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NCBI C++ ToolKit: src/objtools/validator/single_feat_validator.cpp Source File

sequence;

: m_Feat(feat),

(scope), m_Imp(imp), m_ProductIsFar(

)

);

lowerSev =

;

& dbtag = **it;

( dbtag.

() ==

) {

,

, lowerSev);

);

(loc.IsInt() || loc.IsWhole()) {

(CSeq_loc_CI citer(loc); citer; ++citer) {

& this_id = citer.GetSeq_id();

(!

|| !

->Equals(this_id)) {

.Reset(&this_id);

(sid.

()) {

);

);

(id->Which() == sid.

()) {

from_seq =

->AsFastaString();

);

(id->Which()) {

);

is_seqloc_bond =

;

(CSeq_loc_CI it(feat.

()); it; ++it) {

(it.GetEmbeddingSeq_loc().IsBond()

&& (!it.GetEmbeddingSeq_loc().GetBond().IsSetA()

|| it.GetEmbeddingSeq_loc().GetBond().IsSetB())) {

is_seqloc_bond =

;

(CSeq_loc_CI it(feat.

()); it; ++it) {

(it.GetEmbeddingSeq_loc().IsBond()) {

is_seqloc_bond =

;

(CSeq_loc_CI it(feat.

()); it; ++it) {

(it.GetEmbeddingSeq_loc().IsBond()) {

is_seqloc_bond =

;

is_seqloc_bond;

(both || both_rev) {

(both && both_rev) {

suffix =

;

suffix =

;

}

(both_rev) {

suffix =

;

+

+ suffix +

);

(CSeq_loc_CI it(loc); it; ++it) {

(it.IsSetStrand()) {

(both && both_rev) {

has_parent_gene_id =

;

has_parent_gene_id =

;

((*it)->IsSetTag() && (*it)->GetTag().Equals(

)) {

has_parent_gene_id =

;

(!

(parent, (*it)->GetTag(), has_parent_gene_id)) {

(has_parent_gene_id ||

parent = feat_tree->GetParent(parent);

((*pi)->IsEquiv()) {

);

,

,

,

,

,

,

,

,

,

,

,

,

);

);

qual.

() +

);

ec_number = qual.

();

+ ec_number +

);

+ ec_number +

);

(pos == string::npos || !

(ec_number.c_str()[pos + 1])) {

ec_number +

);

ec_number +

);

+ qual.

() +

,

);

has_space =

;

has_char_after_space =

;

(

((

)(*it))) {

}

(has_space) {

has_char_after_space =

;

(has_char_after_space) {

);

+ qual.

() +

);

);

);

);

);

(

it : errors) {

it.first, it.second);

,

);

+ comment +

,

);

(is_partial &&

);

);

is_far_fail =

;

(

);

+=

;

+= is_partial ?

:

;

}

(is_far_fail) {

(

);

+=

;

+=

;

+= is_partial ?

:

;

);

);

prefix =

;

loc_id = os.str();

((*it)->IsGi() || (*it)->IsGibbsq() || (*it)->IsGibbmt()) {

(*it)->WriteAsFasta(os2);

bs_id = os2.str();

);

);

vector<TSeqPos> gap_starts;

);

(

gap_start : gap_starts) {

);

);

);

(

) +

}

(

std::exception&) {

(map_iter && pos <= stop) {

(; pos < map_end && pos <= stop; pos++) {

( (*it)->IsLoc() ) {

num_unknown_gap = 0;

first_in_gap =

, last_in_gap =

;

local_first_gap =

, local_last_gap =

;

startsOrEndsInGap =

;

(CSeq_loc_CI loc_it(loc); loc_it; ++loc_it) {

(!vec.

()) {

(id_it->Equals(loc_it.GetSeq_id())) {

local_first_gap =

;

local_last_gap =

;

string::iterator it = vec_data.begin();

(it != vec_data.end() && pos <

) {

is_gap =

;

unknown_length =

;

unknown_length =

;

unknown_length =

;

local_first_gap =

;

}

(pos ==

- 1) {

local_last_gap =

;

(unknown_length) {

}

(*it ==

) {

first_in_gap = local_first_gap;

last_in_gap = local_last_gap;

(local_first_gap || local_last_gap) {

startsOrEndsInGap =

;

(num_real == 0 && num_n == 0) {

(num_gap == 0 && num_unknown_gap == 0 && num_n == 0) {

}

(first_in_gap || last_in_gap) {

gap_starts.push_back(gap_start);

}

(num_real == 0 && num_gap == 0 && num_unknown_gap == 0 && num_n >= 50) {

}

(startsOrEndsInGap) {

}

(num_unknown_gap > 0) {

((*it)->IsLiteral()) {

= (*it)->GetLiteral().GetLength();

}

((*it)->IsLoc()) {

(CSeq_loc_CI loc_it(loc); loc_it; ++loc_it) {

(!vec.

()) {

=

;

(id_it->Equals(loc_it.GetSeq_id())) {

string::iterator it = vec_data.begin();

(it != vec_data.end()) {

((

)(*it + 1) <= 256 &&

(*it)) {

}

(

std::exception& ) {

(num_n > real_bases);

* protid =

;

(!prot_handle && look_far) {

look_far =

;

);

);

(

.empty())

;

found =

;

reasons_in_cit =

;

annotated_by_transcript_or_proteomic =

;

redundant_with_comment =

;

refseq_except =

;

vector<string> exceptions;

(vector<string>, it, exceptions) {

reasons_in_cit =

;

annotated_by_transcript_or_proteomic =

;

check_refseq =

;

check_refseq =

;

check_refseq =

;

((*id_it)->IsOther()) {

check_refseq =

;

refseq_except =

;

+

);

redundant_with_comment =

;

redundant_with_comment =

;

(redundant_with_comment) {

);

(refseq_except) {

(!found_just_the_exception) {

);

);

(annotated_by_transcript_or_proteomic) {

has_inference =

;

has_inference =

;

(!has_inference) {

);

is_imp =

;

& qual_str = gbq->GetQual();

gbqual = gbqual_and_value.first;

qual_str +

);

+ qual_str);

(

(qual_str,

)) {

(

(qual_str,

)) {

+ qual_str +

+

);

&

= gbq->GetVal();

+

+

+ qual_str);

+

+ qual_str);

+

+ qual_str);

);

);

);

multiple_rpt_unit =

;

}

( *it ==

|| *it ==

||

*it ==

|| *it ==

||

((

)(*it)) ) {

multiple_rpt_unit =

;

!multiple_rpt_unit ) {

just_nuc_letters =

;

,

,

,

,

,

,

,

,

,

( nuc_letters.find(*it) == nuc_letters.end() ) {

just_nuc_letters =

;

( just_nuc_letters ) {

( !vec.

() ) {

);

);

*cp =

.c_str();

badchars =

;

(*cp != 0 && !badchars) {

}

(*cp !=

&& *cp !=

&& *cp !=

&& *cp !=

) {

);

(

.length() > 25) {

(pos == string::npos) {

tmp_from, tmp_to;

}

(

std::exception& ) {

(tmp_from < 0 || tmp_to < 0) {

);

(from - 1 < range.

() || from - 1> range.

() || to - 1 < range.

() || to - 1 > range.

()) {

);

nulls_between =

;

nulls_between =

;

(nulls_between) {

in_range =

;

range = it.GetEmbeddingSeq_loc().GetTotalRange();

(from - 1 < range.

() || from - 1> range.

() || to - 1 < range.

() || to - 1 > range.

()) {

);

only_digits =

,

has_spaces =

;

(

((

)(*it)) ) {

( !

((

)(*it)) ) {

only_digits =

;

(only_digits || has_spaces) {

+

);

+

);

+

);

+

+

);

*src =

.c_str();

*find = consist.c_str();

(*src != 0 && rval) {

(strchr (find, *src) ==

) {

+

+ qual_str

+

);

+

+ qual_str

+

);

+

+ qual_str

+

);

has_fuzz =

;

( objects::CSeq_loc_CI it(

.

