NCBI C++ ToolKit
Macros | Typedefs | Functions | Variables
id_mapper.cpp File Reference
#include <ncbi_pch.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/seqfeat/Gb_qual.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqset/gb_release_file.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/seqfeat/Cdregion.hpp>
#include <objects/seqloc/seqloc__.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/seq_map.hpp>
#include <objmgr/seq_map_ci.hpp>
#include <objmgr/util/obj_sniff.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <objtools/format/ostream_text_ostream.hpp>
#include <serial/iterator.hpp>
#include <serial/objistr.hpp>
#include <objects/genomecoll/genome_collection__.hpp>
#include <algo/id_mapper/id_mapper.hpp>
#include <objmgr/seq_loc_mapper.hpp>
+ Include dependency graph for id_mapper.cpp:

Go to the source code of this file.

Go to the SVN repository for this file.

Macros

#define START_TIMER(X)   TimerMap[#X].Start()
 
#define STOP_TIMER(X)   TimerMap[#X].Stop()
 
#define PRINT_TIMERS(X)
 
#define MARKLINE   cerr << __FILE__ << ":" << __LINE__ << endl;
 

Typedefs

typedef map< string, CStopWatchTTimerMap
 

Functions

 USING_SCOPE (objects)
 
bool s_RevStrLenSort (const string &A, const string &B)
 
bool s_IsNumericString (const string &A)
 
size_t s_CountNumeric (const string &A)
 
bool s_HasMoreDigits (const string &Name, const string &Chromo)
 
CConstRef< CGC_SeqIdAliass_GetSeqIdAlias_GenBankRefSeq (CConstRef< CGC_TypedSeqId > tsid)
 
bool s_DoesBioseqRecurse (const CBioseq &Bioseq)
 

Variables

TTimerMap TimerMap
 
const string DELIM = "%s"
 
const string CHROMO_EXT = "<CHROMOSOME_EXTERNAL>"
 

Macro Definition Documentation

◆ MARKLINE

#define MARKLINE   cerr << __FILE__ << ":" << __LINE__ << endl;

Definition at line 72 of file id_mapper.cpp.

◆ PRINT_TIMERS

#define PRINT_TIMERS (   X)
Value:
ITERATE (TTimerMap, iter, TimerMap) { \
ERR_POST(X << "Timer: " << iter->first << ": " \
<< iter->second.AsString() << "s"); \
}
#define ITERATE(Type, Var, Cont)
ITERATE macro to sequence through container elements.
Definition: ncbimisc.hpp:815
TTimerMap TimerMap
map< string, CStopWatch > TTimerMap

Definition at line 67 of file id_mapper.cpp.

◆ START_TIMER

#define START_TIMER (   X)    TimerMap[#X].Start()

Definition at line 65 of file id_mapper.cpp.

◆ STOP_TIMER

#define STOP_TIMER (   X)    TimerMap[#X].Stop()

Definition at line 66 of file id_mapper.cpp.

Typedef Documentation

◆ TTimerMap

Definition at line 63 of file id_mapper.cpp.

Function Documentation

◆ s_CountNumeric()

size_t s_CountNumeric ( const string A)

Definition at line 95 of file id_mapper.cpp.

References A, isdigit(), and ITERATE.

Referenced by s_HasMoreDigits().

◆ s_DoesBioseqRecurse()

bool s_DoesBioseqRecurse ( const CBioseq Bioseq)

Definition at line 1541 of file id_mapper.cpp.

References CBioseq_Base::GetId(), CBioseq_Base::GetInst(), and ITERATE.

◆ s_GetSeqIdAlias_GenBankRefSeq()

CConstRef<CGC_SeqIdAlias> s_GetSeqIdAlias_GenBankRefSeq ( CConstRef< CGC_TypedSeqId tsid)

◆ s_HasMoreDigits()

bool s_HasMoreDigits ( const string Name,
const string Chromo 
)

Definition at line 106 of file id_mapper.cpp.

References s_CountNumeric().

Referenced by CGencollIdMapper::x_FindChromosomeSequence().

◆ s_IsNumericString()

bool s_IsNumericString ( const string A)

Definition at line 85 of file id_mapper.cpp.

References A, isdigit(), and ITERATE.

Referenced by CGencollIdMapper::x_FindChromosomeSequence().

◆ s_RevStrLenSort()

bool s_RevStrLenSort ( const string A,
const string B 
)

Definition at line 79 of file id_mapper.cpp.

References A.

Referenced by CGencollIdMapper::x_Init().

◆ USING_SCOPE()

USING_SCOPE ( objects  )

Variable Documentation

◆ CHROMO_EXT

const string CHROMO_EXT = "<CHROMOSOME_EXTERNAL>"

◆ DELIM

const string DELIM = "%s"

◆ TimerMap

TTimerMap TimerMap
extern

Definition at line 79 of file id_mapper_app.cpp.

Modified on Sat Mar 02 10:57:48 2024 by modify_doxy.py rev. 669887