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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/Std__seg_8cpp_source.html below:

NCBI C++ ToolKit: src/objects/seqalign/Std_seg.cpp Source File

60 const size_t

& dim =

GetDim

();

63 "CStd_seg::CheckNumRows():" 64 " loc.size is inconsistent with dim"

);

68 "CStd_seg::CheckNumRows():" 69 " ids.size is inconsistent with dim"

);

80 if

(row_i++ ==

row

) {

82 return

(*i)->GetInt().GetFrom();

88 if

(row < 0 || row >=

GetDim

()) {

90 "CStd_seg::GetSeqStart():" 91 " Invalid row number"

);

94 "CStd_seg::GetSeqStart():" 95 " loc.size is inconsistent with dim"

);

105 return

(*i)->GetInt().GetTo();

111 if

(row < 0 || row >=

GetDim

()) {

113 "CStd_seg::GetSeqStop():" 114 " Invalid row number"

);

117 "CStd_seg::GetSeqStop():" 118 " loc.size is inconsistent with dim"

);

139 "CStd_seg::SwapRows():" 140 " Invalid row number"

);

159 if

(row < 0 || row >=

GetDim

()) {

161 "CStd_seg::GetSeqRange():" 162 " Invalid row number"

);

165 "CStd_seg::GetSeqRange():" 166 " loc.size is inconsistent with dim"

);

174 if

(

offset

== 0)

return

;

178 switch

(src_loc.

Which

()) {

184 "Negative offset greater than seq position"

);

195 "Negative offset greater than seq position"

);

204 "CStd_seg::OffsetRow only supports pnt and int source seq-locs"

);

215 switch

(dst_loc.

Which

()) {

222 "CStd_seg::RemapToLoc only supports int target seq-locs"

);

225 if

(row < 0 || row >=

GetDim

()) {

227 "CStd_seg::RemapToLoc():" 228 " Invalid row number"

);

239 const CSeq_id

* single_src_id = 0;

240

src_loc.

CheckId

(single_src_id);

243 const CSeq_id

* single_dst_id = 0;

244

dst_loc.

CheckId

(single_dst_id);

247 if

( !single_src_id->

Equals

(*single_dst_id) ||

250 "CStd_seg::RemapToLoc target seq-loc id does not equal row's id."

);

256 string

errstr(

"CStd_seg::RemapToLoc():" 257 " Target Seq-loc is not long enough to" 258 " cover the Std-seg's seq-loc!" 259 " Maximum row seq pos is "

);

261

errstr +=

". The total seq-loc len is only "

;

263

errstr +=

", it should be at least "

;

265

errstr +=

" (= max seq pos + 1)."

;

270 switch

(src_loc.

Which

()) {

274 if

( !ignore_strand ) {

280 if

( !ignore_strand ) {

288 "CStd_seg::RemapToLoc only supports pnt and int source seq-locs"

);

297 "Invalid row number in CreateRowSeq_interval(): "

@ eExtreme_Positional

numerical value

void Validate(bool full_test=false) const

void SwapRows(TDim row1, TDim row2)

Swap two rows (changing *order*, not content)

TSignedSeqPos GetSeqStop(TDim row) const

TDim CheckNumRows(void) const

TSignedSeqPos GetSeqStart(TDim row) const

void RemapToLoc(TDim row, const CSeq_loc &dst_loc, bool ignore_strand=false)

CRef< CSeq_loc > CreateRowSeq_loc(TDim row) const

CRange< TSignedSeqPos > GetSeqRange(TDim row) const

void OffsetRow(TDim row, TSignedSeqPos offset)

Offset row's coords.

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.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define NCBI_THROW(exception_class, err_code, message)

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

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

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

Override Assign() to incorporate cache invalidation.

bool CheckId(const CSeq_id *&id, bool may_throw=true) const

check that the 'id' field in all parts of the location is the same as the specifies id.

TSeqPos GetStop(ESeqLocExtremes ext) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Convert int to string.

TIds & SetIds(void)

Assign a value to Ids data member.

vector< CRef< CSeq_loc > > TLoc

const TLoc & GetLoc(void) const

Get the Loc member data.

const TIds & GetIds(void) const

Get the Ids member data.

TLoc & SetLoc(void)

Assign a value to Loc data member.

bool IsSetIds(void) const

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

TDim GetDim(void) const

Get the Dim member data.

const TPnt & GetPnt(void) const

Get the variant data.

TPoint GetPoint(void) const

Get the Point member data.

TFrom GetFrom(void) const

Get the From member data.

E_Choice Which(void) const

Which variant is currently selected.

TStrand GetStrand(void) const

Get the Strand member data.

TTo GetTo(void) const

Get the To member data.

const TInt & GetInt(void) const

Get the variant data.

@ e_Empty

to NULL one Seq-id in a collection

const struct ncbi::grid::netcache::search::fields::SIZE size

#define row(bind, expected)

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