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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seqannot__splicer_8cpp_source.html below:

NCBI C++ ToolKit: src/sample/app/serial/seqannot_splicer.cpp Source File

291 for

( ; isc; ++isc ) {

398 "Unexpected exception while preprocessing Seq-annot file."

);

402

sai->ResetLocalHooks();

425

sei->ReadFileHeader();

431

sei->ResetLocalHooks();

434

sei->SetStreamPos(0);

446 virtual void Init

(

void

);

447 virtual int Run

(

void

);

457

arg_desc->SetUsageContext

459 "Seq-annot splicer"

);

463

arg_desc->AddDefaultKey

464

(

"sa"

"SeqAnnotFile"

465 "name of file containing Seq-annot's"

467

arg_desc->AddDefaultKey(

"safmt"

"SeqAnnotFormat"

"format of Seq-annot file"

469

arg_desc->SetConstraint

472

arg_desc->AddDefaultKey

473

(

"sei"

"SeqEntryInputDir"

474 "the directory containing the input Seq-Entry files"

476

arg_desc->AddDefaultKey(

"seifmt"

"SeqEntryInputFormat"

"format of input Seq-entry files"

478

arg_desc->SetConstraint

481

arg_desc->AddDefaultKey

482

(

"seo"

"SeqEntryOutputDir"

483 "the directory containing the output Seq-Entry files"

485

arg_desc->AddDefaultKey(

"seofmt"

"SeqEntryOutputFormat"

"format of output Seq-entry files"

487

arg_desc->SetConstraint

490

arg_desc->AddOptionalKey

491

(

"sasm"

"SeqAnnotChoiceMask"

492 "Seq-annot choice mask"

495

arg_desc->AddOptionalKey

496

(

"sism"

"SeqIdChoiceMask"

497 "Seq-id choice mask"

518

cout <<

"I'm sorry, the Seq_table CHOICE mask for Seq-annot's " 519 "is not currently supported \n" 520 "due to an apparent bug in parsing seq-table CHOICE values.\n" 521 "Please try an alternate CHOICE."

<< endl;

532

(

GetFormat

(args[

"safmt"

].AsString()),

533

args[

"sa"

].AsInputFile()));

538

cout <<

"I'm sorry, ASN.1 text is not currently " 539 "supported for the concatenated \n" 540 "Seq-Annot file due to an apparent bug in " 541 "CObjectIStream::{G|S}etStreamPos().\n" 542 "Please try an alternate format."

<< endl;

552 string

seidir = args[

"sei"

].AsString();

553 string

seodir = args[

"seo"

].AsString();

561 for

(

const auto

file

: dir_entries) {

563 string

name = (*file).GetName();

564 if

(name !=

"."

&& name !=

".."

) {

565 string

seiname = (*file).GetPath();

577

cout <<

"Processing Seq-entry: "

<< name << endl;

618 int main

(

int

argc,

const char

* argv[])

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

Copy hook for a standalone object.

virtual void SkipObject(CObjectIStream &in, const CObjectTypeInfo &passed_info)

unique_ptr< CObjectIStream > & m_sai

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

CHookSeq_entry__Copy__Seq_annot(unique_ptr< CObjectIStream > &sai)

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

virtual void SkipObject(CObjectIStream &in, const CObjectTypeInfo &passed_info)

CHookSeq_entry__Skip(const EContextType context)

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

Writing containers (SET OF, SEQUENCE OF).

virtual void Init(void)

Initialize the application.

virtual int Run(void)

Run the application.

void SeqEntry_Start(void)

void SeqAnnot_Scan_Post(void)

void SeqAnnot_Scan_Pre(void)

Skip hook for a standalone object.

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.

const CNcbiArguments & GetArguments(void) const

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

@ fPreOpen

Open file right away; for eInputFile, eOutputFile, eIOFile.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

#define NCBI_THROW(exception_class, err_code, message)

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

static char GetPathSeparator(void)

Get path separator symbol specific for the current platform.

bool Create(TCreateFlags flags=fCreate_Default) const

Create the directory using "dirname" passed in the constructor.

virtual bool Remove(TRemoveFlags flags=eRecursive) const

Delete existing directory.

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

void SetLocalSkipHook(CObjectIStream &stream, CSkipObjectHook *hook) const

Set local (for the specified stream) skip hook.

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.

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.

CObjectOStream & Out(void) const

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

Default skip.

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

void Copy(const CObjectTypeInfo &type)

Copy data.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines NCBI C++ exception handling.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

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

static void s_PreprocessSeqAnnots(unique_ptr< CObjectIStream > &sai)

static void s_PreprocessSeqEntry(unique_ptr< CObjectIStream > &sei)

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

CSeqAnnotSplicerStats * g_Stats

void SetSeqIdChoiceMask(const string &mask)

void SetSeqAnnotChoiceMask(const string &mask)

void CurrentContextContainsSeqAnnots(void)

ESerialDataFormat GetFormat(const string &name)

void SeqAnnotMapSeqId(TSeqRef seqid_in_annot)

void ResetSeqEntryProcessing(void)

void SeqAnnotSet_Pre(CObjectIStream &in)

void AddSeqIdToCurrentContext(TSeqRef id)

bool IsSeqAnnotChoiceSelected(TSeqAnnotChoiceMaskFlags flags)

void ContextStart(CObjectIStream &in, EContextType type)

void ProcessSeqEntryAnnot(unique_ptr< CObjectIStream > &sai, COStreamContainer &osc)

static CS_CONTEXT * context

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