sesame_street.cpp File Reference

#include <ncbi_pch.hpp>
#include "discrepancy_core.hpp"
#include "utils.hpp"
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/OrgMod.hpp>
#include <objects/seqfeat/PCRPrimer.hpp>
#include <objects/seqfeat/PCRPrimerSet.hpp>
#include <objects/seqfeat/PCRReaction.hpp>
#include <objects/seqfeat/PCRReactionSet.hpp>
#include <objects/seqfeat/SubSource.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include <objmgr/util/sequence.hpp>

Include dependency graph for sesame_street.cpp:

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Classes
class	CDiscrepancyPrivateData< eTestNames::SOURCE_QUALS >
class	CSourseQualsAutofixData

Typedefs
typedef map< const CReportObj *, CRef< CReportObj > >	TReportObjPtrMap
typedef map< string, vector< CRef< CReportObj > > >	TStringObjVectorMap
typedef map< string, TStringObjVectorMap >	TStringStringObjVectorMap

Functions
	USING_SCOPE (objects)
static string	OrderQual (const string &s)
static void	ConvertDuplicates (CReportNode &node)
static void	AddObjToQualMap (const string &qual, const string &val, CReportObj &obj, CReportNode &node)
static bool	GetSubtypeStr (const string &qual, const string &val, const TReportObjectList &objs, string &subtype)
static void	AddObjectToReport (const string &subtype, const string &qual, const string &val, bool unique, CReportObj &obj, CReportNode &report)
static void	AddObjsToReport (const string &diagnosis, CReportNode::TNodeMap &all_objs, const string &qual, CReportNode &report)
static void	AddObjsToReport (const string &diagnosis, const TStringObjVectorMap &all_objs, const string &qual, CReportNode &report)
static size_t	GetNumOfObjects (CReportNode &root)
static size_t	GetSortOrderId (const string &subitem, CReportNode &node)
static float	g_GetSesameStreetCutoff ()
static void	SetSubsource (CRef< CBioSource > bs, CSubSource::ESubtype st, const string &s, size_t &added, size_t &changed)
static void	SetOrgMod (CRef< CBioSource > bs, COrgMod::ESubtype st, const string &s, size_t &added, size_t &changed)

Variables
static constexpr std::initializer_list< const char * >	g_aliases_SOURCE_QUALS = { "SOURCE_QUALS_ASNDISC", "SRC_QUAL_PROBLEM", "MISSING_SRC_QUAL" }
static constexpr CDiscrepancyCaseProps	s_testcase_props_SOURCE_QUALS = { CDiscrepancyVisitorImpl<eTestNames:: SOURCE_QUALS >::Create, eTestTypes:: BIOSRC , eTestNames:: SOURCE_QUALS , "SOURCE_QUALS" , "Some animals are more equal than others..." , eDisc | eOncaller | eSubmitter | eSmart | eBig | eFatal , &g_aliases_SOURCE_QUALS }

Typedef Documentation

TReportObjPtrMap

typedef map<const CReportObj*, CRef<CReportObj> > TReportObjPtrMap

Definition at line 291 of file sesame_street.cpp.

TStringObjVectorMap

typedef map<string, vector<CRef<CReportObj> > > TStringObjVectorMap

Definition at line 292 of file sesame_street.cpp.

TStringStringObjVectorMap

typedef map<string, TStringObjVectorMap > TStringStringObjVectorMap

Definition at line 293 of file sesame_street.cpp.

Function Documentation

AddObjectToReport()

static void AddObjectToReport ( const string &  subtype, const string &  qual, const string &  val, bool  unique, CReportObj &  obj, CReportNode &  report  )

static

Definition at line 310 of file sesame_street.cpp.

References CReportNode::Add(), and val.

Referenced by AddObjsToReport().

AddObjsToReport() [1/2]

static void AddObjsToReport ( const string &  diagnosis, const TStringObjVectorMap &  all_objs, const string &  qual, CReportNode &  report  )

static

Definition at line 333 of file sesame_street.cpp.

References AddObjectToReport(), and GetSubtypeStr().

AddObjsToReport() [2/2]

static void AddObjsToReport ( const string &  diagnosis, CReportNode::TNodeMap &  all_objs, const string &  qual, CReportNode &  report  )

static

Definition at line 321 of file sesame_street.cpp.

References AddObjectToReport(), and GetSubtypeStr().

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

AddObjToQualMap()

static void AddObjToQualMap ( const string &  qual, const string &  val, CReportObj &  obj, CReportNode &  node  )

static

Definition at line 117 of file sesame_street.cpp.

References CReportNode::Add(), and val.

ConvertDuplicates()

static void ConvertDuplicates ( CReportNode &  node )

static

Definition at line 95 of file sesame_street.cpp.

References all, and CReportNode::GetMap().

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

g_GetSesameStreetCutoff()

static float g_GetSesameStreetCutoff ( )

static

Definition at line 365 of file sesame_street.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

GetNumOfObjects()

static size_t GetNumOfObjects ( CReportNode &  root )

static

Definition at line 345 of file sesame_street.cpp.

References CReportNode::GetMap(), and CReportNode::GetObjects().

Referenced by GetSortOrderId().

GetSortOrderId()

static size_t GetSortOrderId ( const string &  subitem, CReportNode &  node  )

static

Definition at line 355 of file sesame_street.cpp.

References NStr::Find(), GetNumOfObjects(), and NPOS.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

GetSubtypeStr()

static bool GetSubtypeStr ( const string &  qual, const string &  val, const TReportObjectList &  objs, string &  subtype  )

static

Definition at line 296 of file sesame_street.cpp.

References val.

Referenced by AddObjsToReport().

OrderQual()

static string OrderQual ( const string &  s )

static

Definition at line 51 of file sesame_street.cpp.

References ArraySize(), i, n, names, and r().

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

SetOrgMod()

static void SetOrgMod ( CRef< CBioSource >  bs, COrgMod::ESubtype  st, const string &  s, size_t &  added, size_t &  changed  )

static

Definition at line 529 of file sesame_street.cpp.

References COrgName_Base::GetMod(), CBioSource::GetOrgname(), COrgMod_Base::GetSubname(), CBioSource_Base::SetOrg(), and COrgMod_Base::SetSubname().

Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix().

SetSubsource()

static void SetSubsource ( CRef< CBioSource >  bs, CSubSource::ESubtype  st, const string &  s, size_t &  added, size_t &  changed  )

static

Definition at line 512 of file sesame_street.cpp.

References CSubSource_Base::GetName(), CBioSource_Base::GetSubtype(), CSubSource_Base::SetName(), and CBioSource_Base::SetSubtype().

Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix().

USING_SCOPE()

USING_SCOPE

(

objects

)

Variable Documentation

g_aliases_SOURCE_QUALS

constexpr std::initializer_list<const char*> g_aliases_SOURCE_QUALS = { "SOURCE_QUALS_ASNDISC", "SRC_QUAL_PROBLEM", "MISSING_SRC_QUAL" }

staticconstexpr

Definition at line 145 of file sesame_street.cpp.

s_testcase_props_SOURCE_QUALS

constexpr CDiscrepancyCaseProps s_testcase_props_SOURCE_QUALS = { CDiscrepancyVisitorImpl<eTestNames:: SOURCE_QUALS >::Create, eTestTypes:: BIOSRC , eTestNames:: SOURCE_QUALS , "SOURCE_QUALS" , "Some animals are more equal than others..." , eDisc | eOncaller | eSubmitter | eSmart | eBig | eFatal , &g_aliases_SOURCE_QUALS }

staticconstexpr

Definition at line 145 of file sesame_street.cpp.