NCBI C++ ToolKit
Functions | Variables
mod_reader.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seq/Seq_hist.hpp>
#include <objects/seq/Seq_hist_rec.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objtools/logging/message.hpp>
#include <objtools/logging/listener.hpp>
#include <objtools/readers/mod_reader.hpp>
#include <objtools/readers/mod_error.hpp>
#include <objtools/readers/message_listener.hpp>
#include <map>
#include <unordered_map>
#include <unordered_set>
#include <cassert>
#include "mod_to_enum.hpp"
#include "descr_mod_apply.hpp"
#include "feature_mod_apply.hpp"
+ Include dependency graph for mod_reader.cpp:

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static string s_GetNormalizedString (const string &unnormalized)


static const unordered_map< string, strings_ModNameMap
static const unordered_map< string, CSeq_inst::EStrands_StrandStringToEnum
static const unordered_map< string, CSeq_inst::EMols_MolStringToEnum
static const unordered_map< string, CSeq_inst::ETopologys_TopologyStringToEnum

Function Documentation

◆ s_GetNormalizedString()

static string s_GetNormalizedString ( const string unnormalized)

Definition at line 424 of file mod_reader.cpp.

References a, b, NStr::ToLower(), and NStr::TruncateSpacesInPlace().

Referenced by CModHandler::x_GetNormalizedString().

Variable Documentation

◆ s_ModNameMap

const unordered_map<string, string> s_ModNameMap

Definition at line 61 of file mod_reader.cpp.

Referenced by CModHandler::GetCanonicalName().

◆ s_MolStringToEnum

const unordered_map<string, CSeq_inst::EMol> s_MolStringToEnum
Initial value:

Definition at line 154 of file mod_reader.cpp.

Referenced by CModAdder::x_SetMolecule().

◆ s_StrandStringToEnum

const unordered_map<string, CSeq_inst::EStrand> s_StrandStringToEnum
Initial value:
{{"single", CSeq_inst::eStrand_ss},
{"double", CSeq_inst::eStrand_ds},
@ eStrand_other
default ds for DNA, ss for RNA, pept
Definition: Seq_inst_.hpp:138
@ eStrand_ds
double strand
Definition: Seq_inst_.hpp:136
@ eStrand_ss
single strand
Definition: Seq_inst_.hpp:135

Definition at line 144 of file mod_reader.cpp.

Referenced by CModAdder::x_SetStrand().

◆ s_TopologyStringToEnum

const unordered_map<string, CSeq_inst::ETopology> s_TopologyStringToEnum
Initial value:
@ eTopology_tandem
some part of tandem repeat
Definition: Seq_inst_.hpp:125

Definition at line 165 of file mod_reader.cpp.

Referenced by CModAdder::x_SetTopology().

Modified on Mon Jul 15 05:34:24 2024 by rev. 669887