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

& output_extension,

binary)

;

process_set_of_any_type =

)

;

arg_desc->SetUsageContext(

,

arg_desc->AddKey(

,

,

,

arg_desc->AddDefaultKey(

,

,

description =

;

description.append(

);

arg_desc->AddKey(

,

,

arg_desc->AddDefaultKey(

,

,

arg_desc->AddDefaultKey(

,

,

arg_desc->AddDefaultKey(

,

,

description =

;

description.append(

);

description.append(

);

description.append(

);

description.append(

);

arg_desc->AddDefaultKey(

,

arg_desc->SetConstraint(

,

,

,

,

));

arg_desc->AddFlag(

,

);

(args[

].AsBoolean() && args[

].AsBoolean()) {

err_msg =

;

err_msg =

;

input_as_seq_entry = args[

].AsBoolean();

list<CRef<CSerialObject>> output_array;

err_msg =

;

output_stub = args[

].AsString();

output_extension =

;

output_index = 0;

unique_ptr<CObjectOStream> ostr;

binary = args[

].AsBoolean();

(

& it: output_array) {

err_msg =

;

err_msg += e.

();

extension =

;

(

.size() > 1) {

extension =

.back();

& output_stub,

& output_extension,

binary)

(output_stub.empty()) {

);

(padded_index.size() < pad_width) {

padded_index =

.substr(0, pad_width - padded_index.size()) + padded_index;

filename = output_stub +

+ padded_index +

+ output_extension;

+ filename);

(

()[

].AsBoolean()) {

unique_ptr<CObjectIStream> istr;

<

Derived>

Derived*

(

)->

(b1, b2);

);

);

);

TSeqEntryArray::iterator seq_entry_it = seq_entry_array.begin();

(seq_entry_it != seq_entry_array.end()) {

(seq_entry_it == seq_entry_array.end()) {

wrapped_entry_array.push_back(seq_entry);

bundle_size = args[

].AsInteger();

wrap_entries = args[

].AsBoolean();

stable_sort(seq_entry_array.begin(), seq_entry_array.end(),

());

(

=0;

<wrapped_entry_array.size(); ++

) {

output_array.push_back(seqsub);

TSeqEntryArray::iterator seq_entry_it = seq_entry_array.begin();

(seq_entry_it != seq_entry_array.end()) {

(seq_entry_it == seq_entry_array.end()) {

output_array.push_back(seqsub);

sub.

().SetEntrys();

(input_sub ==

|| !input_sub->

()) {

(

);

(input_entry ==

|| !input_entry->

()) {

(

);

(upper_level_descr.

()) {

input_entry->

().Assign(*upper_level_descr);

upper_level_descr.

();

);

(args[

].AsBoolean()) {

infile_str = args[

].AsString();

(pInputStream->fail())

+ infile_str +

);

+ infile_str +

);

find(begin(MULTIPLE_ALLOWED), end(MULTIPLE_ALLOWED), choice) != end(MULTIPLE_ALLOWED);

(

& dst_descr: dst.

()) {

(dst_descr->Which() == choice) {

(dst_descr->Equals(descr)) {

(!src.

()) {

(

& descr: src.

())

dst.

().push_back(descr);

(find_if(dst.

().begin(), dst.

().end(), [choice](

& cur_descr) { return cur_descr->Which() == choice; } ) == dst.

().end()) {

dst.

().push_back(descr);

(entry.

()) {

set_of_allowed_type = set_of_any_type_allowed;

(!set_of_any_type_allowed) {

set_of_allowed_type;

process_set_of_any_type)

?

:

;

err_msg =

+ class_string +

;

new_descr.

().push_back(*it);

(seq_descr.

()) {

seq_entry_array.push_back(new_entry);

(

argc,

** argv)

User-defined methods of the data storage class.

const CBioseq & GetNucFromNucProtSet(void) const

const CSeq_id * GetLocalId() const

Find a local ID if present.

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

const CSeq_descr & GetDescr(void) const

void SetDescr(CSeq_descr &value)

bool IsSetDescr(void) const

bool IsEntrys(void) const

Base class for all serializable objects.

virtual CRef< CSerialObject > BuildObject() const =0

virtual TSeqEntryList & GetListOfEntries(CSerialObject &obj) const =0

virtual CRef< CSerialObject > BuildObject() const

virtual TSeqEntryList & GetListOfEntries(CSerialObject &obj) const

CSeqEntryHelper(CSeq_entry &seq_entry)

void xFlattenSeqEntrys(CSeq_submit::TData::TEntrys &entries, TSeqEntryArray &seq_entry_array) const

bool xTryReadInputFile(CRef< CSerialObject > &obj) const

string xGetFileExtension(const string &filename) const

bool xTryProcessSeqSubmit(CRef< CSerialObject > &obj, list< CRef< CSerialObject >> &output_array) const

void xFlattenSeqEntry(CSeq_entry &seq_entry, const CSeq_descr &seq_descr, TSeqEntryArray &seq_entry_array, bool process_set_of_any_type=false) const

bool xTryProcessSeqEntries(const CObjectHelper &builder, TSeqEntryArray &seq_entry_array, list< CRef< CSerialObject >> &output_array) const

