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

(find(ids.begin(), ids.end(),

) == ids.end()) {

(! loc.

())

;

((*it)->IsPacked_int()) {

any_nulls_seen =

;

any_nulls_seen =

;

( any_nulls_seen && ! new_mix_pieces.empty() ) {

new_mix_pieces.push_back( null_piece );

old_piece->

().Assign(seqint);

new_mix_pieces.push_back( old_piece );

( any_nulls_seen && ! new_mix_pieces.empty() ) {

new_mix_pieces.push_back( null_piece );

old_piece->

(curr);

new_mix_pieces.push_back( old_piece );

new_loc->

(*new_mix);

suppress_accession)

( ; loc_ci; ++loc_ci ) {

( cached_handle ) {

(! show_all_accns) {

(

.GetHandle().IsSynonym( loc_ci.

() ) ) {

handles_set.

( handle );

( ! handles_set.

() )

vector<CSeq_id_Handle> handles_vec;

back_inserter(handles_vec) );

.GetScope().GetAccVers( &

, handles_vec );

(

id_idx = 0; id_idx < handles_vec.size(); ++id_idx ) {

handles_vec[id_idx], acc_handle );

(*flat, oss,

,

,

, show_all_accns, add_join, suppress_accession);

(loc, oss,

,

,

, show_all_accns, add_join, suppress_accession);

suppress_accession)

is_flat_order =

;

* prefix =

;

oss <<

;

(*rev_loc, oss,

,

,

, show_all_accns, add_join, suppress_accession);

( loc.

() ) {

is_flat_order =

;

is_flat_order =

;

( loc.

() ) {

(fuzz && fuzz->

() &&

oss << uLength <<

;

(loc.

(), oss,

,

, show_comp, show_all_accns, suppress_accession);

* delim =

;

(!

(**it, oss,

,

, show_comp, show_all_accns, suppress_accession)) {

(loc.

(), oss,

,

, show_comp, show_all_accns, suppress_accession);

oss <<

;

* delim =

;

* delim =

;

( !has_one || add_join ) {

join_inside_order =

;

this_is_virtual = next_is_virtual;

( is_flat_order ) {

( ( this_loc.

() || this_loc.

() ) &&

! join_inside_order && ! this_is_virtual && ! next_is_virtual ) {

join_inside_order =

;

( this_is_virtual && ! print_virtual ) {

(!

(this_loc, oss,

,

, show_comp, show_all_accns,

, suppress_accession)) {

( is_flat_order ) {

( join_inside_order && next_is_virtual ) {

join_inside_order =

;

( join_inside_order ) {

( !has_one || add_join ) {

* delim =

;

(!

(**it, oss,

,

, show_comp, show_all_accns, suppress_accession)) {

(bond.

(), oss,

,

, show_comp, show_all_accns, suppress_accession);

(bond.

(), oss,

,

, show_comp, show_all_accns, suppress_accession);

(!

.IsSetFuzz_to()) {

(to_fuzz.

()) {

( to_fuzz.

() ) {

suppress_accession)

do_html =

.Config().DoHTML();

oss <<

;

(

.GetId(), oss,

,

, show_all_accns, suppress_accession);

suppress_accession)

do_html =

.Config().DoHTML();

oss <<

;

suppress_accession)

( fuzz->

() ) {

oss <<

<< pnt - fuzz->

() <<

;

( bFromSeqPoint ) {

oss << pnt <<

<< pnt <<

;

oss << pnt + fuzz->

() <<

;

oss << ( bFromSeqPoint ?

:

)

<< ( bFromSeqPoint ?

:

)

<< ( bFromSeqPoint ?

:

);

= 0.001 * pnt * fuzz->

();

start =

(pnt -

);

end =

(pnt +

);

( bFromSeqPoint ) {

oss << start <<

<< end;

oss <<

<< start <<

<< end <<

;

( fuzz->

() ) {

( bFromSeqPoint ) {

oss << pnt <<

<< (pnt + 1);

oss << (html ==

?

:

) << pnt;

( bFromSeqPoint ) {

oss << (pnt - 1) <<

<< pnt;

oss << (html ==

?

:

) << pnt;

suppress_accession)

(! show_all_accns) {

(

.GetHandle().IsSynonym(

)) {

oss <<

.GetAccession() <<

;

(suppress_accession) {

( idp->

() ) {

CFlatSeqLoc::TToAccessionMap::const_iterator map_iter =

m_TheMap.find(

);

( map_iter == m_TheMap.end() ) {

map_iter->second;

bool IsReverse(ENa_strand s)

TLength GetLength(void) const

const CInt_fuzz * GetFuzz() const

CFastMutex m_MutexForTheMap

void Insert(CSeq_id_Handle from, CSeq_id_Handle to)

CSeq_id_Handle Get(CSeq_id_Handle query)

bool x_FuzzToDisplayed(const CSeq_interval &si) const

bool x_Add(const CSeq_loc &loc, ostream &oss, CBioseqContext &ctx, TType type, bool show_comp, bool show_all_accns=false, bool join_whole_loc=false, bool suppress_accession=false)