()); it && !has_fuzz; ++it) {

(it.IsPoint() && (it.GetFuzzFrom() || it.GetFuzzTo())) {

+

+

);

}

(

std::exception& ) {

field_name +

);

field_name +

);

field_name +

);

);

(

it = donor_problems.begin(); it != donor_problems.end(); it++) {

(

it = acceptor_problems.begin(); it != acceptor_problems.end(); it++) {

((*it)->IsOther() && (*it)->GetOther().IsSetAccession()

found =

;

((*it)->IsOther()) {

+

);

(strand1 == strand2) {

);

equivalent =

;

g2.

().front())) {

has_gene_id_xref =

;

((*xref)->IsSetId() && (*xref)->GetId().IsLocal()) {

(gene_feats.size() > 0) {

has_gene_id_xref =

;

(has_gene_id_xref) {

num_genes = 0;

num_trans_spliced = 0;

equivalent =

;

=

;

num_match_by_locus = 0;

num_match_by_locus_tag = 0;

( ; gene_it; ++gene_it) {

(gene_xref && gene_xref->

() &&

num_match_by_locus++;

num_match_by_locus_tag++;

);

(

<

|| num_genes == 0) {

num_trans_spliced = 0;

num_trans_spliced++;

equivalent =

;

prev_gene = gene_it;

}

(

==

) {

num_trans_spliced++;

(num_genes > 1 &&

}

(equivalent) {

+

);

+

);

}

(num_genes == 1

& qual = **qual_iter;

+ allele +

);

+ allele +

+ qual.

() +

);

& allele = gene_xref->

();

& qual = **qual_iter;

+ allele +

);

+ allele +

+ qual.

() +

);

(num_match_by_locus == 0 && num_match_by_locus_tag == 0) {

*

= loc.GetId();

);

);

(it->IsSetQual() &&

(it->GetQual(),

)

(

it : feat.

()) {

gene_old_locus_tag;

((*it)->IsSetQual() &&

((*it)->GetQual(),

)

&& (*it)->IsSetVal() && !

((*it)->GetVal())) {

gene_old_locus_tag = (*it)->GetVal();

+ old_locus_tag

+

+ gene_old_locus_tag +

);

);

( imp_loc.find(

) != string::npos ) {

+ imp_loc +

+

);

( imp_loc != temp_loc ) {

+ imp_loc +

+

temp_loc +

+

);

found =

;

((*it)->IsOther()) {

+

);

((*it)->IsOther() && (*it)->GetTextseq_Id()->IsSetAccession()

has_sfp_pseudo =

;

has_gene_pseudo =

;

(it->IsSetQual() &&

sfp_pseudo = it->GetVal();

has_sfp_pseudo =

;

(

it : gene->

()) {

(it->IsSetQual() &&

gene_pseudo = it->GetVal();

has_gene_pseudo =

;

(!has_sfp_pseudo && !has_gene_pseudo) {

}

(!has_sfp_pseudo) {

}

(has_sfp_pseudo && !has_gene_pseudo) {

+=

;

=

;

+=

+ sfp_pseudo +

+ gene_pseudo +

;

);

(

ch : src) {

chu = ch;

(chu > 31 && chu < 128) {

&

= *it;

& ch = *c_it;

chu = ch;

(ch > 127 || (ch < 32 && ch !=

&& ch !=

&& ch !=

)) {

(

it :

.GetName()) {

(

.IsSetEc() && !

.IsSetProcessed()

);

+

.GetDesc() +

);

);

);

(

.IsSetName() &&

.GetName().size() > 0) {

);

(

.CanGetDb () ) {

( (!

.IsSetName() ||

.GetName().empty()) &&

(!

.IsSetProcessed()

);

}

(

.IsSetActivity() && !

.GetActivity().empty()) {

);

}

(

.IsSetEc() && !

.GetEc().empty()) {

);

);

(

.IsSetProcessed() ) {

processed =

.GetProcessed();

(

.IsSetName() &&

!

.GetName().empty() &&

!

.GetName().front().empty() ) {

(

.CanGetDesc() && !

.GetDesc().empty() ) {

(

.CanGetEc() && !

.GetEc().empty() ) {

(

.CanGetActivity() && !

.GetActivity().empty() ) {

(

.CanGetDb() && !

.GetDb().empty() ) {

);

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

(!

.IsSetName()) {

(!

.IsSetProcessed() ||

);

(search.empty()) {

);

}

(sc_BadProtName.find (search.c_str()) != sc_BadProtName.end()

+ it +

);

(it) +

);

& ec_number = it;

+ ec_number +

);

+ ec_number +

);

(pos == string::npos || !

(ec_number.c_str()[pos + 1])) {

ec_number +

);

ec_number +

);

report_name =

;

(pos == string::npos) {

}

(prot_name.length() - pos < 5) {

report_name =

;

);

(id_it->IsOther()

&& id_it->GetOther().IsSetAccession()

prot_name.substr(21))) {

);

);

);

&&

(prot_name,

) == string::npos

(

(prot_name,

)) {

}

(!

(prot_name,

)

&& !

(prot_name,

)) {

);

+ prot_name +

);

(!

)

;

(! mi_i)

;

CSeq_loc& prot_loc =

->GetLocation();

conflict =

;

);

(

.IsSetType()) {

rna_type =

.GetType();

(

.CanGetExt() &&

.GetExt().IsName()) {

& rna_name =

.GetExt().GetName();

+ rna_name +

);

pseudo = feat_pseudo;

rna_typename +

);

);

);

}

(pseudo) {

);

);

);

( anticodon_len != 3 ) {

);

);

);

);

(

.IsSetExt() &&

);

);

isLessThan100 =

;

CSeq_loc_CI li(loc);

last_start = li.GetRange().GetFrom();

last_stop = li.GetRange().GetTo();

last_id->

(li.GetSeq_id());

this_start = li.GetRange().GetFrom();

this_stop = li.GetRange().GetTo();

(

((

)this_start - (

)last_stop) < 100 ||

((

)this_stop - (

)last_start) < 100) {

(li.GetSeq_id().Equals(*last_id)) {

isLessThan100 =

;

(

id_it : last_bsh.

()) {

(id_it.GetSeqId()->Equals(li.GetSeq_id())) {

isLessThan100 =

;

last_start = this_start;

last_stop = this_stop;

last_id->

(li.GetSeq_id());

( grp ==

) {

( !pseudo && grp !=

) {

(isLessThan100 && ! pseudo) {

(

.IsSetLineage()) {

lineage =

.GetLineage();

);

ordered =

;

adjacent =

;

unmarked_strand =

;

mixed_strand =

;

(CSeq_loc_CI curr(anticodon); curr; ++curr) {

(curr.GetEmbeddingSeq_loc().IsInt()) {

}

(curr.GetEmbeddingSeq_loc().IsPnt()) {

curr.GetEmbeddingSeq_loc().GetLabel(&lbl);

+ lbl +

);

(

&& curr &&

(prev_range.

() < curr_range.

()) {

(curr_range.

() + 1 == prev_range.

()) {

(prev_range.

() > curr_range.

()) {

(prev_range.

() + 1 == curr_range.

()) {

( curr_range == prev_range && curr_strand == prev_strand ) {

);

( curr_strand != prev_strand ) {

unmarked_strand =

;

unmarked_strand =

;

mixed_strand =

;

);

ac_strand = anticodon.GetStrand();

);

);

trans_splice =

;

trans_splice =

;

(!trans_splice) {

anticodon.GetLabel(&loc_lbl);

+ loc_lbl +

);

(unmarked_strand) {

+ loc_lbl +

);

+ loc_lbl +

);

[] = { 42, 65, 66, 67, 68, 69, 70, 71, 72, 73,

74, 75, 76, 77, 78, 79, 80, 81, 82, 83,

84, 85, 86, 87, 88, 89, 90 };

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

}

(

std::exception& ) {

list<CRef<CGenetic_code> >& codes = code_table.

