NCBI C++ ToolKit
Enumerations | Functions
agp_read.hpp File Reference
#include <corelib/ncbistd.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seqset/Bioseq_set.hpp>
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Enumerations

enum  EAgpRead_IdRule { eAgpRead_ParseId, eAgpRead_ForceLocalId }
 

Functions

void AgpRead (CNcbiIstream &is, vector< CRef< objects::CBioseq > > &bioseqs, EAgpRead_IdRule component_id_rule=eAgpRead_ParseId, bool set_gap_data=false, vector< vector< char > > *component_types=0)
 Read an agp file from a stream, constructing delta sequences. More...
 
void AgpRead (CNcbiIstream &is, vector< CRef< objects::CSeq_entry > > &entries, EAgpRead_IdRule component_id_rule=eAgpRead_ParseId, bool set_gap_data=false, vector< vector< char > > *component_types=0)
 Same thing, but wrap bioseqs in Seq-entry's. More...
 
CRef< objects::CBioseq_set > AgpRead (CNcbiIstream &is, EAgpRead_IdRule component_id_rule=eAgpRead_ParseId, bool set_gap_data=false, vector< vector< char > > *component_types=0)
 Return a Bioseq-set containing everything. More...
 

Enumeration Type Documentation

Enumerator
eAgpRead_ParseId 
eAgpRead_ForceLocalId 

Definition at line 43 of file agp_read.hpp.

Function Documentation

void AgpRead ( CNcbiIstream is,
vector< CRef< objects::CBioseq > > &  bioseqs,
EAgpRead_IdRule  component_id_rule = eAgpRead_ParseId,
bool  set_gap_data = false,
vector< vector< char > > *  component_types = 0 
)

Read an agp file from a stream, constructing delta sequences.

Referenced by CConversionApp::Read(), and CFileLoader::x_LoadAGP().

void AgpRead ( CNcbiIstream is,
vector< CRef< objects::CSeq_entry > > &  entries,
EAgpRead_IdRule  component_id_rule = eAgpRead_ParseId,
bool  set_gap_data = false,
vector< vector< char > > *  component_types = 0 
)

Same thing, but wrap bioseqs in Seq-entry's.

CRef<objects::CBioseq_set> AgpRead ( CNcbiIstream is,
EAgpRead_IdRule  component_id_rule = eAgpRead_ParseId,
bool  set_gap_data = false,
vector< vector< char > > *  component_types = 0 
)

Return a Bioseq-set containing everything.

Definition at line 52 of file agp_read.cpp.

References entries, ITERATE, and CBioseq_set_Base::SetSeq_set().

Referenced by AgpRead().

Modified on Wed Apr 25 11:16:36 2018 by modify_doxy.py rev. 546573