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NCBI C++ ToolKit: src/objtools/format/flat_file_generator.cpp Source File

(

& annt : bsp.

()) {

(! annt->IsFtable()) {

(

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

(! feat->IsSetQual()) {

(

& qual : feat->GetQual()) {

}

(sep.

()) {

(

& seqentry : bssp.

()) {

(

& annt : bssp.

()) {

(! annt->IsFtable()) {

(

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

(! feat->IsSetQual()) {

(

& qual : feat->GetQual()) {

numInferences = 0;

<

_Pred>

useSeqEntryIndexing =

;

useSeqEntryIndexing =

;

(useSeqEntryIndexing) {

doProt =

;

doFastSets =

;

(showDebugTiming) {

( tseh.

() ) {

.BasicCleanup( *tmp_se, options );

( tmp_se->

() ) {

(showDebugTiming) {

(showDebugTiming) {

(topent && topent->

()) {

formatter->SetContext(*

);

(showDebugTiming) {

(

bioseq_it(entry); bioseq_it; ++bioseq_it) {

(showDebugTiming) {

(! bsh)

;

( ! accn_filt.empty()) {

(

& sid : bsp.

()) {

(sid->Which()) {

accn_string = sid->GetSeqIdString();

( accn_filt == accn_string ) {

fasta_str = sid->AsFastaString();

( accn_filt == fasta_str ) {

(showDebugTiming) {

<<

<< sidh <<

;

is_genomic =

;

is_RNA =

;

(closest_molinfo) {

flatfile_os = mo.

;

( bsh.

() && ! doNuc )

;

( bsh.

() && ! doProt )

;

}

( bsh.

() ) {

flatfile_os = mo.

;

}

((is_genomic || ! closest_molinfo) && mo.

) {

flatfile_os = mo.

;

}

(is_RNA && mo.

) {

flatfile_os = mo.

;

}

( bsh.

() ) {

flatfile_os = mo.

;

flatfile_os = mo.

;

}

(mo.

) {

flatfile_os = mo.

;

( bsh.

() && ! doNuc )

;

( bsh.

() && ! doProt )

;

newitem_os.

(&item_os);

(newitem_os.

())

;

*newitem_os, pCanceled) );

gatherer->Gather(*

, *pItemOS, ent, bsh, useSeqEntryIndexing, doNuc, doProt, doFastSets);

(showDebugTiming) {

formatter->SetContext(*

);

(ftree.

()) {

ftree.

(

feature::CFeatTree (iter));

+ pos +

+ aa +

+ seq +

;

(!

.IsSetType()) {

(!

.IsSetExt()) {

);

loc.

().SetFrom(from);

loc.

().SetStrand(strand);

( entry.

() ) {

);

);

( m_pCanceledCallback && m_pCanceledCallback->IsCanceled() ) {

);

m_pUnderlying->AddItem(item);

User-defined methods of the data storage class.

CBioseq_set_EditHandle –.

CConstRef< CSeqdesc > GetClosestDescriptor(CSeqdesc::E_Choice choice, int *level=NULL) const

@ eClean_FlatfileHTMLMode

@ eClean_FlatfileGenerator

In-memory stream (a la strstream or stringstream)

void SetStyleMaster(void)

const TFormat & GetFormat(void) const

bool IsPolicyInternal(void) const

const ICanceled * GetCanceledCallback(void) const

bool IsPolicyExhaustive(void) const

bool IsPolicyExternal(void) const

CFlatFileConfig & SetUseSeqEntryIndexer(bool val=true)

bool DisableDefaultIndex(void) const

bool OnlyNearFeatures(void) const

bool ShowCDDFeatures(void) const

bool IsPolicyFtp(void) const

bool UseSeqEntryIndexer(void) const

bool ShowSNPFeatures(void) const

bool IsPolicyWeb(void) const

int GetGapDepth(void) const

bool IsViewNuc(void) const

bool IsPolicyGenomes(void) const

bool ShowDebugTiming(void) const

int GetFeatDepth(void) const

bool IsViewAll(void) const

const string & GetSingleAccession(void) const

bool IsViewProt(void) const

bool HideSNPFeatures(void) const

bool HideCDDFeatures(void) const

bool BasicCleanup(void) const

bool FasterReleaseSets(void) const

bool IsStyleNormal(void) const

CFlatFileConfig & SetConfig(void)

void SetLocation(const CSeq_loc *loc)

SAnnotSelector & SetAnnotSelector(void)

const CRef< CSeqEntryIndex > GetSeqEntryIndex(void) const

void SetSubmit(const CSubmit_block &sub)

void SetSeqEntryIndex(CRef< CSeqEntryIndex > idx)

void ResetSeqEntryIndex(void)

bool UsingSeqEntryIndex(void) const

void SetSGS(const bool sgs)

const CFlatFileConfig & GetConfig(void) const

void SetEntry(const CSeq_entry_Handle &entry)

void SetFeatTree(feature::CFeatTree *tree)

Use this class to wrap CFlatItemOStream instances so that they check if canceled for every item added...

void AddItem(CConstRef< IFlatItem > item) override

void SetFormatter(IFormatter *formatter) override

If a subclass overrides this, it must call the parent class's version as its first action.