();

( list<

>::const_iterator code_it = codes.begin(), code_it_end = codes.end(); code_it != code_it_end; ++code_it ) {

((*code_it)->GetId() == gcode) {

(*code_it)->GetName();

aa = 0, orig_aa;

vector<char> seqData;

found =

;

mustbemethionine =

;

mustbemethionine =

;

(mustbemethionine) {

+ aanm +

);

( ncbieaa.length() != 64 ) {

aaname =

;

modified_codon_recognition =

;

rna_editing =

;

modified_codon_recognition =

;

rna_editing =

;

vector<string> recognized_codon_values;

vector<unsigned char> recognized_taa_values;

(*iter == 255)

;

);

}

(*iter < 0) {

);

( !modified_codon_recognition && !rna_editing ) {

= ncbieaa[*iter];

recognized_codon_values.push_back (codon);

recognized_taa_values.push_back (

);

( (aa ==

) && (

==

) && (*iter == 14) ) {

+ codon +

+ aaname +

anticodon =

;

vector<string> codon_values;

vector<unsigned char> taa_values;

(codon.length() > 3) {

codon = codon.substr (0, 3);

ch = anticodon.c_str()[0];

string::iterator str_it = wobble.begin();

(str_it != wobble.end()) {

(index < 64 && index > -1) {

= ncbieaa[index];

taa_values.push_back(

);

codon_values.push_back(codon);

(anticodon.length() > 3) {

anticodon = anticodon.substr(0, 3);

}

(

std::exception& ) {

(codon_values.size() > 0) {

(

= 0;

< codon_values.size();

++) {

(aa ==

&&

(anticodon,

)) {

}

(aa ==

&&

(anticodon,

)) {

}

(aa ==

&&

(anticodon,

)) {

+ anticodon

+

+ aaname +

);

(recognized_codon_values.size() > 0) {

(

= 0;

< codon_values.size() && !

;

++) {

(

j = 0; j < recognized_codon_values.size() && !

; j++) {

(

(codon_values[

], recognized_codon_values[j])) {

}

(

(codon_values[

],

) && aa ==

) {

+ anticodon +

);

(orig_aa == 0 || orig_aa == 255) {

(idx == 0 || idx >= 28) {

found_bad =

;

(

it : scores) {

);

);

mismatches = 0;

);

+

+

);

((*it)->IsOther()) {

+ farstr +

+

+

+ farstr +

+ farstr +

+

+ farstr +

+

+ farstr +

);

);

+

(mismatches)

);

);

);

(

.IsSetExt() &&

.GetExt().IsName()) {

& rna_name =

.GetExt().GetName();

);

+ rna_name +

);

);

);

* genomicgrp =

;

found_match =

;

found_mismatch =

;

(

= 1;

<= 4;

++) {

(

!=

&&

!=

) {

found_match =

;

found_mismatch =

;

(found_mismatch) {

,

}

(found_mismatch) {

,

);

);

);

);

+

+

);

+

+

);

+

+

);

+

+

);

pseudo = feat_pseudo;

pseudo = feat_pseudo;

);

(partial5 && partial3) {

(scores.size() > 0) {

(scores.size() > 0) {

donor_in_gap =

;

acceptor_in_gap =

;

donor_in_gap =

;

acceptor_in_gap =

;

(!partial5 && !partial3) {

(donor_in_gap && acceptor_in_gap) {

donor_good =

;

acceptor_good =

;

(!partial5 && !donor_in_gap) {

donor[0] = vec[end5 - 1];

donor[1] = vec[end5];

donor[0] = vec[end5];

donor[1] = vec[end5 + 1];

(!partial3 && !acceptor_in_gap) {

acceptor[0] = vec[end3];

acceptor[1] = vec[end3 + 1];

acceptor_good =

;

acceptor[0] = vec[end3 - 1];

acceptor[1] = vec[end3];

acceptor_good =

;

(!partial5 && !partial3) {

(donor_good && acceptor_good) {

(!donor_in_gap) {

(!acceptor_in_gap) {

(acceptor_good) {

is_short =

;

}

(partial_right &&

);

content_label;

(

(content_label,

)) {

);

is_far_delta =

;

is_far_delta =

;

( !(*sg) )

;

is_far_delta =

;

(! is_far_delta) {

);

);

);

);

(

= 0;

< sequence.size();

++) {

(sequence[

] !=

) {

((*it)->IsSetQual() &&

((*it)->GetQual(),

)

(estimated_length != loc_len) {

}

(

std::exception& ) {

( !vec.

() ) {

num_gap = 0;

string::iterator it = vec_data.begin();

(it != vec_data.end()) {

}

(*it !=

) {

(num_real > 0 && num_n > 0) {

}

(num_real > 0) {

}

(num_n > 0) {

+

);

}

(

std::exception& ) {

);

);

( subtype ) {

+

);

+

+

);

);

);

);

);

);

+

);

);

&

= (*gbqual)->GetVal();

);

&

= (*gbqual)->GetVal();

missing =

;

);

(

( (*gbqual)->GetQual(),

) != 0 )

;

&

= (*gbqual)->GetVal();

( recomb_values.

(

.c_str()) == recomb_values.

() ) {

);

