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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/shortcuts_8cpp_source.html below:

NCBI C++ ToolKit: src/app/read_blast_result/shortcuts.cpp Source File

43 m_length

= seq->GetInst().GetLength();

54 if

(

->GetData().IsGene())

56 if

(

->GetData().GetGene().CanGetLocus_tag())

58 string

locus_tag =

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

65 ITERATE

(THaveIt, locus, locuses)

67 if

(locus->second<2)

continue

;

69 NcbiCerr

"ERROR: CReadBlastApp::CheckUniqLocusTag : more than one gene with the same locus_tag: " 77 NcbiCerr

"FATAL: sequences or genes with the same locus_tag are not allowed"

NcbiEndl

;

86 if

( ! (*annot)->GetData().IsFtable() )

continue

;

89 if

( ! (*feat)->GetData().IsProt() )

continue

;

90 if

( ! (*feat)->GetData().GetProt().CanGetName() )

continue

;

91 return

*( (*feat)->GetData().GetProt().GetName().begin() );

94 return "default name"

;

103 string type

"unknown rRNA"

;

104 if

rna

.CanGetExt())

return type

;

105 if

rna

.GetExt().IsName())

return type

;

106 string

name =

rna

.GetExt().GetName();

107 if

(name.find(

"5S"

) != string::npos)

return "5S"

;

108 if

(name.find(

"16S"

) != string::npos)

return "16S"

;

109 if

(name.find(

"23S"

) != string::npos)

return "23S"

;

110 if

(name.find(

"SSU"

) != string::npos)

return "16S"

;

111 if

(name.find(

"LSU"

) != string::npos)

return "23S"

;

119 if

rna

.CanGetExt()) {

123 if

rna

.GetExt().IsTRNA()) {

127 if

rna

.GetExt().GetTRNA().CanGetAa()) {

137

let1 =

rna

.GetExt().GetTRNA().GetAa().GetNcbieaa();

141

let1 =

rna

.GetExt().GetTRNA().GetAa().GetIupacaa();

145 NcbiCerr

"Get3type(FATAL)::type e_Ncbi8aa("

rna

.GetExt().GetTRNA().GetAa().GetNcbi8aa() <<

") is not handled now"

NcbiEndl

;

149 NcbiCerr

"Get3type(FATAL)::type e_Ncbistdaa ("

rna

.GetExt().GetTRNA().GetAa().GetNcbistdaa() <<

") is not handled now"

NcbiEndl

;

153 NcbiCerr

"Get3type: INTERNAL FATAL:: you should never be here"

NcbiEndl

;

166 if

( (*desc)->IsTitle() )

168

descr=(*desc)->GetTitle();

break

;

183 if

( descr.find(

"hypothetical"

) != string::npos)

192

"descr "

<< descr <<

", " 199 string

trna_string=

""

;

200 bool

isPseudo=

false

;

218

trna_string = isPseudo ?

"pseudo-tRNA-"

"tRNA-"

;

221 case

0: trna_string+=

"unknown"

;

break

;

222 case 'X'

: trna_string+=

"other"

;

break

;

223 default

: trna_string+=aa;

break

;

231 string

trna_string=

""

;

259

", rna_type= "

<< rna_type

274

(aa>=

'C'

&& aa<=

'I'

) ||

275

(aa>=

'K'

&& aa<=

'N'

) ||

276

(aa>=

'P'

&& aa<=

'T'

) ||

290

", type= "

<< feat_type

305

", type= "

<< feat_type

316 if

(locus_tag !=

""

result

.find(locus_tag) == string::npos)

result

"|"

+ locus_tag;

323

rstr << from2 <<

"..."

<< to2 <<

'\0'

;

324 string r

= rstr.str();

343 typedef

list<pair<int,int> > Tlist;

347

pair<int,int> apair(inter->GetFrom(), inter->GetTo());

348

ints.push_back(apair);

352

pair<int,int> apair(pnt->GetPoint(), pnt->GetPoint());

353

ints.push_back(apair);

360 if

(!ranges.empty()) ranges+=

","

;

396

from = ext_rna.

exons

[0].from;

397

to = ext_rna.

exons

[ext_rna.

exons

.size()-1].to;

401

to = ext_rna.

exons

[0].to;

402

from = ext_rna.

exons

[ext_rna.

exons

.size()-1].from;

408 string printed_range

(

const

TSimpleSeqs::iterator& ext_rna,

const

TSimpleSeqs::iterator& end)

410 if

(ext_rna==end)

return "beyond end...beyond end"

;

423 if

(!(*annot)->GetData().IsAlign())

return len

;

427 string

name = (*score)->GetId().GetStr();

428 if

(name!=

"sbjLen"

)

continue

;

429 len

= (*score)->GetValue().GetInt();

