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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/annotwriter_8cpp_source.html below:

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

79 #if defined(CANCELER_CODE) 84 static const unsigned int

CALLS_UNTIL_CANCELLED = 25;

86 if

(0 == ++mNumCalls % 100) {

87

cerr <<

"Iterations until cancelled: " 88

<< (CALLS_UNTIL_CANCELLED - mNumCalls) <<

"\n"

;

90 return

(mNumCalls > CALLS_UNTIL_CANCELLED);

92 static unsigned int

mNumCalls;

94 unsigned int

TestCanceler::mNumCalls = 0;

107 const auto

* pWriterMessage =

dynamic_cast<const CWriterMessage

>

(&message);

108 if

(!pWriterMessage) {

111 if

(pWriterMessage->GetSeverity() ==

eDiag_Fatal

) {

112 throw

(*pWriterMessage);

121

ostr << message.

GetText

() << endl;

134 void Init

()

override

;

135 int Run

()

override

;

151 const string

id

bool

skipHeaders);

190 const CArgs

& args)

const

;

193 const CArgs

& args)

const

;

222

arg_desc->SetUsageContext(

""

"Convert ASN.1 to alternative file formats"

);

226

arg_desc->AddOptionalKey(

"i"

"InputFile"

228

arg_desc->AddOptionalKey(

"id"

"InputID"

230

arg_desc->AddOptionalKey(

"ids"

"InputIDs"

231 "Comma separated list of Input IDs (accession or GI number)"

237

arg_desc->AddDefaultKey(

243

arg_desc->SetConstraint(

259

arg_desc->AddDefaultKey(

262 "Assembly name to include in GFF3 pragma"

265

arg_desc->AddDefaultKey(

268 "Assembly accession to include in GFF3 pragma"

271

arg_desc->AddDefaultKey(

274 "Default term to use in GFF3 column 2"

282

arg_desc->AddOptionalKey(

"o"

"OutputFile"

284

arg_desc->AddOptionalKey(

"from"

"From"

286

arg_desc->AddOptionalKey(

"to"

"To"

292

arg_desc->AddDefaultKey(

298

arg_desc->SetConstraint(

309 "throw-exception-on-unresolved-gi"

310 "throw if a gi cannot be converted to accession.version"

314 "produce formally invalid output that is easy to read"

318 "limit attributes to inter feature relationships"

321 "skip-gene-features"

322 "GTF only: Do not emit gene features (for GTF 2.2 compliancy)"

325 "skip-exon-numbers"

326 "GTF only: For exon features, do not emit exon numbers"

330 "GFF dialects: Do not generate GFF headers"

334 "GFF dialects: Inherit annots from components, unless prohibited"

338 "GFF dialects: Restore original GFF type and attributes, if possible"

341 "generate-missing-transcripts"

342 "GFF dialects: Generate artificial transcript features for CDS features without one"

346 "GFF3 only: Use Flybase interpretation of the GFF3 spec"

350 "GFF3 alignments only: Do not sort alignments when fetching from ID"

354 "GFF3 only: Incorporate micro introns"

358 "input file is binary ASN.1"

362

arg_desc->AddFlag(

"nocleanup"

363 "Do not perform data cleanup prior to formatting GTF and GFF3"

);

376 auto format

= args[

"format"

].AsString();

393 if

(args[

"throw-exception-on-unresolved-gi"

].AsBoolean()) {

396 #if defined(CANCELER_CODE) 400 if

(args[

"from"

]) {

441 return

&args[

"o"

].AsOutputFile();

445 "annotwriter: Unable to open output stream ["

466 const string

id

bool

skipHeaders)

470

pScope->AddDefaults();

494 if

(!args[

"ids"

]) {

497

vector<string> inputIds;

498 NStr::Split

(args[

"ids"

].AsString(),

","

, inputIds);

499 const bool

skipHeaders = args[

"skip-headers"

];

500 for

(

const auto

& inputId: inputIds) {

521 while

(!instr.EndOfData()) {

522 if

(genbankType ==

"Seq-entry"

) {

528 if

(genbankType ==

"Seq-annot"

) {

534 if

(genbankType ==

"Bioseq"

) {

540 if

(genbankType ==

"Bioseq-set"

) {

546 if

(genbankType ==

"Seq-align"

) {

552 if

(genbankType ==

"Seq-align-set"

) {

558 if

(genbankType ==

"Seq-submit"

) {

580 "annotwriter: Unable to extract object from input stream ["