static CRef< CScope > m_Scope

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

@ eErr_SEQ_FEAT_WrongQualOnImpFeat

@ eErr_SEQ_FEAT_NotSpliceConsensusAcceptor

@ eErr_SEQ_FEAT_rRNADoesNotHaveProduct

@ eErr_SEQ_FEAT_WholeLocation

@ eErr_SEQ_FEAT_MobileElementInvalidQualifier

@ eErr_SEQ_FEAT_DuplicateAnticodonInterval

@ eErr_SEQ_FEAT_ShortTRNAIntron

@ eErr_SEQ_FEAT_MinusStrandProtein

@ eErr_SEQ_FEAT_NotSpliceConsensusDonor

@ eErr_SEQ_FEAT_GeneXrefWithoutLocus

@ eErr_SEQ_FEAT_GenesInconsistent

@ eErr_SEQ_FEAT_PseudoRnaHasProduct

@ eErr_SEQ_FEAT_EcNumberDataMissing

@ eErr_SEQ_FEAT_InvalidProductOnGene

@ eErr_SEQ_FEAT_BadRRNAcomponentOverlapTRNA

@ eErr_SEQ_FEAT_mRNAUnnecessaryException

@ eErr_SEQ_FEAT_UnknownImpFeatQual

@ eErr_SEQ_FEAT_InvalidCompareBadAccession

@ eErr_SEQ_FEAT_InvalidCompareMissingVersion

@ eErr_SEQ_FEAT_InvalidRptUnitRange

@ eErr_GENERIC_SgmlPresentInText

@ eErr_SEQ_FEAT_BadAnticodonAA

@ eErr_SEQ_FEAT_RnaProductMismatch

@ eErr_SEQ_FEAT_FeatureBeginsOrEndsInGap

@ eErr_SEQ_FEAT_EcNumberInProteinName

@ eErr_SEQ_FEAT_InvalidTRNAdata

@ eErr_SEQ_FEAT_UnnecessaryException

@ eErr_SEQ_FEAT_AssemblyGapFeatureProblem

@ eErr_SEQ_FEAT_OldLocusTagWithoutLocusTag

@ eErr_SEQ_FEAT_NotSpliceConsensusAcceptorTerminalIntron

@ eErr_SEQ_FEAT_AnticodonMixedStrand

@ eErr_SEQ_FEAT_UnparsedtRNAProduct

@ eErr_SEQ_FEAT_InconsistentPseudogeneValue

@ eErr_SEQ_FEAT_GeneXrefWithoutGene

@ eErr_SEQ_FEAT_ReplacedEcNumber

@ eErr_SEQ_FEAT_PartialsInconsistent

@ eErr_SEQ_FEAT_InvalidQualifierValue

@ eErr_SEQ_FEAT_DuplicateGeneOntologyTerm

@ eErr_SEQ_FEAT_ProtRefHasNoData

@ eErr_SEQ_FEAT_NotSpliceConsensusDonorTerminalIntron

@ eErr_SEQ_FEAT_BadTrnaAA

@ eErr_SEQ_FEAT_WrongQualOnFeature

@ eErr_SEQ_FEAT_ProductFetchFailure

@ eErr_SEQ_FEAT_MismatchedAllele

@ eErr_SEQ_FEAT_RepeatSeqDoNotMatch

@ eErr_SEQ_FEAT_MissingQualOnImpFeat

@ eErr_SEQ_FEAT_InvalidRptUnitSeqCharacters

@ eErr_SEQ_FEAT_TranscriptLen

@ eErr_SEQ_FEAT_RubiscoProblem

@ eErr_SEQ_FEAT_InvalidAlleleDuplicates

@ eErr_SEQ_FEAT_ImpCDSnotPseudo

@ eErr_SEQ_FEAT_BadCDScomponentOverlapTRNA

@ eErr_SEQ_FEAT_BadEcNumberValue

@ eErr_SEQ_FEAT_EcNumberEmpty

@ eErr_SEQ_FEAT_ImpCDShasTranslation

@ eErr_SEQ_FEAT_PeptideFeatOutOfFrame

@ eErr_SEQ_FEAT_ProteinNameHasPMID

@ eErr_SEQ_FEAT_ImpFeatBadLoc

@ eErr_SEQ_FEAT_MissingQualOnFeature

@ eErr_SEQ_FEAT_PolyAsiteNotPoint

@ eErr_SEQ_FEAT_RepeatRegionNeedsNote

@ eErr_SEQ_FEAT_GeneXrefStrandProblem

@ eErr_SEQ_FEAT_PolyATail

@ eErr_SEQ_FEAT_MissingTrnaAA

@ eErr_GENERIC_NonAsciiAsn

@ eErr_SEQ_FEAT_UnparsedtRNAAnticodon

@ eErr_SEQ_FEAT_RefSeqInText

@ eErr_SEQ_FEAT_ErroneousException

@ eErr_SEQ_FEAT_ImproperBondLocation

@ eErr_SEQ_FEAT_InvalidPseudoQualifier

@ eErr_SEQ_FEAT_FeatureSeqIDCaseDifference

@ eErr_SEQ_FEAT_BadProductSeqId

@ eErr_SEQ_FEAT_PeptideFeatureLacksCDS

@ eErr_SEQ_FEAT_InvalidCompareRefSeqAccession

@ eErr_SEQ_FEAT_InvalidReplace

@ eErr_SEQ_FEAT_UnknownImpFeatKey

@ eErr_SEQ_FEAT_IdenticalMRNAtranscriptIDs

@ eErr_SEQ_FEAT_AssemblyGapCoversSequence

@ eErr_SEQ_FEAT_ShortIntron

@ eErr_SEQ_FEAT_SplitEcNumber

@ eErr_SEQ_FEAT_AssemblyGapAdjacentToNs

@ eErr_SEQ_FEAT_InvalidPunctuation

@ eErr_SEQ_FEAT_LocusTagProductMismatch

@ eErr_SEQ_FEAT_UnknownFeatureQual

@ eErr_SEQ_FEAT_TranscriptMismatches

@ eErr_SEQ_FEAT_IncorrectQualifierCapitalization

@ eErr_SEQ_FEAT_InvalidNumberQualifier

@ eErr_SEQ_FEAT_FeatureInsideGap

@ eErr_SEQ_FEAT_InvalidRNAFeature

@ eErr_SEQ_FEAT_tRNArange

@ eErr_SEQ_FEAT_GeneIdMismatch

@ eErr_SEQ_FEAT_MissingMRNAproduct

@ eErr_SEQ_FEAT_tRNAmRNAmixup

@ eErr_SEQ_FEAT_UndesiredProteinName

@ eErr_SEQ_FEAT_MrnaTransFail

@ eErr_SEQ_FEAT_InvalidInferenceValue

@ eErr_SEQ_FEAT_GeneXrefNeeded

@ eErr_SEQ_FEAT_InvalidType

@ eErr_SEQ_FEAT_SerialInComment

@ eErr_SEQ_FEAT_BadTrailingCharacter

@ eErr_SEQ_FEAT_IntervalBeginsOrEndsInGap

@ eErr_SEQ_FEAT_ProteinNameEndsInBracket

@ eErr_SEQ_FEAT_BadInternalCharacter

@ eErr_SEQ_FEAT_BadProteinName

@ eErr_SEQ_FEAT_MissingLocation

@ eErr_SEQ_FEAT_ExceptionMissingText

@ eErr_SEQ_FEAT_BadAnticodonCodon

@ eErr_SEQ_FEAT_BadTrailingHyphen

@ eErr_SEQ_FEAT_OldLocusTagMismtach

@ eErr_SEQ_FEAT_PseudoRnaViaGeneHasProduct

@ eErr_SEQ_FEAT_DeletedEcNumber

@ eErr_SEQ_FEAT_FeatureIsMostlyNs

@ eErr_SEQ_FEAT_InvalidMatchingReplace

@ eErr_INTERNAL_Exception

@ eErr_SEQ_FEAT_BadEcNumberFormat

@ eErr_SEQ_FEAT_BothStrands

@ eErr_SEQ_FEAT_ExceptionProblem

@ eErr_SEQ_FEAT_RedundantFields

@ eErr_SEQ_FEAT_ColdShockProteinProblem

@ eErr_SEQ_FEAT_TrnaCodonWrong

@ eErr_SEQ_FEAT_NoNameForProtein

@ eErr_SEQ_FEAT_RptUnitRangeProblem

@ eErr_SEQ_FEAT_InvalidVariationReplace

@ eErr_SEQ_FEAT_SeqLocOrder

@ eErr_SEQ_FEAT_AnticodonStrandConflict

@ eErr_SEQ_FEAT_InvalidRepeatUnitLength

@ eErr_SEQ_FEAT_VectorContamination

@ eErr_SEQ_FEAT_AbuttingIntervals

@ eErr_SEQ_FEAT_EcNumberInProteinComment

@ eErr_SEQ_FEAT_UnnecessaryCitPubEquiv

@ eErr_SEQ_FEAT_PartialProblem

@ eErr_SEQ_FEAT_RegulatoryClassOtherNeedsNote

@ eErr_SEQ_FEAT_MiscFeatureNeedsNote

@ eErr_SEQ_FEAT_FocusOnBioSourceFeature

@ eErr_SEQ_FEAT_PolyAsignalNotRange

@ eErr_SEQ_DESCR_BioSourceNeedsFocus

@ eErr_SEQ_FEAT_BadTrnaCodon

@ eErr_SEQ_FEAT_FeatureCrossesGap

@ eErr_SEQ_FEAT_SelfReferentialProduct

@ eErr_SEQ_FEAT_GapFeatureProblem

@ eErr_SEQ_FEAT_HypotheticalProteinMismatch

@ eErr_SEQ_FEAT_MissingGeneXref

@ eErr_SEQ_FEAT_RecombinationClassOtherNeedsNote

@ eErr_SEQ_FEAT_MissingExceptionFlag

bool IsOrganismEukaryote() const

int GetGenCode(int def=1) const

bool IsSkippable(void) const

bool IsKnownGap(size_t offset)

bool IsGap(size_t offset)

bool IsUnknownGap(size_t offset)

map< size_t, EGapType > TGapTypeMap

CGapCache(const CSeq_loc &loc, CBioseq_Handle bsh)

@Gb_qual.hpp User-defined methods of the data storage class.

static bool IsLegalMobileElementValue(const string &val)

static bool IsValidPseudogeneValue(const string &val)

static bool IsValidRptTypeValue(const string &val)

static const TLegalRecombinationClassSet & GetSetOfLegalRecombinationClassValues(void)

static const string & GetNcbieaa(int id)

static string IndexToCodon(int index)

static int CodonToIndex(char base1, char base2, char base3)

static const CGenetic_code_table & GetCodeTable(void)

