NCBI C++ ToolKit
Enumerations | Functions
agp_write.cpp File Reference
#include <ncbi_pch.hpp>
#include <objtools/writers/agp_write.hpp>
#include <objtools/writers/writer_exception.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/Linkage_evidence.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objects/seq/Seq_gap.hpp>
#include <objects/seq/Seq_ext.hpp>
#include <objects/seq/Delta_ext.hpp>
#include <objects/seq/Delta_seq.hpp>
#include <objects/seq/Seq_literal.hpp>
#include <objects/seqblock/GB_block.hpp>
#include <objmgr/seq_map_ci.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/util/sequence.hpp>
+ Include dependency graph for agp_write.cpp:

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Enumerations

enum  EAgpType {
  eO , eP , eD , eA ,
  eF
}
 

Functions

 USING_SCOPE (objects)
 
static char s_DetermineComponentType (const CSeq_id &id, CScope &scope)
 
static string_view GetGapType (const CSeqMap_CI &iter, const string *default_gap_type)
 
static bool GetLinkage (const CSeqMap_CI &iter, const bool *default_linkage)
 
static void WriteLinkageEvidence (CNcbiOstream &os, const CSeqMap_CI &iter)
 
static void s_AgpWrite (CNcbiOstream &os, const CSeqMap &seq_map, TSeqPos start_pos, TSeqPos stop_pos, const string &object_id, const string *default_gap_type, const bool *default_linkage, CScope &scope, const vector< char > &component_types, CAgpWriteComponentIdMapper *comp_id_mapper, int agp_version)
 Write to stream in agp format. More...
 
static CConstRef< CSeqMaps_SeqMapForHandle (const CBioseq_Handle &handle)
 
void AgpWrite (CNcbiOstream &os, const CSeqMap &seq_map, const string &object_id, CScope &scope, const vector< char > &component_types, CAgpWriteComponentIdMapper *comp_id_mapper, int agp_version)
 
void AgpWrite (CNcbiOstream &os, const CBioseq_Handle &handle, const string &object_id, const vector< char > &component_types, CAgpWriteComponentIdMapper *comp_id_mapper, int agp_version)
 
void AgpWrite (CNcbiOstream &os, const CBioseq_Handle &handle, TSeqPos from, TSeqPos to, const string &object_id, const vector< char > &component_types, CAgpWriteComponentIdMapper *comp_id_mapper, int agp_version)
 
void AgpWrite (CNcbiOstream &os, const CSeqMap &seq_map, const string &object_id, const string &default_gap_type, bool default_linkage, CScope &scope, const vector< char > &component_types, CAgpWriteComponentIdMapper *comp_id_mapper, int agp_version)
 
void AgpWrite (CNcbiOstream &os, const CBioseq_Handle &handle, const string &object_id, const string &default_gap_type, bool default_linkage, const vector< char > &component_types, CAgpWriteComponentIdMapper *comp_id_mapper, int agp_version)
 
void AgpWrite (CNcbiOstream &os, const CBioseq_Handle &handle, TSeqPos from, TSeqPos to, const string &object_id, const string &default_gap_type, bool default_linkage, const vector< char > &component_types, CAgpWriteComponentIdMapper *comp_id_mapper, int agp_version)
 

Enumeration Type Documentation

◆ EAgpType

enum EAgpType
Enumerator
eO 
eP 
eD 
eA 
eF 

Definition at line 410 of file agp_write.cpp.

Function Documentation

◆ AgpWrite() [1/6]

void AgpWrite ( CNcbiOstream os,
const CBioseq_Handle handle,
const string object_id,
const string default_gap_type,
bool  default_linkage,
const vector< char > &  component_types,
CAgpWriteComponentIdMapper comp_id_mapper,
int  agp_version 
)

◆ AgpWrite() [2/6]

void AgpWrite ( CNcbiOstream os,
const CBioseq_Handle handle,
const string object_id,
const vector< char > &  component_types,
CAgpWriteComponentIdMapper comp_id_mapper,
int  agp_version 
)

◆ AgpWrite() [3/6]

void AgpWrite ( CNcbiOstream os,
const CBioseq_Handle handle,
TSeqPos  from,
TSeqPos  to,
const string object_id,
const string default_gap_type,
bool  default_linkage,
const vector< char > &  component_types,
CAgpWriteComponentIdMapper comp_id_mapper,
int  agp_version 
)

Definition at line 381 of file agp_write.cpp.

References CBioseq_Handle::GetScope(), s_AgpWrite(), and s_SeqMapForHandle().

◆ AgpWrite() [4/6]

void AgpWrite ( CNcbiOstream os,
const CBioseq_Handle handle,
TSeqPos  from,
TSeqPos  to,
const string object_id,
const vector< char > &  component_types,
CAgpWriteComponentIdMapper comp_id_mapper,
int  agp_version 
)

Definition at line 337 of file agp_write.cpp.

References CBioseq_Handle::GetScope(), s_AgpWrite(), and s_SeqMapForHandle().

◆ AgpWrite() [5/6]

void AgpWrite ( CNcbiOstream os,
const CSeqMap seq_map,
const string object_id,
const string default_gap_type,
bool  default_linkage,
CScope scope,
const vector< char > &  component_types,
CAgpWriteComponentIdMapper comp_id_mapper,
int  agp_version 
)

Definition at line 351 of file agp_write.cpp.

References CSeqMap::GetLength(), and s_AgpWrite().

◆ AgpWrite() [6/6]

void AgpWrite ( CNcbiOstream os,
const CSeqMap seq_map,
const string object_id,
CScope scope,
const vector< char > &  component_types,
CAgpWriteComponentIdMapper comp_id_mapper,
int  agp_version 
)

Definition at line 311 of file agp_write.cpp.

References CSeqMap::GetLength(), and s_AgpWrite().

◆ GetGapType()

static string_view GetGapType ( const CSeqMap_CI iter,
const string default_gap_type 
)
static

◆ GetLinkage()

static bool GetLinkage ( const CSeqMap_CI iter,
const bool default_linkage 
)
static

◆ s_AgpWrite()

static void s_AgpWrite ( CNcbiOstream os,
const CSeqMap seq_map,
TSeqPos  start_pos,
TSeqPos  stop_pos,
const string object_id,
const string default_gap_type,
const bool default_linkage,
CScope scope,
const vector< char > &  component_types,
CAgpWriteComponentIdMapper comp_id_mapper,
int  agp_version 
)
static

◆ s_DetermineComponentType()

static char s_DetermineComponentType ( const CSeq_id id,
CScope scope 
)
static

◆ s_SeqMapForHandle()

static CConstRef<CSeqMap> s_SeqMapForHandle ( const CBioseq_Handle handle)
static

◆ USING_SCOPE()

USING_SCOPE ( objects  )

◆ WriteLinkageEvidence()

static void WriteLinkageEvidence ( CNcbiOstream os,
const CSeqMap_CI iter 
)
static
Modified on Tue Apr 23 07:36:55 2024 by modify_doxy.py rev. 669887