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NCBI C++ ToolKit: src/objtools/writers/agp_write.cpp Source File

;

(default_gap_type) {

*default_gap_type;

runtime_error(

);

(default_linkage) {

*default_linkage;

runtime_error(

);

linkage_evidence_str;

linkage_evidence_str,

os << linkage_evidence_str;

& object_id,

* default_gap_type,

* default_linkage,

vector<char>& component_types,

= 0;

(!component_types.empty()

error_str =

+

seg_pos = iter.GetPosition();

seg_end = iter.GetPosition() + iter.GetLength();

(start_pos > seg_end) {

(start_pos > seg_pos) {

start_offs = start_pos - seg_pos;

(stop_pos < seg_pos) {

(seg_end > stop_pos) {

end_offs = seg_end - stop_pos;

os <<

<< seg_pos + start_offs + 1;

os <<

<< seg_end - end_offs;

os <<

<<

+ 1;

(iter.GetType()) {

(component_types.empty()) {

os << component_types[

];

os <<

<< iter.GetLength();

os <<

<<

(iter, default_gap_type);

os <<

<< (

(iter, default_linkage) ?

:

);

(agp_version >= 2) {

(component_types.empty()) {

os << component_types[

];

(comp_id_mapper) {

comp_id_mapper->

( id_str );

os <<

<< iter.GetRefPosition() + start_offs + 1;

os <<

<< iter.GetRefEndPosition() - end_offs;

(iter.GetRefMinusStrand()) {

treat_as_raw =

;

treat_as_raw =

;

((*iter)->IsLoc() || !(*iter)->GetLiteral().IsSetSeq_data()) {

treat_as_raw =

;

treat_as_raw =

;

loc->

().SetFrom(0);

& object_id,

vector<char>& component_types,

object_id,

,

, scope, component_types,

comp_id_mapper, agp_version);

& object_id,

vector<char>& component_types,

object_id,

,

,

handle.

(), component_types, comp_id_mapper, agp_version);

& object_id,

vector<char>& component_types,

object_id,

,

,

handle.

(), component_types, comp_id_mapper, agp_version);

& object_id,

& default_gap_type,

default_linkage,

vector<char>& component_types,

object_id, &default_gap_type, &default_linkage,

scope, component_types, comp_id_mapper, agp_version);

& object_id,

& default_gap_type,

default_linkage,

vector<char>& component_types,

object_id, &default_gap_type, &default_linkage,

handle.

(), component_types, comp_id_mapper, agp_version);

& object_id,

& default_gap_type,

default_linkage,

vector<char>& component_types,

object_id, &default_gap_type, &default_linkage,

handle.

(), component_types, comp_id_mapper, agp_version);

( ; desc_iter; ++desc_iter) {

(desc_iter->

()) {

(*kw ==

|| *kw ==

) {

(*kw ==

) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

static void WriteLinkageEvidence(CNcbiOstream &os, const CSeqMap_CI &iter)

static char s_DetermineComponentType(const CSeq_id &id, CScope &scope)

void AgpWrite(CNcbiOstream &os, const CSeqMap &seq_map, const string &object_id, CScope &scope, const vector< char > &component_types, CAgpWriteComponentIdMapper *comp_id_mapper, int agp_version)

static bool GetLinkage(const CSeqMap_CI &iter, const bool *default_linkage)

static CConstRef< CSeqMap > s_SeqMapForHandle(const CBioseq_Handle &handle)

static string_view GetGapType(const CSeqMap_CI &iter, const string *default_gap_type)

static void s_AgpWrite(CNcbiOstream &os, const CSeqMap &seq_map, TSeqPos start_pos, TSeqPos stop_pos, const string &object_id, const string *default_gap_type, const bool *default_linkage, CScope &scope, const vector< char > &component_types, CAgpWriteComponentIdMapper *comp_id_mapper, int agp_version)

Write to stream in agp format.

virtual void do_map(string &in_out_component_id)=0

static bool VecToString(string &output_result, const TLinkage_evidence &linkage_evidence)

SeqMap related exceptions.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

CConstRef< CSeq_id > GetSeqId(void) const

@ eContent

Untagged human-readable accession or the like.

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

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

const TInst_Ext & GetInst_Ext(void) const

TSeqPos GetBioseqLength(void) const

const CSeq_id_Handle & GetSeq_id_Handle(void) const

Get handle of id used to obtain this bioseq handle.

TInst_Repr GetInst_Repr(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

const CSeqMap & GetSeqMap(void) const

Get sequence map.

const CSeq_data & GetData(void) const

will allow only regular data segments (whole, plus strand)

vector< CSeqdesc::E_Choice > TDescChoices

static CRef< CSeqMap > CreateSeqMapForSeq_loc(const CSeq_loc &loc, CScope *scope)

CSeqMap_CI Begin(CScope *scope) const

NCBI style methods.

TSeqPos GetLength(CScope *scope) const

size_t GetSegmentsCount(void) const

@ eSeqRef

reference to Bioseq

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

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.

const TKeywords & GetKeywords(void) const

Get the Keywords member data.

bool CanGetKeywords(void) const

Check if it is safe to call GetKeywords method.

TLinkage GetLinkage(void) const

Get the Linkage member data.

const TGap & GetGap(void) const

Get the variant data.

TTech GetTech(void) const

Get the Tech member data.

const TGenbank & GetGenbank(void) const

Get the variant data.

const TLinkage_evidence & GetLinkage_evidence(void) const

Get the Linkage_evidence member data.

const TDelta & GetDelta(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

E_Choice Which(void) const

Which variant is currently selected.

list< CRef< CDelta_seq > > Tdata

const TMolinfo & GetMolinfo(void) const

Get the variant data.

bool IsSetLinkage_evidence(void) const

Check if a value has been assigned to Linkage_evidence data member.

@ eRepr_delta

sequence made by changes (delta) to others

@ eRepr_raw

continuous sequence

@ eTech_htgs_2

ordered High Throughput sequence contig

@ eTech_htgs_3

finished High Throughput sequence

@ eTech_htgs_1

unordered High Throughput sequence contig

@ eTech_wgs

whole genome shotgun sequencing

@ eTech_htgs_0

single genomic reads for coordination

@ e_Genbank

GenBank specific info.

@ e_Molinfo

info on the molecule and techniques

@ eType_clone

Deprecated. Used only for AGP 1.1.

@ eType_fragment

Deprecated. Used only for AGP 1.1.

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