CVectorScreen Class Reference

Search Toolkit Book for CVectorScreen

#include <gui/widgets/edit/vectorscreen.hpp>

Collaboration diagram for CVectorScreen:

Public Member Functions
	CVectorScreen ()
	Constructors. More...
	~CVectorScreen ()
	Destructor. More...
void	Run (objects::CSeq_entry_Handle seh, wxGauge &progress)
const vector< CVecscreenRun::SVecscreenSummary > &	GetVecscreenSummary () const
const TVecscreenSummaryBySeqid &	GetVecscreenSummaryBySeqid () const

Static Public Member Functions
static bool	IsDbAvailable ()

Protected Member Functions
CRef< CSeq_id >	x_SelectSeqId (CBioseq_Handle bioseq_handle)
CRef< CSeq_id >	x_FindAccession (CBioseq_Handle bioseq_handle)
CRef< CSeq_id >	x_FindTypeGeneral (CBioseq_Handle bioseq_handle)
CRef< CSeq_id >	x_FindLocalId (CBioseq_Handle bioseq_handle)

Private Types
typedef vector< CRef< CSeq_loc > >	TSearchLocVec

Private Attributes
objects::CSeq_entry_Handle	m_TopSeqEntry
TSearchLocVec	m_vecSearchLocs
vector< CVecscreenRun::SVecscreenSummary >	m_vecscreen_summary
TVecscreenSummaryBySeqid	m_seqidSummary

Detailed Description

CVectorScreen class declaration

Definition at line 111 of file vectorscreen.hpp.

Member Typedef Documentation

TSearchLocVec

typedef vector< CRef<CSeq_loc> > CVectorScreen::TSearchLocVec

private

Definition at line 138 of file vectorscreen.hpp.

Constructor & Destructor Documentation

CVectorScreen()

CVectorScreen::CVectorScreen

(

)

Constructors.

CVectorScreen constructors

Definition at line 79 of file vectorscreen.cpp.

~CVectorScreen()

CVectorScreen::~CVectorScreen

(

)

Destructor.

CVectorScreen destructor

Definition at line 88 of file vectorscreen.cpp.

Member Function Documentation

GetVecscreenSummary()

const vector< CVecscreenRun::SVecscreenSummary > & CVectorScreen::GetVecscreenSummary

(

)

const

Definition at line 237 of file vectorscreen.cpp.

References m_vecscreen_summary.

GetVecscreenSummaryBySeqid()

const TVecscreenSummaryBySeqid & CVectorScreen::GetVecscreenSummaryBySeqid

(

)

const

Definition at line 244 of file vectorscreen.cpp.

References m_seqidSummary.

Referenced by CVectorTrimPanel::OnRunVecscreen().

IsDbAvailable()

bool CVectorScreen::IsDbAvailable ( )

static

Definition at line 92 of file vectorscreen.cpp.

References CSearchDatabase::eBlastDbIsNucleotide, CSearchDatabase::GetSeqDb(), kUniVecDatabase, and CRef< C, Locker >::NotNull().

Referenced by CVectorTrimPanel::CreateControls().

Run()

void CVectorScreen::Run	(	objects::CSeq_entry_Handle	seh,
		wxGauge &	progress
	)

Definition at line 99 of file vectorscreen.cpp.

