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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/fasta__writer_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/writers/fasta_writer.cpp Source File

m_TranslateCds(

),

& current_id = loc_it.GetSeq_id();

(pFirstId.

()) {

pFirstId.

(&current_id);

(!pFirstId->

(current_id)) {

translate_cds)

(

<<

);

err_msg =

;

err_msg =

;

strand = loc.GetStrand();

translate_cds)

translate_cds)

(id_string.empty()) {

<<

<< id_string;

(frame !=2 && frame != 3) {

err_msg =

+ to_string(frame);

seq_id->Assign(*loc.

());

stop_trim = start_trim;

err_msg =

;

trim_interval =

(

(*seq_id, start_trim, stop_trim, strand));

(protein.

()) {

frame_offset = 0;

(cds_length < 10) {

err_msg =

;

translate_cds =

;

<< defline <<

;

list<CRef<CSeq_id>> idList;

(

idh : scope.

(

)) {

pId->Assign(*(idh.GetSeqId()));

idList.push_back(pId);

FastaRank = isNa ?

(pBestId->IsGeneral() && pBestId->GetGeneral().IsSetTag()) {

&

= pBestId->GetGeneral().GetTag();

.GetStr();

pBestId->GetSeqIdString(

);

(pGeneFeat && pGeneFeat->IsSetData() && pGeneFeat->GetData().IsGene() &&

pGeneFeat->GetData().GetGene().IsSetLocus_tag()) {

pGeneFeat->GetData().GetGene().GetLocus_tag();

translate_cds)

idString +=

;

idString +=

;

idString += productIdOrLocusTag +

;

& feat_data = feat.

();

feat_tag =

;

underscore =

;

= feat_data.GetImp().GetKey();

feat_tag =

+

+

;

id_string += feat_tag;

(

it = kTypeToTag.find(rna_type); it != kTypeToTag.end()) {

rna_tag = it->second;

rna_tag =

;

idString += productIdOrLocusTag +

;

& src_loc =

.GetLocation();

id_string +=

;

(

.IsSetProduct()) {

(!prod_accver.empty()) {

id_string += prod_accver +

;

id_string +=

;

&

,

& defline)

& defline)

defline +=

+

+

;

& defline)

(gene_feat.Empty() ||

!gene_feat->IsSetData() ||

!gene_feat->GetData().IsGene()) {

gene->Assign(gene_feat->GetData().GetGene());

(gene->IsSetLocus()) {

gene_locus = gene->GetLocus();

(gene->IsSetLocus_tag()) {

gene_locus_tag = gene->GetLocus_tag();

& defline)

is_pseudo =

;

(!gene_feat.Empty() &&

gene_feat->IsSetPseudo() &&

gene_feat->GetPseudo()) {

}

(!gene_feat.Empty() &&

gene_feat->GetData().IsGene() &&

gene_feat->GetData().GetGene().GetPseudo()) {

& defline)

list<string> qualifiers;

qualifiers.push_back(

);

qualifiers.push_back(

);

qualifiers.push_back(

);

qualifiers.push_back(

);

qualifiers.push_back(

);

qualifiers.push_back(

);

qualifiers.push_back(

);

(

& qual_name : qualifiers) {

(!

.empty()) {

& defline)

& defline)

(pseudogene.empty()) {

(gene_feat.Empty()) {

pseudogene = gene_feat->GetNamedQual(

);

& defline)

(

&& pDbtag : feat.

()) {

& dbtag = *pDbtag;

(!db_xref.empty()) {

db_xref += dbtag.

() +

;

(db_xref.empty() &&

(gene_feat.Empty()) {

& defline)

pProtXref->IsSetName() &&

!pProtXref->GetName().empty()) {

protein_name = pProtXref->

().front();

(product_handle) {

& defline)

& defline)

partial_string;

partial_string +=

;

(!partial_string.empty()) {

partial_string +=

;

partial_string +=

;

cb_str = (

);

err_msg =

;

( loc.

() ) {

cb_str += aaName +

;

& defline)

transl_exception;

(

&& code_break : code_breaks) {

(!transl_exception.empty()) {

transl_exception +=

;

transl_exception += cb_string;

& defline)

& defline)

& defline)

transcript_id = feat.

