void COffsetReadHook::ReadObject(CObjectIStream &in,
const CObjectInfo &object)
{
CCallStackGuard guard(m_Sniffer->m_CallStack, object);
if (m_EventMode == CObjectsSniffer::eCallAlways) {
// Clear the discard flag before calling sniffer's event reactors
m_Sniffer->SetDiscardCurrObject(false);
m_Sniffer->OnObjectFoundPre(object, in.GetStreamPos());
DefaultRead(in, object);
m_Sniffer->OnObjectFoundPost(object);
// Relay discard flag to the stream
bool discard = m_Sniffer->GetDiscardCurrObject();
in.SetDiscardCurrObject(discard);
}
else {
if (m_EventMode == CObjectsSniffer::eSkipObject) {
DefaultSkip(in, object);
}
else {
DefaultRead(in, object);
}
}
}
virtual void SkipClassMember(CObjectIStream& in,
const CObjectTypeInfoMI& passed_info)
{
cout << in.GetStackPath() << endl;
#if 1
DefaultSkip(in, passed_info);
#else
// get information about the member
// typeinfo of the parent class (Bioseq)
CObjectTypeInfo oti = passed_info.GetClassType();
// typeinfo of the member (SET OF Seq-annot)
CObjectTypeInfo omti = passed_info.GetMemberType();
// index of the member in parent class (4)
TMemberIndex mi = passed_info.GetMemberIndex();
// information about the member, including its name (annot)
const CMemberInfo* minfo = passed_info.GetMemberInfo();
#if 1
// or read the whole SET OF Seq-annot at once
CObjectInfo oi(passed_info);
DefaultRead(in, oi);
cout << MSerial_AsnText << oi << endl;
#endif
#if 0
// or read CSeq_annot objects one by one and write them into stdout
unique_ptr<CObjectOStream> out(CObjectOStream::Open(eSerial_AsnText, "stdout", eSerial_StdWhenStd));
COStreamContainer o(*out, passed_info);
for ( CIStreamContainerIterator i(in, passed_info); i; ++i ) {
CSeq_annot annot;
i >> annot;
// NOTE: this does not produce well formed text ASN, because of missing typeinfo name
// this would work though if we copied data into existing ASN stream
// where typeinfo name ("file header") is not required
o << annot;
// if we needed well formed text ASN, we could write it like this:
// cout << MSerial_AsnText << annot;
}
#endif
#if 0
// or read the whole SET OF Seq-annot at once
CBioseq::TAnnot annot;
CObjectInfo oi(&annot, passed_info.GetMemberType().GetTypeInfo());
in.ReadObject(oi);
// write them one by one
for( const auto& e: annot) {
cout << MSerial_AsnText << *e << endl;
}
// or write them all at once
unique_ptr<CObjectOStream> out(CObjectOStream::Open(eSerial_AsnText, "stdout", eSerial_StdWhenStd));
out->WriteObject(oi);
#endif
#endif
}
// Implement the hook method.
//
// Once the read hook has been set, ReadClassMember() will be called
// whenever the specified class member is encountered while
// reading a hooked input stream. Without the hook, the encountered
// class member would have been automatically read. With the hook, it is
// now the responsibility of the ReadClassMember() method to remove the
// class member from the input stream and process it as desired. It can
// either read it or skip it to remove it from the stream. This is
// easily done by calling DefaultRead() or DefaultSkip() from within
// ReadClassMember(). Subsequent processing is up to the application.
virtual void ReadClassMember(CObjectIStream& in,
const CObjectInfoMI& passed_info)
{
// Perform any pre-read processing here.
//NcbiCout << "In ReadClassMember() hook, before reading." << NcbiEndl;
// You must call DefaultRead() (or perform an equivalent operation)
// if you want the object to be read into memory. You could also
// call DefaultSkip() if you wanted to skip the hooked object while
// reading everything else.