436

CBioseq::TAnnot::const_iterator& annot,

437 int

* qFrom,

int

* qTo,

int

* sFrom,

int

* sTo

445

*qFrom = (*bounds)->GetInt().GetFrom();

446

*qTo = (*bounds)->GetInt().GetTo();

450

*sFrom = (*bounds)->GetInt().GetFrom();

451

*sTo = (*bounds)->GetInt().GetTo();

463 if

( (*desc)->IsName() )

465 return

(*desc)->GetName();

468 return "cannot get name"

;

475 if

( (*desc)->IsComment() )

477 return

(*desc)->GetComment();

480 return "cannot get comment"

;

@ eExtreme_Positional

numerical value

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

static bool PrintDetails(int current_verbosity=m_current_verbosity)

static string GetProtName(const CBioseq &seq)

static bool less_pair(const pair< int, int > &first, const pair< int, int > &second)

static int getQueryLen(const CBioseq &seq)

static string getAnnotComment(CBioseq::TAnnot::const_iterator &annot)

static string getAnnotName(CBioseq::TAnnot::const_iterator &annot)

static void getBounds(CBioseq::TAnnot::const_iterator &annot, int *qFrom, int *qTo, int *sFrom, int *sTo)

static const CSeq_loc & getGenomicLocation(const CBioseq &seq)

static int getLenScore(CBioseq::TAnnot::const_iterator &annot)

static string getLocusTag(const CBioseq &seq)

namespace ncbi::objects::

Template class for iteration on objects of class C (non-medifiable version)

static const char * bounds[]

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.

#define ERR_POST(message)

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

#define NCBI_USER_THROW(message)

Throw a quick-and-dirty runtime exception of type 'CException' with the given error message and error...

void Error(CExceptionArgs_Base &args)

#define MSerial_AsnText

I/O stream manipulators â.

static string GetStringDescr(const CBioseq &bioseq, EStringFormat fmt)

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

TSeqPos GetStop(ESeqLocExtremes ext) const

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

TType GetType(void) const

Get the Type member data.

const TAa & GetAa(void) const

Get the Aa member data.

bool IsTRNA(void) const

Check if variant TRNA is selected.

bool IsNcbieaa(void) const

Check if variant Ncbieaa is selected.

EType

type of RNA feature

TNcbieaa GetNcbieaa(void) const

Get the variant data.

bool CanGetExt(void) const

Check if it is safe to call GetExt method.

TPseudo GetPseudo(void) const

Get the Pseudo member data.

E_Choice

Choice variants.

bool CanGetType(void) const

Check if it is safe to call GetType method.

const TName & GetName(void) const

Get the variant data.

bool CanGetAa(void) const

Check if it is safe to call GetAa method.

bool CanGetPseudo(void) const

Check if it is safe to call GetPseudo method.

const TExt & GetExt(void) const

Get the Ext member data.

const TTRNA & GetTRNA(void) const

Get the variant data.

bool IsName(void) const

Check if variant Name is selected.

vector< CRef< CScore > > TScore

list< CRef< CSeq_loc > > TBounds

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

const TRna & GetRna(void) const

Get the variant data.

bool IsRna(void) const

Check if variant Rna is selected.

list< CRef< CSeqdesc > > Tdata

const TInst & GetInst(void) const

Get the Inst member data.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

const Tdata & Get(void) const

Get the member data.

bool CanGetDescr(void) const

Check if it is safe to call GetDescr method.

TLength GetLength(void) const

Get the Length member data.

list< CRef< CSeq_feat > > TFtable

list< CRef< CSeq_annot > > TAnnot

const TDescr & GetDescr(void) const

Get the Descr member data.

list< CRef< CAnnotdesc > > Tdata

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

@ eMyFeatureType_normal_tRNA

@ eMyFeatureType_atypical_tRNA

@ eMyFeatureType_pseudo_tRNA

@ eMyFeatureType_hypo_CDS

@ eMyFeatureType_normal_CDS

string let1_2_let3(char let1)

string GetLocusTag(const CSeq_feat &f, const LocMap &loc_map)

list< TSimpleSeq > TSimpleSeqs

string get_trna_string(const CSeq_feat &feat)

string GetStringDescr(const CBioseq &bioseq)

string Get3type(const CRNA_ref &rna)

EMyFeatureType get_my_feat_type(const CSeq_feat &feat, const LocMap &loc_map)

string get_title(const CBioseq &seq)

EMyFeatureType get_my_seq_type(const CBioseq &seq)

string printed_ranges(const CSeq_loc &seq_interval)

string GetRNAname(const CSeq_feat &feat)

string GetRRNAtype(const CRNA_ref &rna)

string printed_range(const TSeqPos from2, const TSeqPos to2)

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