(

);

(transcript_id.empty() &&

& defline)

& defline)

& defline)

rna_type =

.IsSetType() ?

product_string;

(

.IsSetExt() &&

.GetExt().IsTRNA()) {

& trna =

.GetExt().GetTRNA();

(product_string.empty() &&

.GetExt().IsName()) {

product_string =

.GetExt().GetName();

(product_string.empty() &&

.GetExt().IsGen() &&

.GetExt().GetGen().IsSetProduct()) {

product_string =

.GetExt().GetGen().GetProduct();

(product_string.empty()) {

: m_filename_without_ext(filename_without_ext),

it->m_fasta_stream; it->m_fasta_stream =

;

it->m_ostream; it->m_ostream =

;

* suffix =

;

suffix =

;

suffix =

;

filename.append(suffix);

* ext =

;

filename.append(ext);

loc2.

().Assign(*it->GetSeqId());

ncbi::objects::CSeq_inst_Base::eMol_dna:

ncbi::objects::CSeq_inst_Base::eMol_rna:

ncbi::objects::CSeq_inst_Base::eMol_aa:

ncbi::objects::CSeq_inst_Base::eMol_na:

)

);

(!pAnnot->IsGraph()) {

(!pGraph->GetGraph().IsByte()) {

(pGraph->IsSetLoc()) {

(current_pos < left) {

& byte_graph = pGraph->GetGraph().GetByte();

(

ch : byte_graph.

()) {

<<

<< setw(2) <<

(ch);

(current_pos < length) {

& graph_title,

header = graph_title;

header +=

;

header +=

;

header +=

;

header +=

;

(values.empty()) {

(

=1;

<values.size(); ++

) {

current_value =

(values[

]);

(current_value >

) {

= current_value;

(current_value <

) {

= current_value;

have_title =

;

has_byte_graph =

;

(!pAnnot->IsGraph()) {

pGraph->IsSetTitle()) {

graph_title = pGraph->GetTitle();

& graph_data = pGraph->GetGraph();

has_byte_graph =

;

& byte_graph = graph_data.GetByte();

(local_min <

) {

(local_max >

) {

(!has_byte_graph) {

->WriteTitle(bioseq, 0,

, ending);

(

== num_columns) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

User-defined methods of the data storage class.

TSeqPos GetLength(void) const

bool IsSetLength(void) const

CFastaOstreamComp(const string &dir, const string &filename_without_ext)

virtual void x_GetNewFilename(string &filename, E_FileSection sel)

vector< TStreams > m_streams

string m_filename_without_ext

void x_Write(const CBioseq_Handle &handle, const CSeq_loc *location)

virtual ~CFastaOstreamComp()

virtual CFastaOstream * x_GetFastaOstream(CNcbiOstream &ostr, E_FileSection sel)

virtual CNcbiOstream * x_GetOutputStream(const string &filename, E_FileSection sel)

void Write(const CSeq_entry_Handle &handle, const CSeq_loc *location=nullptr)

TStreams & x_GetStream(E_FileSection sel)

void x_AddPseudoAttribute(const CSeq_feat &feat, CScope &scope, string &defline) const

void x_AddProteinIdAttribute(const CSeq_feat &feat, CScope &scope, string &defline) const

void x_AddExceptionAttribute(const CSeq_feat &feat, string &defline) const

CRef< CScope > m_InternalScope

void WriteFeatureTitle(const CSeq_feat &feat, CScope &scope, bool translate_cds=false)

void x_AddncRNAClassAttribute(const CSeq_feat &feat, string &defline) const

void x_AddDeflineAttribute(const string &label, const string &value, string &defline) const

void x_AddTranslationExceptionAttribute(const CSeq_feat &feat, CScope &scope, string &defline) const

void ResetFeatureCount(void)

void WriteFeature(const CSeq_feat &feat, CScope &scope, bool translate_cds=false)

string x_GetOtherIdString(const CSeq_feat &feat, CScope &scope)

string x_GetGeneIdString(const CSeq_feat &gene, CScope &scope)

void x_AddGBkeyAttribute(const CSeq_feat &feat, string &defline) const

string x_GetProtIdString(const CSeq_feat &prot, CScope &scope)

void x_AddMiscQualifierAttributes(const CSeq_feat &feat, string &defline) const

void x_AddReadingFrameAttribute(const CSeq_feat &feat, string &defline) const

void x_AddTranscriptIdAttribute(const CSeq_feat &feat, CScope &scope, string &defline) const

string x_GetRNAIdString(const CSeq_feat &rna, CScope &scope)

