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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/primary__item_8cpp_source.html below:

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

61  if

( m_Str.empty() ) {

82  bool

has_bankit =

false

;

83  bool

has_genbank =

false

;

85  bool

has_local =

false

;

86  bool

has_refseq =

false

;

87  bool

has_smart =

false

;

88  bool

has_tpa =

false

;

92  switch

( (*it)->Which() ) {

113  if

( (*it)->GetGeneral().CanGetDb() ) {

114  const string

& db = (*it)->GetGeneral().GetDb();

132  if

(is_tsa)

return true

;

133  if

(has_genbank)

return false

;

134  if

(has_tpa)

return true

;

135  if

(has_refseq)

return true

;

136  if

(has_bankit && has_tpa_assembly)

return true

;

137  if

(has_smart && has_tpa_assembly)

return true

;

138  if

(has_gi)

return false

;

139  if

(has_local && has_tpa_assembly)

return true

;

147  bool

has_bankit =

false

;

148  bool

has_genbank =

false

;

149  bool

has_gi =

false

;

150  bool

has_local =

false

;

151  bool

has_refseq =

false

;

152  bool

has_smart =

false

;

153  bool

has_tpa =

false

;

154  bool

is_tsa =

false

;

157  switch

( (*it)->Which() ) {

178  if

( (*it)->GetGeneral().CanGetDb() ) {

179  const string

& db = (*it)->GetGeneral().GetDb();

197  if

(is_tsa)

return false

;

198  if

(has_genbank)

return true

;

199  if

(has_tpa && has_tpa_assembly)

return true

;

200  if

(has_tpa)

return false

;

201  if

(has_refseq)

return false

;

202  if

(has_bankit && has_tpa_assembly)

return true

;

203  if

(has_smart && has_tpa_assembly)

return true

;

204  if

(has_gi)

return true

;

205  if

(has_local && has_tpa_assembly)

return false

;

213  bool

has_tpa_assembly =

false

;

214  bool

has_tsa =

false

;

216

desc && !has_tpa_assembly && !has_tsa;

221

has_tpa_assembly =

true

;

237  bool

has_hist_assembly =

240  if

(!

ctx

.Config().OldTpaDisplay()) {

242  if

( !has_hist_assembly ) {

254  if

( !

s_IsTPA

(

ctx

, has_tpa_assembly) || !has_hist_assembly ) {

266  if

(

ctx

.IsRefSeq() ) {

267  return "REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP"

;

269  return "TSA_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP"

;

271  return "TPA_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP"

;

300  if

(

ctx

.IsRefSeq() && last_stop > -1 && (this_start > (last_stop + 1)) ) {

301  if

(this_start < (15 + last_stop) ) {

309

v.

GetSeqData

(last_stop + 1, this_start, ss);

323

v.

GetSeqData

(last_stop + 1, last_stop + 5, ss);

327

v.

GetSeqData

(this_start - 4, this_start, ss);

339  ctx

.ThrowIfCanceled();

341

last_stop = this_stop;

350  if

(other_id->

IsGi

()) {

359  if

(other_id->

IsGi

()) {

379  if

(

r

.length() > 20) {

393  if

(!

str

.empty()) {

418

seglist.push_back(

TAln

(&aln) );

User-defined methods of the data storage class.

void x_SetObject(const CSerialObject &obj)

void x_GetStrForPrimary(CBioseqContext &ctx)

void x_GatherInfo(CBioseqContext &ctx) override

list< CConstRef< CSeq_align > > TAlnConstList

CConstRef< CSeq_align > TAln

list< CRef< CSeq_align > > TAlnList

void Format(IFormatter &formatter, IFlatTextOStream &text_os) const override

void x_CollectSegments(TAlnConstList &, const TAlnList &aln_list)

EItem GetItemType() const override

TSeqPos GetSeqStop(TDim row) const

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

TSeqPos GetSeqStart(TDim row) const

ENa_strand GetSeqStrand(TDim row) const

Get strand (the first one if segments have different strands).

virtual void FormatPrimary(const CPrimaryItem &prim, IFlatTextOStream &text_os)=0

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

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.

int TSignedSeqPos

Type for signed sequence position.

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

CConstRef< CSeq_id > GetSeqId(void) const

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

const TInst_Hist & GetInst_Hist(void) const

bool IsSetInst_Hist(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

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.

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

Convert int to string.

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 & 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.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetDb(void) const

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

bool CanGetType(void) const

Check if it is safe to call GetType method.

const TDb & GetDb(void) const

Get the Db member data.

const TStr & GetStr(void) const

Get the variant data.

const TType & GetType(void) const

Get the Type member data.

bool CanGetSegs(void) const

Check if it is safe to call GetSegs method.

bool IsDisc(void) const

Check if variant Disc is selected.

const TDisc & GetDisc(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

ENa_strand

strand of nucleic acid

bool IsGeneral(void) const

Check if variant General is selected.

const TGeneral & GetGeneral(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ e_Tpe

Third Party Annot/Seq EMBL.

@ e_Tpd

Third Party Annot/Seq DDBJ.

@ e_General

for other databases

@ e_Gi

GenInfo Integrated Database.

@ e_Tpg

Third Party Annot/Seq Genbank.

const TAssembly & GetAssembly(void) const

Get the Assembly member data.

list< CRef< CSeq_id > > TId

@ eTech_tsa

transcriptome shotgun assembly

@ e_User

user defined object

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

static bool s_HideTPAPrimary(CBioseqContext &ctx, bool has_tpa_assembly)

static const char * s_PrimaryHeader(CBioseqContext &ctx)

static bool s_IsTPA(CBioseqContext &ctx, bool has_tpa_assembly)

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