NCBI C++ ToolKit
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CAssemblyInfo Class Reference

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#include <gui/objects/assembly_info.hpp>

Static Public Member Functions

static CRef< objects::CDL_AssmInfo > GetAssms_Gi (TGi gi, const string &release_type=NcbiEmptyString)
 
static CRef< objects::CDL_AssmInfo > GetAssms_TaxId (const string &tax_id, const string &release_type=NcbiEmptyString)
 
static CRef< objects::CDL_AssmInfo > GetAssms_Term (const string &term, const string &release_type=NcbiEmptyString, ICanceled *cancel=0)
 
static bool IsSameAssembly (const objects::CGC_Assembly &gc_assm, const string &term)
 Check if assembly name (e.g. hg19, grch37) matches CGC_Assembly. More...
 

Static Private Member Functions

static bool x_ValidateTaxId (const string &tax_id)
 validate if the given tax-id. More...
 
static void x_FilterTaxIds (CSeqUtils::TEntrezIds &uids)
 filter out the tax ids that don't have assembly on them. More...
 
static void x_SearchIds (const string &term, const string &db, CSeqUtils::TEntrezIds &uids)
 search all related links in the given db with a search term. More...
 
static void x_GetAssmInfo (const CSeqUtils::TEntrezIds &uids, objects::CDL_AssmInfo::TAssemblies &assms)
 get detailed assembly information for a list of gencoll ids. More...
 
static void x_FilterAssemblies (objects::CDL_AssmInfo::TAssemblies &assms, const string &release_type)
 filter the assemblies by release type and category=full-assembly. More...
 
static void x_SortAssms (objects::CDL_AssmInfo::TAssemblies &assms)
 sort assemblies based on release date. More...
 
static CRef< objects::CDL_AssmInfo > x_CreateAssmInfo (objects::CDL_AssmInfo::TAssemblies &assms)
 

Detailed Description

Definition at line 48 of file assembly_info.hpp.

Member Function Documentation

◆ GetAssms_Gi()

CRef< CDL_AssmInfo > CAssemblyInfo::GetAssms_Gi ( TGi  gi,
const string release_type = NcbiEmptyString 
)
static

◆ GetAssms_TaxId()

CRef< CDL_AssmInfo > CAssemblyInfo::GetAssms_TaxId ( const string tax_id,
const string release_type = NcbiEmptyString 
)
static

◆ GetAssms_Term()

CRef< CDL_AssmInfo > CAssemblyInfo::GetAssms_Term ( const string term,
const string release_type = NcbiEmptyString,
ICanceled cancel = 0 
)
static

◆ IsSameAssembly()

bool CAssemblyInfo::IsSameAssembly ( const objects::CGC_Assembly &  gc_assm,
const string term 
)
static

◆ x_CreateAssmInfo()

CRef< CDL_AssmInfo > CAssemblyInfo::x_CreateAssmInfo ( objects::CDL_AssmInfo::TAssemblies &  assms)
staticprivate

◆ x_FilterAssemblies()

void CAssemblyInfo::x_FilterAssemblies ( objects::CDL_AssmInfo::TAssemblies &  assms,
const string release_type 
)
staticprivate

filter the assemblies by release type and category=full-assembly.

Definition at line 322 of file assembly_info.cpp.

Referenced by GetAssms_Gi(), GetAssms_TaxId(), and GetAssms_Term().

◆ x_FilterTaxIds()

void CAssemblyInfo::x_FilterTaxIds ( CSeqUtils::TEntrezIds uids)
staticprivate

filter out the tax ids that don't have assembly on them.

Definition at line 200 of file assembly_info.cpp.

References Error(), CException::GetMsg(), kAssmDb, kRetMax, LOG_POST, CEutilsClient::Search(), and CEutilsClient::SetMaxReturn().

Referenced by GetAssms_Term().

◆ x_GetAssmInfo()

void CAssemblyInfo::x_GetAssmInfo ( const CSeqUtils::TEntrezIds uids,
objects::CDL_AssmInfo::TAssemblies &  assms 
)
staticprivate

◆ x_SearchIds()

void CAssemblyInfo::x_SearchIds ( const string term,
const string db,
CSeqUtils::TEntrezIds uids 
)
staticprivate

search all related links in the given db with a search term.

Definition at line 216 of file assembly_info.cpp.

References Error(), CException::GetMsg(), kRetMax, LOG_POST, CEutilsClient::Search(), and CEutilsClient::SetMaxReturn().

Referenced by GetAssms_TaxId(), and GetAssms_Term().

◆ x_SortAssms()

void CAssemblyInfo::x_SortAssms ( objects::CDL_AssmInfo::TAssemblies &  assms)
staticprivate

sort assemblies based on release date.

apply special rules for human, mouse, cow and rat.

Definition at line 352 of file assembly_info.cpp.

References map_checker< Container >::begin(), and s_AssmCompare().

Referenced by x_CreateAssmInfo().

◆ x_ValidateTaxId()

bool CAssemblyInfo::x_ValidateTaxId ( const string tax_id)
staticprivate

validate if the given tax-id.

Definition at line 182 of file assembly_info.cpp.

References CEutilsClient::Count(), Error(), CException::GetMsg(), kTaxDb, and LOG_POST.

Referenced by GetAssms_TaxId().


The documentation for this class was generated from the following files:
Modified on Tue Jun 25 13:34:46 2024 by modify_doxy.py rev. 669887