CObjectOStream * xInitOutputStream(const string &output_stub, const TSeqPos output_index, const TSeqPos pad_width, const string &output_extension, const bool binary) const

void xMergeSeqDescr(const CSeq_descr &src, CSeq_descr &dst) const

CRef< CSerialObject > xGetInputObject() const

void Init()

Initialize the application.

void xWrapSeqEntries(TSeqEntryArray &seq_entry_array, const TSeqPos &bundle_size, TSeqEntryArray &wrapped_entry_array) const

int Run()

Run the application.

CObjectIStream * xInitInputStream() const

bool xTryProcessSeqEntry(CRef< CSerialObject > &obj, list< CRef< CSerialObject >> &output_array) const

CSeq_submit & m_seq_submit

virtual CRef< CSerialObject > BuildObject() const

virtual TSeqEntryList & GetListOfEntries(CSerialObject &obj) const

CSeqSubmitHelper(CSeq_submit &seq_submit)

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

static vector< string > arr

unsigned int TSeqPos

Type for sequence locations and lengths.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

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.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

void SetVersion(const CVersionInfo &version)

Set the version number for the program.

@ eTakeOwnership

An object can take ownership of another.

@ eInputFile

Name of file (must exist and be readable)

@ eBoolean

{'true', 't', 'false', 'f'}, case-insensitive

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

#define ERR_POST(message)

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

@ eDS_ToStderr

To standard error stream.

#define NCBI_THROW(exception_class, err_code, message)

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

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

virtual const CTypeInfo * GetThisTypeInfo(void) const =0

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

int CompareOrdered(const CSeq_id &sid2) const

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

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

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

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

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

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

Convert int to string.

bool IsGeneral(void) const

Check if variant General is selected.

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.

TSet & SetSet(void)

Select the variant.

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 IsSetDescr(void) const

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

bool IsSet(void) const

Check if variant Set is selected.

void SetClass(TClass value)

Assign a value to Class data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

list< CRef< CSeq_entry > > TSeq_set

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

@ eClass_genbank

converted genbank

@ eClass_pub_set

all the seqs from a single publication

list< CRef< CSeqdesc > > Tdata

const TInst & GetInst(void) const

Get the Inst member data.

const TId & GetId(void) const

Get the Id member data.

const Tdata & Get(void) const

Get the member data.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

TLength GetLength(void) const

Get the Length member data.

list< CRef< CSeq_id > > TId

bool IsSetLength(void) const

length of sequence in residues Check if a value has been assigned to Length data member.

E_Choice

Choice variants.

bool IsSet(void) const

Check if a value has been assigned to data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetId(void) const

equivalent identifiers Check if a value has been assigned to Id data member.

Tdata & Set(void)

Assign a value to data member.

@ e_Het

cofactor, etc associated but not bound

@ e_Num

a numbering system

@ e_User

user defined object

@ e_Pub

a reference to the publication

@ e_Dbxref

xref to other databases

@ e_Comment

a more extensive comment

@ e_Modelev

model evidence for XM records

@ e_Region

overall region (globin locus)

@ e_Maploc

map location of this sequence

@ e_Name

a name for this sequence

list< CRef< CSeq_entry > > TEntrys

void SetSub(TSub &value)

Assign a value to Sub data member.

void SetData(TData &value)

Assign a value to Data data member.

static bool MultipleAllowed(CSeqdesc::E_Choice choice)

static bool NeedToInclude(const CSeqdesc &descr, const CSeq_descr &dst)

vector< CRef< CSeq_entry > > TSeqEntryArray

static bool NeedToProcess(const CSeq_entry &entry, bool set_of_any_type_allowed)

list< CRef< CSeq_entry > > TSeqEntryList

#define NCBI_SC_VERSION_PROXY

#define NCBI_TEAMCITY_BUILD_NUMBER_PROXY

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines NCBI C++ diagnostic APIs, classes, and macros.

Defines NCBI C++ exception handling.

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

int main(int argc, const char **argv)

bool operator()(const CRef< CSeq_entry > &e1, const CRef< CSeq_entry > &e2) const

bool compare_seq(const CBioseq &b1, const CBioseq &b2) const

bool compare_seq(const CBioseq &b1, const CBioseq &b2) const

CConstRef< CSeq_id > xGetGeneralId(const CBioseq &bioseq) const

CConstRef< CSeq_id > xGetId(const CBioseq &bioseq) const

bool compare_seq(const CBioseq &b1, const CBioseq &b2) const

bool compare_seq(const CBioseq &b1, const CBioseq &b2) const

static wxAcceleratorEntry entries[3]

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