GC_Assembly.cpp File Reference

#include <ncbi_pch.hpp>
#include <objects/genomecoll/GC_Assembly.hpp>
#include <objects/genomecoll/GC_AssemblyUnit.hpp>
#include <objects/genomecoll/GC_AssemblySet.hpp>
#include <objects/genomecoll/GC_AssemblyDesc.hpp>
#include <objects/genomecoll/GC_Replicon.hpp>
#include <objects/genomecoll/GC_Sequence.hpp>
#include <objects/genomecoll/GC_TaggedSequences.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <serial/serial.hpp>
#include <serial/iterator.hpp>

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Classes
struct	SBestSequence

Functions
static void	s_Extract (const CGC_Assembly &assm, list< CConstRef< CGC_Sequence > > &molecules, CGC_Assembly::ESubset subset)
	Molecule Extraction Routines. More...
static void	s_Extract (const CGC_AssemblyUnit &unit, list< CConstRef< CGC_Sequence > > &molecules, CGC_Assembly::ESubset subset)
static void	s_Extract (const CGC_AssemblySet &set, list< CConstRef< CGC_Sequence > > &molecules, CGC_Assembly::ESubset subset)
static bool	s_RoleFitsSubset (int role, CGC_Assembly::ESubset subset)
static void	s_Extract (const CGC_AssemblySet &set, vector< list< CConstRef< CGC_Sequence > > > &molecules, CGC_Assembly::ESubset subset)
static void	s_Extract (const CGC_Assembly &assm, vector< list< CConstRef< CGC_Sequence > > > &molecules, CGC_Assembly::ESubset subset)

Function Documentation

s_Extract() [1/5]

static void s_Extract ( const CGC_Assembly &  assm, list< CConstRef< CGC_Sequence > > &  molecules, CGC_Assembly::ESubset  subset  )

static

Molecule Extraction Routines.

Definition at line 839 of file GC_Assembly.cpp.

References CGC_Assembly_Base::GetAssembly_set(), CGC_Assembly_Base::GetUnit(), and CGC_Assembly_Base::IsUnit().

Referenced by CGC_Assembly::GetMolecules(), CGC_Assembly::GetMoleculesByUnit(), and s_Extract().

s_Extract() [2/5]

static void s_Extract ( const CGC_Assembly &  assm, vector< list< CConstRef< CGC_Sequence > > > &  molecules, CGC_Assembly::ESubset  subset  )

static

Definition at line 851 of file GC_Assembly.cpp.

References CGC_Assembly_Base::GetAssembly_set(), CGC_Assembly_Base::GetUnit(), CGC_Assembly_Base::IsUnit(), and s_Extract().

s_Extract() [3/5]

static void s_Extract ( const CGC_AssemblySet &  set, list< CConstRef< CGC_Sequence > > &  molecules, CGC_Assembly::ESubset  subset  )

static

Definition at line 807 of file GC_Assembly.cpp.

References ITERATE, and s_Extract().

s_Extract() [4/5]

static void s_Extract ( const CGC_AssemblySet &  set, vector< list< CConstRef< CGC_Sequence > > > &  molecules, CGC_Assembly::ESubset  subset  )

static

Definition at line 821 of file GC_Assembly.cpp.

References ITERATE, s_Extract(), and set< Key, Compare >::size().

s_Extract() [5/5]

static void s_Extract ( const CGC_AssemblyUnit &  unit, list< CConstRef< CGC_Sequence > > &  molecules, CGC_Assembly::ESubset  subset  )

static

Definition at line 768 of file GC_Assembly.cpp.

References count, CGC_Assembly::eAll, eUnknown, ITERATE, NCBI_THROW, and s_RoleFitsSubset().

s_RoleFitsSubset()

static bool s_RoleFitsSubset ( int  role, CGC_Assembly::ESubset  subset  )

static

Definition at line 744 of file GC_Assembly.cpp.

References CGC_Assembly::eChromosome, CGC_Assembly::eComponent, eGC_SequenceRole_chromosome, eGC_SequenceRole_component, eGC_SequenceRole_scaffold, eGC_SequenceRole_submitter_pseudo_scaffold, eGC_SequenceRole_top_level, CGC_Assembly::eScaffold, CGC_Assembly::eSubmitterPseudoScaffold, CGC_Assembly::eTopLevel, eUnknown, and NCBI_THROW.

Referenced by s_Extract().