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NCBI C++ ToolKit: src/algo/id_mapper/app/id_mapper_app.cpp Source File

73 using namespace ncbi

;

85 virtual void Init

(

void

);

104 void

x_RecurseMapSeqAligns(

CSeq_align

& Align,

int

Row,

118

arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),

119 "Annot Fetching Tool"

);

127

arg_desc->AddOptionalKey(

"annot"

"infile"

"input annot file"

129

arg_desc->AddOptionalKey(

"align"

"infile"

"input align file"

131

arg_desc->AddOptionalKey(

"entry"

"infile"

"input entry file"

133

arg_desc->AddOptionalKey(

"row"

"int"

"only update this row in the alignment"

147

arg_desc->AddOptionalKey(

"informat"

"string"

"accepted input formats. Temporarily doesnt work, asn text only."

CArgDescriptions::eString

);

149

SetupArgDescriptions(arg_desc.release());

228 string

GCAsm = args[

"gc"

].AsString();

231

Asm = GcService.

GetAssembly

(GCAsm,

"SequenceNames"

);

238

}

else if

(args[

"gcf"

HasValue

()) {

243

cerr <<

"Rquires either a -gc or a -gcf"

<< endl;

264 if

(args[

"typed"

].AsString() ==

"genbank"

)

266 if

(args[

"typed"

].AsString() ==

"refseq"

)

268 if

(args[

"typed"

].AsString() ==

"external"

)

270 if

(args[

"typed"

].AsString() ==

"private"

)

275 if

(args[

"alias"

].AsString() ==

"public"

)

277 if

(args[

"alias"

].AsString() ==

"gpipe"

)

279 if

(args[

"alias"

].AsString() ==

"gi"

)

281 if

(args[

"alias"

].AsString() ==

"notset"

)

286 if

(args[

"role"

].AsString() ==

"top"

) {

289 if

(args[

"role"

].AsString() ==

"gpipetop"

) {

293 if

(args[

"role"

].AsString() ==

"chro"

)

295 if

(args[

"role"

].AsString() ==

"scaf"

)

297 if

(args[

"role"

].AsString() ==

"comp"

)

300 if

(args[

"role"

].AsString() ==

"notset"

) {

305 if

(args[

"external"

HasValue

())

306

DestSpec.

External

= args[

"external"

].AsString();

309

DestSpec.

Pattern

= args[

"pattern"

].AsString();

320 return

x_HandleFeatures(*Mapper, DestSpec,

Out

);

321 else if

(args[

"align"

HasValue

())

322 return

x_HandleAlignments(*Mapper, DestSpec,

Out

);

323 else if

(args[

"entry"

HasValue

())

324 return

x_HandleEntries(*Mapper, DestSpec,

Out

);

336

list<CRef<CSeq_annot> > Annots;

350

Annots.push_back(Annot);

383

cerr <<

"Map Exception: "

<< e.

ReportAll

() << endl;

386 if

(

Loc

.IsNull()) {

419

Row = args[

"row"

].AsInteger();

427

off_t

Pos

= In.tellg();

435

Alignments->

Set

().insert(Alignments->

Set

().end(),

436

AlignSet->Set().begin(),

437

AlignSet->Set().end());

445

Alignments->

Set

().insert(Alignments->

Set

().end(),

446

Annot->SetData().SetAlign().begin(),

447

Annot->SetData().SetAlign().end());

455

Alignments->

Set

().push_back(Align);

466

Alignments->

Set

().insert(Alignments->

Set

().end(),

467

AlignSet->Set().begin(),

468

AlignSet->Set().end());

477

Alignments->

Set

().insert(Alignments->

Set

().end(),

478

Annot->SetData().SetAlign().begin(),

479

Annot->SetData().SetAlign().end());

487

Alignments->

Set

().push_back(Align);

492 if

(Alignments->

Get

().empty()) {

493

cerr <<

"File reader failure"

;

500 if

(Alignments->

Get

().empty())

505

Alignments->

Set

()) {

506

x_RecurseMapSeqAligns(**AlignIter, Row, Mapper, DestSpec);

529

Row = args[

"row"

].AsInteger();

541

x_RecurseMapSeqAligns(*AlignIter, Row, Mapper, DestSpec);

560

Align.

SetSegs

().SetDisc().Set()) {

561

x_RecurseMapSeqAligns(**AlignIter, Row, Mapper, DestSpec);

572 if

(Row == -1 || Row == Loop) {

582

Mapped = Mapper.