593 if

(

data

.IsEntrys()) {

594 if

GetArgs

()[

"skip-headers"

]) {

597 for

(

auto

pEntry :

data

.SetEntrys()) {

603 if

(

data

.IsAnnots()) {

604 if

GetArgs

()[

"skip-headers"

]) {

607 for

(

auto

pAnnot :

data

.SetAnnots()) {

610 cleanup

.BasicCleanup(*pAnnot);

660 if

GetArgs

()[

"skip-headers"

]) {

682 CBioseq

& bioseq,

bool

skipHeaders)

732 if

GetArgs

()[

"skip-headers"

]) {

747 if

GetArgs

()[

"skip-headers"

]) {

771 bool

bDeleteOnClose =

false

;

773 const char

infile

= args[

"i"

].AsString().c_str();

775

bDeleteOnClose =

true

;

788 "annotwriter: Unsupported input format"

eDiag_Fatal

);

801 "annotwriter: Unable to open input file"

eDiag_Fatal

);

813 if

(args[

"structibutes"

]) {

816 if

(args[

"skip-gene-features"

]) {

819 if

( args[

"skip-exon-numbers"

] ) {

822 if

( args[

"use-extra-quals"

] ) {

825 if

(args[

"micro-introns"

]) {

828 auto

viewType = args[

"view"

].AsString();

829 if

(viewType ==

"all"

) {

832 if

(viewType ==

"prots-only"

) {

836 if

(args[

"generate-missing-transcripts"

]) {

844 const CArgs

& args)

const 847 if

(args[

"from"

]) {

848 return static_cast<TSeqPos>

(args[

"from"

].AsInteger()-1);

857 const CArgs

& args)

const 861 return static_cast<TSeqPos>

(args[

"to"

].AsInteger()-1);

876 "annotwriter: Format writer object needs valid scope and output stream"

880 const string

strFormat = args[

"format"

].AsString();

881 if

(strFormat ==

"gff3"

) {

882 const bool

sortAlignments = args[

"no-sort"

] ?

false

true

;

883 if

(args[

"flybase"

]) {

890 if

(args[

"default-method"

]) {

895 if

(strFormat ==

"gtf"

) {

901 if

(strFormat ==

"gvf"

) {

906 if

(strFormat ==

"wiggle"

|| strFormat ==

"wig"

) {

909 if

(strFormat ==

"bed"

) {

912 if

(strFormat ==

"bedgraph"

) {

915 if

(strFormat ==

"vcf"

) {

918 if

(strFormat ==

"aln"

) {

921 if

(strFormat ==

"psl"

) {

922 unsigned int flags

= 0;

923 if

(args[

"debug-output"

].AsBoolean()) {

931 "annotwriter: No suitable writer for format \""

+ strFormat +

"\""

939 return GetArgs

()[

"assembly-name"

].AsString();

946 return GetArgs

()[

"assembly-accn"

].AsString();

955 if

(args[

"full-annots"

]) {

970 int main

(

int

argc,

const char

** argv)

User-defined methods of the data storage class.

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

static const CDataLoadersUtil::TLoaders default_loaders

string xAssemblyName() const

bool xTryProcessInputId(const CArgs &)

bool xProcessInputObject(CSeq_entry &)

CRef< CWriterBase > m_pWriter

void Init() override

Initialize the application.

TSeqPos xGetTo(const CArgs &args) const

string xAssemblyAccession() const

CWriterBase * xInitWriter(const CArgs &, CNcbiOstream *)

CNcbiOstream * xInitOutputStream(const CArgs &)

int Run() override

Run the application.

bool xProcessBioseqHandle(CBioseq_Handle &bsh, bool skipHeaders)

bool xTryProcessInputIdList(const CArgs &)

bool xTryProcessInputFile(const CArgs &)

CRef< CObjectManager > m_pObjMngr

unsigned int xGffFlags(const CArgs &)

CObjectIStream * xInitInputStream(const CArgs &args, CFileContentInfo &contentInfo)

unique_ptr< CAnnotWriterLogger > m_pErrorHandler

void xTweakAnnotSelector(const CArgs &, SAnnotSelector &)

TSeqPos xGetFrom(const CArgs &args) const

static void xReadObject(CObjectIStream &istr, CSerialObject &object)

bool PutMessage(const IObjtoolsMessage &message)

static void DumpMessage(const CWriterMessage &message, ostream &ostr)

CAnnotWriterLogger()=default

CWriterBase implementation that will render given Genbank objects in the BED file format (http://http...

static void SetupObjectManager(const CArgs &args, objects::CObjectManager &obj_mgr, TLoaders loaders=fDefault)

Set up the standard object manager data loaders according to the arguments provided above.

static void AddArgumentDescriptions(CArgDescriptions &arg_desc, TLoaders loaders=fDefault)

Add a standard set of arguments used to configure the object manager.

static void CreateMicroIntrons(objects::CScope &scope, objects::CBioseq_Handle bsh, const string &annot_name="", TSeqRange *range=NULL, bool ignore_errors=false)

Wraps CFormatGuess, and if CFormatGuess's result is Unknown, it tries every file reader until one wor...

