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NCBI C++ ToolKit: src/app/asn2asn/asn2asn.cpp Source File

<

T> pair<void*, const CTypeInfo*>

(

&

);

<

T> pair<const void*, const CTypeInfo*>

(

&

);

&NCBI_NS_NCBI::objects::CSeq_entry::GetRefChoiceTypeInfo;

make_pair((

*)&

,

(&

)());

make_pair((

*)&

,

(&

)());

NCBI_NS_NCBI::objects;

(

argc,

** argv)

(

)

--m_Counter.m_Counter;

( m_Count % 1000 == 0 )

.GetTypeInfo()->DefaultReadData(

, bioseq);

.SetDiscardCurrObject();

<

Member>

((*member).GetTypeInfo()->GetSize() ==

(

));

<<

<<

<

Object>

(

.GetTypeInfo()->GetSize() ==

(

));

.GetTypeInfo()->GetName() <<

<<

(

.IsSetGenome())

genome =

.GetGenome();

(

.IsSetSubtype()) {

name = (*it)->GetName();

= (*it)->GetSubtype();

(

== 19) subtype =

;

(

.IsSetOrg()) {

taxid = (*it)->GetTag().GetId();

m_Dummy += subtype+biomol+complete+tech;

d->SetUsageContext(

,

);

d->AddKey(

,

,

d->AddOptionalKey(

,

,

);

);

);

);

);

);

);

);

d->AddOptionalKey(

,

,

,

d->AddOptionalKey(

,

,

,

d->AddOptionalKey(

,

,

,

);

d->AddOptionalKey(

,

,

,

d->AddDefaultKey(

,

,

,

d->AddDefaultKey(

,

,

,

);

SetupArgDescriptions(d.release());

: m_Index(index), m_Asn2Asn(asn2asn), m_DoneOk(

)

m_Asn2Asn->RunAsn2Asn(suffix);

(exception& e) {

<< e.what();

threadCount = args[

].AsInteger();

vector< CRef<CAsn2AsnThread> > threads(threadCount);

(

= 1;

< threadCount; ++

) {

(exception& e) {

() <<

<<

<<

<< e.what();

(

= 1;

< threadCount; ++

) {

threads[

]->Join();

( !threads[

]->DoneOk() ) {

: target_gi(target_gi), do_insert(

), annot(annot), annot_in(0) {

: target_gi(target_gi), do_insert(

), annot_in(&annot_in) {

annot || annot_in;

(

.IsGi() &&

.GetGi() == target_gi && HasAnnot() ) {

manager.

(

);

: copier(copier),

(

) {

.WriteElement(copier,

);

( manager.

) {

DefaultCopy(copier, member);

.WriteElement(copier,

);

InsertAnnot(copier,

);

InsertAnnot(copier,

);

& in_file)

: m_DB_Result(db_result) {

* bytes_read) {

( (ret = m_DB_Result->ReadItem(

,

)) == 0 ) {

( !m_DB_Result->Fetch() )

args[

]=

;

args[

]=

;

(

->Connect(

,

,

, 0));

sat = add_ext_feat == 8? 10: 26;

ext_feat(add_ext_feat);

->SetParam(

, &satKeyIn);

->SetParam(

, &satIn);

->SetParam(

, &ext_feat);

( !

&&

->HasMoreResults() ) {

(

->HasFailed() ) {

(

pos = 0; pos < dbr->

(); ++pos ) {

& name = dbr->

(pos);

( name ==

) {

zip_type = v.

