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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/locations_8cpp_source.html below:

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

(loc.

())

(from==0 && to==0)

;

(from2<from ) from = from2;

(from==0 && to==0)

;

(from2<from ) from = from2;

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

;

( !(*gen_feature)->CanGetComment())

;

( (*gen_feature)->GetComment().find(

) == string::npos )

;

<<

<<

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

;

( !(*gen_feature)->CanGetComment())

;

( (*gen_feature)->GetComment().find(

) == string::npos )

;

(*gen_feature)->GetLocation();

<<

<<

mark =

;

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

;

( !(*gen_feature)->CanGetComment())

;

( (*gen_feature)->GetComment().find(mark) == string::npos )

;

= (*gen_feature)->GetComment();

.erase(0, mark.length());

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

;

(! (*gen_feature)->GetLocation().GetInt().CanGetStrand() )

;

(! (*gen_feature)->GetLocation().GetInt().GetId().IsLocal() )

;

<<

<<

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

;

(! (*gen_feature)->GetLocation().GetInt().CanGetStrand() )

;

(! (*gen_feature)->GetLocation().GetInt().GetId().IsLocal() )

;

(*gen_feature)->GetLocation().GetInt();

<<

<<

( !(*f)->GetData().IsGene() )

;

; (*f)->GetData().GetGene().GetLabel(&

);

loc_map[loc_string]=*

;

<< from <<

<< to <<

<< strand_sign <<

;

static bool PrintDetails(int current_verbosity=m_current_verbosity)

void GetLocMap(LocMap &loc_map, const CSeq_annot::C_Data::TFtable &feats)

static void IncreaseVerbosity(void)

static bool hasGenomicInterval(const CBioseq &seq)

static const CSeq_interval & getGenomicInterval(const CBioseq &seq)

static bool hasGenomicLocation(const CBioseq &seq)

static void DecreaseVerbosity(void)

static const CSeq_loc & getGenomicLocation(const CBioseq &seq)

static void getFromTo(const CSeq_loc &loc, TSeqPos &from, TSeqPos &to, ENa_strand &strand)

static string getLocusTag(const CBioseq &seq)

namespace ncbi::objects::

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

static const char label[]

bool IsMix(void) const

Check if variant Mix is selected.

list< CRef< CSeq_interval > > Tdata

ENa_strand

strand of nucleic acid

const Tdata & Get(void) const

Get the member data.

bool CanGetStrand(void) const

Check if it is safe to call GetStrand method.

TFrom GetFrom(void) const

Get the From member data.

list< CRef< CSeq_loc > > Tdata

const Tdata & Get(void) const

Get the member data.

bool IsPacked_int(void) const

Check if variant Packed_int is selected.

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.

bool IsNull(void) const

Check if variant Null is selected.

const TMix & GetMix(void) const

Get the variant data.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

list< CRef< CSeq_feat > > TFtable

list< CRef< CSeq_annot > > TAnnot

template string GetLocationString< CSeq_loc >(const CSeq_loc &loc)

string GetLocationString(const CSeq_feat &f)

string GetStringDescr(const CBioseq &bioseq)

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