rval =
"completedness";
82rval =
"representation";
94rval =
"\"descr..molinfo.biomol\"";
97rval =
"\"descr..molinfo.tech\"";
100rval =
"\"descr..molinfo.completeness\"";
103rval =
"\"inst.mol\"";
106rval =
"\"inst.topology\"";
109rval =
"\"inst.strand\"";
112rval =
"\"inst.repr\"";
160 if(it->second == biomol) {
217 if(it->second == tech) {
264 if(it->second ==
val) {
306 if(it->second ==
val) {
347 if(it->second ==
val) {
388 if(it->second ==
val) {
430 for(
auto& it: k_repr_names) {
431 if(it.second == repr) {
443 for(
auto& it : k_repr_names) {
455vector<string> choices;
457 switch(field_type) {
460choices.push_back(it->first);
462allow_other =
false;
466choices.push_back(it->first);
472choices.push_back(it->first);
474allow_other =
false;
478choices.push_back(it->first);
480allow_other =
false;
484choices.push_back(it->first);
489choices.push_back(it->first);
491allow_other =
false;
494 for(
auto& it : k_repr_names) {
495choices.push_back(it.first);
497allow_other =
false;
507vector<string> values;
508 switch(field_type) {
511values.push_back(
"unknown");
512values.push_back(
"cRNA");
513values.push_back(
"genomic");
514values.push_back(
"genomic-mRNA");
515values.push_back(
"mRNA");
516values.push_back(
"ncRNA");
517values.push_back(
"other");
518values.push_back(
"other-genetic");
519values.push_back(
"peptide");
520values.push_back(
"pre-RNA");
521values.push_back(
"rRNA");
522values.push_back(
"scRNA");
523values.push_back(
"snRNA");
524values.push_back(
"snoRNA");
525values.push_back(
"tRNA");
526values.push_back(
"tmRNA");
527values.push_back(
"transcribed-RNA");
532values.push_back(
"unknown");
533values.push_back(
"est");
534values.push_back(
"fli-cdna");
535values.push_back(
"htc");
536values.push_back(
"htgs-0");
537values.push_back(
"htgs-1");
538values.push_back(
"htgs-2");
539values.push_back(
"htgs-3");
540values.push_back(
"sts");
541values.push_back(
"tsa");
542values.push_back(
"wgs");
543values.push_back(
"both");
544values.push_back(
"composite-wgs-htgs");
545values.push_back(
"concept-trans");
546values.push_back(
"concept-trans-a");
547values.push_back(
"derived");
548values.push_back(
"genemap");
549values.push_back(
"physmap");
550values.push_back(
"seq-pept");
551values.push_back(
"seq-pept-homol");
552values.push_back(
"seq-pept-overlap");
553values.push_back(
"standard");
554values.push_back(
"survey");
559values.push_back(
"unknown");
560values.push_back(
"complete");
561values.push_back(
"has-left");
562values.push_back(
"has-right");
563values.push_back(
"no-ends");
564values.push_back(
"no-left");
565values.push_back(
"no-right");
566values.push_back(
"other");
567values.push_back(
"partial");
572values.push_back(
"not-set");
573values.push_back(
"dna");
574values.push_back(
"rna");
575values.push_back(
"na");
576values.push_back(
"other");
577values.push_back(
"aa");
582values.push_back(
"not-set");
583values.push_back(
"circular");
584values.push_back(
"linear");
585values.push_back(
"other");
586values.push_back(
"tandem");
591values.push_back(
"not-set");
592values.push_back(
"ds");
593values.push_back(
"mixed");
594values.push_back(
"other");
595values.push_back(
"ss");
600values.push_back(
"not-set");
601values.push_back(
"virtual");
602values.push_back(
"raw");
603values.push_back(
"seg");
604values.push_back(
"const");
605values.push_back(
"ref");
606values.push_back(
"consen");
607values.push_back(
"map");
608values.push_back(
"delta");
609values.push_back(
"other");
static string GetBiomolLabel(objects::CMolInfo::TBiomol biomol)
static objects::CSeq_inst::TStrand GetStrandFromLabel(const string &val)
static objects::CSeq_inst::TMol GetMolFromLabel(const string &val)
static vector< string > GetFieldNames()
static vector< string > GetMacroFieldNames()
static string GetTechLabel(objects::CMolInfo::TTech tech)
static objects::CSeq_inst::TTopology GetTopologyFromLabel(const string &val)
static objects::CSeq_inst::TRepr GetReprFromLabel(const string &val)
static EMolInfoFieldType GetFieldType(const string &field_name)
static string GetReprLabel(objects::CSeq_inst::TRepr val)
static objects::CMolInfo::TTech GetTechFromLabel(const string &val)
static string GetStrandLabel(objects::CSeq_inst::TStrand val)
static string GetMolLabel(objects::CSeq_inst::TMol val)
static string GetTopologyLabel(objects::CSeq_inst::TTopology tech)
static objects::CMolInfo::TCompleteness GetCompletenessFromLabel(const string &val)
static string GetMacroFieldName(EMolInfoFieldType field_type)
static objects::CMolInfo::TBiomol GetBiomolFromLabel(const string &val)
static string GetFieldName(EMolInfoFieldType field_type)
static vector< string > GetChoicesForField(CMolInfoFieldType::EMolInfoFieldType field_type, bool &allow_other)
static string GetCompletenessLabel(objects::CMolInfo::TCompleteness tech)
static vector< string > GetValuesForField(EMolInfoFieldType field_type)
class CStaticArrayMap<> is an array adaptor that provides an STLish interface to statically-defined a...
