null)
{
continue;
}
if (tag.Equals(OboFormatTag.TAG_TREAT_XREFS_AS_EQUIVALENT.Tag))
{
AddRule(parts[0], new EquivalenceExpansion());
}
else if (tag.Equals(OboFormatTag.TAG_TREAT_XREFS_AS_GENUS_DIFFERENTIA.Tag))
{
AddRule(idSpace, new GenusDifferentiaExpansion(parts[1], parts[2]));
relationsUseByIdSpace[idSpace] = parts[1];
relation = parts[1];
}
else if (tag.Equals(OboFormatTag.TAG_TREAT_XREFS_AS_REVERSE_GENUS_DIFFERENTIA.Tag))
{
AddRule(idSpace, new ReverseGenusDifferentiaExpansion(parts[1], parts[2]));
relationsUseByIdSpace[idSpace] = parts[1];
relation = parts[1];
}
else if (tag.Equals(OboFormatTag.TAG_TREAT_XREFS_AS_HAS_SUBCLASS.Tag))
{
AddRule(idSpace, new HasSubClassExpansion());
}
else if (tag.Equals(OboFormatTag.TAG_TREAT_XREFS_AS_IS_A.Tag))
{
AddRule(idSpace, new IsaExpansion());
}
else if (tag.Equals(OboFormatTag.TAG_TREAT_XREFS_AS_RELATIONSHIP.Tag))
{
AddRule(idSpace, new RelationshipExpansion(parts[1]));
relationsUseByIdSpace[idSpace] = parts[1];
relation = parts[1];
}
else
{
continue;
}
if (targetBase != null)
{
// create a new bridge ontology for every expansion macro
OBODoc tgt = new OBODoc();
Frame thf = new Frame(FrameType.HEADER);
thf.AddClause(new Clause(OboFormatTag.TAG_ONTOLOGY,
targetBase + "-" + idSpace.ToLower()));
tgt.HeaderFrame = thf;
targetDocMap[idSpace] = tgt;
sourceOBODoc.AddImportedOBODoc(tgt);
if (relation != null)
{
// See 4.4.2
// "In addition, any Typedef frames for relations used
// in a header macro are also copied into the
// corresponding bridge ontology
Frame?tdf = sourceOBODoc.GetTypedefFrame(relation);
if (tdf != null)
{
try
{
tgt.AddTypedefFrame(tdf);
}
catch (FrameMergeException e)
{
LOGGER.Debug("frame merge failed", e);
}
}
}
}
}
}
}
public XrefExpander(OBODoc src, OBODoc tgt)
{
sourceOBODoc = src;
targetOBODoc = tgt;
SetUp();
}
public XrefExpander(OBODoc src, string targetBase)
{
sourceOBODoc = src;
this.targetBase = targetBase;
SetUp();
}