CRef< CFlatItemOStream > m_pUnderlying

void Generate(const CSeq_entry_Handle &entry, CFlatItemOStream &item_os, const multiout &={})

~CFlatFileGenerator(void)

SAnnotSelector & SetAnnotSelector(void)

void SetFeatTree(feature::CFeatTree *tree)

void ResetSeqEntryIndex(void)

static bool HasInference(const CSeq_entry_Handle &topseh)

CFlatFileGenerator(const CFlatFileConfig &cfg)

CBioseq_Handle x_DeduceTarget(const CSeq_entry_Handle &entry)

void SetSeqEntryIndex(CRef< CSeqEntryIndex > idx)

CRef< CFlatFileContext > m_Ctx

static string GetFTableAnticodonText(const CTrna_ext &trna_ext, CBioseqContext &ctx)

void SetConfig(const CFlatFileConfig &cfg)

static string GetSeqFeatText(const CMappedFeat &feat, CScope &scope, const CFlatFileConfig &cfg, CRef< feature::CFeatTree > ftree=null)

void x_GetLocation(const CSeq_entry_Handle &entry, TSeqPos from, TSeqPos to, ENa_strand strand, CSeq_loc &loc)

static CFlatGatherer * New(CFlatFileConfig::TFormat format)

static CFlatItemFormatter * New(CFlatFileConfig::TFormat format)

virtual void SetFormatter(IFormatter *formatter)

If a subclass overrides this, it must call the parent class's version as its first action.

const string & GetString(void) const

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

CRef< CSeqMasterIndex > GetMasterIndex(void) const

void SetFeatDepth(int featDepth)

bool IsIndexFailure(void)

void SetGapDepth(int gapDepth)

CSeq_entry_Handle GetTopSEH(void) const

namespace ncbi::objects::

Interface for testing cancellation request in a long lasting operation.

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

static void x_InferenceInSeqs(const CSeq_entry &sep, int *numInferences)

const int kInferenceCutoff

void VisitAllSeqSets(const objects::CSeq_entry &entry, _Pred m)

static void cleanup(void)

static const char location[]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void ToString(string *)

The CConnMemoryStream::To* methods allow to obtain unread portion of the stream into a single contain...

#define NCBI_THROW(exception_class, err_code, message)

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

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

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

CBioseq_Handle GetBioseqFromSeqLoc(const CSeq_loc &loc, CScope &scope, CScope::EGetBioseqFlag flag=CScope::eGetBioseq_Loaded)

Retrieve the Bioseq Handle from a location.

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...

CSeq_entry_Handle GetSeq_entryHandle(CDataLoader *loader, const TBlobId &blob_id, EMissing action=eMissing_Default)

Get Seq-entry handle by its blob-id, with possible loading.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

TClass GetClass(void) const

TSet SelectSet(TClass set_class=CBioseq_set::eClass_not_set) const

Convert the empty Seq-entry to Bioseq-set.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

CConstRef< TObject > GetCompleteObject(void) const

E_Choice Which(void) const

CSeq_id_Handle GetAccessSeq_id_Handle(void) const

Get any CSeq_id_Handle handle that can be used to access this bioseq Use GetSeq_id_Handle() if it's n...

const CSeqFeatData & GetData(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

TInst_Mol GetInst_Mol(void) const

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

void Remove(ERemoveMode mode=eRemoveSeq_entry) const

void Remove(ERemoveMode mode=eRemoveSeq_entry) const

Remove current seqset-entry from its location.

CConstRef< TObject > GetCompleteObject(void) const

TSeq SelectSeq(CBioseq &seq) const

Make the empty Seq-entry be in seq state with specified Bioseq object.

CSeq_entry_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

TInst_Length GetInst_Length(void) const

bool IsSetClass(void) const

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

TMol GetSequenceType(void) const

CConstRef< TObject > GetCompleteObject(void) const

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

const CSeq_loc & GetLocation(void) const

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

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

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

uint32_t Uint4

4-byte (32-bit) unsigned integer

#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::ostream CNcbiOstream

Portable alias for ostream.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static string & ToLower(string &str)

Convert string to lower case – string& version.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Start(void)

Start the timer.

void Reset(void)

Stop (if running) and reset the timer.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TAnticodon & GetAnticodon(void) const

Get the Anticodon member data.

TNcbi8aa GetNcbi8aa(void) const

Get the variant data.

const TAa & GetAa(void) const

Get the Aa member data.

TNcbistdaa GetNcbistdaa(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetAnticodon(void) const

location of anticodon Check if a value has been assigned to Anticodon data member.

EType

type of RNA feature

TNcbieaa GetNcbieaa(void) const

Get the variant data.

TIupacaa GetIupacaa(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

const TTRNA & GetTRNA(void) const

Get the variant data.

const TLocation & GetLocation(void) const

Get the Location member data.

E_Choice

Choice variants.

const TData & GetData(void) const

Get the Data member data.

bool IsBiosrc(void) const

Check if variant Biosrc is selected.

ENa_strand

strand of nucleic acid

const TSeq & GetSeq(void) const

Get the variant 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 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.

list< CRef< CSeq_entry > > TSeq_set

TSeq & SetSeq(void)

Select the variant.

@ eClass_nuc_prot

nuc acid and coded proteins

@ eClass_gen_prod_set

genomic products, chrom+mRNA+protein

@ eClass_genbank

converted genbank

@ eClass_segset

segmented sequence + parts

@ eClass_small_genome_set

viral segments or mitochondrial minicircles

@ e_not_set

No variant selected.

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 TId & GetId(void) const

Get the Id member data.

TBiomol GetBiomol(void) const

Get the Biomol member data.

EMol

molecule class in living organism

const TMolinfo & GetMolinfo(void) const

Get the variant data.

@ e_Molinfo

info on the molecule and techniques

@ eMol_na

just a nucleic acid

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 IsEntrys(void) const

Check if variant Entrys is selected.

bool CanGetSub(void) const

Check if it is safe to call GetSub method.

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

static void text(MDB_val *v)

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

Defines: CTimeFormat - storage class for time format.

const char * GetAAName(unsigned char aa, bool is_ascii)

#define NCBI_BIOMOL(Type)

CMolInfo definitions.

#define NCBI_SEQID(Type)

@NAME Convenience macros for NCBI objects

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