#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbistr.hpp>
#include "validatorp.hpp"
#include "utilities.hpp"
#include <serial/serialbase.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objmgr/seq_entry_handle.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/util/feature.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqfeat/Code_break.hpp>
#include <objects/seqfeat/Gb_qual.hpp>
#include <objects/seqfeat/Genetic_code.hpp>
#include <objects/seqfeat/Genetic_code_table.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/Prot_ref.hpp>
#include <objects/seqfeat/RNA_ref.hpp>
#include <objects/seqfeat/SubSource.hpp>
#include <objects/seqfeat/Trna_ext.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqloc/Seq_point.hpp>
#include <objects/seqloc/Textseq_id.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/seqport_util.hpp>
#include <objects/pub/Pub.hpp>
#include <objects/pub/Pub_set.hpp>
#include <objects/general/Dbtag.hpp>
#include <util/static_set.hpp>
#include <util/sequtil/sequtil_convert.hpp>
#include <algorithm>
#include <string>
Include dependency graph for validerror_feat.cpp:
Go to the source code of this file.
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Definition at line 1594 of file validerror_feat.cpp. |
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Definition at line 1300 of file validerror_feat.cpp. References CSeq_data_Base::e_Ncbieaa, CSeq_data_Base::e_Ncbistdaa, and CSeqportUtil::GetMapToIndex(). |
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Definition at line 1314 of file validerror_feat.cpp. References CGenetic_code_table_Base::Get(), and CGen_code_table::GetCodeTable(). |
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Definition at line 221 of file validerror_feat.cpp. References CSeq_id::eAcc_gb_embl_ddbj, CSeq_id::eAcc_local, FOR_EACH_SEQID_ON_BIOSEQ, CBioseq_Handle::GetBioseqCore(), and CScope::GetBioseqHandle(). |
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Definition at line 206 of file validerror_feat.cpp. References CSeq_id::eAcc_refseq_mrna, FOR_EACH_SEQID_ON_BIOSEQ, CBioseq_Handle::GetBioseqCore(), and CScope::GetBioseqHandle(). |
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Definition at line 1572 of file validerror_feat.cpp. |
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Definition at line 1700 of file validerror_feat.cpp. |
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Definition at line 1603 of file validerror_feat.cpp. References eAccessionFormat_null, eAccessionFormat_too_long, and NStr::IsBlank(). |
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Initial value: { "---", "Ala", "Asx", "Cys", "Asp", "Glu", "Phe", "Gly", "His", "Ile", "Lys", "Leu", "Met", "Asn", "Pro", "Gln", "Arg", "Ser", "Thr", "Val", "Trp", "OTHER", "Tyr", "Glx", "Sec", "TERM" } Definition at line 1293 of file validerror_feat.cpp. |
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Initial value: { "(5'site:YES, 3'site:YES)", "(5'site:YES, 3'site:NO)", "(5'site:YES, 3'site:ABSENT)", "(5'site:NO, 3'site:YES)", "(5'site:NO, 3'site:NO)", "(5'site:NO, 3'site:ABSENT)", "(5'site:ABSENT, 3'site:YES)", "(5'site:ABSENT, 3'site:NO)", "(5'site:ABSENT, 3'site:ABSENT)" } Definition at line 193 of file validerror_feat.cpp. |
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Initial value: { "RNA editing", "reasons given in citation", "rearrangement required for product", "ribosomal slippage", "trans-splicing", "alternative processing", "artificial frameshift", "nonconsensus splice site", "modified codon recognition", "alternative start codon", "dicistronic gene", "transcribed product replaced", "translated product replaced", "transcribed pseudogene", } Definition at line 2554 of file validerror_feat.cpp. |
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Initial value: { 42, 65, 66, 67, 68, 69, 70, 71, 72, 73, 75, 76, 77, 78, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90 } Definition at line 1288 of file validerror_feat.cpp. |
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Initial value: { "tandem", "inverted", "flanking", "terminal", "direct", "dispersed", "other" } Definition at line 187 of file validerror_feat.cpp. Referenced by CValidError_feat::ValidateImpGbquals(). |
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Initial value: { "", "", "chloroplast", "chromoplast", "", "", "plastid", "", "", "", "", "", "cyanelle", "", "", "", "apicoplast", "leucoplast", "proplastid", "" } Definition at line 163 of file validerror_feat.cpp. |
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Initial value: { "unclassified transcription discrepancy", "unclassified translation discrepancy", "mismatches in transcription", "mismatches in translation", "adjusted for low-quality genome", } Definition at line 2572 of file validerror_feat.cpp. |
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Initial value: { "RNA editing", "artificial frameshift", "mismatches in translation", "rearrangement required for product", "reasons given in citation", "unclassified translation discrepancy" } Definition at line 2673 of file validerror_feat.cpp. |
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Initial value: { "RNA editing", "artificial frameshift", "mismatches in transcription" "reasons given in citation", "unclassified transcription discrepancy", } Definition at line 2029 of file validerror_feat.cpp. |