#define ITERATE(Type, Var, Cont)
ITERATE macro to sequence through container elements.
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)
Check if a string is blank (has no text).
static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)
Case-insensitive equality of a substring with another string.
ERepr
representation class
ETopology
topology of molecule
EMol
molecule class in living organism
EStrand
strandedness in living organism
@ eRepr_const
constructed sequence
@ eRepr_ref
reference to another sequence
@ eRepr_seg
segmented sequence
@ eRepr_delta
sequence made by changes (delta) to others
@ eRepr_map
ordered map of any kind
@ eRepr_consen
consensus sequence or pattern
@ eRepr_raw
continuous sequence
@ eRepr_virtual
no seq data
@ eCompleteness_has_left
5' or NH3 end present
@ eCompleteness_complete
complete biological entity
@ eCompleteness_has_right
3' or COOH end present
@ eCompleteness_no_left
missing 5' or NH3 end
@ eCompleteness_partial
partial but no details given
@ eCompleteness_no_right
missing 3' or COOH end
@ eCompleteness_no_ends
missing both ends
@ eTech_htgs_2
ordered High Throughput sequence contig
@ eTech_physmap
from physical mapping techniques
@ eTech_other
use Source.techexp
@ eTech_htc
high throughput cDNA
@ eTech_both
concept transl. w/ partial pept. seq.
@ eTech_seq_pept_homol
sequenced peptide, ordered by homology
@ eTech_composite_wgs_htgs
composite of WGS and HTGS
@ eTech_sts
Sequence Tagged Site.
@ eTech_htgs_3
finished High Throughput sequence
@ eTech_seq_pept_overlap
sequenced peptide, ordered by overlap
@ eTech_htgs_1
unordered High Throughput sequence contig
@ eTech_concept_trans
conceptual translation
@ eTech_tsa
transcriptome shotgun assembly
@ eTech_standard
standard sequencing
@ eTech_wgs
whole genome shotgun sequencing
@ eTech_seq_pept
peptide was sequenced
@ eTech_survey
one-pass genomic sequence
@ eTech_htgs_0
single genomic reads for coordination
@ eTech_derived
derived from other data, not a primary entity
@ eTech_fli_cdna
full length insert cDNA
@ eTech_est
Expressed Sequence Tag.
@ eTech_concept_trans_a
conceptual transl. supplied by author
@ eTech_genemap
from genetic mapping techniques
@ eBiomol_pre_RNA
precursor RNA of any sort really
@ eBiomol_cRNA
viral RNA genome copy intermediate
@ eBiomol_snoRNA
small nucleolar RNA
@ eBiomol_genomic_mRNA
reported a mix of genomic and cdna sequence
@ eBiomol_transcribed_RNA
transcribed RNA other than existing classes
@ eBiomol_other_genetic
other genetic material
@ eTopology_tandem
some part of tandem repeat
@ eMol_not_set
> cdna = rna
@ eMol_na
just a nucleic acid
@ eStrand_other
default ds for DNA, ss for RNA, pept
@ eStrand_ds
double strand
@ eStrand_ss
single strand
CStaticPairArrayMap< const char *, CSeq_inst::TRepr, PCase_CStr > TCStringReprPairsMap
CStaticPairArrayMap< const char *, CSeq_inst::TMol, PCase_CStr > TCStringMolPairsMap
static const SStaticPair< const char *, CMolInfo::TCompleteness > s_map_completeness_names[]
CStaticPairArrayMap< const char *, CSeq_inst::TTopology, PCase_CStr > TCStringTopologyPairsMap
static const SStaticPair< const char *, CSeq_inst::TTopology > s_map_topology_names[]
DEFINE_STATIC_ARRAY_MAP(TCStringBiomolPairsMap, k_biomol_names, s_map_biomol_names)
static const SStaticPair< const char *, CSeq_inst::TRepr > s_map_repr_names[]
CStaticPairArrayMap< const char *, CMolInfo::TCompleteness, PCase_CStr > TCStringCompletenessPairsMap
static const SStaticPair< const char *, CSeq_inst::TMol > s_map_mol_names[]
CStaticPairArrayMap< const char *, CSeq_inst::TStrand, PCase_CStr > TCStringStrandPairsMap
CStaticPairArrayMap< const char *, CMolInfo::TBiomol, PCase_CStr > TCStringBiomolPairsMap
static const SStaticPair< const char *, CMolInfo::TBiomol > s_map_biomol_names[]
static const SStaticPair< const char *, CMolInfo::TTech > s_map_tech_names[]
static const SStaticPair< const char *, CSeq_inst::TStrand > s_map_strand_names[]
CStaticPairArrayMap< const char *, CMolInfo::TBiomol, PCase_CStr > TCStringTechPairsMap
static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)
bool QualifierNamesAreEquivalent(string name1, string name2)
Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...
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