();

( name ==

) {

(

);

PubSeqOS::CDB_Result_Reader reader(

.get());

( zip_type & 2 ) {

unique_ptr<CObjectIStream> annot_in

unique_ptr<CObjectIStream> annot_in

inFile = args[

].AsString();

( args[

] )

( args[

] )

outFile += outFileSuffix;

EDataType eDataType = eDataType_BioseqSet;

eDataType = eDataType_SeqEntry;

}

( args[

] ) {

eDataType = eDataType_SeqSubmit;

skip = args[

];

merge = args[

] && (args[

] || args[

]);

( args[

] ) {

ext = args[

].AsInteger();

( ext == 0 || (ext & (ext-1)) != 0 ) {

(

);

readHook = args[

];

writeHook = args[

];

usePool = args[

];

= args[

];

multi = args[

];

= args[

].AsInteger();

(

= 1;

<=

; ++

) {

displayMessages =

!= 1 && !

;

( displayMessages )

->UseMemoryPool();

unique_ptr<CObjectOStream>

(!haveOutput? 0:

( eDataType == eDataType_SeqEntry ||

eDataType == eDataType_SeqSubmit )

eDataType == eDataType_SeqEntry ?

( displayMessages )

.SetLocalSkipHook

.FindMember(

).SetLocalSkipHook

.FindMember(

).SetLocalSkipHook

->Skip(objectTypeInfo);

->Skip(objectTypeInfo);

(

&& haveOutput ) {

( displayMessages )

( eDataType == eDataType_SeqEntry &&

merge && haveOutput )

( displayMessages )

( args[

] ) {

args[

].AsString());

args[

].AsInteger());

( displayMessages )

( eDataType == eDataType_SeqEntry ) {

pObjectFromIn = pEntry;

*

>> *pSeqSubmit;

pObjectFromIn = pSeqSubmit;

( pInnerSeqEntry ) {

( displayMessages )

*

<< *pObjectFromIn;

( displayMessages )

(

&& haveOutput ) {

( displayMessages )

( displayMessages )

( displayMessages )

( !multi ||

->EndOfData() )

( m_Level == 1 ) {

.ReadClassMember(member);

( m_Level == 1 ) {

.GetTypeInfo()->DefaultWriteData(

,

.GetObjectPtr());

.GetTypeInfo()->DefaultWriteData(

,

.GetObjectPtr());

( m_Level == 1 ) {

( TSeq_set::const_iterator

=

.begin();

!=

.end(); ++

) {

.WriteClassMember(member);

User-defined methods of the data storage class.

void MergeExternal(CObjectIStream &in, CObjectOStream &out, TGi gi, int add_ext_feat)

static void SeqEntryProcess(CSeq_entry &entry)

void MergeFromFile(CObjectIStream &in, CObjectOStream &out, TGi gi, const string &in_file)

DEFINE_STATIC_FAST_MUTEX(s_ArgsMutex)

int main(int argc, char **argv)

void MergeAnnot(CObjectIStream &in, CObjectOStream &out, TGi gi, CObjectIStream &annot_in)

void * Main()

Derived (user-created) class must provide a real thread function.

CAsn2AsnThread(int index, CAsn2Asn *asn2asn)

int Run(void)

Run the application.

void Init(void)

Initialize the application.

Copy hook for data member of a containing object (eg, SEQUENCE)

ERW_Result PendingCount(size_t *)

Via parameter "count" (which is guaranteed to be supplied non-NULL) return the number of bytes that a...

ERW_Result Read(void *buf, size_t count, size_t *bytes_read)

Read as many as "count" bytes into a buffer pointed to by the "buf" argument.

CDB_Result_Reader(CDB_Result *db_result)

virtual void ReadObject(CObjectIStream &in, const CObjectInfo &info)

This method will be called at approriate time when the object of requested type is to be read.

void Release()

Manually force the resource to be released.

Reading (iterating through) elements of containers (SET OF, SEQUENCE OF).