References CScope::AddDataLoader(), CScope::AddScope(), CSeq_id::AsFastaString(), ASSERT, map_checker< Container >::clear(), CBlastOptionsFactory::CreateTask(), CSearchDatabase::eBlastDbIsNucleotide, CSeq_inst_Base::eMol_na, CVecscreen::eNoMatch, CObjectManager::eNonDefault, CBlastDbDataLoader::eNucleotide, NStr::FindNoCase(), CVecscreen::GetAlnInfoList(), CSeq_loc::GetId(), CObjectManager::GetInstance(), GetLength(), SRegisterLoaderInfo< TLoader >::GetLoader(), CDataLoader::GetName(), CSysPath::GetResourcePath(), CVecscreen::GetStrengthString(), map_checker< Container >::insert(), CRef< C, Locker >::IsNull(), CObjectManager::kPriority_NotSet, kUniVecDatabase, SVecscreenResult::m_arrRangeMatch, SRangeMatch::m_match_type, SRangeMatch::m_range, m_seqidSummary, m_TopSeqEntry, m_vecscreen_summary, m_vecSearchLocs, CVecscreenRun::SVecscreenSummary::match_type, NON_CONST_ITERATE, NPOS, CVecscreen::ProcessSeqAlign(), query, CVecscreenRun::SVecscreenSummary::range, CBlastDbDataLoader::RegisterInObjectManager(), results, CLocalBlast::Run(), CVecscreenRun::SVecscreenSummary::seqid, CBlastOptionsHandle::SetHitlistSize(), CVecscreen::SetImagePath(), CSeq_loc::SetWhole(), CVecscreen::VecscreenPrint(), and x_SelectSeqId().

Referenced by CVectorTrimPanel::OnRunVecscreen().

x_FindAccession()

CRef< CSeq_id > CVectorScreen::x_FindAccession ( CBioseq_Handle  bioseq_handle )

protected

Definition at line 281 of file vectorscreen.cpp.

References CTextseq_id_Base::CanGetAccession(), CTextseq_id_Base::GetAccession(), CBioseq_Handle::GetId(), CSeq_id_Handle::GetSeqIdOrNull(), ITERATE, and NULL.

Referenced by x_SelectSeqId().

x_FindLocalId()

CRef< CSeq_id > CVectorScreen::x_FindLocalId ( CBioseq_Handle  bioseq_handle )

protected

Definition at line 327 of file vectorscreen.cpp.

References CSeq_id_Base::e_Local, CObject_id_Base::GetId(), CBioseq_Handle::GetId(), CSeq_id_Handle::GetSeqIdOrNull(), CObject_id_Base::GetStr(), CObject_id_Base::IsId(), CSeq_id_Base::IsLocal(), CObject_id_Base::IsStr(), and ITERATE.

Referenced by x_SelectSeqId().

x_FindTypeGeneral()

CRef< CSeq_id > CVectorScreen::x_FindTypeGeneral ( CBioseq_Handle  bioseq_handle )

protected

Definition at line 304 of file vectorscreen.cpp.

References CSeq_id_Base::GetGeneral(), CBioseq_Handle::GetId(), CSeq_id_Handle::GetSeqIdOrNull(), CSeq_id_Base::IsGeneral(), and ITERATE.

Referenced by x_SelectSeqId().

x_SelectSeqId()

CRef< CSeq_id > CVectorScreen::x_SelectSeqId ( CBioseq_Handle  bioseq_handle )

protected

Definition at line 250 of file vectorscreen.cpp.

References CBioseq_Handle::CanGetId(), x_FindAccession(), x_FindLocalId(), and x_FindTypeGeneral().

Referenced by Run().

Member Data Documentation

m_seqidSummary

TVecscreenSummaryBySeqid CVectorScreen::m_seqidSummary

private

Definition at line 145 of file vectorscreen.hpp.

Referenced by GetVecscreenSummaryBySeqid(), and Run().

m_TopSeqEntry

objects::CSeq_entry_Handle CVectorScreen::m_TopSeqEntry

private

Definition at line 137 of file vectorscreen.hpp.

Referenced by Run().

m_vecscreen_summary

vector<CVecscreenRun::SVecscreenSummary> CVectorScreen::m_vecscreen_summary

private

Definition at line 142 of file vectorscreen.hpp.

Referenced by GetVecscreenSummary(), and Run().

m_vecSearchLocs

TSearchLocVec CVectorScreen::m_vecSearchLocs

private

Definition at line 139 of file vectorscreen.hpp.

Referenced by Run().

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The documentation for this class was generated from the following files:

• include/gui/widgets/edit/vectorscreen.hpp
• src/gui/widgets/edit/vectorscreen.cpp