CRef< CSeq_loc > x_TrimLocation(TSeqPos frame, ENa_strand strand, CScope &scope, const CSeq_loc &loc)

void x_AddProteinNameAttribute(const CSeq_feat &feat, CScope &scope, string &defline) const

void x_AddPartialAttribute(const CSeq_feat &feat, CScope &scope, string &defline) const

void x_AddRNAProductAttribute(const CSeq_feat &feat, string &defline) const

virtual bool xWriteFeature(CFeat_CI feat_it) override

void x_WriteTranslatedCds(const CSeq_feat &cds, CScope &scope)

bool xWriteFeatureTitle(const CSeq_feat &feat, CScope &scope, bool translate_cds=false)

string x_GetCDSIdString(const CSeq_feat &cds, CScope &scope, bool translate_cds=false)

CFastaOstreamEx(CNcbiOstream &out)

void x_AddGeneAttributes(const CSeq_feat &feat, CScope &scope, string &defline) const

void x_AddLocationAttribute(const CSeq_feat &feat, CScope &scope, string &defline) const

void x_AddDbxrefAttribute(const CSeq_feat &feat, CScope &scope, string &defline) const

virtual void x_WriteBuffer(const char *buf, unsigned int count) override

bool WriteFeatures(CFeat_CI feat_it, bool translate_cds)

void x_AddPseudoGeneAttribute(const CSeq_feat &feat, CScope &scope, string &defline) const

bool x_GetCodeBreak(const CSeq_feat &feat, const CCode_break &code_break, CScope &scope, string &cbstring) const

void x_WriteFeatureAttributes(const CSeq_feat &feat, CScope &scope) const

FASTA-format output; see also ReadFasta in <objtools/readers/fasta.hpp>

bool WriteFeatures(CFeat_CI &first)

const string & GetString(void) const

CQualScoreWriter(CNcbiOstream &ostr, bool enable_gi=false)

bool x_WriteHeader(const CBioseq &bioseq)

void x_Advance(int &column, const int num_columns)

unique_ptr< CFastaOstreamEx > m_FastaOstr

void Write(const CBioseq &bioseq)

string x_ComposeHeaderEnding(const string &graph_title, TSeqPos length, int max, int min)

virtual ~CQualScoreWriter(void)

bool IsLegalQualifier(EQualifier qual) const

Test wheather a certain qualifier is legal for the feature.

ESubtype GetSubtype(void) const

string GetKey(EVocabulary vocab=eVocabulary_full) const

namespace ncbi::objects::

const CProt_ref * GetProtXref(void) const

get protein (if present) from Seq-feat.xref list

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

static bool GetAaName(const CCode_break &, string &)

static bool GetTrnaProductName(const CTrna_ext &, string &)

#define MAKE_CONST_MAP(name, type1, type2,...)

std::ofstream out("events_result.xml")

main entry point for tests

static bool x_GetMaxMin(const CByte_graph::TValues &values, int &max, int &min)

static string s_GetDeflineIdString(const CSeq_id &id, CScope &scope, const bool isNa=true)

MAKE_CONST_SET(s_TrnaList, ct::tagStrNocase, { "tRNA-Gap", "tRNA-Ala", "tRNA-Asx", "tRNA-Cys", "tRNA-Asp", "tRNA-Glu", "tRNA-Phe", "tRNA-Gly", "tRNA-His", "tRNA-Ile", "tRNA-Xle", "tRNA-Lys", "tRNA-Leu", "tRNA-Met", "tRNA-Asn", "tRNA-Pyl", "tRNA-Pro", "tRNA-Gln", "tRNA-Arg", "tRNA-Ser", "tRNA-Thr", "tRNA-Sec", "tRNA-Val", "tRNA-Trp", "tRNA-OTHER", "tRNA-Tyr", "tRNA-Glx", "tRNA-TERM" })

static string s_GetProductIdOrLocusTag(const CSeq_feat &feat, CScope &scope)

