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NCBI C++ ToolKit: src/misc/discrepancy/discrepancy_stream.cpp Source File

(!line_reader.

());

(header.empty()) {

header = default_header;

(header == CSeq_submit::GetTypeInfo()->GetName()) {

(header == CSeq_entry::GetTypeInfo()->GetName()) {

(header == CBioseq_set::GetTypeInfo()->GetName()) {

(header == CBioseq::GetTypeInfo()->GetName()) {

handle =

->AddTopLevelSeqEntry(*se);

->ResetDataAndHistory();

(

& entry : root.

()) {

(root.

()) {

(root.

()) {

(

& desc : bioseq.

().

()) {

(desc->IsMolinfo()) {

(desc->IsSource()) {

(desc->IsTitle()) {

(

& annot : bioseq.

()) {

(annot->IsFtable()) {

(

& feat : annot->GetData().GetFtable()) {

((!

(

->m_Type) &&

->m_Type !=

) || !

->m_Ref->m_Text.empty()) {

=

->m_Ref->GetText();

(

& desc : seqset.

().

()) {

(desc->IsMolinfo()) {

(desc->IsSource()) {

(desc->IsTitle()) {

(

& annot : seqset.

()) {

(annot->IsFtable()) {

(

& feat : annot->GetData().GetFtable()) {

(

& feat :

) {

(&*feat == &old_feat) {

feat.Reset(&new_feat);

unique_ptr<CNcbiIstream> InputStream(

(fname, ios::binary));

unique_ptr<CObjectIStream> objectStream;

(!tofix.empty()) {

in_file =

;

(node->m_Type ==

) in_file =

;

(

& fix : tofix) {

vector<vector<CDiscrepancyObject*>> all_fixes;

(

& fix : tofix) {

(node->m_Type ==

) {

(path != current_path) {

vector<CDiscrepancyObject*> fixes;

all_fixes.push_back(fixes);

all_fixes.back().push_back(&obj);

(

& fix : all_fixes) {

(node->m_Type ==

) {

compressed =

;

cout <<

<< path <<

;

dot = path.find_last_of(

);

(dot != string::npos) {

slash = path.find_last_of(

);

(slash != string::npos && slash >= dot) {

fixed_path = !compressed && (dot != string::npos) ? path.substr(0, dot) +

+ path.substr(dot) : path +

;

header =

->ReadFileHeader();

(header.empty()) {

header = default_header;

(header == CSeq_submit::GetTypeInfo()->GetName()) {

(header == CSeq_entry::GetTypeInfo()->GetName()) {

(header == CBioseq_set::GetTypeInfo()->GetName()) {

(header == CBioseq::GetTypeInfo()->GetName()) {

(

->EndOfData()) {

header =

->ReadFileHeader();

(

->m_Index !=

->m_Index) {

(

* fix : *

) {

(

->m_Index !=

->m_Index) {

(

* fix : *

) {

(

->m_Index !=

->m_Index) {

(

* fix : *

) {

(

->m_Index !=

->m_Index) {

(

* fix : *

) {

(

->m_Index !=

->m_Index) {

(

* fix : *

) {

(

* fix : *

) {

(

* fix : *

) {

(

* fix : *

) {

(

& annot : bss->

()) {

(annot->IsFtable()) {

(

& feat : annot->GetData().GetFtable()) {

(

* fix : *

) {

(

& annot : bs->

()) {

(annot->IsFtable()) {

(

& feat : annot->GetData().GetFtable()) {

(

* fix : *

) {

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

CCopyHook_Bioseq_set(CDiscrepancyContext *context)

CDiscrepancyContext * m_Context

void CopyObject(CObjectStreamCopier &copier, const CObjectTypeInfo &passed_info) override

CDiscrepancyContext * m_Context

void CopyObject(CObjectStreamCopier &copier, const CObjectTypeInfo &passed_info) override

CCopyHook_Bioseq(CDiscrepancyContext *context)

void CopyObject(CObjectStreamCopier &copier, const CObjectTypeInfo &passed_info) override

CCopyHook_Seq_annot(CDiscrepancyContext *context)

CDiscrepancyContext * m_Context

CDiscrepancyContext * m_Context

void CopyObject(CObjectStreamCopier &copier, const CObjectTypeInfo &passed_info) override

CCopyHook_Seq_descr(CDiscrepancyContext *context)

void CopyObject(CObjectStreamCopier &copier, const CObjectTypeInfo &passed_info) override

CCopyHook_Submit_block(CDiscrepancyContext *context)

CDiscrepancyContext * m_Context

Copy hook for a standalone object.

friend class CReadHook_Bioseq_set

BIG FILE.

