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NCBI C++ ToolKit: include/gui/widgets/seq_text/seq_text_ds.hpp Source File

(

splice_buffer,

before_loc,

is_minus)

;

ChooseBetterSubtype (

subtype1,

subtype2);

SequencePosToSourcePos (

sequence_pos,

*found_in_source =

);

GetToolTipForSourcePos (

source_pos);

vector<CConstRef<objects::CSeq_feat> > GetFeaturesAtPosition(

source_pos);

FindSequenceFragment (

& fragment,

start_search);

IsmRNASequence ();

objects::CSeq_loc*

()

;

objects::CBioseq_Handle

() {

m_SubjectHandle;}

x_PopulateFeatureIterators();

@ eExtreme_Positional

numerical value

bool GetSeqData(ParserPtr pp, const DataBlk &entry, CBioseq &bioseq, Int4 nodetype, unsigned char *seqconv, Uint1 seq_data_type)

bool SourcePosToIntervalPos(TSeqPos &pos) const

void GetFeaturesAtPosition(TSeqPos source_pos, vector< CConstRef< objects::CSeq_feat > > &features)

bool IntersectingSourceInterval(TSeqPos &src_start, TSeqPos &src_stop) const

void GetSeqData(TSeqPos src_start, TSeqPos src_stop, string &buffer, objects::SAnnotSelector *feat_sel) const

void RenderFeatureExtras(ISeqTextGeometry *pParent, TSeqPos start_offset, TSeqPos stop_offset)

objects::CBioseq_Handle m_Seq

objects::CBioseq_Handle GetSeq()

~CSeqTextDataSourceInterval()

objects::CSeqVector m_Vect

bool SequencePosToIntervalPos(TSeqPos &pos) const

TSeqPos GetLength() const

TSeqPos GetSequenceStart() const

void GetSubtypesForAlternatingExons(TSeqPos start_offset, TSeqPos stop_offset, ISeqTextGeometry *pParent, CSeqTextDefs::TSubtypeVector &subtypes, bool &even)

void x_AddVariationsFromFeature(const objects::CSeq_feat &feat, const objects::CSeq_loc &loc, CSeqTextDefs::TVariationGraphVector &variations) const

void GetSeqString(TSeqPos src_start, TSeqPos src_stop, string &buffer) const

void LookForSpliceJunctions(const objects::CMappedFeat &feat, CSeqTextDefs::TSpliceSiteVector &splice_sites, TSeqPos start_offset, TSeqPos stop_offset) const

CSeqTextDataSourceInterval(const objects::CSeq_loc &loc, objects::CScope &scope, TSeqPos offset)

bool x_IsSpliceSite(string splice_buffer, bool before_loc, bool is_minus) const

void GetFeatureData(TSeqPos start_offset, TSeqPos stop_offset, CSeqTextConfig *cfg, ISeqTextGeometry *pParent, CSeqTextDefs::TSubtypeVector &subtypes, CSeqTextDefs::TSpliceSiteVector &splice_sites, CSeqTextDefs::TVariationGraphVector &variations)

CRef< objects::CSeq_loc > m_Loc

void GetToolTipForPosition(TSeqPos src_pos, string &tooltip_text)

CRef< objects::CSeq_loc > x_GetSeqLocForInterval(TSeqPos interval_start, TSeqPos interval_stop) const

TSeqPos GetSourceStart() const

TSeqPos GetSourceStop() const

TSeqPos GetSequenceStop() const

objects::ENa_strand GetStrand() const

void GetVariations(TSeqPos start_offset, TSeqPos stop_offset, CSeqTextDefs::TVariationGraphVector &variations)

CSeqTextDataSource implements Adapter design pattern.

vector< CSeqTextDataSourceInterval > TIntervalList

CRef< objects::CSeq_entry > m_Sep

CConstRef< objects::CSeq_id > TIdRef

CRef< objects::CSeq_loc > m_Loc

vector< bool > TAvailableSubtypeVector

objects::CBioseq_Handle m_SubjectHandle

CSeqTextDataSource(objects::CSeq_entry &sep, objects::CScope &scope)

CSeqTextDataSource(objects::CBioseq_Handle handle, objects::CScope &scope)

CSeqTextDataSource(objects::CSeq_loc &loc, objects::CScope &scope)

TIntervalList m_Intervals

objects::CBioseq_Handle GetSeq()

CRef< objects::CScope > m_Scope

vector< CSeqTextVariationGraph > TVariationGraphVector

vector< bool > TSpliceSiteVector

vector< int > TSubtypeVector

vector< TSeqPos > TSeqPosVector

Interface for testing cancellation request in a long lasting operation.

Include a standard set of the NCBI C++ Toolkit most basic headers.

unsigned int TSeqPos

Type for sequence locations and lengths.

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,...

NCBI_XOBJUTIL_EXPORT string GetTitle(const CBioseq_Handle &hnd, TGetTitleFlags flags=0)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_GUIWIDGETS_SEQTEXT_EXPORT

ENa_strand

strand of nucleic acid

Defines to provide correct exporting from DLLs in Windows.

Miscellaneous common-use basic types and functionality.

int GetLoc(const string &acc, const string &pat, CSeq_loc &loc, CScope &scope)

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