NCBI C++ ToolKit
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source_mod_parser.cpp File Reference
#include <ncbi_pch.hpp>
#include <sstream>
#include <objtools/readers/source_mod_parser.hpp>
#include <objtools/readers/message_listener.hpp>
#include <corelib/ncbiutil.hpp>
#include <util/static_map.hpp>
#include <serial/enumvalues.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/User_field.hpp>
#include <objects/misc/sequence_macros.hpp>
#include <objects/pub/Pub.hpp>
#include <objects/pub/Pub_equiv.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Pubdesc.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objects/seq/Seq_hist_rec.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/OrgMod.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objects/seqfeat/PCRReactionSet.hpp>
#include <objects/seqfeat/PCRReaction.hpp>
#include <objects/seqfeat/PCRPrimer.hpp>
#include <objects/seqfeat/PCRPrimerSet.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/SubSource.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/general/User_object.hpp>
+ Include dependency graph for source_mod_parser.cpp:

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class  CAutoInitDesc< _T >
 CSourceModParser. More...
class  CAutoAddDBLink
struct  SMolTypeInfo


#define STATIC_SMOD(key_str)


typedef SStaticPair< const char *, SMolTypeInfoTBiomolMapEntry
typedef CStaticPairArrayMap< const char *, SMolTypeInfo, CSourceModParser::PKeyCompareTBiomolMap
typedef SStaticPair< const char *, CMolInfo::TTechTTechMapEntry
typedef CStaticPairArrayMap< const char *, CMolInfo::TTech, CSourceModParser::PKeyCompareTTechMap
typedef SStaticPair< const char *, CMolInfo::TCompletenessTCompletenessMapEntry
typedef CStaticPairArrayMap< const char *, CMolInfo::TCompleteness, CSourceModParser::PKeyCompareTCompletenessMap


 DEFINE_STATIC_ARRAY_MAP (TBiomolMap, sc_BiomolMap, sc_BiomolArray)
static void s_AddPrimers (const pair< string, string > &primer_info, CPCRPrimerSet &primer_set)
static void s_GetPrimerInfo (const CSourceModParser::SMod *pNamesMod, const CSourceModParser::SMod *pSeqsMod, vector< pair< string, string >> &reaction_info)
 DEFINE_STATIC_ARRAY_MAP (TTechMap, sc_TechMap, sc_TechArray)
 DEFINE_STATIC_ARRAY_MAP (TCompletenessMap, sc_CompletenessMap, sc_CompletenessArray)
static void s_PopulateUserObject (CUser_object &uo, const string &type, CUser_object::TData &data)
static CRef< CSeqdescs_SetDBLinkDesc (CBioseq &bioseq)
static void s_SetDBLinkFieldVals (const string &label, const list< CTempString > &vals, CSeqdesc &dblink_desc)
static void s_SetDBLinkField (const string &label, const string &vals, CRef< CSeqdesc > &pDBLinkDesc, CBioseq &bioseq)
static void s_ApplyPubMods (CBioseq &bioseq, const CSourceModParser::TModsRange &range)


CSafeStaticRef< CSeq_descrfake_descr
static const TBiomolMapEntry sc_BiomolArray []
static const TTechMapEntry sc_TechArray []
static const TCompletenessMapEntry sc_CompletenessArray []

Macro Definition Documentation


#define STATIC_SMOD (   key_str)
const char s_Mod_s_##key_str[] = #key_str; \
const size_t s_Mod_n_##key_str = sizeof(#key_str)-1; \
const CTempString s_Mod_##key_str(s_Mod_s_##key_str, s_Mod_n_##key_str)
CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...
Definition: tempstr.hpp:65

Definition at line 98 of file source_mod_parser.cpp.

Typedef Documentation

◆ TBiomolMap

Definition at line 750 of file source_mod_parser.cpp.

◆ TBiomolMapEntry

Definition at line 729 of file source_mod_parser.cpp.

◆ TCompletenessMap

Definition at line 1209 of file source_mod_parser.cpp.

◆ TCompletenessMapEntry

Definition at line 1198 of file source_mod_parser.cpp.

◆ TTechMap

Definition at line 1195 of file source_mod_parser.cpp.

◆ TTechMapEntry

Definition at line 1166 of file source_mod_parser.cpp.

Function Documentation


sc_BiomolMap  ,


sc_CompletenessMap  ,


sc_TechMap  ,

◆ s_AddPrimers()

static void s_AddPrimers ( const pair< string, string > &  primer_info,
CPCRPrimerSet primer_set 

◆ s_ApplyPubMods()

static void s_ApplyPubMods ( CBioseq bioseq,
const CSourceModParser::TModsRange range 

◆ s_GetPrimerInfo()

static void s_GetPrimerInfo ( const CSourceModParser::SMod pNamesMod,
const CSourceModParser::SMod pSeqsMod,
vector< pair< string, string >> &  reaction_info 

◆ s_PopulateUserObject()

static void s_PopulateUserObject ( CUser_object uo,
const string type,
CUser_object::TData data 

◆ s_SetDBLinkDesc()

static CRef<CSeqdesc> s_SetDBLinkDesc ( CBioseq bioseq)

◆ s_SetDBLinkField()

static void s_SetDBLinkField ( const string label,
const string vals,
CRef< CSeqdesc > &  pDBLinkDesc,
CBioseq bioseq 

◆ s_SetDBLinkFieldVals()

static void s_SetDBLinkFieldVals ( const string label,
const list< CTempString > &  vals,
CSeqdesc dblink_desc 

Variable Documentation

◆ fake_descr

Definition at line 440 of file source_mod_parser.cpp.