CConstRef< CSeq_feat > s_GetBestGeneForFeat(const CSeq_feat &feat, CScope &scope)

static bool s_LocationSpansMultipleSeqs(const CSeq_loc &loc)

static const string s_TrnaList[]

static const char * column

static const char location[]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define ERR_POST(message)

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

#define NCBI_THROW(exception_class, err_code, message)

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

const string & GetMsg(void) const

Get message string.

void Warning(CExceptionArgs_Base &args)

static string AddTrailingPathSeparator(const string &path)

Add trailing path separator, if needed.

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

static int FastaNARank(const CRef< CSeq_id > &id)

static int FastaAARank(const CRef< CSeq_id > &id)

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

TSeqPos GetStop(ESeqLocExtremes ext) const

CMappedFeat GetBestGeneForMrna(const CMappedFeat &mrna_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)

CMappedFeat GetBestGeneForCds(const CMappedFeat &cds_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)

CMappedFeat GetBestOverlappingFeat(const CMappedFeat &feat, CSeqFeatData::ESubtype need_subtype, sequence::EOverlapType overlap_type, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

TSeqPos LocationOffset(const CSeq_loc &outer, const CSeq_loc &inner, EOffsetType how=eOffset_FromStart, CScope *scope=0)

returns (TSeqPos)-1 if the locations don't overlap

int SeqLocPartialCheck(const CSeq_loc &loc, CScope *scope)

CRef< CSeq_loc > Seq_loc_Subtract(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)

Subtract the second seq-loc from the first one.

int TestForOverlap(const CSeq_loc &loc1, const CSeq_loc &loc2, EOverlapType type, TSeqPos circular_len=kInvalidSeqPos, CScope *scope=0)

Calls TestForOverlap64() and if the result is greater than kMax_Int truncates it to kMax_Int.

@ eOverlap_Simple

any overlap of extremes

@ eOverlap_Interval

at least one pair of intervals must overlap

@ eOffset_FromStart

For positive-orientation strands, start = left and end = right; for reverse-orientation strands,...

static CRef< CBioseq > TranslateToProtein(const CSeq_feat &cds, CScope &scope)

virtual void Write(const CSeq_entry_Handle &handle, const CSeq_loc *location=0)

Unspecified locations designate complete sequences; non-empty custom titles override the usual title ...

virtual void WriteSequence(const CBioseq_Handle &handle, const CSeq_loc *location=0, CSeq_loc::EOpFlags merge_flags=CSeq_loc::fMerge_AbuttingOnly)

virtual void x_WriteBuffer(const char *buf, unsigned int count)

void SetAllFlags(TFlags flags)

@ fHideGenBankPrefix

Hide gb| prefix for genbank only seq_id's.

@ fNoDupCheck

skip check for duplicate sequence IDs

@ fEnableGI

Use this flag to enable GI output in the defline.

TIds GetIds(const CSeq_id &id, TGetFlags flags=0)

Get "native" bioseq ids without filtering and matching.

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

Add bioseq, return bioseq handle.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_inst::TMol GetSequenceType(const CSeq_id &id, TGetFlags flags=0)

Get molecular type of sequence (protein/dna/rna) Return CSeq_inst::eMol_not_set if sequence is not fo...

const CSeqFeatData & GetData(void) const

TInst_Mol GetInst_Mol(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CScope & GetScope(void) const

Get scope this handle belongs to.

bool IsSetData(void) const

bool CanGetInst_Mol(void) const

SAnnotSelector & SetExcludeExternal(bool exclude=true)

External annotations for the Object Manger are annotations located in top level Seq-entry different f...

SAnnotSelector & SetSortOrder(ESortOrder sort_order)

Set sort order of annotations.