CRef< CBioseq > m_AF_Bioseq

friend class CReadHook_Bioseq_set_class

bool CanFixSubmit_block()

vector< CDiscrepancyObject * > * m_Fixes

CRef< CSeq_descr > m_AF_Seq_descr

void PopulateSeqSet(CParseNode &node)

CRef< objects::CScope > m_Scope

void Populate(CParseNode &node)

CParseNode * FindNode(const CRefNode &obj)

bool CanFixDesc(CRefNode &refnode)

CRef< CBioseq_set > m_AF_Bioseq_set

friend class CCopyHook_Seq_annot

CRef< CParseNode > m_RootNode

void AutofixFile(vector< CDiscrepancyObject * > &fixes, const string &default_header)

void ParseObject(const CBioseq &root)

CRef< feature::CFeatTree > m_FeatTree

friend class CCopyHook_Seq_descr

void ReplaceSeq_feat(CReportObj &obj, const CSeq_feat &old_feat, CSeq_feat &new_feat, bool alt=false)

CRef< CParseNode > m_CurrentNode

bool InGenProdSet() const

const CSerialObject * FindObject(CReportObj &obj, bool alt=false) override

objects::CScope & GetScope() const

map< string, size_t > Autofix() override

friend class CCopyHook_Bioseq_set

friend class CCopyHook_Bioseq

bool CanFixFeat(CRefNode &refnode)

void BuildSeqSummary(const CBioseq &bs, CSeqSummary &summary)

void PopulateSubmit(CParseNode &node)

void PopulateBioseq(CParseNode &node)

void Extend(CParseNode &node, CObjectIStream &stream)

friend class CReadHook_Bioseq

map< const CRefNode *, CParseNode * > m_NodeMap

friend class CCopyHook_Submit_block

CRef< CSeq_annot > m_AF_Seq_annot

static bool InNucProtSet(const CParseNode *node)

static bool CompareRefs(CRef< CReportObj > a, CRef< CReportObj > b)

void ReplaceObject(CReportObj &obj, CSerialObject *, bool alt=false)

void ParseAll(CParseNode &node)

CRef< CSubmit_block > m_AF_Submit_block

void ParseStrings(const string &fname) override

void ParseStream(CObjectIStream &stream, const string &fname, bool skip, const string &default_header=kEmptyStr) override

static bool IsSeqSet(EObjType n)

void AutofixSubmit_block()

virtual CRef< CAutofixReport > Autofix(CDiscrepancyObject *obj, CDiscrepancyContext &context) const =0

CRef< CDiscrepancyContext::CRefNode > m_Ref

CRef< CDiscrepancyContext::CRefNode > m_Fix

CRef< CDiscrepancyCore > m_Case

EFormat

The formats are checked in the same order as declared here.

@ eBZip2

bzip2 compressed file

@ eBinaryASN

Binary ASN.1.

@ eLzo

lzo compressed file

@ eGZip

GNU zip compressed file.

static EFormat Format(const string &path, EOnError onerror=eDefault)

Guess file format.

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

void ReadClassMember(CObjectIStream &stream, const CObjectInfoMI &passed_info) override

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

CDiscrepancyContext * m_Context

CReadHook_Bioseq_set_class(CDiscrepancyContext *context)

CReadHook_Bioseq_set(CDiscrepancyContext *context)

void ReadObject(CObjectIStream &stream, const CObjectInfo &passed_info) override

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

CDiscrepancyContext * m_Context

CReadHook_Bioseq(CDiscrepancyContext *context)

CDiscrepancyContext * m_Context

void ReadObject(CObjectIStream &stream, const CObjectInfo &passed_info) override

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

Read hook for a standalone object.

bool IsFtable(void) const

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

CSeq_feat_EditHandle –.

namespace ncbi::objects::

Base class for all serializable objects.

Simple implementation of ILineReader for i(o)streams.

vector< CRef< CReportObj > > TReportObjectList

unique_ptr< CObjectIStream > OpenUncompressedStream(const string &fname, bool &compressed)

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

main entry point for tests

@ eTakeOwnership

An object can take ownership of another.

EMethod

Compression/decompression methods.

@ eNone

no compression method (copy "as is")

@ eGZipFile

.gz file (including concatenated files)

@ fDefault

Use algorithm-specific defaults.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

bool AtEOF(void) const

Indicates (negatively) whether there is any more input.

void DefaultRead(CObjectIStream &in, const CObjectInfoMI &object)

void Read(const CObjectInfo &object)

Read object of know type.

void DefaultRead(CObjectIStream &in, const CObjectInfo &object)

Default read.