◆ sc_BiomolArray

const TBiomolMapEntry sc_BiomolArray[]
Initial value:
= {
@ eBiomol_pre_RNA
precursor RNA of any sort really
Definition: MolInfo_.hpp:102
@ eBiomol_cRNA
viral RNA genome copy intermediate
Definition: MolInfo_.hpp:111
@ eBiomol_transcribed_RNA
transcribed RNA other than existing classes
Definition: MolInfo_.hpp:113
@ eBiomol_other_genetic
other genetic material
Definition: MolInfo_.hpp:109

Definition at line 730 of file source_mod_parser.cpp.

◆ sc_CompletenessArray

const TCompletenessMapEntry sc_CompletenessArray[]
Initial value:
= {
@ eCompleteness_has_left
5' or NH3 end present
Definition: MolInfo_.hpp:161
@ eCompleteness_complete
complete biological entity
Definition: MolInfo_.hpp:156
@ eCompleteness_has_right
3' or COOH end present
Definition: MolInfo_.hpp:162
@ eCompleteness_no_left
missing 5' or NH3 end
Definition: MolInfo_.hpp:158
@ eCompleteness_partial
partial but no details given
Definition: MolInfo_.hpp:157
@ eCompleteness_no_right
missing 3' or COOH end
Definition: MolInfo_.hpp:159
@ eCompleteness_no_ends
missing both ends
Definition: MolInfo_.hpp:160

Definition at line 1199 of file source_mod_parser.cpp.

◆ sc_TechArray

const TTechMapEntry sc_TechArray[]
Initial value:
= {
{ "barcode", CMolInfo::eTech_barcode },
{ "both", CMolInfo::eTech_both },
{ "composite-wgs-htgs", CMolInfo::eTech_composite_wgs_htgs },
{ "concept-trans", CMolInfo::eTech_concept_trans },
{ "concept-trans-a", CMolInfo::eTech_concept_trans_a },
{ "derived", CMolInfo::eTech_derived },
{ "EST", CMolInfo::eTech_est },
{ "fli cDNA", CMolInfo::eTech_fli_cdna },
{ "genetic map", CMolInfo::eTech_genemap },
{ "htc", CMolInfo::eTech_htc },
{ "htgs 0", CMolInfo::eTech_htgs_0 },
{ "htgs 1", CMolInfo::eTech_htgs_1 },
{ "htgs 2", CMolInfo::eTech_htgs_2 },
{ "htgs 3", CMolInfo::eTech_htgs_3 },
{ "physical map", CMolInfo::eTech_physmap },
{ "seq-pept", CMolInfo::eTech_seq_pept },
{ "seq-pept-homol", CMolInfo::eTech_seq_pept_homol },
{ "seq-pept-overlap", CMolInfo::eTech_seq_pept_overlap },
{ "standard", CMolInfo::eTech_standard },
{ "STS", CMolInfo::eTech_sts },
{ "survey", CMolInfo::eTech_survey },
{ "targeted", CMolInfo::eTech_targeted },
{ "tsa", CMolInfo::eTech_tsa },
@ eTech_htgs_2
ordered High Throughput sequence contig
Definition: MolInfo_.hpp:138
@ eTech_physmap
from physical mapping techniques
Definition: MolInfo_.hpp:129
@ eTech_htc
high throughput cDNA
Definition: MolInfo_.hpp:142
@ eTech_both
concept transl. w/ partial pept. seq.
Definition: MolInfo_.hpp:133
@ eTech_targeted
targeted locus sets/studies
Definition: MolInfo_.hpp:147
@ eTech_seq_pept_homol
sequenced peptide, ordered by homology
Definition: MolInfo_.hpp:135
@ eTech_composite_wgs_htgs
composite of WGS and HTGS
Definition: MolInfo_.hpp:145
@ eTech_sts
Sequence Tagged Site.
Definition: MolInfo_.hpp:126
@ eTech_htgs_3
finished High Throughput sequence
Definition: MolInfo_.hpp:139
@ eTech_seq_pept_overlap
sequenced peptide, ordered by overlap
Definition: MolInfo_.hpp:134
@ eTech_htgs_1
unordered High Throughput sequence contig
Definition: MolInfo_.hpp:137
@ eTech_concept_trans
conceptual translation
Definition: MolInfo_.hpp:131
@ eTech_tsa
transcriptome shotgun assembly
Definition: MolInfo_.hpp:146
@ eTech_standard
standard sequencing
Definition: MolInfo_.hpp:124
@ eTech_wgs
whole genome shotgun sequencing
Definition: MolInfo_.hpp:143
@ eTech_seq_pept
peptide was sequenced
Definition: MolInfo_.hpp:132
@ eTech_survey
one-pass genomic sequence
Definition: MolInfo_.hpp:127
@ eTech_barcode
barcode of life project
Definition: MolInfo_.hpp:144
@ eTech_htgs_0
single genomic reads for coordination
Definition: MolInfo_.hpp:141
@ eTech_derived
derived from other data, not a primary entity
Definition: MolInfo_.hpp:130
@ eTech_fli_cdna
full length insert cDNA
Definition: MolInfo_.hpp:140
@ eTech_est
Expressed Sequence Tag.
Definition: MolInfo_.hpp:125
@ eTech_concept_trans_a
conceptual transl. supplied by author
Definition: MolInfo_.hpp:136
@ eTech_genemap
from genetic mapping techniques
Definition: MolInfo_.hpp:128

Definition at line 1167 of file source_mod_parser.cpp.

Referenced by CDeflineGenerator::x_GetModifiers().

Modified on Mon May 27 04:35:56 2024 by rev. 669887