CFlatSeqLoc(const CSeq_loc &loc, CBioseqContext &ctx, TType type=eType_location, bool show_all_accns=false, bool add_join=false, bool suppress_accession=false)

static CGuardedToAccessionMap m_ToAccessionMap

void x_AddID(const CSeq_id &id, ostream &oss, CBioseqContext &ctx, TType type, bool show_all_accns=false, bool suppress_accession=false)

bool x_IsAccessionVersion(CSeq_id_Handle id)

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

static const char si[8][64]

static bool s_NeedsFlattening(const CSeq_loc &loc)

static bool s_IsVirtualSeqInt(const CSeq_interval &seqint, const CBioseq_Handle &seq)

static bool s_IsVirtualLocation(const CSeq_loc &loc, const CBioseq_Handle &seq)

static CConstRef< CSeq_loc > s_FlattenLoc(const CSeq_loc &loc)

static bool s_IsVirtualId(const CSeq_id_Handle &id, const CBioseq_Handle &seq)

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

void Rewind(void)

Reset the iterator to the initial state.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Override Assign() to incorporate cache invalidation.

CSeq_id_Handle GetSeq_id_Handle(void) const

const CSeq_loc & GetEmbeddingSeq_loc(void) const

Get the nearest seq-loc containing the current range.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

const CSeq_id & GetSeq_id(void) const

Get seq_id of the current location.

void SetNull(void)

Override all setters to incorporate cache invalidation.

@ eEmpty_Allow

ignore empty locations

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

CSeq_loc * SeqLocRevCmpl(const CSeq_loc &loc, CScope *scope)

Get reverse complement of the seq-loc (?)

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

vector< CSeq_id_Handle > TSeq_id_Handles

Bulk retrieval methods Common argument typedef - vector of requested ids.

@ eGetBioseq_Loaded

Search in all loaded TSEs in the scope.

vector< CSeq_id_Handle > TId

TInst_Repr GetInst_Repr(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

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.

bool IsLim(void) const

Check if variant Lim is selected.

TPct GetPct(void) const

Get the variant data.

TLim GetLim(void) const

Get the variant data.

TMin GetMin(void) const

Get the Min member data.

E_Choice Which(void) const

Which variant is currently selected.

TMax GetMax(void) const

Get the Max member data.

TP_m GetP_m(void) const

Get the variant data.

const TRange & GetRange(void) const

Get the variant data.

@ eLim_tl

space to left of position

@ eLim_tr

space to right of position

@ e_Pct

% plus or minus (x10) 0-1000

@ e_P_m

plus or minus fixed amount

bool IsMix(void) const

Check if variant Mix is selected.

const TB & GetB(void) const

Get the B member data.

list< CRef< CSeq_interval > > Tdata

ENa_strand

strand of nucleic acid

const Tdata & Get(void) const

Get the member data.

TStrand GetStrand(void) const

Get the Strand member data.

const TId & GetId(void) const

Get the Id member data.

const TPnt & GetPnt(void) const

Get the variant data.

TPoint GetPoint(void) const

Get the Point member data.

const TWhole & GetWhole(void) const

Get the variant data.

bool IsSetStrand(void) const

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

bool IsSetFuzz(void) const

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

list< CRef< CSeq_loc > > Tdata

const TFuzz & GetFuzz(void) const

Get the Fuzz member data.

bool CanGetA(void) const

Check if it is safe to call GetA method.

E_Choice Which(void) const

Which variant is currently selected.

const TId & GetId(void) const

Get the Id member data.

E_Choice Which(void) const

Which variant is currently selected.

const TId & GetId(void) const

Get the Id member data.

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.

const Tdata & Get(void) const

Get the member data.

const TEquiv & GetEquiv(void) const

Get the variant data.

list< CRef< CSeq_loc > > Tdata

vector< TSeqPos > TPoints

bool IsPacked_int(void) const

Check if variant Packed_int is selected.

const TA & GetA(void) const

Get the A member data.

bool CanGetB(void) const

Check if it is safe to call GetB method.

bool CanGetPoint(void) const

Check if it is safe to call GetPoint method.

bool CanGetFuzz(void) const

Check if it is safe to call GetFuzz method.

bool IsSetStrand(void) const

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

const TPoints & GetPoints(void) const

Get the Points member data.

bool IsSetId(void) const

WARNING: this used to be optional Check if a value has been assigned to Id data member.

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 TFuzz & GetFuzz(void) const

Get the Fuzz member 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.

@ e_Gi

GenInfo Integrated Database.

@ e_Equiv

equivalent sets of locations

@ e_Empty

to NULL one Seq-id in a collection

@ e_Feat

indirect, through a Seq-feat

@ eRepr_virtual

no seq data

double value_type

The numeric datatype used by the parser.

const CharType(& source)[N]

Int4 delta(size_t dimension_, const Int4 *score_)

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

const char * strLinkBaseEntrezViewer

Generic utility macros and templates for exploring NCBI objects.

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