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

Set local (for the specified stream) read hook.

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

virtual bool EndOfData(void)

Check if there is still some meaningful data that can be read; in text streams this function will ski...

void ReadObject(const CObjectInfo &object)

Read child object.

TObjectPtr GetObjectPtr(void) const

Get pointer to object.

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.

virtual string ReadFileHeader(void)

Read file header.

CObjectInfo GetMember(void) const

Get class member data.

void SetStreamPos(CNcbiStreampos pos)

Set the current read position in underlying input stream This is the same as istream::seekg()

void WriteObject(const CConstObjectInfo &object)

CNcbiStreampos GetStreamPos(void) const

Get the current stream position.

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

void DefaultCopy(CObjectStreamCopier &copier, const CObjectTypeInfo &type)

void SetLocalCopyHook(CObjectStreamCopier &stream, CCopyObjectHook *hook) const

Set local (for the specified stream) copy hook.

void DefaultSkip(CObjectIStream &in, const CObjectTypeInfo &object)

Default skip.

CObjectOStream & Out(void) const

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

void Copy(const CObjectTypeInfo &type)

Copy data.

@ eDelayBufferPolicyAlwaysParse

Parse always.

void Replace(const CSeq_feat &new_feat) const

Replace the feature with new Seq-feat object.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

TObjectType * GetPointerOrNull(void) const THROWS_NONE

Get pointer value.

#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.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

IO_PREFIX::streampos CNcbiStreampos

Portable alias for streampos.

static const char label[]

const TAuthors & GetAuthors(void) const

Get the Authors member data.

bool CanGetAuthors(void) const

Check if it is safe to call GetAuthors method.

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSetClass(void) const

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

const TDescr & GetDescr(void) const

Get the Descr member data.

bool CanGetDescr(void) const

Check if it is safe to call GetDescr method.

TSet & SetSet(void)

Select the variant.

bool CanGetSeq_set(void) const

Check if it is safe to call GetSeq_set method.

TClass GetClass(void) const

Get the Class member data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSetAnnot(void) const

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

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

TSeq & SetSeq(void)

Select the variant.

@ eClass_pop_set

population study

@ eClass_phy_set

phylogenetic study

@ eClass_mut_set

set of mutations

@ eClass_eco_set

ecological sample study

@ eClass_nuc_prot

nuc acid and coded proteins

@ eClass_gen_prod_set

genomic products, chrom+mRNA+protein

@ eClass_segset

segmented sequence + parts

@ eClass_small_genome_set

viral segments or mitochondrial minicircles

void SetData(TData &value)

Assign a value to Data data member.

bool CanGet(void) const

Check if it is safe to call Get method.

bool IsSetAnnot(void) const

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

const TAnnot & GetAnnot(void) const

Get the Annot member data.

const Tdata & Get(void) const

Get the member data.

bool CanGetDescr(void) const

Check if it is safe to call GetDescr method.

const TFtable & GetFtable(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TDescr & GetDescr(void) const

Get the Descr member data.

const TCit & GetCit(void) const

Get the Cit member data.

const TEntrys & GetEntrys(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TSub & GetSub(void) const

Get the Sub member data.

bool IsSetSub(void) const

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

bool IsEntrys(void) const

Check if variant Entrys is selected.

bool IsSetCit(void) const

citation for this submission Check if a value has been assigned to Cit data member.

bool CanGetData(void) const

Check if it is safe to call GetData method.

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

Lightweight interface for getting lines of data with minimal memory copying.

constexpr auto sort(_Init &&init)

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

C++ I/O stream wrappers to compress/decompress data on-the-fly.

CConstRef< CSeqdesc > m_Molinfo

CParseNode & AddDescriptor(const CSeqdesc &seqdesc)

CConstRef< CSeqdesc > m_Title

vector< CRef< CParseNode > > m_Children

vector< CRef< CParseNode > > m_Features

vector< CRef< CParseNode > > m_Descriptors

CConstRef< CSerialObject > m_Obj

CParseNode & AddFeature(const CSeq_feat &feat)

CConstRef< CSeqdesc > m_Biosource

map< const CAuth_list *, CParseNode * > m_AuthorMap

shared_ptr< CSeqSummary > m_BioseqSummary

vector< const CAuth_list * > m_Authors

CRef< CRefNode > m_Parent

static CS_CONTEXT * context

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