CInsertAnnotHookAnnot(CInsertAnnotManager &manager)

CInsertAnnotManager & manager

void CopyClassMember(CObjectStreamCopier &copier, const CObjectTypeInfoMI &member)

void CopyMissingClassMember(CObjectStreamCopier &copier, const CObjectTypeInfoMI &member)

void InsertAnnot(CObjectStreamCopier &copier, COStreamContainer &out)

CInsertAnnotHookCopy(CObjectStreamCopier &copier, COStreamContainer &out)

CObjectStreamCopier & copier

void SkipObject(CObjectIStream &in, const CObjectTypeInfo &type)

CInsertAnnotHookId(CInsertAnnotManager &manager)

void CopyClassMember(CObjectStreamCopier &copier, const CObjectTypeInfoMI &member)

CInsertAnnotManager & manager

bool HasAnnot(void) const

CConstRef< CSeq_annot > annot

void AddId(const CSeq_id &id)

CInsertAnnotManager(TGi target_gi, CConstRef< CSeq_annot > annot)

CInsertAnnotManager(TGi target_gi, CObjectIStream &annot_in)

bool SkipInsert(void) const

CObjectIStream * annot_in

Writing containers (SET OF, SEQUENCE OF).

Helper class: installs hooks in constructor, and uninstalls in destructor.

CObjectIStreamAsnBinary –.

CObjectOStreamAsnBinary –.

Note about the "buf_size" parameter for streams in this API.

Read hook for data member of a containing object (eg, SEQUENCE)

void SkipClassMember(CObjectIStream &in, const CObjectTypeInfoMI &member)

CReadInSkipClassMemberHook()

void SkipObject(CObjectIStream &in, const CObjectTypeInfo &type)

Read hook for a standalone object.

void ReadClassMember(CObjectIStream &in, const CObjectInfo::CMemberIterator &member)

This method will be called at approriate time when the object of requested type is to be read.

@Seq_descr.hpp User-defined methods of the data storage class.

Skip hook for data member of a containing object (eg, SEQUENCE)

Skip hook for a standalone object.

virtual void ReadClassMember(CObjectIStream &in, const CObjectInfo::CMemberIterator &member)

This method will be called at approriate time when the object of requested type is to be read.

CTypeInfo class contains all information about C++ types (both basic and classes): members and layout...

Write hook for data member of a containing object (eg, SEQUENCE)

Write hook for a standalone object.

void WriteObject(CObjectOStream &out, const CConstObjectInfo &object)

This method will be called at approriate time when the object of requested type is to be written.

void WriteClassMember(CObjectOStream &out, const CConstObjectInfo::CMemberIterator &member)

CZipStreamDecompressor – zlib based decompression stream processor.

A very basic data-read interface.

Include a standard set of the NCBI C++ Toolkit most basic headers.

std::ofstream out("events_result.xml")

main entry point for tests

static CS_CONNECTION * conn

static TDSRET convert(TDSSOCKET *tds, TDSICONV *conv, TDS_ICONV_DIRECTION direction, const char *from, size_t from_len, char *dest, size_t *dest_len)

#define GI_FROM(T, value)

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

element_type * get(void) const

Get pointer.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

virtual const string & AsString(void) const =0

Get the argument's string value.

@ eExcludes

One argument excludes another.

@ eInputFile

Name of file (must exist and be readable)

@ eIntId

Convertible to TIntId (int or Int8 depending on NCBI_INT8_GI)

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

void DBAPI_RegisterDriver_FTDS(void)

I_DriverContext * GetDriverContext(const string &driver_name, string *err_msg=0, const map< string, string > *attr=0)

virtual EDB_ResType ResultType() const

Get type of the result.

virtual bool SkipItem()

Skip result item.

virtual CDB_Object * GetItem(CDB_Object *item_buf=0, EGetItem policy=eAppendLOB)

Get a result item (you can use either GetItem or ReadItem).

virtual const char * ItemName(unsigned int item_num) const

Get name of a result item.

virtual unsigned int NofItems() const

Get # of items (columns) in the result.

virtual bool Fetch()

Fetch next row.

#define ERR_FATAL(message)

Posting fatal error and abort.