CConstRef< CSeq_feat > GetSeq_feat(void) const

Get current seq-feat.

@ eSortOrder_Normal

default - increasing start, decreasing length

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.

void Reset(void)

Reset reference object.

TObjectType & GetObject(void)

Get object.

bool Empty(void) const THROWS_NONE

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

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

Convert int to string.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

static const char label[]

bool IsSetDb(void) const

name of database or system Check if a value has been assigned to Db data member.

const TTag & GetTag(void) const

Get the Tag member data.

bool IsId(void) const

Check if variant Id is selected.

bool IsSetTag(void) const

appropriate tag Check if a value has been assigned to Tag data member.

const TDb & GetDb(void) const

Get the Db member data.

const TStr & GetStr(void) const

Get the variant data.

TId GetId(void) const

Get the variant data.

const TName & GetName(void) const

Get the Name member data.

bool IsSetName(void) const

protein name Check if a value has been assigned to Name data member.

EType

type of RNA feature

bool IsSetExt(void) const

generic fields for ncRNA, tmRNA, miscRNA Check if a value has been assigned to Ext data member.

bool IsGen(void) const

Check if variant Gen is selected.

const TGen & GetGen(void) const

Get the variant data.

bool IsSetClass(void) const

for ncRNAs, the class of non-coding RNA: examples: antisense_RNA, guide_RNA, snRNA Check if a value h...

const TExt & GetExt(void) const

Get the Ext member data.

const TClass & GetClass(void) const

Get the Class member data.

@ eType_scRNA

will become ncRNA, with RNA-gen.class = scRNA

@ eType_snoRNA

will become ncRNA, with RNA-gen.class = snoRNA

@ eType_ncRNA

non-coding RNA; subsumes snRNA, scRNA, snoRNA

@ eType_snRNA

will become ncRNA, with RNA-gen.class = snRNA

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

E_Choice Which(void) const

Which variant is currently selected.

bool IsProt(void) const

Check if variant Prot is selected.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

const TLoc & GetLoc(void) const

Get the Loc member data.

const TLocation & GetLocation(void) const

Get the Location member data.

E_Choice

Choice variants.

bool IsGene(void) const

Check if variant Gene is selected.

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

const TExcept_text & GetExcept_text(void) const

Get the Except_text member data.

bool IsSetExcept_text(void) const

explain if except=TRUE Check if a value has been assigned to Except_text data member.

const TDbxref & GetDbxref(void) const

Get the Dbxref member data.

const TCdregion & GetCdregion(void) const

Get the variant data.

TPseudo GetPseudo(void) const

Get the Pseudo member data.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsSetPseudo(void) const

annotated on pseudogene? Check if a value has been assigned to Pseudo data member.

const TGene & GetGene(void) const

Get the variant data.

const TProt & GetProt(void) const

Get the variant data.

const TRna & GetRna(void) const

Get the variant data.

bool IsSetDbxref(void) const

support for xref to other databases Check if a value has been assigned to Dbxref data member.

const TCode_break & GetCode_break(void) const

Get the Code_break member data.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

bool IsSetLoc(void) const

location of exception Check if a value has been assigned to Loc data member.

bool IsRna(void) const

Check if variant Rna is selected.

bool IsSetCode_break(void) const

individual exceptions Check if a value has been assigned to Code_break data member.

bool IsSetFrame(void) const

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

@ e_Region

named region (globin locus)

@ eFrame_three

reading frame

ENa_strand

strand of nucleic acid

TFrom GetFrom(void) const

Get the From member data.

E_Choice Which(void) const

Which variant is currently selected.

TTo GetTo(void) const

Get the To member data.

const TInt & GetInt(void) const

Get the variant data.

const TGraph & GetGraph(void) const

Get the Graph member data.

bool IsSetValues(void) const

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

const TValues & GetValues(void) const

Get the Values member data.

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.

EMol

molecule class in living organism

std::false_type tagStrNocase

const struct ncbi::grid::netcache::search::fields::KEY key

const GenericPointer< typename T::ValueType > T2 value

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

CFastaOstream * m_fasta_stream

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4