CRef< feature::CFeatTree > GetFeatTreeFromCache(const CSeq_loc &loc, CScope &scope)

CConstRef< CSeq_feat > GetGeneFromCache(const CSeq_feat *feat, CScope &scope)

bool IsSuppressed(void) const

bool x_IsIntronShort(bool pseudo)

CMRNAValidator(const CSeq_feat &feat, CScope &scope, CValidError_imp &imp)

void x_ValidateMrnaGene()

CConstRef< CSeq_feat > m_Gene

void x_ValidateCommonMRNAProduct()

CPeptideValidator(const CSeq_feat &feat, CScope &scope, CValidError_imp &imp)

void x_ValidatePeptideOnCodonBoundary()

CConstRef< CSeq_feat > m_CDS

void x_ValidateSeqFeatLoc() override

void x_ValidateSeqFeatLoc() override

void x_ValidateECNumbers()

void x_ValidateProteinName(const string &prot_name)

void x_ReportUninformativeNames()

void x_ValidateMolinfoPartials()

static EECNumberFileStatus GetECNumAmbiguousStatus()

static EECNumberFileStatus GetECNumSpecificStatus()

@ eECFile_not_found

File was not found in expected directory.

static bool IsECNumberSplit(const string &old_ecno)

static bool IsValidECNumberFormat(const string &ecno)

Verify correct form of EC number.

static EECNumberFileStatus GetECNumDeletedStatus()

EECNumberStatus

Enzyme Commission number status.

@ eEC_replaced

Obsolete synonym for some other EC number.

@ eEC_unknown

Unrecognized; possibly malformed.

@ eEC_deleted

Withdrawn, with no (single?) replacement.

static EECNumberFileStatus GetECNumReplacedStatus()

static EECNumberStatus GetECNumberStatus(const string &ecno)

Determine an EC number's validity and specificity.

void x_ValidateTrnaOverlap()

void x_ValidateRnaTrans()

void x_ValidateRnaProductType()

void x_ValidateTrnaCodons()

void x_ReportRNATranslationProblems(size_t problems, size_t mismatches)

void x_ValidateAnticodon(const CSeq_loc &anticodon)

void x_ValidateTrnaData()

void x_ValidateTrnaType()

void x_ValidateRnaProduct(bool feat_pseudo, bool pseudo)

@RNA_ref.hpp User-defined methods of the data storage class.

static string GetRnaTypeName(const CRNA_ref::EType rna_type)

static SIZE_TYPE Convert(const CTempString &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst, TCoding dst_coding)

bool IsLegalQualifier(EQualifier qual) const

Test wheather a certain qualifier is legal for the feature.

@ eQual_mobile_element_type

static bool AllowStrandBoth(ESubtype subtype)

ESubtype GetSubtype(void) const

string GetKey(EVocabulary vocab=eVocabulary_full) const

const TQualifiers & GetMandatoryQualifiers(void) const

Get the list of all mandatory qualifiers for the feature.

static std::pair< EQualifier, CTempString > GetQualifierTypeAndValue(CTempString qual)

@ eSubtype_transit_peptide

@ eSubtype_bad

These no longer need to match the FEATDEF values in the C toolkit's objfdef.h.

@ eSubtype_mobile_element

static EQualifier GetQualifierType(CTempString qual)

convert qual string to enumerated value

static CTempString GetQualifierAsString(EQualifier qual)

Convert a qualifier from an enumerated value to a string representation or empty if not found.

static CTempString SubtypeValueToName(ESubtype eSubtype)

Turns a ESubtype into its string value which is NOT necessarily related to the identifier of the enum...

static const vector< string > & GetRegulatoryClassList()

namespace ncbi::objects::

static bool IsExceptionTextInLegalList(const string &exception_text, bool allow_refseq)

Indicates whether this specific text occurs in the list of legal exceptions.

const CGene_ref * GetGeneXref(void) const

See related function in util/feature.hpp.

static bool IsExceptionTextRefSeqOnly(const string &exception_text)

Indicates whether this specific text is a RefSeq-only exception.

static TIndex GetMapToIndex(CSeq_data::E_Choice from_type, CSeq_data::E_Choice to_type, TIndex from_idx)

static bool x_IsMostlyNs(const CSeq_loc &loc, CBioseq_Handle bsh)

CBioseq_Handle x_GetFeatureProduct(bool look_far, bool &is_far)

EDiagSev x_SeverityForConsensusSplice()

void x_ValidateBothStrands()

void ValidateCharactersInField(string value, string field_name)

void PostErr(EDiagSev sv, EErrType et, const string &msg)

void x_ValidateLabelVal(const string &val)

CSingleFeatValidator(const CSeq_feat &feat, CScope &scope, CValidError_imp &imp)

void x_ReportAcceptorSpliceSiteReadErrors(const CSpliceProblems::TSpliceProblem &problem, const string &label)

void x_ValidateRptUnitVal(const string &val, const string &key)

void x_ValidateGeneXRef()

void x_ValidateReplaceQual(const string &key, const string &qual_str, const string &val)

void x_CheckForNonAsciiCharacters()

CBioseq_Handle x_GetBioseqByLocation(const CSeq_loc &loc)

void x_ValidateSeqFeatDataType()

CBioseq_Handle m_ProductBioseq

static bool s_IsPseudo(const CSeq_feat &feat)

virtual bool x_ReportOrigProteinId()

CBioseq_Handle m_LocationBioseq

void x_ValidateCompareVal(const string &val)

void x_ValidateRptUnitSeqVal(const string &val, const string &key)

void x_ValidateExtUserObject()

void x_ValidateSeqFeatProduct()

void x_ReportDonorSpliceSiteReadErrors(const CSpliceProblems::TSpliceProblem &problem, const string &label)

void x_ValidateImpFeatQuals()

static bool s_GeneRefsAreEquivalent(const CGene_ref &g1, const CGene_ref &g2, string &label)

void x_ReportECNumFileStatus()

void x_ValidateGbQual(const CGb_qual &qual)

void x_ValidateGeneFeaturePair(const CSeq_feat &gene)

void x_ValidateOldLocusTag(const string &old_locus_tag)

virtual void x_ValidateFeatComment()

void x_ValidateNonImpFeat()

bool x_HasNamedQual(const string &qual_name)

void x_ValidateLocusTagGeneralMatch(CConstRef< CSeq_feat > gene)

static bool x_HasSeqLocBond(const CSeq_feat &feat)

void x_ReportPseudogeneConflict(CConstRef< CSeq_feat > gene)

void x_ValidateRptUnitRangeVal(const string &val)

void x_ValidateFeatPartialness()

static bool x_BioseqHasNmAccession(CBioseq_Handle bsh)

void ValidateSplice(bool gene_pseudo, bool check_all)

void x_ReportSpliceProblems(const CSpliceProblems &problems, const string &label)

bool x_AllowFeatureToMatchGapExactly()

static TSeqPos x_FindStartOfGap(CBioseq_Handle bsh, TSeqPos pos, CScope *scope)

static size_t x_CalculateLocationGaps(CBioseq_Handle bsh, const CSeq_loc &loc, vector< TSeqPos > &gap_starts)

virtual void x_ValidateSeqFeatLoc()

virtual void x_ValidateExceptText(const string &text)

static bool s_BioseqHasRefSeqThatStartsWithPrefix(CBioseq_Handle bsh, string prefix)

@ eLocationGapInternalIntervalEndpointInGap

@ eLocationGapCrossesUnknownGap

@ eLocationGapContainedInGapOfNs

@ eLocationGapContainedInGap

@ eLocationGapFeatureMatchesGap

static void x_LocHasStrandBoth(const CSeq_loc &feat, bool &both, bool &both_rev)

void x_ValidateImpFeatLoc()

const TSpliceProblemList & GetDonorProblems() const

void CalculateSpliceProblems(const CSeq_feat &feat, bool check_all, bool pseudo, CBioseq_Handle loc_handle)

vector< TSpliceProblem > TSpliceProblemList

@ eSpliceSiteRead_WrongNT

bool IsExceptionUnnecessary() const

bool AreErrorsUnexpected() const

pair< size_t, TSeqPos > TSpliceProblem

const TSpliceProblemList & GetAcceptorProblems() const

const_iterator find(const key_type &key) const

Return a const_iterator pointing to the specified element, or to the end if the element is not found.

