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NCBI C++ ToolKit: include/gui/widgets/hit_matrix/dense_ds.hpp Source File

(

objects::CSeq_id&

) : m_SeqId(&id) {}

()

{

m_Row; }

CanCreateRowBased()

;

SelectIds(

& q_id,

SelectDefaultIds();

& GetHitSeqIds();

GetHitSeqIdsForParams(

& ids,

& params)

;

GetAlignedIdsForParams(

&

,

objects::CScope&

();

& GetSubjectId()

;

objects::CBioseq_Handle GetQueryHandle();

objects::CBioseq_Handle GetSubjectHandle();

objects::CBioseq_Handle GetBioseqHandle(

&

);

GetScoreNames(vector<string>&

)

;

GetScoreRange(

& name)

;

objects::CSeq_align::TSegs::TStd

;

x_TestAndSelectAlign(

objects::CSeq_align& align);

x_GoodSeg(

& std_list);

x_CanCreateRowBased();

x_UpdateScoreMap();

x_GetSeqAlignIds(

objects::CSeq_align& align,

x_GetAlignedSeqIds(

& align,

x_CreateHits(

objects::CSeq_align& align);

x_CreateHit(

objects::CSeq_align& align,

q_index,

s_index);

x_CreateHit_Denseg(

objects::CSeq_align& align,

q_index,

s_index);

x_CreateHit_Std(

objects::CSeq_align& align,

q_index,

s_index);

x_CreateHits_Diagonal(

objects::CSeq_align& align,

q_index,

s_index);

x_CalculateHitsRange();

User-defined methods of the data storage class.

Container mapping seq-aligns to vectors of participating seq-ids.

Helper class which collects seq-align statistics: seq-ids participating in alignments and rows,...

objects::CBioseq_Handle m_QueryHandle

vector< const CSeq_align * > TAlnPtrVector

vector< CConstRef< objects::CSeq_id > > TSeqIdRefVector

TSeqRange m_SubjectHitsRange

objects::CBioseq_Handle m_SubjectHandle

map< string, TValueRange > TScoreMap

THIdToHandleMap m_HIdToHandleMap

list of Ids for all sequences

unique_ptr< IHitSeqId > m_QueryID

set< objects::CBioseq_Handle > THIdToHandleMap

CAlnIdMap< TAlnPtrVector, TIdExtract > TAlnIdMap

vector< TSeqIdPtr > TSeqIdVector

objects::CSeq_align::TSegs::TStd TStd

const CSeq_id * TSeqIdPtr

unique_ptr< IHitSeqId > m_SubjectID

CAlnStats< TAlnIdMap > TAlnStats

unique_ptr< TAlnIdMap > m_AlnIdMap

CAlnSeqIdsExtract< CAlnSeqId > TIdExtract

CRef< objects::CScope > m_Scope

TSeqRange m_QueryHitsRange

CRef< TAlnStats > m_AlnStats

CConstRef< objects::CSeq_id > m_SeqId

CHitSeqId(const objects::CSeq_id &id)

CHitSeqId(const CHitSeqId &id)

virtual CConstRef< objects::CSeq_id > GetSeqId() const

returns CSeq_id associated with IHitSeqId

CConstRef< objects::CSeq_id > m_SeqId

IHitMatrixDataSource - abstract Data Source for Hit Matrix Widget.

vector< CConstRef< objects::CSeq_align > > TAlignVector

vector< IHitSeqId * > TIdVector

vector< IHit * > THitAdapterCont

pair< double, double > TValueRange

IHitSeqId - abstract identifier of a sequence in an alignment.

virtual CConstRef< objects::CSeq_id > GetSeqId() const =0

returns CSeq_id associated with IHitSeqId

virtual IHitSeqId * Clone() const =0

virtual bool Equals(const IHitSeqId &id) const =0

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

static const struct name_t names[]

string GetLabel(const CSeq_id &id)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

virtual void SetParams()

Called at the beginning of Run, before creating thread pool.

#define NCBI_GUIWIDGETS_HIT_MATRIX_EXPORT

Defines to provide correct exporting from DLLs in Windows.

static CRef< CUser_object > GetParams()

#define row(bind, expected)

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