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

index = prot_id;

vector<CSeq_id_Handle> ids = bsh.

();

(

hid: ids) {

index = nuc_id;

vector<CSeq_id_Handle> ids = bsh.

();

(

hid: ids) {

+= acc_id +

+ acc_id;

+= gi_str +

+ gi_str;

+=

;

t_taxname = taxname;

replace(t_taxname.begin(), t_taxname.end(),

,

);

+=

;

(add_comma) loc_str +=

;

(add_comma) loc_str +=

;

loc_str +=

+ pnt_str +

;

(add_comma) loc_str +=

;

loc_str +=

+ pnt_str +

;

(loc.

()) {

is_prot =

;

(

& loc_ci: loc) {

strLink.reserve(100);

strLink =

;

strLink +=

;

strLink +=

;

}

(visible_text !=

) {

add_comma =

;

strLink +=

;

strLink += visible_text;

+=

;

+=

;

((me.

.first >= 0) && (me.

.second >= me.

.first)) {

kPadAmount = 500;

+=

;

*mol_type = (is_prot ?

:

);

os <<

<< gap_size <<

<< mol_type <<

<<

<<

+ link_base <<

<<

;

@ eExtreme_Positional

numerical value

User-defined methods of the data storage class.

void FormatNucId(string &str, const CSeq_id &seq_id, TIntId gi, const string &acc_id) const override

FIXME: Shouldn't gi have type TGi, not TIntId???

void FormatTranscriptId(string &, const CSeq_id &seq_id, const string &nuc_id) const override

void FormatTranscript(string &str, const string &name) const override

void FormatUniProtId(string &str, const string &prot_id) const override

void FormatTaxid(string &str, const TTaxId taxid, const string &taxname) const override

void FormatLocation(string &str, const CSeq_loc &loc, TIntId gi, const string &visible_text) const override

void FormatGeneralId(CNcbiOstream &os, const string &id) const override

void FormatGapLink(CNcbiOstream &os, TSeqPos gap_size, const string &id, bool is_prot) const override

~CHTMLFormatterEx() override

void FormatModelEvidence(string &str, const SModelEvidance &me) const override

void FormatNucSearch(CNcbiOstream &os, const string &id) const override

void FormatProteinId(string &, const CSeq_id &seq_id, const string &prot_id) const override

static void s_AddSeqPackedPointString(const CPacked_seqpnt &packed_pnt, string &loc_str, bool &add_comma)

static void s_AddLocString(const CSeq_loc &loc, string &loc_str, bool &add_comma)

static void s_AddSeqPointString(const CSeq_point &seqpnt, string &loc_str, bool &add_comma)

static void s_AddSeqIntString(const CSeq_interval &seqint, string &loc_str, bool &add_comma)

static void s_AddSeqBondString(const CSeq_bond &seqbond, string &loc_str, bool &add_comma)

const string sLinkBaseNuc

const string sLinkBaseProt

const string sLinkBaseTaxonomy

const string sLinkBaseNucSearch

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

SStrictId_Tax::TId TTaxId

Taxon id type.

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

Wrappers for use with FindBestChoice from <corelib/ncbiutil.hpp>

string GetLabel(const CSeq_id &id)

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

TSeqPos GetStop(ESeqLocExtremes ext) const

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

const TId & GetId(void) const

TMol GetBioseqMolType(void) const

Get some values from core:

int64_t Int8

8-byte (64-bit) signed 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 string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

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.

@ eNocase

Case insensitive compare.

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

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

bool CanGetStrand(void) const

Check if it is safe to call GetStrand method.

const TB & GetB(void) const

Get the B member data.

list< CRef< CSeq_interval > > Tdata

const Tdata & Get(void) const

Get the member data.

bool CanGetStrand(void) const

Check if it is safe to call GetStrand method.

TStrand GetStrand(void) const

Get the Strand member data.

const TPnt & GetPnt(void) const

Get the variant data.

TPoint GetPoint(void) const

Get the Point member data.

TFrom GetFrom(void) const

Get the From member data.

list< CRef< CSeq_loc > > Tdata

bool CanGetA(void) const

Check if it is safe to call GetA method.

E_Choice Which(void) const

Which variant is currently selected.

TStrand GetStrand(void) const

Get the Strand member data.

const Tdata & Get(void) const

Get the member data.

const TPacked_pnt & GetPacked_pnt(void) const

Get the variant data.

bool CanGetStrand(void) const

Check if it is safe to call GetStrand method.

vector< TSeqPos > TPoints

const TA & GetA(void) const

Get the A member data.

bool CanGetB(void) const

Check if it is safe to call GetB method.

const TPoints & GetPoints(void) const

Get the Points member data.

TStrand GetStrand(void) const

Get the Strand member data.

TTo GetTo(void) const

Get the To member data.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

const TMix & GetMix(void) const

Get the variant data.

bool IsPnt(void) const

Check if variant Pnt is selected.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

const TBond & GetBond(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

Defines command line argument related classes.

const char * strLinkBaseUniProt

void TryToSanitizeHtml(std::string &str)

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