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NCBI C++ ToolKit: src/gui/objects/assembly_info.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <objmgr/util/sequence.hpp>
#include <misc/xmlwrapp/xmlwrapp.hpp>
#include <util/xregexp/regexp.hpp>
#include <gui/objutils/gui_eutils_client.hpp>
#include <gui/objutils/gencoll_svc.hpp>
#include <gui/objutils/entrez_conversion.hpp>
#include <gui/objects/DL_Assembly.hpp>
#include <gui/objects/DL_TaxId.hpp>
#include <util/icanceled.hpp>
#include <gui/objects/assembly_info.hpp>
#include <objects/genomecoll/GCClient_EquivalentAssembl.hpp>
#include <objects/genomecoll/GCClient_GetEquivalentAsse.hpp>

Include dependency graph for assembly_info.cpp:

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Functions   USING_SCOPE (objects)   static bool  s_AssmCompare (const CRef< CDL_Assembly > &assm1, const CRef< CDL_Assembly > &assm2)   static void  s_GetAssmEquiv (CGenomicCollectionsService &gc, const string &acc, set< string > &equiv_accs)   static bool  s_IsAsmAccEquiv (CGenomicCollectionsService &gc, const string &acc1, const string &acc2)   Variables static const string  kTaxDb = "taxonomy"   static const string  kNucDb = "nucleotide"   static const string  kAssmDb = "assembly"   static const int  kRetMax = 5000   Function Documentation ◆ s_AssmCompare() static bool s_AssmCompare ( const CRef< CDL_Assembly > &  assm1, const CRef< CDL_Assembly > &  assm2  ) static

Definition at line 340 of file assembly_info.cpp.

Referenced by CAssemblyInfo::x_SortAssms().

◆ s_GetAssmEquiv() static void s_GetAssmEquiv ( CGenomicCollectionsService &  gc, const string &  acc, set< string > &  equiv_accs  ) static

Definition at line 402 of file assembly_info.cpp.

References set< Key, Compare >::clear(), CGCClient_GetEquivalentAssembliesRequest_Base::eEquivalency_all_types_same_coordinates, CGenomicCollectionsService::GetEquivalentAssemblies(), set< Key, Compare >::insert(), and ITERATE.

Referenced by CAssemblyInfo::IsSameAssembly(), and s_IsAsmAccEquiv().

◆ s_IsAsmAccEquiv() static bool s_IsAsmAccEquiv ( CGenomicCollectionsService &  gc, const string &  acc1, const string &  acc2  ) static

Definition at line 413 of file assembly_info.cpp.

References set< Key, Compare >::end(), NStr::EqualNocase(), Error(), set< Key, Compare >::find(), LOG_POST, and s_GetAssmEquiv().

Referenced by CAssemblyInfo::IsSameAssembly().

◆ USING_SCOPE() USING_SCOPE ( objects  ) Variable Documentation ◆ kAssmDb const string kAssmDb = "assembly" static

Definition at line 57 of file assembly_info.cpp.

Referenced by CAssemblyInfo::GetAssms_Gi(), CAssemblyInfo::GetAssms_TaxId(), CAssemblyInfo::GetAssms_Term(), CAssemblyInfo::IsSameAssembly(), CAssemblyInfo::x_FilterTaxIds(), and CAssemblyInfo::x_GetAssmInfo().

◆ kNucDb const string kNucDb = "nucleotide" static

Definition at line 56 of file assembly_info.cpp.

Referenced by CAssemblyInfo::GetAssms_Gi().

◆ kRetMax const int kRetMax = 5000 static

Definition at line 58 of file assembly_info.cpp.

Referenced by CAssemblyInfo::IsSameAssembly(), CAssemblyInfo::x_FilterTaxIds(), CAssemblyInfo::x_GetAssmInfo(), and CAssemblyInfo::x_SearchIds().

◆ kTaxDb const string kTaxDb = "taxonomy" static

Definition at line 55 of file assembly_info.cpp.

Referenced by CAssemblyInfo::GetAssms_Term(), and CAssemblyInfo::x_ValidateTaxId().

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