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void SetDiagStream(CNcbiOstream *os, bool quick_flush=true, FDiagCleanup cleanup=0, void *cleanup_data=0, const string &stream_name="")

Set diagnostic stream.

@ eDS_Default

Try standard log file (app.name + ".log") in /log/, use stderr on failure.

@ eDiag_Error

Error message.

void Error(CExceptionArgs_Base &args)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

const CMemberId & GetId(void) const

const string & GetName(void) const

TTypeInfoGetter GetTypeRef(const T *object)

CNcbiOstream & WriteObject(CNcbiOstream &str, TConstObjectPtr ptr, TTypeInfo info)

#define MSerial_AsnText

I/O stream manipulators –.

ESerialDataFormat

Data file format.

@ eFNP_Allow

pass through unchanged, post no error message

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

static C * GetUnchecked(const CObjectInfo &object)

pair< TObjectPtr, TTypeInfo > ObjectInfo(C &obj)

const CMemberInfo * GetMemberInfo(void) const

CObjectTypeInfo GetMemberType(void) const

Get data type information.

CMemberIterator FindMember(const string &memberName) const

Find class member by its name.

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

CObjectTypeInfo GetClassType(void) const

Get containing class type.

TTypeInfo GetTypeInfo(void) const

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

CObjectIStream & In(void) const

pair< TConstObjectPtr, TTypeInfo > ConstObjectInfo(const C &obj)

CObjectOStream & Out(void) const

void SetLocalReadHook(CObjectIStream &stream, CReadClassMemberHook *hook) const

void SetLocalWriteHook(CObjectOStream &stream, CWriteObjectHook *hook) const

Set local (for the specified stream) write hook.

const string & GetName(void) const

Get type name.

void Copy(const CObjectTypeInfo &type)

Copy data.

void SetLocalWriteHook(CObjectOStream &stream, CWriteClassMemberHook *hook) const

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

ERW_Result

Result codes for I/O operations.

@ eRW_NotImplemented

Action / information is not available.

@ eRW_Eof

End of data, should be considered permanent.

@ eRW_Success

Everything is okay, I/O completed.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static string & ToLower(string &str)

Convert string to lower case – string& version.

const string & GetName(void) const

Get name of this type.

const TTaxname & GetTaxname(void) const

Get the Taxname member data.

const TDb & GetDb(void) const

Get the Db member data.

list< CRef< CSeq_entry > > TSeq_set

bool IsSetCompleteness(void) const

Check if a value has been assigned to Completeness data member.

bool IsMolinfo(void) const

Check if variant Molinfo is selected.

const TTitle & GetTitle(void) const

Get the variant data.

const TSource & GetSource(void) const

Get the variant data.

bool IsSource(void) const

Check if variant Source is selected.

bool IsSetBiomol(void) const

Check if a value has been assigned to Biomol data member.

TTech GetTech(void) const

Get the Tech member data.

const Tdata & Get(void) const

Get the member data.

TBiomol GetBiomol(void) const

Get the Biomol member data.

bool IsSetTech(void) const

Check if a value has been assigned to Tech data member.

TCompleteness GetCompleteness(void) const

Get the Completeness member data.

bool IsTitle(void) const

Check if variant Title is selected.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

const TEntrys & GetEntrys(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

unsigned int

A callback function used to compare two keys in a database.

const CharType(& source)[N]

#define NCBI_SC_VERSION_PROXY

#define NCBI_TEAMCITY_BUILD_NUMBER_PROXY

#define GetArgs

Avoid preprocessor name clash with the NCBI C Toolkit.

Defines command line argument related classes.

Defines unified interface to application:

Memory pool for fast allocation of memory for localized set of CObjects, e.g.

Multi-threading – classes, functions, and features.

Useful/utility classes and methods.

std::istream & in(std::istream &in_, double &x_)

Reader-writer based streams.

static SLJIT_INLINE sljit_ins st(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static CS_CONTEXT * context

static wxAcceleratorEntry entries[3]

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