CFormatGuess::EFormat GuessFormatAndContent(CFileContentInfo &contentInfo)

CFormatGuess::CFormatHints & GetFormatHints(void)

Get format hints.

CFormatHints & AddPreferredFormat(TFormat fmt)

Mark the format as preferred.

CFormatHints & DisableAllNonpreferred(void)

Disable all formats not marked as preferred.

EFormat

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

@ eBinaryASN

Binary ASN.1.

void SetThrowOnUnresolvedGi(bool doThrow)

@ fGenerateMissingTranscripts

void SetDefaultMethod(const string &defaultMethod)

void SetCanceler(ICanceled *pCanceller)

Base class for all serializable objects.

Defines and provides stubs for a general interface to a variety of file formatters.

virtual bool WriteAnnot(const CSeq_annot &, const string &="", const string &="")

Write a raw Seq-annot to the internal output stream.

virtual bool WriteFooter()

Write a file trailer.

void SetMessageListener(CWriterListener *pMessageListener)

virtual bool WriteAlign(const CSeq_align &, const string &="", const string &="")

Write a raw Seq-align to the internal output stream.

virtual bool WriteBioseqHandle(CBioseq_Handle, const string &="", const string &="")

Write a Bioseq handle to the internal output stream.

virtual bool WriteHeader()

Write a file header.

virtual SAnnotSelector & SetAnnotSelector(void)

CGenbankIdResolve & SetIdResolve(void)

virtual bool WriteSeqEntryHandle(CSeq_entry_Handle, const string &="", const string &="")

Write a Seq-entry handle to the internal output stream.

virtual CRange< TSeqPos > & SetRange(void)

Interface for testing cancellation request in a long lasting operation.

static void cleanup(void)

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

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.

void SetVersion(const CVersionInfo &version)

Set the version number for the program.

@ eTakeOwnership

An object can take ownership of another.

@ eNoOwnership

No ownership is assumed.

@ 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)

static const char * SeverityName(EDiagSev sev)

Get a common symbolic name for the severity levels.

@ eDiag_Fatal

Fatal error â guarantees exit(or abort)

const string & GetMsg(void) const

Get message string.

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

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

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

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

void RemoveBioseq(const CBioseq_Handle &seq)

Revoke Bioseq previously added using AddBioseq().

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

void RemoveEntry(CSeq_entry &entry)

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

SAnnotSelector & SetExactDepth(bool value=true)

SetExactDepth() specifies that annotations will be searched on the segment level specified by SetReso...

SAnnotSelector & SetResolveAll(void)

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

SAnnotSelector & SetAdaptiveDepth(bool value=true)

SetAdaptiveDepth() requests to restrict subsegment resolution depending on annotations found on lower...

SAnnotSelector & SetResolveDepth(int depth)

SetResolveDepth sets the limit of subsegment resolution in searching annotations.

CRef< C > Ref(C *object)

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

void Reset(void)

Reset reference object.

static position_type GetWholeFrom(void)

static position_type GetWholeTo(void)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

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.

void CONNECT_Init(const IRWRegistry *reg=0, CRWLock *lock=0, TConnectInitFlags flag=eConnectInit_OwnNothing, FSSLSetup ssl=0)

Init [X]CONNECT library with the specified "reg" and "lock" (ownership for either or both can be deta...

void SetFrom(TFrom value)

Assign a value to From data member.

void SetTo(TTo value)

Assign a value to To data member.

list< CRef< CSeq_align > > Tdata

const Tdata & Get(void) const

Get the member data.

TSet & SetSet(void)

Select the variant.

void SetData(TData &value)

Assign a value to Data data member.

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

#define NCBI_SC_VERSION_PROXY

#define NCBI_TEAMCITY_BUILD_NUMBER_PROXY

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

CFileContentInfoGenbank mInfoGenbank

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