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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gbseq__formatter_8cpp_source.html below:

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

149 const string

value

)

159 return

spaces +

"<"

tag

">"

"\n"

;

165 return

spaces +

"<"

tag

">"

;

172 return

spaces +

"</"

tag

">"

"\n"

;

252 bool

firstOfPair =

true

;

256

firstOfPair =

false

;

330 if

( pBiomolEnumInfo ) {

334 const string

*psBiomolName = find_iter->second;

378 if

(biomol_str.find(

"RNA"

) !=

NPOS

)

414 return "01-JAN-1900"

;

431 if

( ! sStrandedness.empty() ) {

436 if

( ! sMolType.empty() ) {

438

}

else if

(

ctx

.IsProt()) {

473

def.resize(def.length() - 1);

495 if

(acc.length() !=

.length()) {

499 for

(

= 0;

< acc.length() && !

isdigit

((

unsigned char

) acc[

]); ++

) {

500 if

(acc[

] !=

[

]) {

504 if

(

< acc.length()) {

531 bool

hasOthers =

false

;

541 static const size_t

kAccCutoff = 20;

542 static const size_t

kBinCutoff = 5;

544 bool

hasExtras =

false

;

549 if

(xtra.size() < kAccCutoff) {

562 typedef

vector<string> TAccBin;

563 typedef

vector <TAccBin> TAccBins;

565

TAccBin* curr_bin =

nullptr

;

568

CAccessionItem::TExtra_accessions::const_iterator

= xtra.begin();

571

bins.push_back(TAccBin());

572

curr_bin = &bins.back();

574

curr_bin->push_back(*it);

578 ITERATE

(TAccBins, bin_it, bins) {

579 if

(bin_it->size() <= kBinCutoff) {

585 string

rnge = bin_it->front() +

"-"

+ bin_it->back();

615 str

.append(

s_OpenTag

(

" "

"GBSeq_secondary-accessions"

));

617 str

.append(

s_CloseTag

(

" "

"GBSeq_secondary-accessions"

));

642 if

(dblinklines.size() == 0)

return

;

645 string

line = *gp_it;

706 string

source_line =

source

.GetOrganelle() +

source

.GetTaxname();

707 if

( !

source

.GetCommon().empty() ) {

708

source_line.append( (

source

.IsUsingAnamorph() ?

" (anamorph: "

" ("

) +

source

.GetCommon() +

")"

);

714 const string

& sTaxonomy =

source

.GetLineage();

715 string

staxon = sTaxonomy;

717

staxon.resize( staxon.length() - 1);

740 if

( csh.

Skip

() ) {

744

vector<string>* rcx = csh.

GetCache

();

746 for

(

auto

str

: *rcx) {

810 const char

* pchDelim =

""

;

821

list<string> authors;

824 bool

hasAuthors =

false

;

825 ITERATE

(list<string>, it, authors) {

827 str

.append(

s_OpenTag

(

" "

"GBReference_authors"

));

842

title.resize(title.length() - 1);

852 if

( (*it ==

'\n'

) || (*it ==

'\t'

) || (*it ==

'\r'

) ) {

859 string

doi = ref.

GetDOI

();

860 if

( ! doi.empty() ) {

971 str

.append(

s_OpenTag

(

" "

"GBSeq_feature-table"

));

982 string location

= feat->GetLoc().GetString();

986 str

.append(

s_OpenTag

(

" "

"GBFeature_intervals"

));

989 CScope

& scope =

.GetContext()->GetScope();

1003

to = range.

GetTo

() + 1;

1015 if

( best->

IsGi

() ) {

1017

list< CConstRef<CSeq_id> > ids;

1018 for

(

auto

& syn_id: *syns) {

1019

ids.push_back(syn_id.GetSeqId());

1038 str

.append(

" <GBFeature_partial5 value=\"true\"/>\n"

);

1041 str

.append(

" <GBFeature_partial3 value=\"true\"/>\n"

);

1044 if

( !feat->GetQuals().empty() ) {

1113 TSeqPos

total = from <= to? to - from + 1 : 0;

1227 str

.append(

s_OpenTag

(

" "

"GBSeq_feature-table"

));

1242 const bool

isGapOfLengthZero = ( gapStart > gapEnd );

1245 if

( isGapOfLengthZero ) {

1256 str

.append(

s_OpenTag

(

" "

"GBFeature_intervals"

));

1270 if

( isGapOfLengthZero ) {

1274 "Non-consecutive residues"

));

1279 string

estimated_length;

1283

estimated_length =

"unknown"

;

1328

name =

"WGS"

;

break

;

1330

name =

"WGS_SCAFLD"

;

break

;

1332

name =

"WGS_CONTIG"

;

break

;

1345

name =

"TSA"

;

break

;

1347

name =

"TLS"

;

break

;

1354 template

typename

void 1402 str

.append(

s_OpenTag

(

" "

"GBAltSeqData_items"

));

1407 string

first_id = item.GetFirstID();

1408 string

last_id = item.GetLastID();

1411 if

(first_id != last_id)

1455 for

(

string

str

) {

1464 #ifdef NCBI_SHUN_OSTRSTREAM

User-defined methods of the data storage class.