const_iterator end() const

Return the end of the controlled sequence.

vector< CSeq_feat_Handle > TSeq_feat_Handles

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

Template class for iteration on objects of class C (non-medifiable version)

@ eInferenceValidCode_valid

static EInferenceValidCode ValidateInference(string inference, bool fetch_accession, CScope *scope=nullptr)

bool DoRubiscoTest() const

bool ReportSpliceAsError() const

void PostErr(EDiagSev sv, EErrType et, const string &msg, const CSerialObject &obj)

const CBioSourceKind & BioSourceKind() const

bool IsRemoteFetch() const

CConstRef< CSeq_feat > GetmRNAGivenProduct(const CBioseq &seq)

bool DoesAnyFeatLocHaveGI() const

bool IsLocusTagGeneralMatch() const

bool IgnoreInferences() const

void ValidateDbxref(const CDbtag &xref, const CSerialObject &obj, bool biosource=false, const CSeq_entry *ctx=nullptr)

bool IsSerialNumberInComment(const string &comment)

bool IsFarSequence(const CSeq_id &id)

const CTSE_Handle & GetTSE_Handle()

bool ValidateInferenceAccessions() const

bool IsHugeFileMode() const

void IncrementPseudogeneCount()

CConstRef< CSeq_feat > GetCDSGivenProduct(const CBioseq &seq)

CBioseq_Handle GetLocalBioseqHandle(const CSeq_id &id)

bool x_IsFarFetchFailure(const CSeq_loc &loc)

bool IsGenomeSubmission() const

void ValidateBioSource(const CBioSource &bsrc, const CSerialObject &obj, const CSeq_entry *ctx=nullptr)

void IncrementGeneXrefCount()

bool IsFarFetchCDSproducts() const

bool IsValidateExons() const

size_t GetCumulativeInferenceCount(void) const

bool IgnoreExceptions() const

void SetFarFetchFailure()

bool IsRefSeqConventions() const

SValidatorContext & SetContext()

bool IsIndexerVersion() const

CGeneCache & GetGeneCache()

bool IsSmallGenomeSet() const

bool HasRefSeq(void) const

void ValidateSeqLoc(const CSeq_loc &loc, const CBioseq_Handle &seq, bool report_abutting, const string &prefix, const CSerialObject &obj, bool lowerSev=false)

bool IsFarFetchMRNAproducts() const

bool IsTransgenic(const CBioSource &bsrc)

void ValidatePubdesc(const CPubdesc &pub, const CSerialObject &obj, const CSeq_entry *ctx=nullptr)

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

#define MAKE_CONST_SET(name, type,...)

Include a standard set of the NCBI C++ Toolkit most basic headers.

The NCBI C++ standard methods for dealing with std::string.

static void chk(int check, const char *fmt,...)

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

static const char * expected[]

static const char * str(char *buf, int n)

Public API for finding the gene(s) on a given feature using the same criteria as the flatfile generat...

vector< TGoTermError > GetGoTermErrors(const CSeq_feat &feat)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

EDiagSev

Severity level for the posted diagnostics.

@ eDiag_Info

Informational message.

@ eDiag_Error

Error message.

@ eDiag_Warning

Warning message.

@ eDiag_Fatal

Fatal error – guarantees exit(or abort)

@ eDiag_Critical

Critical error message.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

const string AsFastaString(void) const

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

virtual void WriteAsFasta(ostream &out) const

Implement serializable interface.

string GetLabel(const CSeq_id &id)

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

ENa_strand GetStrand(void) const

Get the location's strand.

TRange GetTotalRange(void) const

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

bool IsSetStrand(EIsSetStrand flag=eIsSetStrand_Any) const

Check if strand is set for any/all part(s) of the seq-loc depending on the flag.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

CRef< CSeq_loc > Intersect(const CSeq_loc &other, TOpFlags flags, ISynonymMapper *syn_mapper) const

Find the intersection with the seq-loc, merge/sort resulting ranges depending on flags.

TSeqPos GetStop(ESeqLocExtremes ext) const

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

ELocationInFrame IsLocationInFrame(const CSeq_feat_Handle &cds, const CSeq_loc &loc)

Determines whether location loc is in frame with coding region cds.

CMappedFeat GetBestOverlappingFeat(const CMappedFeat &feat, CSeqFeatData::ESubtype need_subtype, sequence::EOverlapType overlap_type, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

@ eLocationInFrame_InFrame

@ eLocationInFrame_BadStart

@ eLocationInFrame_BadStop

@ eLocationInFrame_BadStartAndStop

@ fFGL_Content

Include its content if there is any.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

bool IsValid(const CSeq_point &pt, CScope *scope)

Checks that point >= 0 and point < length of Bioseq.

Int8 TestForOverlapEx(const CSeq_loc &loc1, const CSeq_loc &loc2, EOverlapType type, CScope *scope=0, TOverlapFlags flags=fOverlap_Default)

Updated version of TestForOverlap64().

int SeqLocPartialCheck(const CSeq_loc &loc, CScope *scope)

sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

Returns the sequence::ECompare containment relationship between CSeq_locs.

bool IsOneBioseq(const CSeq_loc &loc, CScope *scope)

Returns true if all embedded CSeq_ids represent the same CBioseq, else false.

bool IsSameBioseq(const CSeq_id &id1, const CSeq_id &id2, CScope *scope, CScope::EGetBioseqFlag get_flag=CScope::eGetBioseq_All)

Determines if two CSeq_ids represent the same CBioseq.

CSeq_loc * SeqLocRevCmpl(const CSeq_loc &loc, CScope *scope)

Get reverse complement of the seq-loc (?)

@ eSeqlocPartial_Internal

@ eSeqlocPartial_Complete

@ fCompareOverlapping

Check if seq-locs are overlapping.

@ eOverlap_Simple

any overlap of extremes

@ eOverlap_Interval

at least one pair of intervals must overlap

@ eOverlap_Contained

2nd contained within 1st extremes

@ eOverlap_Subset

2nd is a subset of 1st ranges

@ eContains

First CSeq_loc contains second.

@ eSame

CSeq_locs contain each other.

@ eContained

First CSeq_loc contained by second.

const CSeq_feat * GetCDSForProduct(const CBioseq &product, CScope *scope)

Get the encoding CDS feature of a given protein sequence.

bool IsPseudo(const CSeq_feat &feat, CScope &scope)

Determines whether given feature is pseudo, using gene associated with feature if necessary Checks to...

CConstRef< CSeq_feat > GetOverlappingGene(const CSeq_loc &loc, CScope &scope, ETransSplicing eTransSplicing=eTransSplicing_Auto)

CConstRef< CSeq_feat > GetOverlappingCDS(const CSeq_loc &loc, CScope &scope)

vector< TFeatScore > TFeatScores

void GetOverlappingFeatures(const CSeq_loc &loc, CSeqFeatData::E_Choice feat_type, CSeqFeatData::ESubtype feat_subtype, EOverlapType overlap_type, TFeatScores &feats, CScope &scope, const TBestFeatOpts opts=0, CGetOverlappingFeaturesPlugin *plugin=NULL)

Find all features overlapping the location.

CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id &id, const CTSE_Handle &tse)

Get bioseq handle for sequence withing one TSE.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

bool IsSetExcept(void) const

const CTSE_Handle & GetTSE_Handle(void) const

Get CTSE_Handle of containing TSE.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

TClass GetClass(void) const

const TInst_Ext & GetInst_Ext(void) const

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

bool IsSetInst_Ext(void) const

bool IsSetDbxref(void) const

const CSeqFeatData & GetData(void) const

TSeqPos GetBioseqLength(void) const

bool IsSetExcept_text(void) const

TInst_Length GetInst_Length(void) const

const string & GetExcept_text(void) const

bool IsSetInst_Repr(void) const

bool IsSetClass(void) const

TInst_Repr GetInst_Repr(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

const CSeq_feat::TDbxref & GetDbxref(void) const

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

const TId & GetId(void) const

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

const TInst & GetInst(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

const CSeq_loc & GetLocation(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

CSeqMap::ESegmentType GetType(void) const

bool IsUnknownLength(void) const

return true if current segment is a gap of unknown length

TSeqPos GetPosition(void) const

return position of current segment in sequence

TSeqPos GetLength(void) const

return length of current segment

CConstRef< CSeq_feat > GetSeq_feat(void) const

Get current seq-feat.

ENa_strand GetStrand(void) const

bool IsInGap(TSeqPos pos) const

true if sequence at 0-based position 'pos' has gap Note: this method is not MT-safe,...

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

char Char

Alias for char.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static string SizetToString(size_t value, TNumToStringFlags flags=0, int base=10)

Convert size_t to string.

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static bool EqualCase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-sensitive equality of a substring with another string.

static SIZE_TYPE FindWord(const CTempString str, const CTempString word, ECase use_case=eCase, EDirection direction=eForwardSearch)

Find given word in the string.

static SIZE_TYPE FindCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case sensitive search.

static int Compare(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Compare of a substring with another string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

static string & ToLower(string &str)

Convert string to lower case – string& version.

@ eReverseSearch

Search in a backward direction.

@ eNocase

Case insensitive compare.

static const char label[]

const TOrg & GetOrg(void) const

Get the Org member data.

bool IsSetIs_focus(void) const

to distinguish biological focus Check if a value has been assigned to Is_focus data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsSetSyn(void) const

synonyms for locus Check if a value has been assigned to Syn data member.

const TSyn & GetSyn(void) const

Get the Syn member data.

const TDesc & GetDesc(void) const

Get the Desc member data.

bool IsSetPseudo(void) const

pseudogene Check if a value has been assigned to Pseudo data member.

bool CanGetLocus(void) const

Check if it is safe to call GetLocus method.

bool IsSetLocus_tag(void) const

systematic gene name (e.g., MI0001, ORF0069) Check if a value has been assigned to Locus_tag data mem...

bool CanGetLocus_tag(void) const

Check if it is safe to call GetLocus_tag method.

bool IsSetLocus(void) const

Official gene symbol Check if a value has been assigned to Locus data member.

bool IsSetAllele(void) const

Official allele designation Check if a value has been assigned to Allele data member.

bool CanGetAllele(void) const

Check if it is safe to call GetAllele method.

bool CanGetDesc(void) const

Check if it is safe to call GetDesc method.

const TLocus_tag & GetLocus_tag(void) const

Get the Locus_tag member data.

const TLocus & GetLocus(void) const

Get the Locus member data.

TPseudo GetPseudo(void) const

Get the Pseudo member data.

const TAllele & GetAllele(void) const

Get the Allele member data.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetDb(void) const

name of database or system Check if a value has been assigned to Db data member.

const TTag & GetTag(void) const

Get the Tag member data.

bool IsSetTag(void) const

appropriate tag Check if a value has been assigned to Tag data member.

const TDb & GetDb(void) const

Get the Db member data.

const TStr & GetStr(void) const

Get the variant data.

const TTaxname & GetTaxname(void) const

Get the Taxname member data.

bool CanGetTaxname(void) const

Check if it is safe to call GetTaxname method.

EProcessed

processing status

const TName & GetName(void) const

Get the Name member data.

bool IsSetEc(void) const

E.C.

const TEc & GetEc(void) const

Get the Ec member data.

@ eProcessed_signal_peptide

@ eProcessed_transit_peptide

const TPub & GetPub(void) const

Get the variant data.

list< CRef< CPub > > TPub

bool IsPub(void) const

Check if variant Pub is selected.

const TAnticodon & GetAnticodon(void) const

Get the Anticodon member data.

TType GetType(void) const

Get the Type member data.

TNcbi8aa GetNcbi8aa(void) const

Get the variant data.

const TAa & GetAa(void) const

Get the Aa member data.

const TCodon & GetCodon(void) const

Get the Codon member data.

bool IsSetAa(void) const

Check if a value has been assigned to Aa data member.

bool IsTRNA(void) const

Check if variant TRNA is selected.

bool IsSetAnticodon(void) const

location of anticodon Check if a value has been assigned to Anticodon data member.

EType

type of RNA feature

bool IsSetExt(void) const

generic fields for ncRNA, tmRNA, miscRNA Check if a value has been assigned to Ext data member.

TNcbieaa GetNcbieaa(void) const

Get the variant data.

bool IsGen(void) const

Check if variant Gen is selected.

TIupacaa GetIupacaa(void) const

Get the variant data.

bool CanGetAnticodon(void) const

Check if it is safe to call GetAnticodon method.

const TGen & GetGen(void) const

Get the variant data.

bool IsSetType(void) const

Check if a value has been assigned to Type data member.

bool IsSetClass(void) const

for ncRNAs, the class of non-coding RNA: examples: antisense_RNA, guide_RNA, snRNA Check if a value h...

E_Choice Which(void) const

Which variant is currently selected.

const TExt & GetExt(void) const

Get the Ext member data.

const TTRNA & GetTRNA(void) const

Get the variant data.

const TClass & GetClass(void) const

Get the Class member data.

@ e_not_set

No variant selected.

@ e_Name

for naming "other" type

@ eType_scRNA

will become ncRNA, with RNA-gen.class = scRNA

@ eType_snoRNA

will become ncRNA, with RNA-gen.class = snoRNA

@ eType_snRNA

will become ncRNA, with RNA-gen.class = snRNA

bool CanGetDbxref(void) const

Check if it is safe to call GetDbxref method.

const TVal & GetVal(void) const

Get the Val member data.

const TKey & GetKey(void) const

Get the Key member data.

bool IsSetLoc(void) const

original location string Check if a value has been assigned to Loc data member.

bool IsSetComment(void) const

Check if a value has been assigned to Comment data member.

vector< CRef< CDbtag > > TDbxref

const TPub & GetPub(void) const

Get the variant data.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

bool IsSetQual(void) const

qualifiers Check if a value has been assigned to Qual data member.

E_Choice Which(void) const

Which variant is currently selected.

bool IsBond(void) const

Check if variant Bond is selected.

bool IsProt(void) const

Check if variant Prot is selected.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

bool IsImp(void) const

Check if variant Imp is selected.

const TCit & GetCit(void) const

Get the Cit member data.

const TQual & GetQual(void) const

Get the Qual member data.

bool IsSetPartial(void) const

incomplete in some way? Check if a value has been assigned to Partial data member.

bool IsSetKey(void) const

Check if a value has been assigned to Key data member.

bool IsSetXref(void) const

cite other relevant features Check if a value has been assigned to Xref data member.

const TLocation & GetLocation(void) const

Get the Location member data.

E_Choice

Choice variants.

bool IsGene(void) const

Check if variant Gene is selected.

const TData & GetData(void) const

Get the Data member data.

bool IsSetExcept(void) const

something funny about this? Check if a value has been assigned to Except data member.

const TExcept_text & GetExcept_text(void) const

Get the Except_text member data.

bool IsPub(void) const

Check if variant Pub is selected.

bool IsSetExcept_text(void) const

explain if except=TRUE Check if a value has been assigned to Except_text data member.

const TDbxref & GetDbxref(void) const

Get the Dbxref member data.

bool CanGetVal(void) const

Check if it is safe to call GetVal method.

bool IsHet(void) const

Check if variant Het is selected.

bool IsSetExp_ev(void) const

Check if a value has been assigned to Exp_ev data member.

const TBiosrc & GetBiosrc(void) const

Get the variant data.

bool CanGetExcept_text(void) const

Check if it is safe to call GetExcept_text method.

