#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 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, CStopWatch >	TTimerMap

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_SeqIdAlias >	s_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");   \
        }