@ eExtreme_Biological

5' and 3'

const TExtra_accessions & GetExtraAccessions(void) const

const string & GetAccession(void) const

vector< string > TExtra_accessions

const string & GetAccession(void) const

const TCache & GetCache(void) const

const CSeq_loc & GetLoc(void) const

const TDBSource & GetDBSource(void) const

const string & GetDefline(void) const

vector< CRef< CFormatQual > > TQuals

void x_FormatRefJournal(const CReferenceItem &ref, string &journal, CBioseqContext &ctx) const

CBioseqContext * GetContext(void)

const CSerialObject * GetObject(void) const

const string & GetString(void) const

~CGBSeqFormatter() override

void FormatPrimary(const CPrimaryItem &primary, IFlatTextOStream &text_os) override

void x_WriteFileHeader(IFlatTextOStream &text_os)

void End(IFlatTextOStream &) override

void EndSection(const CEndSectionItem &, IFlatTextOStream &) override

void FormatDBSource(const CDBSourceItem &dbs, IFlatTextOStream &text_os) override

void FormatSource(const CSourceItem &source, IFlatTextOStream &text_os) override

void FormatDefline(const CDeflineItem &defline, IFlatTextOStream &text_os) override

void FormatTSA(const CTSAItem &tsa, IFlatTextOStream &text_os) override

void FormatLocus(const CLocusItem &locus, IFlatTextOStream &text_os) override

void FormatReference(const CReferenceItem &keys, IFlatTextOStream &text_os) override

void x_FormatAltSeq(const T &item, const string &name, IFlatTextOStream &text_os)

list< string > m_Dbsource

void FormatSegment(const CSegmentItem &seg, IFlatTextOStream &text_os) override

void FormatSequence(const CSequenceItem &seq, IFlatTextOStream &text_os) override

void FormatGenomeProject(const CGenomeProjectItem &, IFlatTextOStream &) override

void FormatVersion(const CVersionItem &version, IFlatTextOStream &text_os) override

void FormatKeywords(const CKeywordsItem &keys, IFlatTextOStream &text_os) override

void x_StrOStreamToTextOStream(IFlatTextOStream &text_os)

void FormatContig(const CContigItem &contig, IFlatTextOStream &text_os) override

void FormatComment(const CCommentItem &keys, IFlatTextOStream &text_os) override

void FormatWGS(const CWGSItem &wgs, IFlatTextOStream &text_os) override

void FormatCache(const CCacheItem &csh, IFlatTextOStream &text_os) override

void FormatGap(const CGapItem &gap, IFlatTextOStream &text_os) override

void FormatFeature(const CFeatureItemBase &feat, IFlatTextOStream &text_os) override

void FormatAccession(const CAccessionItem &acc, IFlatTextOStream &text_os) override

unique_ptr< CObjectOStream > m_Out

void x_WriteGBSeq(IFlatTextOStream &text_os)

CGBSeqFormatter(bool isInsd=false)

void StartSection(const CStartSectionItem &, IFlatTextOStream &) override

list< string > m_Comments

TSeqPos GetTo(void) const

TSeqPos GetEstimatedLength(void) const

TSeqPos GetFrom(void) const

std::vector< std::string > TEvidence

const std::string & GetType(void) const

bool HasEstimatedLength(void) const

const TEvidence & GetEvidence(void) const

const std::string & GetFeatureName(void) const

const TDBLinkLineVec & GetDBLinkLines(void) const

vector< TDBLinkLine > TDBLinkLineVec

vector< string > TKeywords

const TKeywords & GetKeywords(void) const

const string & GetName(void) const

size_t GetLength(void) const

TBiomol GetBiomol(void) const

TTopology GetTopology(void) const

const string & GetDivision(void) const

TStrand GetStrand(void) const

const string & GetString(void) const

const string & GetTitle(void) const

static void GetAuthNames(const CAuth_list &alp, TStrList &authors)