TPseudo GetPseudo(void) const

Get the Pseudo member data.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsSetQual(void) const

Check if a value has been assigned to Qual data member.

bool CanGetExcept(void) const

Check if it is safe to call GetExcept method.

bool IsSetPseudo(void) const

annotated on pseudogene? Check if a value has been assigned to Pseudo data member.

const TComment & GetComment(void) const

Get the Comment member data.

bool IsSetCit(void) const

citations for this feature Check if a value has been assigned to Cit data member.

bool IsBiosrc(void) const

Check if variant Biosrc is selected.

const TGene & GetGene(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

TPartial GetPartial(void) const

Get the Partial member data.

const TProt & GetProt(void) const

Get the variant data.

TExcept GetExcept(void) const

Get the Except member data.

const TXref & GetXref(void) const

Get the Xref member data.

vector< CRef< CSeqFeatXref > > TXref

vector< CRef< CGb_qual > > TQual

const TQual & GetQual(void) const

Get the Qual member data.

const TRna & GetRna(void) const

Get the variant data.

bool IsSetDbxref(void) const

support for xref to other databases Check if a value has been assigned to Dbxref data member.

bool IsSetVal(void) const

Check if a value has been assigned to Val data member.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

bool CanGetQual(void) const

Check if it is safe to call GetQual method.

const TLoc & GetLoc(void) const

Get the Loc member data.

bool IsRna(void) const

Check if variant Rna is selected.

TExp_ev GetExp_ev(void) const

Get the Exp_ev member data.

const TImp & GetImp(void) const

Get the variant data.

bool IsSetLocation(void) const

feature made from Check if a value has been assigned to Location data member.

@ e_Het

cofactor, prosthetic grp, etc, bound to seq

@ e_Region

named region (globin locus)

@ e_Seq

to annotate origin from another seq

@ e_Txinit

transcription initiation

@ e_Num

a numbering system

@ e_Pub

publication applies to this seq

@ e_User

user defined structure

@ e_Rsite

restriction site (for maps really)

@ e_Comment

just a comment

@ e_Non_std_residue

non-standard residue here in seq

bool IsSetAccession(void) const

Check if a value has been assigned to Accession data member.

const TName & GetName(void) const

Get the Name member data.

ENa_strand

strand of nucleic acid

TFrom GetFrom(void) const

Get the From member data.

bool IsGeneral(void) const

Check if variant General is selected.

bool CanGetName(void) const

Check if it is safe to call GetName method.

E_Choice Which(void) const

Which variant is currently selected.

bool CanGetAccession(void) const

Check if it is safe to call GetAccession method.

const TGeneral & GetGeneral(void) const

Get the variant data.

TTo GetTo(void) const

Get the To member data.

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

bool IsSetName(void) const

Check if a value has been assigned to Name data member.

@ eNa_strand_both_rev

in reverse orientation

@ eNa_strand_both

in forward orientation

@ e_Tpe

Third Party Annot/Seq EMBL.

@ e_Tpd

Third Party Annot/Seq DDBJ.

@ e_Tpg

Third Party Annot/Seq Genbank.

@ eClass_gen_prod_set

genomic products, chrom+mRNA+protein

TRepr GetRepr(void) const

Get the Repr member data.

bool IsSetCompleteness(void) const

Check if a value has been assigned to Completeness data member.

bool CanGetBiomol(void) const

Check if it is safe to call GetBiomol method.

ERepr

representation class

const TInst & GetInst(void) const

Get the Inst member data.

const TSource & GetSource(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

bool IsSetExt(void) const

extensions for special types Check if a value has been assigned to Ext data member.

bool IsDelta(void) const

Check if variant Delta is selected.

const TExt & GetExt(void) const

Get the Ext member data.

TBiomol GetBiomol(void) const

Get the Biomol member data.

const TDelta & GetDelta(void) const

Get the variant data.

TCompleteness GetCompleteness(void) const

Get the Completeness member data.

const Tdata & Get(void) const

Get the member data.

list< CRef< CDelta_seq > > Tdata

const TMolinfo & GetMolinfo(void) const

Get the variant data.

@ eRepr_delta

sequence made by changes (delta) to others

@ eRepr_raw

continuous sequence

@ 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

@ e_Ncbieaa

extended ASCII 1 letter aa codes

@ e_Ncbistdaa

consecutive codes for std aas

@ e_Molinfo

info on the molecule and techniques

@ e_Source

source of materials, includes Org-ref

@ e_Loc

point to a sequence

static void text(MDB_val *v)

constexpr bool empty(list< Ts... >) noexcept

const struct ncbi::grid::netcache::search::fields::KEY key

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

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)

#define FOR_EACH_SEQID_ON_BIOSEQ(Itr, Var)

FOR_EACH_SEQID_ON_BIOSEQ EDIT_EACH_SEQID_ON_BIOSEQ.

#define FOR_EACH_GBQUAL_ON_FEATURE

#define FOR_EACH_GBQUAL_ON_SEQFEAT(Itr, Var)

FOR_EACH_GBQUAL_ON_SEQFEAT EDIT_EACH_GBQUAL_ON_SEQFEAT.

#define FOR_EACH_STRING_IN_VECTOR(Itr, Var)

FOR_EACH_STRING_IN_VECTOR EDIT_EACH_STRING_IN_VECTOR.

#define FOR_EACH_CHAR_IN_STRING(Itr, Var)

FOR_EACH_CHAR_IN_STRING EDIT_EACH_CHAR_IN_STRING.

bool ContainsSgml(const string &str)

static string s_AsciiString(const string &src)

static bool s_LocationStrandsIncompatible(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

CSingleFeatValidator * FeatValidatorFactory(const CSeq_feat &feat, CScope &scope, CValidError_imp &imp)

bool s_HasNamedQual(const CSeq_feat &feat, const string &qual)

const string kInferenceMessage[]

static bool s_StringConsistsOf(string str, string consist)

static string GetGeneticCodeName(int gcode)

const string kOrigProteinId

int s_LegalNcbieaaValues[]

static const char *const sc_BadProtNameText[]

CStaticArraySet< const char *, PCase_CStr > TBadProtNameSet

static bool s_IsBioseqPartial(CBioseq_Handle bsh)

const char * GetAAName(unsigned char aa, bool is_ascii)

DEFINE_STATIC_ARRAY_MAP(TBadProtNameSet, sc_BadProtName, sc_BadProtNameText)

static const char * kAANames[]

static string s_GetGeneRefFields(const CGene_ref &gene, int field)

bool HasGeneIdXref(const CMappedFeat &sf, const CObject_id &tag, bool &has_parent_gene_id)

static bool s_RptUnitIsBaseRange(string str, TSeqPos &from, TSeqPos &to)

static bool xf_IsDeltaLitOnly(CBioseq_Handle bsh)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

bool CheckIntronAcceptor(ENa_strand strand, TConstSpliceSite acceptor)

bool CheckIntronSpliceSites(ENa_strand strand, TConstSpliceSite donor, TConstSpliceSite acceptor)

bool CheckIntronDonor(ENa_strand strand, TConstSpliceSite donor)

Selector used in CSeqMap methods returning iterators.

atomic_bool CheckECNumFileStatus

size_t GetMRNATranslationProblems(const CSeq_feat &feat, size_t &mismatches, bool ignore_exceptions, CBioseq_Handle nuc, CBioseq_Handle rna, bool far_fetch, bool is_gpipe, bool is_genomic, CScope *scope)

@ eMRNAProblem_UnnecessaryException

@ eMRNAProblem_UnableToFetch

@ eMRNAProblem_TranscriptLenLess

@ eMRNAProblem_PolyATail95

@ eMRNAProblem_TranscriptLenMore

@ eMRNAProblem_ProductReplaced

@ eMRNAProblem_ErroneousException

@ eMRNAProblem_PolyATail100

const int InferenceAccessionCutoff

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