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NCBI C++ ToolKit: src/algo/blast/unit_tests/api/test_objmgr.cpp Source File

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47 #ifndef SKIP_DOXYGEN_PROCESSING 59 throw

std::runtime_error(

"Could not initialize object manager"

);

90

seqloc->SetInt().SetFrom(0);

92

seqloc->SetInt().SetStrand(strand);

93

seqloc->SetInt().SetId().Assign(

id

);

95 return new SSeqLoc

(seqloc, scope);

100

pair<TSeqPos, TSeqPos> range,

105

scope->AddDefaults();

107

seqloc->SetInt().SetFrom(range.first);

108

seqloc->SetInt().SetTo(range.second);

109

seqloc->SetInt().SetStrand(strand);

110

seqloc->SetInt().SetId().Assign(

id

);

112 return new SSeqLoc

(seqloc, scope);

132 return new SSeqLoc

(seqloc, scope);

144 return new SSeqLoc

(seqloc, scope);

154

seqloc->

SetInt

().SetFrom(0);

156

seqloc->

SetInt

().SetStrand(strand);

157

seqloc->

SetInt

().SetId().Assign(

id

);

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

This class wraps the C++ Object Manager to control its lifetime and to facilitate the creation of SSe...

blast::SSeqLoc * CreateSSeqLoc(objects::CSeq_id &id, objects::ENa_strand s=objects::eNa_strand_unknown)

CRef< blast::CBlastSearchQuery > CreateBlastSearchQuery(objects::CSeq_id &id, objects::ENa_strand s=objects::eNa_strand_unknown)

objects::CObjectManager & GetObjMgr()

blast::SSeqLoc * CreateEmptySSeqLoc(objects::CSeq_id &id)

static CTestObjMgr & Instance()

static unique_ptr< CTestObjMgr > m_Instance

blast::SSeqLoc * CreateWholeSSeqLoc(objects::CSeq_id &id)

CRef< objects::CObjectManager > m_ObjMgr

Collection of masked regions for a single query sequence.

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

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

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

ENa_strand

strand of nucleic acid

Definition of SSeqLoc structure.

Structure to represent a single sequence to be fed to BLAST.

Utility stuff for more convenient using of Boost.Test library.

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