const string & GetRemark(void) const

int GetSerial(void) const

TEntrezId GetPMID(void) const

const CAuth_list & GetAuthors(void) const

const CSeq_loc & GetLoc(void) const

const string & GetDOI(void) const

const string & GetConsortium(void) const

bool IsSetAuthors(void) const

size_t GetNum(void) const

size_t GetCount(void) const

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

const CSeqVector & GetSequence(void) const

TSeqPos GetTo(void) const

TSeqPos GetFrom(void) const

TTSAType GetType(void) const

TWGSType GetType(void) const

virtual void AddLine(const CTempString &, const CSerialObject *=nullptr, EAddNewline=eAddNewline_Yes)

This adds its given argument, appending a newline only if the add_newline argument is eAddNewline_Yes...

virtual void AddParagraph(const list< string > &, const CSerialObject *=nullptr)

This adds a list of strings to the stream one at a time, unconditionally adding a newline to each one...

container_type::const_iterator const_iterator

const_iterator end() const

const_iterator find(const key_type &key) const

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

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

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

static const char * str(char *buf, int n)

static const char location[]

static string s_OpenTag(const string &spaces, const string &tag)

static void s_GBSeqStringCleanup(string &str, bool location=false)

CGBSeq::TMoltype s_GBSeqMoltype(CMolInfo::TBiomol biomol)

static string s_OpenTagNoNewline(const string &spaces, const string &tag)

static bool s_IsSuccessor(const string &acc, const string &prev)

static string s_CloseTag(const string &spaces, const string &tag)

string s_GetDate(const CBioseq_Handle &bsh, CSeqdesc::E_Choice choice)

CGBSeq::TTopology s_GBSeqTopology(CSeq_inst::TTopology topology)

static string s_AddAttribute(const string &spaces, const string &tag, const string &attribute, const string &value)

static string s_CombineStrings(const string &spaces, const string &tag, const string &value)

CGBSeq::TStrandedness s_GBSeqStrandedness(CSeq_inst::TStrand strand, CMolInfo::TBiomol eBiomol)

#define ENTREZ_ID_TO(T, entrez_id)

unsigned int TSeqPos

Type for sequence locations and lengths.

#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.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

const TValueToName & ValueToName(void) const

Get value-to-name map.

#define ENUM_METHOD_NAME(EnumName)

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

static int ConstScore(const CConstRef< CSeq_id > &id)

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

bool IsPartialStop(ESeqLocExtremes ext) const

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

pair< TConstObjectPtr, TTypeInfo > ConstObjectInfo(const C &obj)

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

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

CConstRef< CSynonymsSet > GetSynonyms(const CSeq_id &id)

Get bioseq synonyms, resolving to the bioseq in this scope.

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

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.

position_type GetLength(void) const

#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.

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.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

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

Replace occurrences of a substring within a string.

static string XmlEncode(const CTempString str, TXmlEncode flags=eXmlEnc_Contents)

Encode a string for XML.

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

Convert UInt to string.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

static unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

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 enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value 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.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

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

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

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetTo(TTo value)

Assign a value to To data member.

bool IsGi(void) const

Check if variant Gi is selected.

bool IsUpdate_date(void) const

Check if variant Update_date is selected.

const TUpdate_date & GetUpdate_date(void) const

Get the variant data.

list< CRef< CSeq_id > > TId

E_Choice

Choice variants.

ETopology

topology of molecule

EStrand

strandedness in living organism

const TCreate_date & GetCreate_date(void) const

Get the variant data.

@ eBiomol_cRNA

viral RNA genome copy intermediate

@ eBiomol_genomic_mRNA

reported a mix of genomic and cdna sequence

@ e_Update_date

date of last update

@ e_Create_date

date entry first created/released

@ eStrand_other

default ds for DNA, ss for RNA, pept

@ eStrand_ds

double strand

@ eStrand_ss

single strand

const string version

version string

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

void DateToString(const CDate &date, string &str, EDateToString format_choice=eDateToString_regular)

CRef< CPub > journal(ParserPtr pp, char *bptr, char *eptr, CRef< CAuth_list > &auth_list, CRef< CTitle::C_E > &title, bool has_muid, CRef< CCit_art > &cit_art, Int4 er)

#define FOR_EACH_STRING_IN_LIST(Itr, Var)

FOR_EACH_STRING_IN_LIST EDIT_EACH_STRING_IN_LIST.

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static SLJIT_INLINE sljit_ins xr(sljit_gpr dst, sljit_gpr src)

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