DefaultRead(in, passed_info);
#if 0
// call DefaultRead to read member data, or DefaultSkip to skip it
DefaultSkip(in, passed_info);
// get information about the member
// typeinfo of the parent class
CObjectTypeInfo oti = passed_info.GetClassType();
// typeinfo and data of the parent class
const CObjectInfo& oi = passed_info.GetClassObject();
// typeinfo of the member
CObjectTypeInfo omti = passed_info.GetMemberType();
// typeinfo and data of the member
CObjectInfo om = passed_info.GetMember();
// index of the member in parent class
TMemberIndex mi = passed_info.GetMemberIndex();
// information about the member, including its name
const CMemberInfo* minfo = passed_info.GetMemberInfo();
#endif
// Perform any post-read processing here. Once the object has been
// read, its data can be used for processing.
CNcbiOstrstream oss;
oss << MSerial_AsnText << passed_info.GetClassObject();
string s = CNcbiOstrstreamToString(oss);
NcbiCout << s << NcbiEndl;
}
virtual void SkipChoiceVariant(CObjectIStream& in,
const CObjectTypeInfoCV& passed_info)
{
cout << in.GetStackPath() << endl;
#if 1
DefaultSkip(in, passed_info);
#else
// get information about the variant
// typeinfo of the parent class (Seq-annot.data)
CObjectTypeInfo oti = passed_info.GetChoiceType();
// typeinfo of the variant (SET OF Seq-feat)
CObjectTypeInfo omti = passed_info.GetVariantType();
// index of the variant in parent class (1)
TMemberIndex mi = passed_info.GetVariantIndex();
// information about the variant, including its name (ftable)
const CVariantInfo* minfo = passed_info.GetVariantInfo();
#if 1
// or read the whole SET OF Seq-feat at once
CObjectInfo oi(passed_info);
DefaultRead(in, oi);
cout << MSerial_AsnText << oi << endl;
#endif
#if 0
// or read CSeq_feat objects one by one
for ( CIStreamContainerIterator i(in, passed_info.GetVariantType()); i; ++i ) {
CSeq_feat feat;
i >> feat;
cout << MSerial_AsnText << feat << endl;
}
#endif
#if 0
// or read CSeq_feat objects one by one and write them into stdout
unique_ptr<CObjectOStream> out(CObjectOStream::Open(eSerial_AsnText, "stdout", eSerial_StdWhenStd));
COStreamContainer o(*out, passed_info.GetVariantType());
for ( CIStreamContainerIterator i(in, passed_info.GetVariantType()); i; ++i ) {
CSeq_feat feat;
i >> feat;
// NOTE: this does not produce well formed text ASN, because of missing typeinfo name
// this would work though if we copied data into existing ASN stream
// where typeinfo name ("file header") is not required
// o << feat;
// if we needed well formed text ASN, we could write it like this:
cout << MSerial_AsnText << feat;
}
#endif
#if 0
// or read the whole SET OF Seq-feat at once
CSeq_annot::TData::TFtable ft;
CObjectInfo oi(&ft, passed_info.GetVariantType().GetTypeInfo());
// or, like this:
// CObjectInfo oi(passed_info.GetVariantType());
in.ReadObject(oi);
// write them one by one
for( const auto& e: ft) {
cout << MSerial_AsnText << *e << endl;
}
// or write them all at once
unique_ptr<CObjectOStream> out(CObjectOStream::Open(eSerial_AsnText, "stdout", eSerial_StdWhenStd));
out->WriteObject(oi);
#endif
#endif
}
void CPreReadChoiceVariantHook::ReadChoiceVariant(CObjectIStream& in,
const CObjectInfoCV& variant)
{
PreReadChoiceVariant(in, variant);
DefaultRead(in, variant);
}
void CPreReadClassMemberHook::ReadClassMember(CObjectIStream& in,
const CObjectInfoMI& member)
{
PreReadClassMember(in, member);
DefaultRead(in, member);
}