Map

(Whole, DestSpec);

588 if

(Whole.Equals(*Mapped)) {

595

}

else if

(Mapped->

IsInt

()) {

597

cerr << __LINE__ <<

" : "

"Can not perfectly map from " 598

<< Whole.GetInt().GetId().AsFastaString() <<

" to " 600

"The first is not entirely represented in the second."

<< endl;

605

MapAlign = Mapper.

Map

(Align, Row);

607

cerr <<__LINE__<<

" : "

"CSeq_loc_Mapper ctor or Map exception"

<< endl;

613

Align.

Assign

(*MapAlign);

618

cerr << __LINE__ <<

" FAIL_MAP "

<< endl;

668 int main

(

int

argc,

const char

* argv[])

static CRef< CScope > m_Scope

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

bool Guess(const objects::CSeq_loc &Loc, SIdSpec &Spec) const

CRef< objects::CSeq_loc > Map(const objects::CSeq_loc &Loc, const SIdSpec &Spec) const

CRef< CGC_Assembly > GetAssembly(const string &acc, const string &mode)

int x_HandleFeatures(CGencollIdMapper &Mapper, CGencollIdMapper::SIdSpec &DestSpec, CNcbiOstream &Out)

int x_HandleEntries(CGencollIdMapper &Mapper, CGencollIdMapper::SIdSpec &DestSpec, CNcbiOstream &Out)

void x_RecurseMapSeqAligns(CSeq_align &Align, int Row, CGencollIdMapper &Mapper, CGencollIdMapper::SIdSpec &DestSpec)

int x_HandleAlignments(CGencollIdMapper &Mapper, CGencollIdMapper::SIdSpec &DestSpec, CNcbiOstream &Out)

CRef< CSeq_loc > CreateRowSeq_loc(TDim row) const

TSeqPos GetLength(void) const

Template class for iteration on objects of class C.

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

The NCBI C++ standard methods for dealing with std::string.

User-defined methods of the data storage class.

#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.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

void DBAPI_RegisterDriver_FTDS(void)

CDiagContext & GetDiagContext(void)

Get diag context instance.

void SetSplitLogFile(bool value=true)

Split log files flag.

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.

static void SetOldPostFormat(bool value)

Set old/new format flag.

@ eDS_Default

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

@ eDiag_Info

Informational message.

void Warning(CExceptionArgs_Base &args)

string ReportAll(TDiagPostFlags flags=eDPF_Exception) const

Report all exceptions.

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

Set object to copy of another one.

#define MSerial_AsnBinary

#define MSerial_AsnText

I/O stream manipulators â.

const string AsFastaString(void) const

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

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

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

void Run(void)

Enter the main loop.

@ eGC_SequenceRole_top_level

@ eGC_SequenceRole_component

@ eGC_SequenceRole_scaffold

@ eGC_SequenceRole_chromosome

Tdata & Set(void)

Assign a value to data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

TExons & SetExons(void)

Assign a value to Exons data member.

vector< CRef< CSeq_id > > TIds

bool IsDisc(void) const

Check if variant Disc is selected.

bool IsSpliced(void) const

Check if variant Spliced is selected.

list< CRef< CSeq_align > > Tdata

TIds & SetIds(void)

Assign a value to Ids data member.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

void SetLocation(TLocation &value)

Assign a value to Location data member.

const TLocation & GetLocation(void) const

Get the Location member data.

bool IsEmpty(void) const

Check if variant Empty is selected.

const TId & GetId(void) const

Get the Id member data.

const TWhole & GetWhole(void) const

Get the variant data.

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

bool IsNull(void) const

Check if variant Null is selected.

void SetData(TData &value)

Assign a value to Data data member.

list< CRef< CSeq_feat > > TFtable

list< CRef< CSeq_annot > > TAnnot

map< string, CStopWatch > TTimerMap

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

Magic spell ;-) needed for some weird compilers... very empiric.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

#define GetArgs

Avoid preprocessor name clash with the NCBI C Toolkit.

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

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

void Out(T t, int w, CNcbiOstream &to=cout)

Reader-writer based streams.

CRef< objects::CObjectManager > om

string ToString(void) const

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Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/id__mapper__app_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/id_mapper/app/id_mapper_app.cpp Source File

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/idmapperapp_8cpp_source.html below: