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NCBI C++ ToolKit: Sequence utilities

Conversions between seq-id types

Searching for features

Definition at line 1566 of file sequence.hpp.

Storage for features and scores.

Definition at line 352 of file sequence.hpp.

For relative ranges (ONLY), id is irrelevant and normally unset.

Definition at line 1131 of file sequence.hpp.

Multiple STrimRules are allowed, which are applied from smallest bases_to_check to largest bases_to_check, and redundant rules are automatically removed.

When a rule is applied, we start over at the first sorted rule again.

Definition at line 1322 of file sequence.hpp.

accession.version (when possible)

accession only, even if version is available

Definition at line 90 of file sequence.hpp.

requires explicit association, rather than analysis based on overlaps

don't perform any expensive tests, such as ones that require fetching additional sequences

favor longer features over shorter features

Pay no attention to strands when finding the best feat.

This may be useful for, e.g., trans-spliced genes.

default options: do everything

Definition at line 330 of file sequence.hpp.

Definition at line 752 of file sequence.hpp.

This indicates what happened when we tried to run x_FindNextGapOnBioseq.

No more relevant gaps were found on this bioseq.

The other output parameters will be in an undefined state.

Another relevant gap was found, and the output parameters are filled in to represent information about it.

Definition at line 1689 of file sequence.hpp.

assemble FAR delta sequences; on by dflt

honor specifed gap mode; on by default

never include location details in defline

flip the (implicit) location

don't convert '>' to '_' in title

honor masks specified at a lower level

honor masks specified at a higher level

don't try too hard to find titles

show key-value pair modifiers (e.g. "[organism=Homo sapiens]")

skip check for duplicate sequence IDs

show gap key-value pair modifiers (e.g. "[linkage-evidence=map;strobe]"). Only works if gap mode is eGM_count.

Keep unknown gap's nominal length. That is, when a gap has an unknown length but nominal length, use that instead of just making it 100.

Use this to show gaps of size zero as a lone hyphen at the end of a line.

Use this flag to enable GI output in the defline.

Hide gb| prefix for genbank only seq_id's.

Encode the title string for HTML display.

Disregard original ID when constructing defline.

Disregard original ID when constructing defline.

first avalailabe for derived classes

Show general id and accession in the defline.

Definition at line 772 of file sequence.hpp.

don't merge adjacent intervals

Definition at line 1125 of file sequence.hpp.

0x01 ("Beginning" as defined by CSeqVector)

0x02 ("End" as defined by CSeqVector)

0x04 (Seq-gaps are not considered trimmable if this flag is set, only letter gaps (e.g. N's for nucs))

Definition at line 1300 of file sequence.hpp.

How to represent gaps with fInstantiateGaps enabled, as it is by default.

(Disabling fInstantiateGaps is equivalent to requesting eGM_one_dash.)

A single dash, followed by a line break.

Multiple inline dashes.

Multiple inline Ns or Xs as appropriate (default).

>?N or >?unk100, as appropriate.

Definition at line 803 of file sequence.hpp.

Retrieve a particular seq-id from a given bioseq handle.

This uses CSynonymsSet internally to decide which seq-id should be used.

return only a gi-based seq-id

return only an accession based seq-id

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

returns the ID associated with a bioseq-handle

use CSeq_id::Score() as the scoring function

use CSeq_id::BestRank() as the scoring function

use CSeq_id::WorstRank() as the scoring function

use CSeq_id::FastaAARank() as the scoring function

use CSeq_id::FastaNARank() as the scoring function

"canonical" here means "most specific"; this differs from "best" in that "best" is intended for display purposes

Mask for requested id type.

Check if the seq-id is present in the scope.

Throw exception on errors. If not set, an empty value is returned.

Definition at line 98 of file sequence.hpp.

This function is here rather than in CBioseq because it may need to inspect other sequences.

The reconstruct flag indicates that it should ignore any existing title Seqdesc.

ignore existing title Seqdesc.

append [organism]

normally just names the first

skip potential expensive operations

Definition at line 281 of file sequence.hpp.

Which residues to mask out in subsequent output.

These do NOT automatically reset between calls to Write; you must do so yourself by setting them to null.

write as lowercase rather than uppercase

write as N for nucleotides, X for peptides

Definition at line 847 of file sequence.hpp.

This enum is used to set what is meant by "ambiguous".

Here, only N for nucleotides and X for amino acids is considered ambiguous.

Here, anything that's not certain is considered ambiguous.

That is, anything but A, C, G, T for nucleotides, and most amino acids except, for example, B (which can be aspartic acid or asparagine), X (completely ambiguous), etc.

Definition at line 1289 of file sequence.hpp.

if hitting ends, extend to include partial codons

Definition at line 313 of file sequence.hpp.

This indicates what happened with the trim.

Error states are indicated by an exception, not EResult.

Bioseq is now trimmed.

Bioseq is left unchanged because it did not need to be trimmed at all.

This is NOT an error.

Definition at line 1352 of file sequence.hpp.

don't merge adjacent intervals on the product

map the termination codon as a legal location

Definition at line 302 of file sequence.hpp.

Definition at line 1214 of file sequence.hpp.

See also

TTranslationFlags

= 0x1 Do not include stop in translation

= 0x2 Remove trailing Xs from protein

= 0x4 Translate first codon even if not start codon (because sequence is 5' partial)

= 0x8 May not end in stop codon (because sequence is 3' partial)

Definition at line 980 of file sequence.hpp.

Definition at line 948 of file sequence.hpp.

Convenience functions for popular overlapping types.

Ignore overlap strand if the source location has mixed/both strand.

Definition at line 579 of file sequence.hpp.

User-settable flags for tuning behavior.

Generate fresh titles unconditionally.

List all relevant proteins, not just one.

Never use related sequences' annotations.

Refrain from anything that could add substantial overhead.

Use GPipe defaults.

Do not add organism suffix to proteins.

Development mode for testing new features.

Show key-value pair modifiers (e.g. "[organism=Homo sapiens]")

Run auto-def for nucleotides if user object is present.

Generate FASTA defline.

Disable internal call to auto-def.

Do not remove and recreate prefix or suffix.

Definition at line 83 of file create_defline.hpp.

Add nucleotide pattern or restriction site to sequence search.

Uses ambiguity codes, e.g., R = A and G, H = A, C and T

Parameters

sequence pattern's name cut_site pattern's sequence

Definition at line 4871 of file sequence.cpp.

References eNa_strand_both, eNa_strand_minus, eNa_strand_plus, flags, NStr::IsBlank(), NCBI_THROW, revcomp(), s_GetReverseComplement(), NStr::ToUpper(), NStr::TruncateSpaces(), CSeqSearch::x_AddNucleotidePattern(), and CSeqSearch::x_IsJustTopStrand().

constructors

Parameters

client pointer to a client object (receives pattern match notifications) flags specify search flags

Definition at line 4797 of file sequence.cpp.

This sets up the parameters for how this trimmer will act.

Parameters

eMeaningOfAmbig This indicates exactly what ambiguous means (e.g. just "N" or do all ambiguous symbols count? ) fFlags miscellaneous parameters to control this. See TFlags. vecTrimRules This indicates how trimming will occur. See TTrimRuleVec. uMinSeqLen Trimming tries to halt if the sequence becomes smaller than this size. It is possible for the resulting sequence to be below the uMinSeqLen size (or even trimmed to nothing), but the trimmer will at least try not to do that.

Definition at line 163 of file seq_trimmer.cpp.

References _ASSERT, ArraySize(), CSequenceAmbigTrimmer::eMeaningOfAmbig_AnyAmbig, CSequenceAmbigTrimmer::eMeaningOfAmbig_OnlyCompletelyUnknown, CSequenceAmbigTrimmer::m_arrNucAmbigLookupTable, CSequenceAmbigTrimmer::m_arrProtAmbigLookupTable, CSequenceAmbigTrimmer::m_eMeaningOfAmbig, CSequenceAmbigTrimmer::m_vecTrimRules, NCBI_USER_THROW_FMT, and CSequenceAmbigTrimmer::x_NormalizeVecTrimRules().

This trims the given bioseq, using params set in the CSequenceAmbigTrimmer constructor.

It will properly handle the annots and descs inside the bioseq, too, if requested.

Parameters

bioseq_handle The bioseq to trim. trimmed_ranges The ranges trimmed by DoTrim will be added to this.

Returns

This returns how the trimming went. On error, an exception is thrown and the bioseq may be in an undefined state.

Definition at line 213 of file seq_trimmer.cpp.

References _ASSERT, CBioseq_Handle::eCoding_Iupac, CSequenceAmbigTrimmer::eResult_NoTrimNeeded, CSequenceAmbigTrimmer::eResult_SuccessfullyTrimmed, CSequenceAmbigTrimmer::fFlags_DoNotTrimBeginning, CSequenceAmbigTrimmer::fFlags_DoNotTrimEnd, CBioseq_Handle::GetBioseqLength(), CRangeCollection< Position >::GetCoveredLength(), CSequenceAmbigTrimmer::x_FindWhereToTrim(), CSequenceAmbigTrimmer::x_SliceBioseq(), CSequenceAmbigTrimmer::x_TestFlag(), and CSequenceAmbigTrimmer::x_TrimToNothing().

Find "best" frame for a coding region.

"Best" frame has no internal stop codons.

Definition at line 4376 of file sequence.cpp.

Referenced by CEditSequence::AdjustFeatureLocations(), BOOST_AUTO_TEST_CASE(), CRetranslateCDS::GetCommand(), CEditCdsFrame::GetCommand(), ApplyCDSFrame::s_SetCDSFrame(), CMacroFunction_ApplyCDSFrame::s_SetCDSFrame(), CCleanup::SetBestFrame(), CMacroFunction_ApplyCDS::TheFunction(), UpdateFeat(), CFeaturePropagator::x_PropagateCds(), and CFeatureTableReader::xMoveCdRegions().

Definition at line 4272 of file sequence.cpp.

References CSerialObject::Assign(), map_checker< Container >::begin(), eExtreme_Biological, CCdregion_Base::eFrame_not_set, CCdregion_Base::eFrame_one, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, map_checker< Container >::end(), NStr::Find(), CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), GetLength(), CSeq_feat_Base::GetLocation(), CSeqFeatData_Base::IsCdregion(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_feat_Base::IsSetData(), CCdregion_Base::IsSetFrame(), CSeq_feat_Base::IsSetLocation(), NPOS, NULL, prot, CSeq_feat_Base::SetData(), NStr::StartsWith(), and CSeqTranslator::Translate().

Main method.

Definition at line 3931 of file create_defline.cpp.

References CSeqdesc_Base::e_User, ctll::empty(), CTempString::empty(), NStr::eNocase, CUser_object::eObjectType_AutodefOptions, CDeflineGenerator::fDoNotUseAutoDef, flags, CDeflineGenerator::fLeavePrefixSuffix, CDeflineGenerator::fShowModifiers, CUser_object::GetObjectType(), CAutoDef::GetOneDefLine(), CSeqdesc_Base::GetUser(), NStr::HtmlDecode(), i, CAutoDefOptions::InitFromUserObject(), islower(), CDeflineGenerator::m_Feat_Tree, CDeflineGenerator::m_GpipeMode, CDeflineGenerator::m_Idx, CDeflineGenerator::m_IsAA, CDeflineGenerator::m_IsEST_STS_GSS, CDeflineGenerator::m_IsMap, CDeflineGenerator::m_IsNA, CDeflineGenerator::m_IsNC, CDeflineGenerator::m_IsNM, CDeflineGenerator::m_IsNR, CDeflineGenerator::m_IsNZ, CDeflineGenerator::m_IsPatent, CDeflineGenerator::m_IsPDB, CDeflineGenerator::m_IsSeg, CDeflineGenerator::m_IsTLS, CDeflineGenerator::m_IsTSA, CDeflineGenerator::m_IsWGS, CDeflineGenerator::m_LocalAnnotsOnly, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_MetaGenomeSource, CDeflineGenerator::m_MICompleteness, CDeflineGenerator::m_Reconstruct, CDeflineGenerator::m_TLSMaster, CDeflineGenerator::m_WGSMaster, NCBI_COMPLETENESS, NPOS, NULL, CRef< C, Locker >::Reset(), s_tpaPrefixList, s_TrimMainTitle(), CAutoDefModifierCombo::SetOptions(), CAutoDef::SetOptionsObject(), NStr::StartsWith(), str(), toupper(), CDeflineGenerator::x_AdjustProteinTitleSuffix(), CDeflineGenerator::x_AdjustProteinTitleSuffixIdx(), x_CleanAndCompress(), CDeflineGenerator::x_GetModifiers(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetBioSrcIdx(), CDeflineGenerator::x_SetFlags(), CDeflineGenerator::x_SetFlagsIdx(), CDeflineGenerator::x_SetPrefix(), CDeflineGenerator::x_SetSuffix(), CDeflineGenerator::x_SetTitleFromBioSrc(), CDeflineGenerator::x_SetTitleFromGPipe(), CDeflineGenerator::x_SetTitleFromMap(), CDeflineGenerator::x_SetTitleFromNC(), CDeflineGenerator::x_SetTitleFromNM(), CDeflineGenerator::x_SetTitleFromNR(), CDeflineGenerator::x_SetTitleFromPatent(), CDeflineGenerator::x_SetTitleFromPDB(), CDeflineGenerator::x_SetTitleFromProtein(), CDeflineGenerator::x_SetTitleFromProteinIdx(), CDeflineGenerator::x_SetTitleFromSegSeq(), and CDeflineGenerator::x_SetTitleFromWGS().

Referenced by CDeflineGenerator::GenerateDefline(), s_GetCdsSequence(), s_SetCloneInfo(), s_SetIdList(), CShowBlastDefline::x_FillDeflineAndId(), CAlnGraphic::x_GetAlnInfo(), and CDisplaySeqalign::x_InitDefLinesHeader().

Retrieve the accession for a given GI.

If no accession was found returns an empty string or throws CSeqIdFromHandleException depending on the flags. Id type in the flags is ignored, only VerifyId and ThrowOnError flags are checked.

Definition at line 686 of file sequence.cpp.

References CSeq_id_Base::e_Gi, eGetId_ForceAcc, eGetId_ThrowOnError, eGetId_VerifyId, eWithAccessionVersion, flags, GetId(), CSeq_id_Handle::GetSeqId(), CSeq_id::GetSeqIdString(), kEmptyStr, and NCBI_THROW.

Referenced by CDemoApp::GetIds(), ReplaceWellknownSeqs(), s_CheckQuals_cdregion(), s_ChrName(), s_CreateHistCommentString(), variation::CHgvsParser::s_SeqIdToHgvsStr(), CFeatureItem::x_AddQualProteinId(), and CAppHitFilter::x_LoadConstraints().

Retrieve the accession string for a Seq-id.

If no accession was found returns an empty string or throws CSeqIdFromHandleException depending on the flags. Id type in the flags is ignored, only VerifyId and ThrowOnError flags are checked.

Definition at line 708 of file sequence.cpp.

References eGetId_ForceAcc, eGetId_ThrowOnError, eGetId_VerifyId, eWithAccessionVersion, flags, GetId(), CSeq_id_Handle::GetSeqId(), CSeq_id::GetSeqIdString(), kEmptyStr, and NCBI_THROW.

Referenced by CLocMapper_Default::CLocMapper_Default(), SCompareAlignments::operator()(), SFlybaseCompareAlignments::operator()(), CCreateGeneModelTask::x_AssignIDsAndUpdateGenes(), CGuiObjectInfoSeq_feat::x_GetAccession(), variation_ref::CHgvsParser::x_SeqIdToHgvsHeader(), CGff3Writer::x_WriteBioseqHandle(), and CSrcWriter::xGatherId().

Definition at line 1874 of file sequence.cpp.

References _ASSERT, CSeqFeatData_Base::e_Cdregion, eOverlap_CheckIntervals, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_mRNA, SAnnotSelector::ExcludeNamedAnnots(), fBestFeat_FavorLonger, fBestFeat_NoExpensive, fBestFeat_StrictMatch, CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CSeq_id_Handle::GetHandle(), GetId(), CScope::GetIds(), CSeq_feat_Base::GetLocation(), CSeq_feat::GetNamedQual(), GetOverlappingFeatures(), CSeq_feat_Base::GetProduct(), CMappedFeat::GetProduct(), CSeqFeatData::GetSubtype(), CSeq_feat_Base::IsSetExt(), CSeq_feat_Base::IsSetProduct(), CSeq_feat_Handle::IsSetProduct(), CBioseq_Handle::IsSynonym(), ITERATE, CConstRef< C, Locker >::Reset(), SAnnotSelector::SetFeatSubtype(), SAnnotSelector::SetOverlapIntervals(), and SAnnotSelector::SetResolveTSE().

Referenced by GetBestCdsForMrna(), GetBestOverlappingFeat(), and GetCdssForGene().

Definition at line 2128 of file sequence.cpp.

References _ASSERT, CSeqFeatData_Base::e_Gene, eOverlap_Contained, CSeqFeatData::eSubtype_any, CSeqFeatData::eSubtype_cdregion, fBestFeat_NoExpensive, fBestFeat_StrictMatch, GetBestGeneForMrna(), GetBestMrnaForCds(), CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetGene(), CSeq_feat::GetGeneXref(), CGene_ref::GetLabel(), CSeq_feat_Base::GetLocation(), GetOverlappingFeatures(), CSeqFeatData::GetSubtype(), CGene_ref::IsSuppressed(), and ITERATE.

Referenced by GetBestGeneForCds(), and GetBestOverlappingFeat().

Definition at line 2040 of file sequence.cpp.

References _ASSERT, CSeqFeatData_Base::e_Gene, eOverlap_Contained, CSeqFeatData::eSubtype_any, CSeqFeatData::eSubtype_mRNA, fBestFeat_FavorLonger, fBestFeat_StrictMatch, CSeq_feat_Base::GetData(), CSeq_feat_Base::GetDbxref(), CSeqFeatData_Base::GetGene(), CSeq_feat::GetGeneXref(), CGene_ref::GetLabel(), CSeq_feat_Base::GetLocation(), GetOverlappingFeatures(), CSeqFeatData::GetSubtype(), CSeq_feat_Base::IsSetDbxref(), CGene_ref::IsSuppressed(), and ITERATE.

Referenced by GetBestGeneForCds(), GetBestGeneForMrna(), and GetBestOverlappingFeat().

Definition at line 1609 of file sequence.cpp.

References _ASSERT, CSeqFeatData_Base::e_Rna, eOverlap_CheckIntRev, eOverlap_SubsetRev, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_mRNA, SAnnotSelector::ExcludeNamedAnnots(), fBestFeat_FavorLonger, fBestFeat_NoExpensive, fBestFeat_StrictMatch, CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetExcept(), CSeq_feat_Base::GetExcept_text(), CSeq_id_Handle::GetHandle(), GetId(), CScope::GetIds(), CSeq_feat_Base::GetLocation(), CSeq_feat::GetNamedQual(), CMappedFeat::GetOriginalFeature(), GetOverlappingFeatures(), CSeq_feat_Base::GetProduct(), CSeqFeatData::GetSubtype(), CSeq_feat_Base::IsSetExcept(), CSeq_feat_Base::IsSetExcept_text(), CSeq_feat_Base::IsSetExt(), CSeq_feat_Base::IsSetProduct(), CBioseq_Handle::IsSynonym(), ITERATE, kRibosomalSlippageText, CSeq_id::Match(), CConstRef< C, Locker >::Reset(), SAnnotSelector::SetFeatSubtype(), SAnnotSelector::SetOverlapIntervals(), and SAnnotSelector::SetResolveTSE().

Referenced by GetBestGeneForCds(), GetBestMrnaForCds(), and GetBestOverlappingFeat().

Get the best overlapping feature for a SNP (variation)

Parameters

snp_feat SNP feature object subtype subtype of overlapping feature scope search_both_strands search is performed on both strands, starting with the one specified by the feature's location.

Returns

the overlapping fetaure or NULL if not found

Definition at line 1355 of file sequence.cpp.

References CSeqFeatData::GetTypeFromSubtype(), and x_GetBestOverlapForSNP().

Definition at line 2386 of file sequence.cpp.

References CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_variation, GetBestCdsForMrna(), GetBestGeneForCds(), GetBestGeneForMrna(), GetBestMrnaForCds(), GetBestOverlapForSNP(), GetBestOverlappingFeat(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetLocation(), and CSeqFeatData::GetSubtype().

See the note above on 'overlap_type' meaning.

Definition at line 1208 of file sequence.cpp.

References CSeqFeatData::eSubtype_any, fBestFeat_FavorLonger, and GetOverlappingFeatures().

Referenced by GetBestOverlappingFeat(), GetCdssForGene(), GetmRNAforCDS(), GetMrnasForGene(), GetOverlappingCDS(), GetOverlappingGene(), GetOverlappingmRNA(), GetOverlappingOperon(), GetOverlappingPub(), GetOverlappingSource(), and GetSourceFeatForProduct().

Retrieve the Bioseq Handle from a location.

location refers to a single bioseq: return the bioseq location referes to multiple bioseqs: if parts of a segmentd bioseq, returns the segmentd bioseq. otherwise, return the first bioseq that could be found (first localy then, if flag is eGetBioseq_All, remote)

Definition at line 307 of file sequence.cpp.

References CScope::eGetBioseq_All, CScope::eGetBioseq_Loaded, CScope::GetBioseqHandle(), GetId(), GetParentForPart(), IsOneBioseq(), and CBioseq_Handle::Reset().

Referenced by CFlatFileGenerator::Generate(), CFlatFileGenerator::GetFTableAnticodonText(), GetGeneForFeature(), GetProductName(), CFlatFileGenerator::GetSeqFeatText(), GetStop(), GetTextObjectDescription(), CDiscrepancyObject::GetTextObjectDescription(), s_GetProductName(), sGetCdsProductName(), CFlatGatherer::x_GatherCDSReferences(), CFlatGatherer::x_GatherReferences(), CFlatGatherer::x_GatherReferencesIdx(), CFlatFeatureRetrieveJob::x_Run(), and CBioseqContext::x_SetMapper().

Retrieve the BioSource object for a given bioseq handle.

If the supplied sequence does not have a MolInfo associated with it, this will return NULL

Definition at line 104 of file sequence.cpp.

References ITERATE, and NULL.

Referenced by CopyOrg(), fg::GetGeneticCode(), IAlignRowHandle::GetOrgLabel(), IAlignRowHandle::GetTaxonomy(), variation::IsMitochondrion(), CMakeBadSpecificHostTable::MakeTable(), CNewCleanup_imp::RemoveSingleStrand(), CTreeBuilderJob::x_CreateProjectItems(), CSparseAln::x_GetGenCode(), and CDeflineGenerator::x_GetModifiers().

Get the encoding CDS feature of a given protein sequence.

Definition at line 2549 of file sequence.cpp.

References CScope::GetBioseqHandle().

Referenced by CValidError_bioseq::CdError(), CConvertProtToImp::Convert(), CNewCleanup_imp::CreateMissingMolInfo(), IEditingActionFeat::FindRelated(), CEditingActionFeatGeneLocus::FindRelated(), CProductColumn::GetApplyObjects(), CCodonStartColumn::GetApplyObjects(), NMacroUtil::GetLocusTagFromProtRef(), GetNucleotideParent(), GetRelatedFeatureApplyObjects(), GetRelatedFeatures(), GetSourceFeatForProduct(), GetTextObjectDescription(), CDiscrepancyObject::GetTextObjectDescription(), IEditingAction::GetUpdateMRNAProductNameCmd(), CLocationConstraintMatcher::Match(), CNewCleanup_imp::ResynchProteinPartials(), s_GetProtApplyObjectsFeatures(), s_GetProteinName(), CMacroFunction_UpdateProteinSeqs::TheFunction(), UpdatemRNAProduct(), CValidError_bioseq::ValidateRawConst(), CCmdFeatIdXrefsFromQualifiers::x_CreateActionCmd(), CCdsGlyph::x_DrawProjectedProtSeq(), CCdsGlyph::x_DrawProtSeqWithMapping(), CFlatGatherer::x_GatherCDSReferences(), CDBSourceItem::x_GatherInfo(), x_GetDivisionProc(), x_GetDivisionProcIdx(), x_GetSourceFeatViaCDS(), CMacroFunction_ParsedText::x_GetSpecialField(), CCdregionValidator::x_ValidateCommonProduct(), and CSingleFeatValidator::x_ValidateGeneXRef().

Definition at line 2318 of file sequence.cpp.

References _ASSERT, eOverlap_Subset, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, GetBestCdsForMrna(), GetBestOverlappingFeat(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetLocation(), GetMrnasForGene(), CSeqFeatData::GetSubtype(), and ITERATE.

Referenced by GetCdssForGene().

Given a CSeq_gap object, this outputs the Gap information.

Parameters

seq_gap This is the seq_gap information we're using to figure out the gap mod text out_gap_mod_text This holds the result.

Definition at line 3483 of file sequence.cpp.

References CSeq_gap_Base::CanGetLinkage(), CSeq_gap_Base::CanGetLinkage_evidence(), CLinkage_evidence_Base::CanGetType(), CSeq_gap_Base::CanGetType(), CSeq_gap_Base::eLinkage_linked, CLinkage_evidence_Base::eType_align_genus, CLinkage_evidence_Base::eType_align_trnscpt, CLinkage_evidence_Base::eType_align_xgenus, CSeq_gap_Base::eType_centromere, CSeq_gap_Base::eType_clone, CLinkage_evidence_Base::eType_clone_contig, CSeq_gap_Base::eType_contamination, CSeq_gap_Base::eType_contig, CSeq_gap_Base::eType_fragment, CSeq_gap_Base::eType_heterochromatin, CLinkage_evidence_Base::eType_map, CLinkage_evidence_Base::eType_other, CSeq_gap_Base::eType_other, CLinkage_evidence_Base::eType_paired_ends, CLinkage_evidence_Base::eType_pcr, CLinkage_evidence_Base::eType_proximity_ligation, CSeq_gap_Base::eType_repeat, CSeq_gap_Base::eType_scaffold, CSeq_gap_Base::eType_short_arm, CLinkage_evidence_Base::eType_strobe, CSeq_gap_Base::eType_telomere, CSeq_gap_Base::eType_unknown, CLinkage_evidence_Base::eType_unspecified, CLinkage_evidence_Base::eType_within_clone, CFastaOstream::SGapModText::gap_linkage_evidences, CFastaOstream::SGapModText::gap_type, CSeq_gap_Base::GetLinkage(), CSeq_gap_Base::GetLinkage_evidence(), CLinkage_evidence_Base::GetType(), CSeq_gap_Base::GetType(), NStr::IntToString(), CSeq_gap_Base::IsSetLinkage_evidence(), and ITERATE.

Referenced by s_NewGapItem(), CBioseqIndex::x_InitGaps(), and CFastaOstream::x_WriteSequence().

Finds gene for feature, but obeys SeqFeatXref directives.

Definition at line 1529 of file sequence.cpp.

Referenced by AddExceptionsToShortIntron(), CAutoDefFeatureClause::AddGene(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), CNewCleanup_imp::CdRegionEC(), CDiscrepancyContext::GeneForFeature(), CGeneCache::GetGeneFromCache(), GetLocusTagForFeature(), CFeatureSeqTableColumnBase::GetRelatedGeneApplyObjects(), GetTargetedLocusName(), CBioseqEditor::OnDeleteSelection(), CMacroFunction_ConvertLocStrand::TheFunction(), CMacroFunction_ConvertLocType::TheFunction(), CCleanupApp::x_FixCDS(), CValidErrorFormat::x_FormatECNumberForSubmitterReport(), and CValidErrorFormat::x_GetLocusTag().

Given an accession string retrieve the GI id.

If no GI was found returns 0 or throws CSeqIdFromHandleException depending on the flags. Id type in the flags is ignored, only VerifyId and ThrowOnError flags are checked.

Definition at line 638 of file sequence.cpp.

References CSeq_id::AvoidGi(), eGetId_ForceGi, eGetId_ThrowOnError, eGetId_VerifyId, flags, CSeq_id_Handle::GetGi(), GetId(), CSeq_id::GetTextseq_Id(), CSeq_id_Handle::IsGi(), NCBI_THROW, and ZERO_GI.

Referenced by BOOST_AUTO_TEST_CASE(), CSequenceDataTester::x_Init(), and CAppHitFilter::x_LoadConstraints().

Given a Seq-id retrieve the corresponding GI.

If no GI was found returns 0 or throws CSeqIdFromHandleException depending on the flags. Id type in the flags is ignored, only VerifyId and ThrowOnError flags are checked.

Definition at line 668 of file sequence.cpp.

References CSeq_id::AvoidGi(), eGetId_ForceGi, eGetId_ThrowOnError, eGetId_VerifyId, flags, CSeq_id_Handle::GetGi(), GetId(), CSeq_id_Handle::IsGi(), NCBI_THROW, and ZERO_GI.

Referenced by fta_get_gi_for_seq_id(), CSeqIdListSet::GetGiList(), CSeqLocListSet::GetGiList(), CLocationListCtrl::GetIdFromForm(), CBinsTrack::InitHTMLActiveArea(), CVarTrack::InitHTMLActiveArea(), CSeqUtils::isTopLevel(), CBinsGlyph::x_BuildNonEmptyBinList(), CGeneMarkerGlyph::x_BuildSignatures(), and CCreateGeneModelTask::x_GetCommand().

Return a selected ID type for a given bioseq handle.

This function will try to use the most efficient method possible to determine which ID fulfills the requested parameter. This version will call sequence::GetId() with the bioseq handle's seq-id.

Parameters

id Source id to evaluate scope Scope for seq-id resolution. type Type of ID to return

Returns

A requested seq-id. Depending on the flags set in 'type' this function can verify if the requested ID exists in the scope and throw CSeqIdFromHandleException if the request cannot be satisfied.

Definition at line 621 of file sequence.cpp.

References _ASSERT, eGetId_ThrowOnError, CBioseq_Handle::GetId(), NCBI_THROW, and x_GetId().

Return a selected ID type for a seq-id.

This function will try to use the most efficient method possible to determine which ID fulfills the requested parameter. The following logic is used:

• For seq-id type eGetId_HandleDefault, the original seq-id is returned. This satisfies the condition of returning a bioseq-handle's seq-id if sequence::GetId() is applied to a CBioseq_Handle.
• For seq-id type eGetId_ForceAcc, the returned set of seq-ids will first be evaluated for a "best" id (which, given seq-id scoring, will be a textseq-id if one exists). If the returned best ID is a textseq-id, this id will be returned. Otherwise, an exception is thrown or an empty handle returned.
• For seq-id type eGetId_ForceGi, the returned set of IDs is scanned for an ID of type gi. If this is found, it is returned; otherwise, an exception is thrown or an empty handle returned. If the supplied ID is already a gi and eGetId_VerifyId flag is not set, no work is done.

Parameters

id Source id to evaluate scope Scope for seq-id resolution. type Type of ID to return

Returns

A requested seq-id. Depending on the flags set in 'type' this function can verify if the requested ID exists in the scope and throw CSeqIdFromHandleException if the request cannot be satisfied.

Definition at line 552 of file sequence.cpp.

References CSeq_id_Handle::GetHandle(), and GetId().

Return a selected ID type for a seq-id handle.

Arguments (except 'id') and behavior is the same as of GetId(const CSeq_id& id, ...).

Definition at line 558 of file sequence.cpp.

References _ASSERT, CSeq_id_Base::e_General, eGetId_Canonical, eGetId_ForceAcc, eGetId_ForceGi, eGetId_ThrowOnError, eGetId_TypeMask, eGetId_VerifyId, ERR_POST, CScope::GetAccVer(), CScope::GetGi(), CSeq_id_Handle::GetGiHandle(), CScope::GetIds(), CSeq_id_Handle::GetSeqId(), CSeq_id_Base::IsGeneral(), CSeq_id_Handle::IsGi(), NCBI_THROW, CSeq_id::PreferAccessionOverGi(), CSeq_id_Handle::Reset(), CSeq_id_Handle::Which(), x_GetId(), and ZERO_GI.

Retrieve the MolInfo object for a given bioseq handle.

If the supplied sequence does not have a MolInfo associated with it, this will return NULL

Definition at line 284 of file sequence.cpp.

References CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), ITERATE, and NULL.

Referenced by AddDefaultSentinelFeats(), CAlignCollapser::GetCollapsedAlgnments(), variation::CVariationUtil::GetMolType(), CAlignCollapser::GetOnlyOtherAlignments(), GetSequenceType(), CSGUtils::IsmRNA(), CGuiObjectInfoSeq_align::IsPolyA(), CDiscrepancyPanel::OnListClk(), CFeatureGenerator::SImplementation::SMapper::SMapper(), and CDeflineGenerator::x_GetModifiers().

GetmRNAforCDS A function to find a CSeq_feat representing the appropriate mRNA for a given CDS.

Parameters

cds The feature for which the mRNA to be found scope The scope

Returns

CConstRef<CSeq_feat> for new mRNA (will be NULL if none is found)

Definition at line 1261 of file sequence.cpp.

Referenced by CAdjustForConsensusSpliceSite::AdjustmRNAandExonEnds(), CAdjustForConsensusSpliceSite::AdjustmRNAandExonFeatures(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), CNewCleanup_imp::CdRegionEC(), CCleanup::ExtendToStopIfShortAndNotPartial(), CTruncateCDS::GetCommand(), IEditingAction::GetUpdateMRNAProductNameCmd(), CBulkCDS::GetUpdateMRNAProductNameCmd(), UpdatemRNAProduct(), CCleanup::WGSCleanup(), CCleanupApp::x_FixCDS(), and CCdregionValidator::x_ValidateParentPartialness().

Definition at line 2195 of file sequence.cpp.

References _ASSERT, Compare(), count, eContains, eOverlap_Contains, eSame, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, fCompareOverlapping, GetBestOverlappingFeat(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetDbxref(), CSeq_feat_Handle::GetDbxref(), CSeqFeatData_Base::GetGene(), CSeq_feat::GetGeneXref(), CGene_ref::GetLabel(), CSeq_feat_Base::GetLocation(), CMappedFeat::GetLocation(), CMappedFeat::GetOriginalFeature(), CAnnotTypes_CI::GetSize(), CSeqFeatData::GetSubtype(), SAnnotSelector::IncludeFeatSubtype(), CSeq_feat_Base::IsSetDbxref(), CSeq_feat_Handle::IsSetDbxref(), CGene_ref::IsSuppressed(), ITERATE, CFeat_CI::Rewind(), SAnnotSelector::SetAdaptiveDepth(), and SAnnotSelector::SetResolveTSE().

Referenced by GetCdssForGene(), and GetMrnasForGene().

Return the org-ref associated with a given sequence.

This will throw a CException if there is no org-ref associated with the sequence

Definition at line 264 of file sequence.cpp.

References eUnknown, GetOrg_refOrNull(), and NCBI_THROW.

Referenced by BOOST_AUTO_TEST_CASE(), CProteinAlignText::CProteinAlignText(), CProSplign::CImplementation::FindGlobalAlignment_stage1(), CScoreBuilder::GetBlastScoreProtToNucl(), CSequenceTrack::GetTooltip(), CGuiObjectInfoComponent::GetToolTip(), s_GetGeneticCode(), s_GetSplicedSegIdentityMismatch(), CFeatureGenerator::SImplementation::x_ConstructRnaName(), CTreeBuilderJob::x_CreateProjectItems(), CAlnVecRow::x_GetDescrTooltip(), CAlignSeqTableModel::x_GetOrganism(), CSFTranslationJob::x_InitGeneticCode(), and CPhyTreeFormatter::x_InitTreeFeatures().

Find an Org-ref for the given Bioseq: If it's a protein then look on the source feature of the product.

Otherwise find a source descriptor for the sequence. Otherwise, try to find a source feature for the sequence. Return nullptr if we still turn up empty.

Definition at line 211 of file sequence.cpp.

References GetBioSourceForBioseq().

Return the pointer to org-ref associated with a given sequence or null if there is no org-ref associated with the sequence.

Definition at line 245 of file sequence.cpp.

References CSeqdesc_Base::e_Org, CSeqdesc_Base::e_Source, CSeqdesc_Base::GetOrg(), CBioSource_Base::GetOrg(), CSeqdesc_Base::GetSource(), CSeqdesc_Base::IsOrg(), CSeqdesc_Base::IsSource(), and types.

Referenced by CFeatureGenerator::ConvertLocToAnnot(), GetOrg_ref(), GetTaxId(), CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript(), and CSparseAln::x_GetGenCode().

Find all features overlapping the location.

Features and corresponding scores are stored in the 'feats' vector. The scores are calculated as difference between the input location and each feature's location. NOTE: 'overlap_type' defines how the location must be related to the feature. For eOverlap_Subset, eOverlap_SubsetRev, eOverlap_CheckIntervals, eOverlap_CheckIntRev and eOverlap_Interval the relationship is reversed. E.g. with eOverlap_Contains, the location will contain the feature, but with eOverlap_Subset the feature will be defined on a subset of the location.

Definition at line 945 of file sequence.cpp.

References _DEBUG_ARG, _TRACE, CSeq_loc::Assign(), CSeq_loc::CheckId(), Compare(), ConstRef(), eContains, eExtreme_Positional, eNa_strand_plus, eNa_strand_unknown, eOverlap_CheckIntervals, eOverlap_CheckIntRev, eOverlap_Contained, eOverlap_Contains, eOverlap_Interval, SAnnotSelector::eOverlap_Intervals, eOverlap_Simple, eOverlap_Subset, eOverlap_SubsetRev, SAnnotSelector::eOverlap_TotalRange, eSame, CSeq_inst_Base::eTopology_circular, fBestFeat_IgnoreStrand, fCompareOverlapping, fOverlap_Default, fOverlap_IgnoreTopology, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), COpenRange< Position >::GetEmpty(), CRange_Base::GetFrom(), CSeq_loc::GetId(), CBioseq_Handle::GetInst_Topology(), CSeq_feat_Base::GetLocation(), CMappedFeat::GetLocation(), CMappedFeat::GetMappedFeature(), CMappedFeat::GetOriginalFeature(), CBioseq_Handle::GetSeqId(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), CRange_Base::GetTo(), COpenRange< Position >::GetWhole(), CSeq_loc_Base::GetWhole(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsPacked_int(), CSeq_loc_Base::IsPacked_pnt(), CSeq_loc_Base::IsPnt(), IsReverse(), CBioseq_Handle::IsSetInst_Topology(), CSeq_loc::IsSetStrand(), CSeq_loc_Base::IsWhole(), kInvalidSeqPos, NULL, CGetOverlappingFeaturesPlugin::postProcessDiffAmount(), CGetOverlappingFeaturesPlugin::processLoc(), CGetOverlappingFeaturesPlugin::processMainLoop(), CGetOverlappingFeaturesPlugin::processSAnnotSelector(), CRef< C, Locker >::Reset(), CConstRef< C, Locker >::Reset(), SAnnotSelector::SetFeatSubtype(), SAnnotSelector::SetFeatType(), CRange_Base::SetFrom(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), SAnnotSelector::SetIgnoreStrand(), SAnnotSelector::SetOverlapType(), CSeq_loc::SetPacked_int(), SAnnotSelector::SetResolveTSE(), SAnnotSelector::SetSearchUnresolved(), CSeq_loc::SetStrand(), CSeq_interval_Base::SetStrand(), CRange_Base::SetTo(), CSeq_interval_Base::SetTo(), CGetOverlappingFeaturesPlugin::setUpFeatureIterator(), TestForOverlap64(), and TestForOverlapEx().

Referenced by CCdsMatchInfo::AssignOverlapMatch(), BOOST_AUTO_TEST_CASE(), CCdsToMatPeptide::ConvertInner(), GetBestCdsForMrna(), GetBestGeneForCds(), GetBestGeneForMrna(), GetBestMrnaForCds(), GetBestOverlappingFeat(), GetRelatedFeatureApplyObjects(), GetRelatedFeatures(), CCleanup::IsGeneXrefUnnecessary(), CMrnaMatchInfo::OkWithoutCds(), s_GetCdsByLocation(), s_HasMobileElementForInterval(), CIntronValidator::Validate(), x_GetBestOverlapForSNP(), CValidError_bioseq::x_MatchesOverlappingFeaturePartial(), CCdregionValidator::x_ValidateParentPartialness(), and CRNAValidator::x_ValidateTrnaOverlap().

Definition at line 1366 of file sequence.cpp.

References eNa_strand_both, eNa_strand_other, eOverlap_Contained, CSeqFeatData::eSubtype_gene, eTransSplicing_Auto, eTransSplicing_No, eTransSplicing_Yes, fBestFeat_IgnoreStrand, GetBestOverlappingFeat(), CSeq_feat_Base::GetLocation(), CSeq_loc::GetStrand(), and CConstRef< C, Locker >::Reset().

Referenced by AddColumnsToFeatureTable(), AdjustGene(), CRecomputeIntervals::apply(), CConvertBadCdsAndRnaToMiscFeat::apply(), ApplyFeatureSeqTableToSeqEntry(), ApplyPolicyToFeature(), CConvertCDSToPseudoGene::Convert(), CFeatureGenePanel::CreateControls(), CTruncateCDS::GetCommand(), GetGeneForFeature(), NMacroUtil::GetLocusTagFromProtRef(), GetRelatedFeatureApplyObjects(), GetRelatedFeatures(), CCleanup::IsGeneXrefUnnecessary(), CCdsToMatPeptide::MergeConvert(), CHugeFileDemoApp::ProcessHugeSeqEntry(), s_CheckQuals_cdregion(), s_GetProteinName(), s_TitleFromSegment(), SetTranslExcept(), CMytestApplication::TestFeatureGeneOverlap(), CGeneOverlapProcess::TestFeatureGeneOverlap(), CHugeFileDemoApp::x_ProcessFileTraditionally(), CConvertFeatureBase::x_SimpleConversion(), and CRNAValidator::x_ValidateTrnaType().

Return protein name from corresponding Prot-ref feature.

Throws exception if the sequence is not a protein, or if there is no unambiguously best Prot-ref feature, or if the feature doesn't return non-empty label.

Definition at line 356 of file sequence.cpp.

References CSeqFeatData_Base::e_Prot, eGetId_Best, CBioseq_Handle::GetBioseqLength(), GetId(), COpenRange< Position >::GetLength(), COpenRange< Position >::GetToOpen(), CBioseq_Handle::IsProtein(), NCBI_THROW, NCBI_THROW_FMT, and COpenRange< Position >::SetToOpen().

Referenced by CAlnVecRow::x_GetAlignmentTooltip_General().

Definition at line 133 of file sequence.cpp.

References CSeq_loc::Assign(), eOverlap_SubsetRev, CSeqFeatData::eSubtype_biosrc, GetBestOverlappingFeat(), GetCDSForProduct(), CSeq_feat_Base::GetLocation(), CBioseq_Handle::GetScope(), CSeq_feat_Base::IsSetData(), and SeqLocRevCmpl().

Referenced by GetBioSourceForBioseq(), GetOrg_refForProduct(), GetTaxIdForProduct(), CFlatGatherer::x_CollectBioSourcesOnBioseq(), and CSourceItem::x_GatherInfo().

return the tax-id associated with a given sequence.

This will return 0 if no tax-id can be found.

Definition at line 274 of file sequence.cpp.

References GetOrg_refOrNull(), COrg_ref::GetTaxId(), and ZERO_TAX_ID.

Referenced by CLinkUtils::AddSequenceLinks(), IAlignRowHandle::GetTaxId(), CTaxTreeDS_ObjMgr::GetTaxMap(), CSeqDBTaxInfo::GetTaxNames(), CFeatGlyph::GetTooltip(), CBioSource::RemoveLineageSourceNotes(), CWindowMaskerPanel::TaxonsLoaded(), CAsn2FlatApp::x_AddSNPAnnots(), CTaxTreeToolJob::x_CreateProjectItems(), CAlignGroup::x_GetTaxId(), CWindowMaskerPanel::x_InitTaxons(), CAltValidator::x_QueryAccessions(), and CBlastTabularInfo::x_SetTaxInfo().

Definition at line 551 of file seqtitle.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeqdesc_Base::e_Molinfo, CSeqdesc_Base::e_Org, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeqdesc_Base::e_Source, CSeqdesc_Base::e_Title, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CSeq_id::eAcc_division_mask, CSeq_id::eAcc_refseq_chromosome, CSeq_id::eAcc_refseq_mrna, CSeq_id::eAcc_refseq_ncrna, CSeq_id::eAcc_tsa, CSeq_id::eAcc_wgs, CMolInfo_Base::eBiomol_genomic, CMolInfo_Base::eBiomol_other_genetic, NStr::EndsWith(), NStr::eNocase, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_seg, CMolInfo_Base::eTech_est, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, CMolInfo_Base::eTech_sts, CMolInfo_Base::eTech_survey, CMolInfo_Base::eTech_tsa, CMolInfo_Base::eTech_unknown, CMolInfo_Base::eTech_wgs, fGetTitle_Organism, fGetTitle_Reconstruct, flags, fON_wgs, CMolInfo_Base::GetBiomol(), CBioseq::GetClosestDescriptor(), CSeq_id_Base::GetGeneral(), CBioseq_Base::GetId(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetRepr(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), CMolInfo_Base::GetTech(), CSeq_id::IdentifyAccession(), NStr::IntToString(), CBioseq::IsAa(), CConstRef< C, Locker >::IsNull(), CBioseq_Base::IsSetInst(), CDbtag::IsSkippable(), CObject_id_Base::IsStr(), ITERATE, kEmptyStr, kMax_Int, CConstRef< C, Locker >::NotEmpty(), NPOS, NULL, s_OrganelleName(), s_TitleFromBioSource(), s_TitleFromChromosome(), rapidjson::source, NStr::StartsWith(), string, t, and CSeq_id_Base::Which().

Definition at line 106 of file seqtitle.cpp.

References BREAK, CSeqFeatData_Base::e_Cdregion, CSeq_id_Base::e_Ddbj, CSeqdesc_Base::e_Embl, CSeq_id_Base::e_Embl, CSeqdesc_Base::e_Genbank, CSeq_id_Base::e_Genbank, CSeqFeatData_Base::e_Gene, CSeq_id_Base::e_General, CSeqdesc_Base::e_Molinfo, CSeqdesc_Base::e_Org, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeqdesc_Base::e_Pdb, CSeq_id_Base::e_Pdb, CSeqFeatData_Base::e_Prot, CSeqdesc_Base::e_Source, CSeqdesc_Base::e_Title, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CSeq_id::eAcc_division_mask, CSeq_id::eAcc_refseq_chromosome, CSeq_id::eAcc_refseq_mrna, CSeq_id::eAcc_refseq_ncrna, CSeq_id::eAcc_tsa, CSeq_id::eAcc_wgs, CMolInfo_Base::eBiomol_cRNA, CMolInfo_Base::eBiomol_genomic, CMolInfo_Base::eBiomol_mRNA, CMolInfo_Base::eBiomol_ncRNA, CMolInfo_Base::eBiomol_other_genetic, CMolInfo_Base::eBiomol_pre_RNA, CMolInfo_Base::eBiomol_rRNA, CMolInfo_Base::eBiomol_scRNA, CMolInfo_Base::eBiomol_snoRNA, CMolInfo_Base::eBiomol_snRNA, CMolInfo_Base::eBiomol_tmRNA, CMolInfo_Base::eBiomol_transcribed_RNA, CMolInfo_Base::eBiomol_tRNA, CSeq_inst_Base::eMol_aa, NStr::EndsWith(), NStr::eNocase, NStr::EqualNocase(), CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_seg, CMolInfo_Base::eTech_est, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, CMolInfo_Base::eTech_sts, CMolInfo_Base::eTech_survey, CMolInfo_Base::eTech_tsa, CMolInfo_Base::eTech_unknown, CMolInfo_Base::eTech_wgs, fFGL_Content, CSeqMap::fFindGap, fGetTitle_NoExpensive, fGetTitle_Organism, fGetTitle_Reconstruct, flags, fON_wgs, CMolInfo_Base::GetBiomol(), CBioseq_Handle::GetBioseqMolType(), CSeq_entry_Handle::GetCompleteSeq_entry(), CPDB_block_Base::GetCompound(), CSeq_id_Base::GetGeneral(), CBioseq_Handle::GetId(), CBioseq_Handle::GetInst_Repr(), GetLabel(), CSeqdesc_Base::GetOrg(), CSeqdesc_Base::GetPdb(), CBioseq_Handle::GetScope(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), CMolInfo_Base::GetTech(), CSeqdesc_Base::GetTitle(), CBioseq_Handle::GetTopLevelEntry(), CSeq_id::IdentifyAccession(), NStr::IntToString(), CConstRef< C, Locker >::IsNull(), isprint(), CDbtag::IsSkippable(), CObject_id_Base::IsStr(), ITERATE, kEmptyStr, NCBI_UNUSED, CConstRef< C, Locker >::NotEmpty(), NPOS, NULL, NStr::Replace(), CConstRef< C, Locker >::Reset(), s_FlyCG_PtoR(), s_OrganelleName(), s_TitleFromBioSource(), s_TitleFromChromosome(), s_TitleFromProtein(), s_TitleFromSegment(), rapidjson::source, NStr::StartsWith(), string, t, and CSeq_id_Base::Which().

Referenced by PT::CWorkspace::BeginLabelEdit(), CEditingBtnsPanel::CEditingBtnsPanel(), CFeedbackWizard::Create(), CSubjectMap_Factory_Base::extractSeqVector(), ExtractSeqVector(), CWinMaskUtil::CIdSet_TextMatch::find(), CPub::GetTitles(), and CTitleProcess::SeqEntryProcess().

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

Looks for pseudo flag set on feature, looks for pseudogene qualifier on feature, performs same checks for gene associated with feature

Parameters

feat Seq-feat to check scope CScope to use when looking for associated gene

Returns

Boolean return value indicates whether any of the "pseudo" markers are found

Definition at line 1428 of file sequence.cpp.

References NStr::EqualNocase(), CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetGene(), GetGeneForFeature(), CGene_ref_Base::GetPseudo(), CSeq_feat_Base::GetPseudo(), CSeq_feat_Base::GetQual(), CSeq_feat_Base::GetXref(), CSeqFeatData_Base::IsGene(), CGene_ref_Base::IsSetPseudo(), CSeq_feat_Base::IsSetPseudo(), CSeq_feat_Base::IsSetQual(), CSeq_feat_Base::IsSetXref(), and ITERATE.

Referenced by CGenericPropsPanel::CreateControls(), DoesFeatureHaveUnnecessaryException(), CCleanup::ExtendToStopIfShortAndNotPartial(), g_InstantiateMissingProteins(), CRetranslateCDS::GetCommand(), CCDSTranslationProblems::GetNonsenseIntrons(), CCleanup::RemovePseudoProduct(), s_TranslateCds(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), CImpFeatValidator::Validate(), CValidError_bioseqset::ValidateGenProdSet(), CValidError_imp::ValidateSeqLoc(), CCleanup::WGSCleanup(), CCleanup::x_AddLowQualityException(), CCleanupApp::x_BatchExtendCDS(), CCDSTranslationProblems::x_CountNonsenseIntrons(), CImportFeatTable::x_DoImportCDS(), CCDSTranslationPanel::x_IsPseudo(), CMacroFunction_EditFeatLocation::x_RetranslateCDS(), CValidError_bioseq::x_TranscriptIDsMatch(), and CFeatTableEdit::xGenerate_mRNA_Product().

Default ctor gives params which are usually reasonable.

Definition at line 1579 of file sequence.hpp.

Definition at line 841 of file sequence.cpp.

References _ASSERT, flags, fP2S_Extend, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), GetLength(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetProduct(), CSeqFeatData_Base::IsCdregion(), IsReverse(), SRelLoc::m_ParentLoc, SRelLoc::m_Ranges, max(), NON_CONST_ITERATE, CConstRef< C, Locker >::Reset(), and SRelLoc::Resolve().

Referenced by CCdregionValidator::MapToNTCoords().

Definition at line 4583 of file sequence.cpp.

References _ASSERT, delta(), CInt_fuzz::eAmplify, eNa_strand_unknown, CSerialObject::Equals(), ERR_POST_X, f, first(), CSeq_loc_mix_Base::Get(), CSeq_loc::GetLabel(), GetLength(), CConstRef< C, Locker >::GetPointer(), IsReverse(), ITERATE, label, SRelLoc::m_Ranges, CConstRef< C, Locker >::Reset(), result, Reverse(), CSeq_loc_mix_Base::Set(), CSeq_interval_Base::SetFrom(), CSeq_point_Base::SetFuzz(), CSeq_interval_Base::SetFuzz_from(), CSeq_interval_Base::SetFuzz_to(), CSeq_interval_Base::SetId(), CSeq_point_Base::SetId(), CSeq_loc::SetInt(), CSeq_loc::SetPnt(), CSeq_point_Base::SetPoint(), CSeq_interval_Base::SetStrand(), CSeq_point_Base::SetStrand(), CSeq_interval_Base::SetTo(), and Warning().

Reverse complement a Bioseq in place.

If delta sequence, will also need to reverse order of segments

Definition at line 5142 of file sequence.cpp.

References CDelta_seq_Base::e_Literal, CDelta_seq_Base::e_Loc, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_raw, CSeq_inst_Base::GetExt(), CSeq_inst_Base::GetLength(), CSeq_literal_Base::GetLength(), CSeq_inst_Base::GetRepr(), CSeq_literal_Base::GetSeq_data(), CSeq_ext_Base::IsDelta(), CSeq_data_Base::IsGap(), CSeq_inst_Base::IsSetExt(), NCBI_THROW, NON_CONST_ITERATE, CSeqportUtil::ReverseComplement(), SeqLocRevCmpl(), CSeq_inst_Base::SetExt(), CSeq_inst_Base::SetSeq_data(), and CSeq_literal_Base::SetSeq_data().

Constructor initializes to state that it should be when the iterator first starts.

Definition at line 1629 of file sequence.hpp.

Definition at line 3456 of file sequence.cpp.

References AutoPtr< X, Del >::get(), CFastaOstream::m_Dashes, CFastaOstream::m_LC_Ns, CFastaOstream::m_LC_Xs, CFastaOstream::m_UC_Ns, CFastaOstream::m_UC_Xs, CFastaOstream::m_Width, and AutoPtr< X, Del >::reset().

Referenced by CBlastDB_FastaFormatter::CBlastDB_FastaFormatter(), CVdbFastaExtractor::DumpAll(), CSeqFormatter::DumpAll(), CBlastDBExtractor::ExtractFasta(), s_CheckIdLookup(), and CVdbFastaExtractor::Write().

Definition at line 790 of file sequence.cpp.

References _ASSERT, ERR_POST_X, flags, SRelLoc::fNoMerge, fS2P_AllowTer, fS2P_NoMerge, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), GetLength(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetProduct(), CSeqFeatData_Base::IsCdregion(), IsReverse(), SRelLoc::m_ParentLoc, SRelLoc::m_Ranges, max(), NON_CONST_ITERATE, CConstRef< C, Locker >::Reset(), SRelLoc::Resolve(), and Warning().

Referenced by TestOneCDS(), and CCdregionValidator::x_ValidateCodebreak().

Beware: treats locations corresponding to different sequences as disjoint, even if one is actually a segment of the other.

:-/

Definition at line 4421 of file sequence.cpp.

References delta(), CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, eNa_strand_unknown, f, flags, SRelLoc::fNoMerge, GetLength(), IsReverse(), IsSameBioseq(), SRelLoc::m_Ranges, CInt_fuzz::Negative(), CConstRef< C, Locker >::Reset(), Reverse(), and SameOrientation().

For manual work. As noted above, ranges need not contain any IDs.

Definition at line 1140 of file sequence.hpp.

Translate a CDRegion into a protein.

Definition at line 4183 of file sequence.cpp.

References CBioseq_Handle::eCoding_Iupac, eExtreme_Biological, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, eOffset_FromStart, CCode_break_Base::GetAa(), CSeqFeatData_Base::GetCdregion(), CCdregion_Base::GetCode(), CCdregion_Base::GetCode_break(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), CCode_break_Base::GetLoc(), CSeq_feat_Base::GetLocation(), CCode_break_Base::C_Aa::GetNcbieaa(), i, CSeqFeatData_Base::IsCdregion(), CCode_break_Base::C_Aa::IsNcbieaa(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CCdregion_Base::IsSetCode(), CCdregion_Base::IsSetCode_break(), CCdregion_Base::IsSetFrame(), ITERATE, LocationOffset(), NULL, prot, and x_Translate().

Translate a seq-vector using a specified genetic code if the code is NULL, then the default genetic code is used.

Parameters

seq CSeqVector of sequence to be translated code Genetic code to use for translation (NULL to use default) include_stop If true, translate through stop codons and include trailing stop (true by default) remove_trailing_X If true, remove trailing Xs from protein translation (false by default) alt_start Pointer to bool to indicate whether an alternative start codon was used is_5prime_complete If true, only translate first codon if start codon, otherwise translate as dash (-) to indicate problem with sequence

Definition at line 4123 of file sequence.cpp.

References prot, and x_Translate().

Translate a seq-vector using a specified genetic code if the code is NULL, then the default genetic code is used.

Parameters

seq CSeqVector of sequence to be translated code Genetic code to use for translation (NULL to use default) flags Binary OR of "ETranslationFlags" alt_start Pointer to bool to indicate whether an alternative start codon was used

Definition at line 4136 of file sequence.cpp.

References flags, prot, and x_Translate().

Translate a string using a specified genetic code.

Parameters

seq String containing IUPAC representation of sequence to be translated code Genetic code to use for translation (NULL to use default) include_stop If true, translate through stop codons and include trailing stop (true by default) remove_trailing_X If true, remove trailing Xs from protein translation (false by default) alt_start Pointer to bool to indicate whether an alternative start codon was used is_5prime_complete If true, only translate first codon if start codon, otherwise translate as dash (-) to indicate problem with sequence

Definition at line 4095 of file sequence.cpp.

References prot, and x_Translate().

Referenced by CCDSTranslationPanel::AdjustForStopCodonHyperlinkClicked(), CFeatGapInfo::AdjustProteinSeq(), AdjustSingleFeature(), BOOST_AUTO_TEST_CASE(), CNewCleanup_imp::CdRegionEC(), CConvertCdsToMiscFeat::DetectStartStopCodons(), DoesCodingRegionEndWithStopCodon(), CCleanup::ExtendToStopIfShortAndNotPartial(), CSeqTranslator::FindBestFrame(), CScore_CdsInternalStops::Get(), GetRetranslateCDSCommand(), CLocationEditPolicy::Interpret3Policy(), CLocationEditPolicy::Interpret5Policy(), CMakeCdrProds::MakeCdrProds(), variation_ref::CVariationUtil::PrecursorToProt(), CTabularFormatter_StopCodonChanges::Print(), CGlimmerReader::Read(), CRetranslateCDS::RetranslateCDSCommand(), CAddGlobalCodeBreak::RetranslateCDSCommand(), CExtendCDSToStop::RetranslateCDSCommand(), CTestSingleAln_All::RunTest(), s_CompareProtProdToTrans(), ApplyCDSFrame::s_FindMatchingFrame(), CMacroFunction_ApplyCDSFrame::s_FindMatchingFrame(), s_GetCdsSequence(), s_GetGermlineTranslation(), CCmdCreateCDS::s_GetProductSequence(), variation_ref::CVariationUtil::s_UntranslateProt(), variation::CVariationUtil::s_UntranslateProt(), CIgBlastTabularInfo::SetAirrFormatData(), SetCdrFwrSeq(), CCleanup::SetCDSPartialsByFrameAndTranslation(), CIgBlastTabularInfo::SetIgAnnotation(), CIgBlastTabularInfo::SetIgCDR3FWR4Annotation(), CValidError_bioseq::SuppressTrailingXMsg(), TestTrimForFrame(), variation::Translate(), Translate(), CCdregion_translate::TranslateCdregion(), CPaintSequence::TranslateCDS(), TranslateCodingRegionForValidation(), TruncateCDSAtStop(), CTruncateCDS::TruncateProteinFeat(), CPaintSequence::UpdateData(), CFeatureItem::x_AddQualTranslation(), CDisplaySeqalign::x_AddTranslationForLocalSeq(), CCleanupApp::x_BatchExtendCDS(), CFeaturePropagator::x_CdsCleanupPartials(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CImportFeatTable::x_DoImportCDS(), CAdjustFeaturesForGaps::x_DoOne(), COrfSearchJob::x_DoSearch(), CCdsGlyph::x_Draw(), CAlignGlyph::x_DrawAlignRowSequence(), CCdsGlyph::x_DrawProjectedProtSeq(), CCdsGlyph::x_DrawProtSeqWithMapping(), CAlignGlyph::x_DrawUnalignedRowSequence(), CGuiObjectInfoSeq_feat::x_GetProductSequence(), CCDSTranslationProblems::x_GetTranslExceptProblems(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CReportTrim::x_RetranslateCDS(), variation::CHgvsParser::x_SeqLiteralToStr(), CCDSTranslationPanel::x_Translate(), and CCdregionValidator::x_ValidateConflict().

Translate a string using a specified genetic code.

Parameters

seq String containing IUPAC representation of sequence to be translated code Genetic code to use for translation (NULL to use default) flags Binary OR of "ETranslationFlags" alt_start Pointer to bool to indicate whether an alternative start codon was used

Definition at line 4108 of file sequence.cpp.

References flags, prot, and x_Translate().

Definition at line 3839 of file sequence.cpp.

References AddAAToDeltaSeq(), AddGapToDeltaSeq(), CSeqVector::begin(), data, CBioseq_Handle::eCoding_Iupac, eExtreme_Biological, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, CSeq_inst_Base::eMol_aa, NStr::EndsWith(), eOffset_FromStart, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_raw, CSeqMap::eSeqGap, NStr::Find(), CCode_break_Base::GetAa(), CSeqFeatData_Base::GetCdregion(), CCdregion_Base::GetCode(), CCdregion_Base::GetCode_break(), CTrans_table::GetCodonResidue(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), CCode_break_Base::GetLoc(), CSeq_feat_Base::GetLocation(), CCode_break_Base::C_Aa::GetNcbieaa(), CSeqVector::GetSeqMap(), CTrans_table::GetStartResidue(), CGen_code_table::GetTransTable(), CSeqMap_CI::GetType(), CSeqVector_CI::HasZeroGapBefore(), i, CSeqFeatData_Base::IsCdregion(), CSeqVector::IsInGap(), CCode_break_Base::C_Aa::IsNcbieaa(), CSeq_loc::IsPartialStart(), CCdregion_Base::IsSetCode(), CCdregion_Base::IsSetCode_break(), CCdregion_Base::IsSetFrame(), CSeqMap_CI::IsUnknownLength(), ITERATE, LocationOffset(), mod(), CTrans_table::NextCodonState(), NON_CONST_ITERATE, NULL, offset, prot, and CSeqVector::size().

Referenced by CCleanup::AddProtein(), BOOST_AUTO_TEST_CASE(), CCmdAddCDS::Execute(), GetRetranslateCDSCommand(), CCdsToMatPeptide::MergeConvert(), RetranslateCDS(), RetranslateCdsForNucProtSet(), SetNewProteinSequence(), TestOneGapSeq(), TranslateCDSCommand(), TruncateCDSAtStop(), CFeaturePropagator::x_CdsStopAtStopCodon(), CVectorTrimPanel::x_RetranslateCDS(), CFastaOstreamEx::x_WriteTranslatedCds(), CFeatTableEdit::xGenerate_mRNA_Product(), and CFeatureTableReader::xTranslateProtein().

Definition at line 3389 of file sequence.cpp.

References CScope::AddBioseq(), CDelta_seq_Base::e_Loc, CSeq_data_Base::e_Ncbieaa, CBioseq_Handle::eCoding_Iupac, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_raw, CDelta_ext_Base::Get(), CSeq_ext_Base::GetDelta(), CSeq_inst_Base::GetExt(), CBioseq_Base::GetInst(), CObjectManager::GetInstance(), CSeq_inst_Base::GetRepr(), CSeqVector::IsProtein(), ITERATE, location, NULL, CSeqVector::SetCoding(), CFastaOstream::Write(), CFastaOstream::x_GetMaskingStates(), CFastaOstream::x_WriteSeqIds(), CFastaOstream::x_WriteSeqTitle(), and CFastaOstream::x_WriteSequence().

These versions may set up a temporary object manager scope In the common case of a raw bioseq, no scope is needed.

Definition at line 3365 of file sequence.cpp.

References CScope::AddTopLevelSeqEntry(), CSeq_entry_Base::e_Seq, CSeq_entry_Base::e_Set, CObjectManager::GetInstance(), CSeq_entry_Base::GetSeq(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), ITERATE, location, CSeq_entry_Base::Which(), and CFastaOstream::Write().

Unspecified locations designate complete sequences; non-empty custom titles override the usual title determination logic.

Definition at line 2727 of file sequence.cpp.

References eOverlap_Interval, CSeq_entry_Handle::GetScope(), kInvalidSeqPos, location, CSeq_loc::SetWhole(), CFastaOstream::SkipBioseq(), and TestForOverlap().

Referenced by BOOST_AUTO_TEST_CASE(), CMytestApplication::DoProcessStreamFasta(), CReadBlastApp::dump_fasta_for_pretty_blast(), CVdbFastaExtractor::DumpAll(), CSeqFormatter::DumpAll(), CBlastDBExtractor::ExtractFasta(), CAsn2FastaApp::HandleSeqEntry(), CFastaExportJob::Run(), s_CheckIdLookup(), CFastaProcess::SeqEntryProcess(), CFastaTextDisplay::Update(), CSortedProteins::View(), CFastaOstream::Write(), CVdbFastaExtractor::Write(), CBlastDB_FastaFormatter::Write(), CBLASTSeqToolJob::x_CreateProjectItems(), CWindowMaskerJob::x_CreateProjectItems(), and CFastaOstreamComp::x_Write().

Definition at line 3322 of file sequence.cpp.

References CSeqMap::CanResolveRange(), CSeq_data_Base::e_Ncbieaa, CBioseq_Handle::eCoding_Iupac, eSeqLocCheck_error, CFastaOstream::fAssembleParts, CSeqMap::fFindInnerRef, CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeqId(), CBioseq_Handle::GetSeqMap(), CBioseq_Handle::GetSeqVector(), CBioseq_Handle::GetTSE_Handle(), CSeqVector::IsProtein(), CBioseq_Handle::IsSetInst_Seq_data(), label, location, CFastaOstream::m_Flags, CFastaOstream::m_HardMask, CFastaOstream::m_SoftMask, NCBI_THROW, CConstRef< C, Locker >::NotEmpty(), Seq_loc_Merge(), SeqLocCheck(), CSeqVector::SetCoding(), SSeqMapSelector::SetLinkUsedTSE(), CFastaOstream::x_GetMaskingStates(), and CFastaOstream::x_WriteSequence().

Referenced by CSeqFormatter::DumpAll(), CBlastDBExtractor::ExtractFasta(), GetSequenceStringFromLoc(), CFastaOstream::Write(), CBlastDB_FastaFormatter::Write(), CFastaOstreamEx::WriteFeature(), and CFastaOstreamEx::x_WriteTranslatedCds().

Definition at line 3265 of file create_defline.cpp.

References CTempString::empty(), CConstRef< C, Locker >::Empty(), NStr::EndsWith(), NStr::eNocase, NStr::EqualNocase(), NStr::eReverseSearch, CTempString::find(), NStr::Find(), COrgName_Base::C_Name::GetBinomial(), CBioseqIndex::GetBioseqForProduct(), CSeqEntryIndex::GetBioseqIndex(), CBioSource_Base::GetGenome(), CBinomialOrgName_Base::GetGenus(), COrgName_Base::GetName(), CBioSource::GetOrgname(), CBinomialOrgName_Base::GetSpecies(), CBioSource::GetTaxname(), int, COrgName_Base::C_Name::IsBinomial(), CBioSource_Base::IsSetGenome(), CBinomialOrgName_Base::IsSetGenus(), COrgName_Base::IsSetName(), CBioSource::IsSetOrgname(), CBinomialOrgName_Base::IsSetSpecies(), CBioSource::IsSetTaxname(), CTempString::length(), CWeakRef< C, Locker >::Lock(), CDeflineGenerator::m_FirstSuperKingdom, CDeflineGenerator::m_Genome, CDeflineGenerator::m_Genus, CDeflineGenerator::m_Idx, CDeflineGenerator::m_IsCrossKingdom, CDeflineGenerator::m_LocalAnnotsOnly, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_OmitTaxonomicName, CDeflineGenerator::m_SecondSuperKingdom, CDeflineGenerator::m_Source, CDeflineGenerator::m_Species, CDeflineGenerator::m_Taxname, NCBI_GENOME, CConstRef< C, Locker >::NotEmpty(), NPOS, s_proteinOrganellePrefix, s_TitleEndsInOrganism(), s_TrimMainTitle(), str(), string, x_GetSourceFeatViaCDS(), and CDeflineGenerator::x_IsComplete().

Referenced by CDeflineGenerator::GenerateDefline().

Definition at line 3115 of file create_defline.cpp.

References CTempString::empty(), CConstRef< C, Locker >::Empty(), NStr::EndsWith(), NStr::eNocase, NStr::EqualNocase(), NStr::eReverseSearch, CTempString::find(), NStr::Find(), CBioseqIndex::GetBioseqForProduct(), CSeqEntryIndex::GetBioseqIndex(), CBioseqIndex::GetBioSource(), CBioseqIndex::GetDescTaxname(), CBioseqIndex::GetGenome(), CBioseqIndex::GetGenus(), CBioseqIndex::GetOrganelle(), CBioseqIndex::GetSpecies(), CBioseqIndex::GetTaxname(), CBioSource::GetTaxname(), int, CBioSource::IsSetTaxname(), CTempString::length(), CWeakRef< C, Locker >::Lock(), CDeflineGenerator::m_FirstSuperKingdom, CDeflineGenerator::m_Genome, CDeflineGenerator::m_Genus, CDeflineGenerator::m_Idx, CDeflineGenerator::m_IsCrossKingdom, CDeflineGenerator::m_LocalAnnotsOnly, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_OmitTaxonomicName, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_SecondSuperKingdom, CDeflineGenerator::m_Source, CDeflineGenerator::m_Species, CDeflineGenerator::m_Taxname, NCBI_GENOME, CConstRef< C, Locker >::NotEmpty(), NPOS, s_proteinOrganellePrefix, s_TitleEndsInOrganism(), s_TrimMainTitle(), str(), string, x_GetSourceFeatViaCDS(), and CDeflineGenerator::x_IsComplete().

Referenced by CDeflineGenerator::GenerateDefline().

Definition at line 2100 of file create_defline.cpp.

References FEATURE_CHOICE_IS, FOR_EACH_CHAR_IN_STRING, CSeq_feat_Base::GetExcept(), CSeq_feat_Base::GetExcept_text(), CSeq_feat_Base::IsSetExcept(), CSeq_feat_Base::IsSetExcept_text(), CDeflineGenerator::ms_p_Low_Quality_Fsa, NCBI_SEQFEAT, and str().

Referenced by CDeflineGenerator::x_SetPrefix(), CDeflineGenerator::x_SetTitleFromProtein(), and CDeflineGenerator::x_SetTitleFromProteinIdx().

This counts the number of ambiguous bases in the range [leftmost_pos_to_check, rightmost_pos_to_check].

Note that rightmost_pos_to_check is inclusive.

Parameters

out_result This will store the result. Pass in a struct initialized by the default constructor. seqvec This is used to get the bases. iStartPosInclusive This is where we start our count. iEndPosInclusive This is where we end our count. Note that it can be < or > iStartPosInclusive, depending on trim direction. iTrimDirection 1 to trim from left to right, -1 to trim from right to left.

Definition at line 571 of file seq_trimmer.cpp.

References abs, CSeqMap::eSeqData, CSeqMap::eSeqGap, CSequenceAmbigTrimmer::fFlags_DoNotTrimSeqGap, CSeqMap::FindSegment(), CSeqVector::GetScope(), CSeqVector::GetSeqMap(), CSeqVector::GetSequenceType(), CSeqMap_CI::GetType(), CSeqVector::IsNucleotide(), CSeqVector::IsProtein(), CSequenceAmbigTrimmer::m_arrNucAmbigLookupTable, CSequenceAmbigTrimmer::m_arrProtAmbigLookupTable, CSequenceAmbigTrimmer::m_fFlags, max(), min(), NCBI_USER_THROW_FMT, NULL, CSequenceAmbigTrimmer::SAmbigCount::num_ambig_bases, CSequenceAmbigTrimmer::SAmbigCount::pos_after_last_gap, CSequenceAmbigTrimmer::x_SegmentGetBeginningInclusive(), CSequenceAmbigTrimmer::x_SegmentGetEndInclusive(), and CSequenceAmbigTrimmer::x_SeqMapIterDoNext().

Referenced by CSequenceAmbigTrimmer::x_FindWhereToTrim().

Definition at line 1439 of file create_defline.cpp.

References buf, count, CTempString::empty(), CTempString::find(), CDeflineGenerator::m_Clone, CDeflineGenerator::m_has_clone, CDeflineGenerator::m_HTGSPooled, CDeflineGenerator::m_HTGSUnfinished, NPOS, and NStr::NumericToString().

Referenced by CDeflineGenerator::x_SetTitleFromBioSrc(), CDeflineGenerator::x_SetTitleFromGPipe(), CDeflineGenerator::x_SetTitleFromSegSeq(), and CDeflineGenerator::x_SetTitleFromWGS().

This adjusts in_out_uStartOfGoodBasesSoFar if we're at a CSeqMap gap.

It does not notice ambiguous bases that are inside a normal sequence.

Parameters

seqvec This is used to access information about the sequence. in_out_uStartOfGoodBasesSoFar This is the start of where we check for a gap. It will be updated to be past the gap, if a gap is found. in_out_uRightmostGoodBaseSoFar Analogous to in_out_uLeftmostGoodBaseSoFar. It's inclusive. uEndOfGoodBasesSoFar This limits how far this function may search (inclusive) when looking for the end of a gap segment. iTrimDirection 1 to trim from left to right, -1 to trim from right to left. uChunkSize The gap size that we chop off must be a multiple of uChunkSize. We will chop off less if we would go more than 1 past the uEndOfGoodBasesSoFar. A uChunkSize of 1 means no chunking for obvious math reasons.

Definition at line 497 of file seq_trimmer.cpp.

References abs, CSeqMap::eSeqData, CSeqMap::eSeqGap, CSequenceAmbigTrimmer::fFlags_DoNotTrimSeqGap, CSeqMap::FindSegment(), CSeqVector::GetScope(), CSeqVector::GetSeqMap(), CSeqMap_CI::GetType(), CSeqVector::IsNucleotide(), CSeqVector::IsProtein(), CSequenceAmbigTrimmer::m_arrNucAmbigLookupTable, CSequenceAmbigTrimmer::m_arrProtAmbigLookupTable, CSequenceAmbigTrimmer::m_fFlags, NCBI_USER_THROW, NULL, and CSequenceAmbigTrimmer::x_SegmentGetEndInclusive().

Referenced by CSequenceAmbigTrimmer::x_FindWhereToTrim().

This finds the next gap on the bioseq, starting at given pos.

Parameters

bioseq_h the bioseq on which we're seeking the next relevant gap. pos_to_start_looking This is the position on bioseq_h to start looking for a relevant gap. out_pos_of_gap If a gap is found, this holds the 0-based position of the start of that gap. This is undefined if no gap was found. out_len_of_gap If a gap is found, this holds the length of the gap. This is undefined if no gap was found.

Returns

This indicates whether or not a relevant gap was found.

Definition at line 191 of file bioseqgaps_ci.cpp.

References CBioseq_Handle::eCoding_Iupac, CBioseqGaps_CI::eFindNext_Found, CBioseqGaps_CI::eFindNext_NotFound, CSeqMap::eSeqData, CSeqMap::eSeqGap, CSeqMap::FindSegment(), CSeqMap_CI::GetEndPosition(), CSeqVector::GetGapChar(), CBioseq_Handle::GetScope(), CSeqVector::GetSeqMap(), CSeqMap_CI::GetType(), NCBI_USER_THROW_FMT, and CSeqVector::size().

Referenced by CBioseqGaps_CI::x_Next().

This returns the last good base that won't be trimmed (note: last really means "first" when we're starting from the end)

Parameters

seqvec This lets us explore the Bioseq to find out where to trim. iStartPosInclusive_arg This is the where we start our trimming. Depending on direction, this could be < or > iEndPosInclusive_arg. iEndPosInclusive_arg This is where the trimming ends (inclusive). Analogous to iStartPosInclusive_arg. iTrimDirection 1 to trim from left to right, -1 to trim from right to left.

Returns

The last good base (remember: last means "lower number" when we're checking from the end). If trimming would trim off the entire sequence, it returns a position past the end of the sequence.

Definition at line 362 of file seq_trimmer.cpp.

References _ASSERT, abs, CSequenceAmbigTrimmer::STrimRule::bases_to_check, ITERATE, CSequenceAmbigTrimmer::m_uMinSeqLen, CSequenceAmbigTrimmer::m_vecTrimRules, max(), CSequenceAmbigTrimmer::STrimRule::max_bases_allowed_to_be_ambig, min(), CSequenceAmbigTrimmer::SAmbigCount::num_ambig_bases, CSequenceAmbigTrimmer::SAmbigCount::pos_after_last_gap, s_IsValidDirection(), CSequenceAmbigTrimmer::x_CountAmbigInRange(), and CSequenceAmbigTrimmer::x_EdgeSeqMapGapAdjust().

Referenced by CSequenceAmbigTrimmer::DoTrim().

Definition at line 2812 of file sequence.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Other, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CSeq_inst_Base::eMol_aa, CSeq_id::FastaAARank(), CSeq_id::FastaNARank(), CFastaOstream::fEnableGI, CFastaOstream::fHideGenBankPrefix, FindBestChoice(), CBioseq_Base::GetId(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetMol(), ITERATE, CFastaOstream::m_Flags, CConstRef< C, Locker >::NotEmpty(), and CSeq_id_Base::Which().

Referenced by CFastaOstream::x_WriteAsFasta().

Definition at line 1991 of file create_defline.cpp.

References CRef< C, Locker >::Empty(), FOR_EACH_SEQFEATXREF_ON_FEATURE, GetBestGeneForCds(), CSeq_feat_Base::GetData(), CSeqFeatXref_Base::GetData(), CSeqFeatData_Base::GetGene(), CMappedFeat::GetOriginalFeature(), CSeqFeatData_Base::IsGene(), CSeqFeatXref_Base::IsSetData(), CDeflineGenerator::m_ConstructedFeatTree, CDeflineGenerator::m_Feat_Tree, CDeflineGenerator::m_InitializedFeatTree, CDeflineGenerator::m_TopSEH, and CRef< C, Locker >::Reset().

Referenced by CDeflineGenerator::x_SetTitleFromProtein().

Definition at line 1918 of file create_defline.cpp.

References CSeqFeatData_Base::e_Prot, eOverlap_Contained, CProt_ref_Base::eProcessed_not_set, FOR_EACH_SEQFEAT_ON_BIOSEQ_HANDLE, GetBestOverlappingFeat(), CSeq_feat_Base::GetData(), CBioseq_Handle::GetInst_Length(), GetLength(), CSeq_feat_Base::GetLocation(), CProt_ref_Base::GetProcessed(), CSeqFeatData_Base::GetProt(), CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeqId(), CSeq_feat_Base::IsSetData(), CBioseq_Handle::IsSetInst(), CBioseq_Handle::IsSetInst_Length(), CSeq_feat_Base::IsSetLocation(), CProt_ref_Base::IsSetProcessed(), prot, and CSeq_loc::SetWhole().

Referenced by CDeflineGenerator::x_SetTitleFromProtein().

Definition at line 3450 of file create_defline.cpp.

References CDefLineJoiner::Add(), CPCRPrimerSet_Base::CanGet(), CPCRReactionSet_Base::CanGet(), CBioSource_Base::CanGetGenome(), CBioseq_Handle::CanGetInst_Topology(), DEFINE_STATIC_ARRAY_MAP, CBioSource_Base::eGenome_apicoplast, CBioSource_Base::eGenome_chloroplast, CBioSource_Base::eGenome_chromatophore, CBioSource_Base::eGenome_chromoplast, CBioSource_Base::eGenome_cyanelle, CBioSource_Base::eGenome_hydrogenosome, CBioSource_Base::eGenome_kinetoplast, CBioSource_Base::eGenome_leucoplast, CBioSource_Base::eGenome_mitochondrion, CBioSource_Base::eGenome_plasmid_in_mitochondrion, CBioSource_Base::eGenome_plasmid_in_plastid, CBioSource_Base::eGenome_plastid, CBioSource_Base::eGenome_proplastid, CBioSource_Base::eGenome_unknown, CTempString::empty(), ERR_POST_X, COrgMod_Base::eSubtype_acronym, CSubSource_Base::eSubtype_altitude, COrgMod_Base::eSubtype_anamorph, COrgMod_Base::eSubtype_authority, COrgMod_Base::eSubtype_bio_material, COrgMod_Base::eSubtype_biotype, COrgMod_Base::eSubtype_biovar, COrgMod_Base::eSubtype_breed, CSubSource_Base::eSubtype_cell_line, CSubSource_Base::eSubtype_cell_type, COrgMod_Base::eSubtype_chemovar, CSubSource_Base::eSubtype_chromosome, CSubSource_Base::eSubtype_clone, CSubSource_Base::eSubtype_clone_lib, CSubSource_Base::eSubtype_collected_by, CSubSource_Base::eSubtype_collection_date, COrgMod_Base::eSubtype_common, CSubSource_Base::eSubtype_country, COrgMod_Base::eSubtype_cultivar, COrgMod_Base::eSubtype_culture_collection, CSubSource_Base::eSubtype_dev_stage, COrgMod_Base::eSubtype_dosage, COrgMod_Base::eSubtype_ecotype, CSubSource_Base::eSubtype_endogenous_virus_name, CSubSource_Base::eSubtype_environmental_sample, COrgMod_Base::eSubtype_forma, COrgMod_Base::eSubtype_forma_specialis, CSubSource_Base::eSubtype_frequency, COrgMod_Base::eSubtype_gb_acronym, COrgMod_Base::eSubtype_gb_anamorph, COrgMod_Base::eSubtype_gb_synonym, CSubSource_Base::eSubtype_genotype, CSubSource_Base::eSubtype_germline, COrgMod_Base::eSubtype_group, CSubSource_Base::eSubtype_haplogroup, CSubSource_Base::eSubtype_haplotype, CSubSource_Base::eSubtype_identified_by, CSubSource_Base::eSubtype_insertion_seq_name, COrgMod_Base::eSubtype_isolate, CSubSource_Base::eSubtype_isolation_source, CSubSource_Base::eSubtype_lab_host, CSubSource_Base::eSubtype_lat_lon, CSubSource_Base::eSubtype_linkage_group, CSubSource_Base::eSubtype_map, CSubSource_Base::eSubtype_mating_type, COrgMod_Base::eSubtype_metagenome_source, CSubSource_Base::eSubtype_metagenomic, COrgMod_Base::eSubtype_nat_host, COrgMod_Base::eSubtype_nomenclature, COrgMod_Base::eSubtype_other, CSubSource_Base::eSubtype_other, COrgMod_Base::eSubtype_pathovar, CSubSource_Base::eSubtype_phenotype, CSubSource_Base::eSubtype_plasmid_name, CSubSource_Base::eSubtype_plastid_name, CSubSource_Base::eSubtype_pop_variant, CSubSource_Base::eSubtype_rearranged, CSubSource_Base::eSubtype_segment, COrgMod_Base::eSubtype_serogroup, COrgMod_Base::eSubtype_serotype, COrgMod_Base::eSubtype_serovar, CSubSource_Base::eSubtype_sex, COrgMod_Base::eSubtype_specimen_voucher, COrgMod_Base::eSubtype_strain, COrgMod_Base::eSubtype_sub_species, CSubSource_Base::eSubtype_subclone, COrgMod_Base::eSubtype_subgroup, COrgMod_Base::eSubtype_substrain, COrgMod_Base::eSubtype_subtype, COrgMod_Base::eSubtype_synonym, COrgMod_Base::eSubtype_teleomorph, CSubSource_Base::eSubtype_tissue_lib, CSubSource_Base::eSubtype_tissue_type, CSubSource_Base::eSubtype_transgenic, CSubSource_Base::eSubtype_transposon_name, COrgMod_Base::eSubtype_type, COrgMod_Base::eSubtype_type_material, COrgMod_Base::eSubtype_variety, CSubSource_Base::eSubtype_whole_replicon, CMolInfo_Base::eTech_barcode, CMolInfo_Base::eTech_both, CMolInfo_Base::eTech_composite_wgs_htgs, CMolInfo_Base::eTech_concept_trans, CMolInfo_Base::eTech_concept_trans_a, CMolInfo_Base::eTech_derived, CMolInfo_Base::eTech_est, CMolInfo_Base::eTech_fli_cdna, CMolInfo_Base::eTech_genemap, CMolInfo_Base::eTech_htc, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, CMolInfo_Base::eTech_physmap, CMolInfo_Base::eTech_seq_pept, CMolInfo_Base::eTech_seq_pept_homol, CMolInfo_Base::eTech_seq_pept_overlap, CMolInfo_Base::eTech_standard, CMolInfo_Base::eTech_sts, CMolInfo_Base::eTech_survey, CMolInfo_Base::eTech_tsa, CMolInfo_Base::eTech_unknown, CMolInfo_Base::eTech_wgs, CSeq_inst_Base::eTopology_circular, CPCRPrimerSet_Base::Get(), CPCRReactionSet_Base::Get(), GetBioSource(), COrgName_Base::GetGcode(), CBioSource_Base::GetGenome(), CBioseq_Handle::GetInst_Topology(), COrgName_Base::GetMgcode(), COrgName_Base::GetMod(), GetMolInfo(), CSubSource_Base::GetName(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), CBioSource_Base::GetPcr_primers(), COrgName_Base::GetPgcode(), CBioSource_Base::GetSubtype(), CSubSource_Base::GetSubtype(), COrg_ref_Base::GetTaxname(), CMolInfo_Base::GetTech(), COrgName_Base::IsSetGcode(), COrgName_Base::IsSetMgcode(), COrgName_Base::IsSetMod(), CSubSource_Base::IsSetName(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), CBioSource_Base::IsSetPcr_primers(), COrgName_Base::IsSetPgcode(), CBioSource_Base::IsSetSubtype(), CSubSource_Base::IsSetSubtype(), COrg_ref_Base::IsSetTaxname(), CMolInfo_Base::IsSetTech(), ITERATE, CDefLineJoiner::Join(), kEmptyStr, CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_IsChromosome, CDeflineGenerator::m_IsPlasmid, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_MICompleteness, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_Plasmid, mod(), NCBI_COMPLETENESS, CSubSource::NCBI_UseGeoLocNameForCountry(), NULL, sc_TechArray, subname, Warning(), and CDeflineGenerator::x_SetBioSrc().

Referenced by CDeflineGenerator::GenerateDefline().

Definition at line 2978 of file sequence.cpp.

This moves this iterator to the next relevant gap.

Throws if this iterator has finished.

Definition at line 92 of file bioseqgaps_ci.cpp.

References _ASSERT, CBioseqGaps_CI::eFindNext_Found, CBioseq_Handle::GetAccessSeq_id_Handle(), kInvalidSeqPos, CBioseqGaps_CI::SCurrentGapInfo::length, CBioseqGaps_CI::m_bioseq_CI, CBioseqGaps_CI::m_infoOnCurrentGap, CBioseqGaps_CI::m_Params, CBioseqGaps_CI::Params::max_gap_len_to_ignore, CBioseqGaps_CI::Params::max_num_gaps_per_seq, NCBI_USER_THROW, CBioseqGaps_CI::SCurrentGapInfo::num_gaps_seen_so_far_on_this_seq, CBioseqGaps_CI::SCurrentGapInfo::num_seqs_seen_so_far, CBioseqGaps_CI::SCurrentGapInfo::seq_id, CBioseqGaps_CI::SCurrentGapInfo::start_pos, CBioseqGaps_CI::x_FindNextGapOnBioseq(), and CBioseqGaps_CI::x_NextBioseq().

Referenced by CBioseqGaps_CI::operator++().

This returns the (inclusive) position at the beginning of the segment.

Parameters

segment This is the segment we're trying to find the beginning of. iTrimDirection This is which direction in which we're trimming. The beginning will be in the opposite direction.

Returns

This returns the (inclusive) position at the beginning of the given segment. As always, the definition of "beginning" depends on iTrimDirection.

Definition at line 1521 of file sequence.hpp.

References CSequenceAmbigTrimmer::x_SegmentGetEndInclusive().

Referenced by CSequenceAmbigTrimmer::x_CountAmbigInRange().

Returns the "next" segment.

The definition of "next" depends on iTrimDirection

Parameters

in_out_segment Caller gives the current CSeqMap_CI, which will be returned adjusted in the trim direction. iTrimDirection The direction in which to increment. 1 means normal incrementing and -1 really means decrementing.

Returns

Reference to in_out_segment_it.

Definition at line 692 of file seq_trimmer.cpp.

References _ASSERT, and s_IsValidDirection().

Referenced by CSequenceAmbigTrimmer::x_CountAmbigInRange().

Definition at line 1266 of file create_defline.cpp.

References CSeqFeatData_Base::e_Biosrc, CTempString::empty(), NStr::EqualNocase(), FOR_EACH_ORGMOD_ON_BIOSOURCE, FOR_EACH_SUBSOURCE_ON_BIOSOURCE, CPartialOrgName_Base::Get(), COrgName_Base::C_Name::GetBinomial(), CSeqFeatData_Base::GetBiosrc(), CSeq_feat_Base::GetData(), CTaxElement_Base::GetFixed_level(), CBioSource_Base::GetGenome(), CBinomialOrgName_Base::GetGenus(), CTaxElement_Base::GetLevel(), COrgName_Base::GetName(), CSubSource_Base::GetName(), CBioSource::GetOrgname(), CMappedFeat::GetOriginalFeature(), COrgName_Base::C_Name::GetPartial(), CBinomialOrgName_Base::GetSpecies(), COrgMod_Base::GetSubname(), CBioSource::GetTaxname(), COrgName_Base::C_Name::IsBinomial(), COrgName_Base::C_Name::IsPartial(), CPartialOrgName_Base::IsSet(), CSeq_feat_Base::IsSetData(), CTaxElement_Base::IsSetFixed_level(), CBioSource_Base::IsSetGenome(), CBinomialOrgName_Base::IsSetGenus(), CTaxElement_Base::IsSetLevel(), COrgName_Base::IsSetName(), CSubSource_Base::IsSetName(), CBioSource::IsSetOrgname(), CBinomialOrgName_Base::IsSetSpecies(), COrgMod_Base::IsSetSubname(), CBioSource::IsSetTaxname(), ITERATE, CDeflineGenerator::m_Breed, CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_Clone, CDeflineGenerator::m_Cultivar, CDeflineGenerator::m_Genome, CDeflineGenerator::m_Genus, CDeflineGenerator::m_has_clone, CDeflineGenerator::m_IsChromosome, CDeflineGenerator::m_Isolate, CDeflineGenerator::m_IsPlasmid, CDeflineGenerator::m_LinkageGroup, CDeflineGenerator::m_Map, CDeflineGenerator::m_MetaGenomeSource, CDeflineGenerator::m_Multispecies, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_Plasmid, CDeflineGenerator::m_Segment, CDeflineGenerator::m_Source, CDeflineGenerator::m_Species, CDeflineGenerator::m_SpecimenVoucher, CDeflineGenerator::m_Strain, CDeflineGenerator::m_Substrain, CDeflineGenerator::m_Taxname, NCBI_GENOME, NCBI_ORGMOD, NCBI_SUBSOURCE, CConstRef< C, Locker >::NotEmpty(), rapidjson::source, str(), SWITCH_ON_ORGMOD_CHOICE, SWITCH_ON_SUBSOURCE_CHOICE, and CDeflineGenerator::x_OrganelleName().

Referenced by CDeflineGenerator::GenerateDefline(), and CDeflineGenerator::x_GetModifiers().

Definition at line 1197 of file create_defline.cpp.

References CSeqFeatData_Base::e_Biosrc, FOR_EACH_SUBSOURCE_ON_BIOSOURCE, CSeqEntryIndex::GetBioseqIndex(), CBioseqIndex::GetBioSource(), CSeqFeatData_Base::GetBiosrc(), CBioseqIndex::GetBreed(), CBioseqIndex::GetChromosome(), CBioseqIndex::GetClone(), CBioseqIndex::GetCultivar(), CSeq_feat_Base::GetData(), CBioseqIndex::GetGenome(), CBioseqIndex::GetGenus(), CBioseqIndex::GetIsolate(), CBioseqIndex::GetLinkageGroup(), CBioseqIndex::GetMap(), CBioseqIndex::GetMetaGenomeSource(), CBioseqIndex::GetOrganelle(), CMappedFeat::GetOriginalFeature(), CBioseqIndex::GetPlasmid(), CBioseqIndex::GetSegment(), CBioseqIndex::GetSpecies(), CBioseqIndex::GetSpecimenVoucher(), CBioseqIndex::GetStrain(), CBioseqIndex::GetSubstrain(), CBioseqIndex::GetTaxname(), CBioseqIndex::HasClone(), CBioseqIndex::IsChromosome(), CBioseqIndex::IsMultispecies(), CBioseqIndex::IsPlasmid(), CSeq_feat_Base::IsSetData(), CSubSource_Base::IsSetName(), CDeflineGenerator::m_Breed, CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_Clone, CDeflineGenerator::m_Cultivar, CDeflineGenerator::m_Genome, CDeflineGenerator::m_Genus, CDeflineGenerator::m_has_clone, CDeflineGenerator::m_Idx, CDeflineGenerator::m_IsChromosome, CDeflineGenerator::m_Isolate, CDeflineGenerator::m_IsPlasmid, CDeflineGenerator::m_LinkageGroup, CDeflineGenerator::m_Map, CDeflineGenerator::m_MetaGenomeSource, CDeflineGenerator::m_Multispecies, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_Plasmid, CDeflineGenerator::m_Segment, CDeflineGenerator::m_Source, CDeflineGenerator::m_Species, CDeflineGenerator::m_SpecimenVoucher, CDeflineGenerator::m_Strain, CDeflineGenerator::m_Substrain, CDeflineGenerator::m_Taxname, NCBI_SUBSOURCE, rapidjson::source, and SWITCH_ON_SUBSOURCE_CHOICE.

Referenced by CDeflineGenerator::GenerateDefline().

Definition at line 612 of file create_defline.cpp.

References _ASSERT, _TROUBLE, CTempString::clear(), data, CSeqdesc_Base::e_Comment, CSeqdesc_Base::e_Embl, CSeqdesc_Base::e_Genbank, CSeqdesc_Base::e_Molinfo, CSeqdesc_Base::e_Pdb, CSeqdesc_Base::e_Source, CSeqdesc_Base::e_Title, CSeqdesc_Base::e_User, CTempString::empty(), NStr::EqualNocase(), CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_map, CSeq_inst_Base::eRepr_seg, CSeq_inst_Base::eRepr_virtual, COrgMod_Base::eSubtype_metagenome_source, CSeq_id::fAcc_master, CDeflineGenerator::fAllProteinNames, CDeflineGenerator::fDevMode, CDeflineGenerator::fFastaFormat, CDeflineGenerator::fGpipeMode, FIELD_IS_SET_AND_IS, CDeflineGenerator::fIgnoreExisting, NStr::Find(), flags, CDeflineGenerator::fLocalAnnotsOnly, CDeflineGenerator::fOmitTaxonomicName, FOR_EACH_COMPOUND_ON_PDBBLOCK, FOR_EACH_SEQID_ON_BIOSEQ_HANDLE, FOR_EACH_STRING_IN_LIST, FOR_EACH_USERFIELD_ON_USEROBJECT, NStr::fSplit_Tokenize, CMap_ext_Base::Get(), CPartialOrgName_Base::Get(), GET_FIELD, CTextseq_id_Base::GetAccession(), CMolInfo_Base::GetBiomol(), CPDB_seq_id_Base::GetChain(), CPDB_seq_id_Base::GetChain_id(), CPatent_seq_id_Base::GetCit(), CMolInfo_Base::GetCompleteness(), CId_pat_Base::GetCountry(), CUser_field_Base::GetData(), CSeq_feat_Base::GetData(), CTaxElement_Base::GetFixed_level(), CObject_id_Base::GetId(), CBioseq_Handle::GetInst_Ext(), CBioseq_Handle::GetInst_Length(), CBioseq_Handle::GetInst_Repr(), CBioseq_Handle::GetInst_Topology(), CEMBL_block_Base::GetKeywords(), CGB_block_Base::GetKeywords(), CUser_field_Base::GetLabel(), CTaxElement_Base::GetLevel(), CSeq_ext_Base::GetMap(), COrgName_Base::GetMod(), COrgName_Base::GetName(), CTaxElement_Base::GetName(), CBioSource::GetOrgname(), COrgName_Base::C_Name::GetPartial(), CSeq_id_Handle::GetSeqId(), CPatent_seq_id_Base::GetSeqid(), CId_pat::GetSomeNumber(), CObject_id_Base::GetStr(), CUser_field_Base::C_Data::GetStr(), CRsite_ref_Base::GetStr(), CDbtag_Base::GetTag(), CMolInfo_Base::GetTech(), CUser_object_Base::GetType(), CSeq_id::IdentifyAccession(), CBioseq_Handle::IsAa(), CObject_id_Base::IsId(), CSeq_ext_Base::IsMap(), CBioseq_Handle::IsNa(), COrgName_Base::C_Name::IsPartial(), CMap_ext_Base::IsSet(), CPartialOrgName_Base::IsSet(), CTextseq_id_Base::IsSetAccession(), CPDB_seq_id_Base::IsSetChain(), CPDB_seq_id_Base::IsSetChain_id(), CPatent_seq_id_Base::IsSetCit(), CUser_field_Base::IsSetData(), CTaxElement_Base::IsSetFixed_level(), CBioseq_Handle::IsSetInst(), CBioseq_Handle::IsSetInst_Ext(), CBioseq_Handle::IsSetInst_Repr(), CEMBL_block_Base::IsSetKeywords(), CGB_block_Base::IsSetKeywords(), CTaxElement_Base::IsSetLevel(), COrgName_Base::IsSetMod(), CTaxElement_Base::IsSetName(), CBioSource::IsSetOrgname(), CPatent_seq_id_Base::IsSetSeqid(), CDbtag_Base::IsSetTag(), CDbtag::IsSkippable(), CObject_id_Base::IsStr(), CUser_field_Base::C_Data::IsStr(), CRsite_ref_Base::IsStr(), CUser_object::IsUnreviewed(), CUser_object::IsUnreviewedUnannotated(), CUser_object::IsUnverified(), CUser_object::IsUnverifiedContaminant(), CUser_object::IsUnverifiedFeature(), CUser_object::IsUnverifiedMisassembled(), CUser_object::IsUnverifiedOrganism(), ITERATE, CDeflineGenerator::m_AllProtNames, CDeflineGenerator::m_Breed, CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_Clone, CDeflineGenerator::m_Comment, CDeflineGenerator::m_Cultivar, CDeflineGenerator::m_DevMode, CDeflineGenerator::m_FastaFormat, CDeflineGenerator::m_FirstSuperKingdom, CDeflineGenerator::m_GeneralId, CDeflineGenerator::m_GeneralStr, CDeflineGenerator::m_Genome, CDeflineGenerator::m_Genus, CDeflineGenerator::m_GpipeMode, CDeflineGenerator::m_has_clone, CDeflineGenerator::m_HTGSCancelled, CDeflineGenerator::m_HTGSDraft, CDeflineGenerator::m_HTGSPooled, CDeflineGenerator::m_HTGSUnfinished, CDeflineGenerator::m_HTGTech, CDeflineGenerator::m_IsAA, CDeflineGenerator::m_IsChromosome, CDeflineGenerator::m_IsCrossKingdom, CDeflineGenerator::m_IsDelta, CDeflineGenerator::m_IsEST_STS_GSS, CDeflineGenerator::m_IsMap, CDeflineGenerator::m_IsNA, CDeflineGenerator::m_IsNC, CDeflineGenerator::m_IsNM, CDeflineGenerator::m_IsNR, CDeflineGenerator::m_IsNZ, CDeflineGenerator::m_Isolate, CDeflineGenerator::m_IsPatent, CDeflineGenerator::m_IsPDB, CDeflineGenerator::m_IsPlasmid, CDeflineGenerator::m_IsPseudogene, CDeflineGenerator::m_IsSeg, CDeflineGenerator::m_IsTLS, CDeflineGenerator::m_IsTSA, CDeflineGenerator::m_IsUnreviewed, CDeflineGenerator::m_IsUnverified, CDeflineGenerator::m_IsVirtual, CDeflineGenerator::m_IsWGS, CDeflineGenerator::m_IsWP, CDeflineGenerator::m_Length, CDeflineGenerator::m_LinkageGroup, CDeflineGenerator::m_LocalAnnotsOnly, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_Map, CDeflineGenerator::m_MetaGenomeSource, CDeflineGenerator::m_MIBiomol, CDeflineGenerator::m_MICompleteness, CDeflineGenerator::m_MITech, CDeflineGenerator::m_Multispecies, CDeflineGenerator::m_OmitTaxonomicName, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_PatentCountry, CDeflineGenerator::m_PatentNumber, CDeflineGenerator::m_PatentSequence, CDeflineGenerator::m_PDBChain, CDeflineGenerator::m_PDBChainID, CDeflineGenerator::m_PDBCompound, CDeflineGenerator::m_Plasmid, CDeflineGenerator::m_Reconstruct, CDeflineGenerator::m_rEnzyme, CDeflineGenerator::m_SecondSuperKingdom, CDeflineGenerator::m_Segment, CDeflineGenerator::m_Source, CDeflineGenerator::m_Species, CDeflineGenerator::m_SpecimenVoucher, CDeflineGenerator::m_Strain, CDeflineGenerator::m_Substrain, CDeflineGenerator::m_TargetedLocus, CDeflineGenerator::m_Taxname, CDeflineGenerator::m_ThirdParty, CDeflineGenerator::m_TLSMaster, CDeflineGenerator::m_Topology, CDeflineGenerator::m_TPAExp, CDeflineGenerator::m_TPAInf, CDeflineGenerator::m_TPAReasm, CDeflineGenerator::m_TSAMaster, CDeflineGenerator::m_Unordered, CDeflineGenerator::m_UnreviewedPrefix, CDeflineGenerator::m_UnverifiedPrefix, CDeflineGenerator::m_UseBiosrc, CDeflineGenerator::m_UsePDBCompoundForDefline, CDeflineGenerator::m_WGSMaster, NCBI_ACCN, NCBI_BIOMOL, NCBI_COMPLETENESS, NCBI_GENOME, NCBI_SEQID, NCBI_SEQTOPOLOGY, NCBI_TECH, NPOS, NULL, CConstRef< C, Locker >::Reset(), NStr::Split(), str(), Type, and CSeq_id_Handle::Which().

Referenced by CDeflineGenerator::GenerateDefline().

Definition at line 430 of file create_defline.cpp.

References CTempString::clear(), CTempString::empty(), CDeflineGenerator::fAllProteinNames, CDeflineGenerator::fDevMode, CDeflineGenerator::fFastaFormat, CDeflineGenerator::fGpipeMode, CDeflineGenerator::fIgnoreExisting, NStr::Find(), flags, CDeflineGenerator::fLocalAnnotsOnly, CDeflineGenerator::fOmitTaxonomicName, CBioseqIndex::GetBiomol(), CSeqEntryIndex::GetBioseqIndex(), CBioseqIndex::GetBioSource(), CBioseqIndex::GetBreed(), CBioseqIndex::GetChromosome(), CBioseqIndex::GetClone(), CBioseqIndex::GetComment(), CBioseqIndex::GetCompleteness(), CBioseqIndex::GetCultivar(), CBioseqIndex::GetFirstSuperKingdom(), CBioseqIndex::GetGeneralId(), CBioseqIndex::GetGeneralStr(), CBioseqIndex::GetGenome(), CBioseqIndex::GetGenus(), CBioseqIndex::GetIsolate(), CBioseqIndex::GetLength(), CBioseqIndex::GetLinkageGroup(), CBioseqIndex::GetMap(), CBioseqIndex::GetMetaGenomeSource(), CBioseqIndex::GetOrganelle(), CBioseqIndex::GetPatentCountry(), CBioseqIndex::GetPatentNumber(), CBioseqIndex::GetPatentSequence(), CBioseqIndex::GetPDBChain(), CBioseqIndex::GetPDBChainID(), CBioseqIndex::GetPDBCompound(), CBioseqIndex::GetPlasmid(), CBioseqIndex::GetrEnzyme(), CBioseqIndex::GetSecondSuperKingdom(), CBioseqIndex::GetSegment(), CBioseqIndex::GetSpecies(), CBioseqIndex::GetSpecimenVoucher(), CBioseqIndex::GetStrain(), CBioseqIndex::GetSubstrain(), CBioseqIndex::GetTargetedLocus(), CBioseqIndex::GetTaxname(), CBioseqIndex::GetTech(), CBioseqIndex::GetTitle(), CBioseqIndex::GetTopology(), CBioseqIndex::HasClone(), CBioseqIndex::IsAA(), CBioseqIndex::IsChromosome(), CBioseqIndex::IsCrossKingdom(), CBioseqIndex::IsDelta(), CBioseqIndex::IsEST_STS_GSS(), CBioseqIndex::IsHTGSCancelled(), CBioseqIndex::IsHTGSDraft(), CBioseqIndex::IsHTGSPooled(), CBioseqIndex::IsHTGSUnfinished(), CBioseqIndex::IsHTGTech(), CBioseqIndex::IsMap(), CBioseqIndex::IsMultispecies(), CBioseqIndex::IsNA(), CBioseqIndex::IsNC(), CBioseqIndex::IsNM(), CBioseqIndex::IsNR(), CBioseqIndex::IsNZ(), CBioseqIndex::IsPatent(), CBioseqIndex::IsPDB(), CBioseqIndex::IsPlasmid(), CBioseqIndex::IsPseudogene(), CBioseqIndex::IsThirdParty(), CBioseqIndex::IsTLS(), CBioseqIndex::IsTLSMaster(), CBioseqIndex::IsTPAExp(), CBioseqIndex::IsTPAInf(), CBioseqIndex::IsTPAReasm(), CBioseqIndex::IsTSA(), CBioseqIndex::IsTSAMaster(), CBioseqIndex::IsUnordered(), CBioseqIndex::IsUnreviewed(), CBioseqIndex::IsUnreviewedUnannotated(), CBioseqIndex::IsUnverified(), CBioseqIndex::IsUnverifiedContaminant(), CBioseqIndex::IsUnverifiedFeature(), CBioseqIndex::IsUnverifiedMisassembled(), CBioseqIndex::IsUnverifiedOrganism(), CBioseqIndex::IsUseBiosrc(), CBioseqIndex::IsVirtual(), CBioseqIndex::IsWGS(), CBioseqIndex::IsWGSMaster(), CBioseqIndex::IsWP(), CDeflineGenerator::m_AllProtNames, CDeflineGenerator::m_Breed, CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_Clone, CDeflineGenerator::m_Comment, CDeflineGenerator::m_Cultivar, CDeflineGenerator::m_DevMode, CDeflineGenerator::m_FastaFormat, CDeflineGenerator::m_FirstSuperKingdom, CDeflineGenerator::m_GeneralId, CDeflineGenerator::m_GeneralStr, CDeflineGenerator::m_Genome, CDeflineGenerator::m_Genus, CDeflineGenerator::m_GpipeMode, CDeflineGenerator::m_has_clone, CDeflineGenerator::m_HTGSCancelled, CDeflineGenerator::m_HTGSDraft, CDeflineGenerator::m_HTGSPooled, CDeflineGenerator::m_HTGSUnfinished, CDeflineGenerator::m_HTGTech, CDeflineGenerator::m_Idx, CDeflineGenerator::m_IsAA, CDeflineGenerator::m_IsChromosome, CDeflineGenerator::m_IsCrossKingdom, CDeflineGenerator::m_IsDelta, CDeflineGenerator::m_IsEST_STS_GSS, CDeflineGenerator::m_IsMap, CDeflineGenerator::m_IsNA, CDeflineGenerator::m_IsNC, CDeflineGenerator::m_IsNM, CDeflineGenerator::m_IsNR, CDeflineGenerator::m_IsNZ, CDeflineGenerator::m_Isolate, CDeflineGenerator::m_IsPatent, CDeflineGenerator::m_IsPDB, CDeflineGenerator::m_IsPlasmid, CDeflineGenerator::m_IsPseudogene, CDeflineGenerator::m_IsSeg, CDeflineGenerator::m_IsTLS, CDeflineGenerator::m_IsTSA, CDeflineGenerator::m_IsUnreviewed, CDeflineGenerator::m_IsUnverified, CDeflineGenerator::m_IsVirtual, CDeflineGenerator::m_IsWGS, CDeflineGenerator::m_IsWP, CDeflineGenerator::m_Length, CDeflineGenerator::m_LinkageGroup, CDeflineGenerator::m_LocalAnnotsOnly, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_Map, CDeflineGenerator::m_MetaGenomeSource, CDeflineGenerator::m_MIBiomol, CDeflineGenerator::m_MICompleteness, CDeflineGenerator::m_MITech, CDeflineGenerator::m_Multispecies, CDeflineGenerator::m_OmitTaxonomicName, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_PatentCountry, CDeflineGenerator::m_PatentNumber, CDeflineGenerator::m_PatentSequence, CDeflineGenerator::m_PDBChain, CDeflineGenerator::m_PDBChainID, CDeflineGenerator::m_PDBCompound, CDeflineGenerator::m_Plasmid, CDeflineGenerator::m_Reconstruct, CDeflineGenerator::m_rEnzyme, CDeflineGenerator::m_SecondSuperKingdom, CDeflineGenerator::m_Segment, CDeflineGenerator::m_Source, CDeflineGenerator::m_Species, CDeflineGenerator::m_SpecimenVoucher, CDeflineGenerator::m_Strain, CDeflineGenerator::m_Substrain, CDeflineGenerator::m_TargetedLocus, CDeflineGenerator::m_Taxname, CDeflineGenerator::m_ThirdParty, CDeflineGenerator::m_TLSMaster, CDeflineGenerator::m_Topology, CDeflineGenerator::m_TPAExp, CDeflineGenerator::m_TPAInf, CDeflineGenerator::m_TPAReasm, CDeflineGenerator::m_TSAMaster, CDeflineGenerator::m_Unordered, CDeflineGenerator::m_UnreviewedPrefix, CDeflineGenerator::m_UnverifiedPrefix, CDeflineGenerator::m_UseBiosrc, CDeflineGenerator::m_UsePDBCompoundForDefline, CDeflineGenerator::m_WGSMaster, and NPOS.

Referenced by CDeflineGenerator::GenerateDefline().

Definition at line 2801 of file create_defline.cpp.

References CBioseqIndex::GetBioseqForProduct(), CSeqEntryIndex::GetBioseqIndex(), CBioseqIndex::GetFeatureForProduct(), CFeatureIndex::GetMappedFeat(), CMappedFeat::GetOriginalFeature(), kEmptyCStr, CWeakRef< C, Locker >::Lock(), CDeflineGenerator::m_Idx, CDeflineGenerator::m_IsAA, CDeflineGenerator::m_IsPseudogene, CDeflineGenerator::m_IsTLS, CDeflineGenerator::m_IsTSA, CDeflineGenerator::m_IsUnreviewed, CDeflineGenerator::m_IsUnverified, CDeflineGenerator::m_IsWP, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_Multispecies, CDeflineGenerator::m_ThirdParty, CDeflineGenerator::m_TPAExp, CDeflineGenerator::m_TPAInf, CDeflineGenerator::m_TPAReasm, CDeflineGenerator::m_UnreviewedPrefix, CDeflineGenerator::m_UnverifiedPrefix, NPOS, and CDeflineGenerator::x_CDShasLowQualityException().

Referenced by CDeflineGenerator::GenerateDefline().

Definition at line 2871 of file create_defline.cpp.

References CTempString::empty(), NStr::EqualNocase(), CSeqMap::fFindGap, NStr::IntToString(), CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_Genome, CDeflineGenerator::m_HTGSCancelled, CDeflineGenerator::m_HTGSDraft, CDeflineGenerator::m_IsChromosome, CDeflineGenerator::m_IsDelta, CDeflineGenerator::m_IsPlasmid, CDeflineGenerator::m_LinkageGroup, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_MIBiomol, CDeflineGenerator::m_MICompleteness, CDeflineGenerator::m_MITech, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_TargetedLocus, CDeflineGenerator::m_TLSMaster, CDeflineGenerator::m_TSAMaster, CDeflineGenerator::m_Unordered, CDeflineGenerator::m_WGSMaster, NCBI_BIOMOL, NCBI_COMPLETENESS, NCBI_GENOME, NCBI_TECH, NPOS, and type.

Referenced by CDeflineGenerator::GenerateDefline().

Definition at line 1547 of file create_defline.cpp.

References CDefLineJoiner::Add(), eHideType, CTempString::empty(), CTempString::find(), ITERATE, CDefLineJoiner::Join(), CDeflineGenerator::m_Breed, CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_Cultivar, CDeflineGenerator::m_has_clone, CDeflineGenerator::m_Isolate, CDeflineGenerator::m_LinkageGroup, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_Map, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_Plasmid, CDeflineGenerator::m_SpecimenVoucher, CDeflineGenerator::m_Strain, CDeflineGenerator::m_Substrain, CDeflineGenerator::m_Taxname, s_AddVoucherAndIsolate(), s_EndsWithStrain(), CTempString::substr(), NStr::TruncateSpacesInPlace(), and CDeflineGenerator::x_DescribeClones().

Referenced by CDeflineGenerator::GenerateDefline().

Definition at line 1863 of file create_defline.cpp.

References CDefLineJoiner::Add(), eHideType, CTempString::empty(), CTempString::find(), NStr::FindNoCase(), ITERATE, CDefLineJoiner::Join(), CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_has_clone, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_Map, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_Plasmid, CDeflineGenerator::m_Strain, CDeflineGenerator::m_Substrain, CDeflineGenerator::m_Taxname, NPOS, s_EndsWithStrain(), NStr::TruncateSpacesInPlace(), CDeflineGenerator::x_DescribeClones(), and CDeflineGenerator::x_IsComplete().

Referenced by CDeflineGenerator::GenerateDefline().

Definition at line 2761 of file create_defline.cpp.

References CDefLineJoiner::Add(), eHideType, CTempString::empty(), CTempString::find(), CDefLineJoiner::Join(), CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_IsChromosome, CDeflineGenerator::m_Isolate, CDeflineGenerator::m_IsPlasmid, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_Plasmid, CDeflineGenerator::m_rEnzyme, CDeflineGenerator::m_Strain, CDeflineGenerator::m_Substrain, CDeflineGenerator::m_Taxname, s_EndsWithStrain(), CTempString::substr(), and NStr::TruncateSpacesInPlace().

Referenced by CDeflineGenerator::GenerateDefline().

Definition at line 1605 of file create_defline.cpp.

References CDefLineJoiner::Add(), eHideType, CTempString::empty(), CTempString::find(), NStr::FindNoCase(), CDefLineJoiner::Join(), CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_Genome, CDeflineGenerator::m_IsChromosome, CDeflineGenerator::m_IsPlasmid, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_MIBiomol, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_Plasmid, CDeflineGenerator::m_Segment, CDeflineGenerator::m_Taxname, NCBI_BIOMOL, NCBI_GENOME, NPOS, NStr::ReplaceInPlace(), and CDeflineGenerator::x_IsComplete().

Referenced by CDeflineGenerator::GenerateDefline().

Definition at line 1708 of file create_defline.cpp.

References CTextJoiner< num_prealloc, TIn, TOut >::Add(), CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Gene, CTempString::empty(), NStr::EqualNocase(), fFGL_Content, FOR_SELECTED_SEQFEAT_ON_BIOSEQ_HANDLE, GetLabel(), CBioseq_Handle::GetScope(), SAnnotSelector::IncludeFeatType(), CTextJoiner< num_prealloc, TIn, TOut >::Join(), CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_Taxname, NStr::ReplaceInPlace(), CConstRef< C, Locker >::Reset(), SAnnotSelector::SetFeatType(), SAnnotSelector::SetResolveTSE(), SWITCH_ON_FEATURE_CHOICE, and x_FlyCG_PtoR().

Referenced by CDeflineGenerator::GenerateDefline().

Definition at line 1817 of file create_defline.cpp.

References CTextJoiner< num_prealloc, TIn, TOut >::Add(), NStr::IntToString(), CTextJoiner< num_prealloc, TIn, TOut >::Join(), CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_PatentCountry, CDeflineGenerator::m_PatentNumber, and CDeflineGenerator::m_PatentSequence.

Referenced by CDeflineGenerator::GenerateDefline().

Definition at line 1827 of file create_defline.cpp.

References CTextJoiner< num_prealloc, TIn, TOut >::Add(), CTempString::find_first_not_of(), isprint(), CTextJoiner< num_prealloc, TIn, TOut >::Join(), CTempString::length(), CDeflineGenerator::m_Comment, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_PDBChain, CDeflineGenerator::m_PDBChainID, CDeflineGenerator::m_PDBCompound, CDeflineGenerator::m_UsePDBCompoundForDefline, and CTempString::substr().

Referenced by CDeflineGenerator::GenerateDefline().

Definition at line 2388 of file create_defline.cpp.

References delta(), CTempString::empty(), NStr::EqualNocase(), CTempString::find(), NStr::FindNoCase(), FOR_EACH_ACTIVITY_ON_PROT, FOR_EACH_NAME_ON_PROT, FOR_EACH_SYNONYM_ON_GENE, CSeq_feat_Base::GetData(), CGene_ref_Base::GetDesc(), CProt_ref_Base::GetDesc(), CGene_ref_Base::GetLocus(), CGene_ref_Base::GetLocus_tag(), GetMappedCDSForProduct(), CMappedFeat::GetOriginalFeature(), CSeqFeatData_Base::GetProt(), CBioSource::GetTaxname(), CGene_ref_Base::IsSetDesc(), CProt_ref_Base::IsSetDesc(), CGene_ref_Base::IsSetLocus(), CGene_ref_Base::IsSetLocus_tag(), CBioSource::IsSetTaxname(), CDeflineGenerator::m_AllProtNames, CDeflineGenerator::m_FirstSuperKingdom, CDeflineGenerator::m_Genome, CDeflineGenerator::m_IsCrossKingdom, CDeflineGenerator::m_LocalAnnotsOnly, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_OmitTaxonomicName, CDeflineGenerator::m_SecondSuperKingdom, CDeflineGenerator::m_Taxname, NCBI_GENOME, CConstRef< C, Locker >::NotEmpty(), NPOS, offset, prot, s_proteinOrganellePrefix, s_RemoveBracketedOrgFromEnd(), NStr::StartsWith(), str(), string, tmp, CDeflineGenerator::x_CDShasLowQualityException(), CDeflineGenerator::x_GetGeneRefViaCDS(), CDeflineGenerator::x_GetLongestProtein(), x_GetSourceFeatViaCDS(), and CDeflineGenerator::x_IsComplete().

Referenced by CDeflineGenerator::GenerateDefline().

Definition at line 2175 of file create_defline.cpp.

References delta(), CTempString::empty(), NStr::EqualNocase(), CTempString::find(), NStr::FindNoCase(), FOR_EACH_ACTIVITY_ON_PROT, FOR_EACH_NAME_ON_PROT, FOR_EACH_SYNONYM_ON_GENE, CFeatureIndex::GetBestGene(), CBioseqIndex::GetBestProteinFeature(), CSeqEntryIndex::GetBioseqIndex(), CSeq_feat_Handle::GetData(), CGene_ref_Base::GetDesc(), CProt_ref_Base::GetDesc(), CBioseqIndex::GetFeatureForProduct(), CSeqFeatData_Base::GetGene(), CGene_ref_Base::GetLocus(), CGene_ref_Base::GetLocus_tag(), CFeatureIndex::GetMappedFeat(), CMappedFeat::GetOriginalFeature(), CSeqFeatData_Base::GetProt(), CBioSource::GetTaxname(), CGene_ref_Base::IsSetDesc(), CProt_ref_Base::IsSetDesc(), CGene_ref_Base::IsSetLocus(), CGene_ref_Base::IsSetLocus_tag(), CBioSource::IsSetTaxname(), CDeflineGenerator::m_AllProtNames, CDeflineGenerator::m_FirstSuperKingdom, CDeflineGenerator::m_Genome, CDeflineGenerator::m_Idx, CDeflineGenerator::m_IsCrossKingdom, CDeflineGenerator::m_LocalAnnotsOnly, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_OmitTaxonomicName, CDeflineGenerator::m_SecondSuperKingdom, CDeflineGenerator::m_Taxname, NCBI_GENOME, CConstRef< C, Locker >::NotEmpty(), NPOS, offset, prot, s_proteinOrganellePrefix, s_RemoveBracketedOrgFromEnd(), NStr::StartsWith(), str(), string, tmp, CDeflineGenerator::x_CDShasLowQualityException(), x_GetSourceFeatViaCDS(), and CDeflineGenerator::x_IsComplete().

Referenced by CDeflineGenerator::GenerateDefline().

Definition at line 2648 of file create_defline.cpp.

References CDefLineJoiner::Add(), eHideType, CTempString::empty(), ITERATE, CDefLineJoiner::Join(), CDeflineGenerator::m_Clone, CDeflineGenerator::m_Isolate, CDeflineGenerator::m_LocalAnnotsOnly, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_Strain, CDeflineGenerator::m_Taxname, s_EndsWithStrain(), string, NStr::TruncateSpacesInPlace(), CDeflineGenerator::x_DescribeClones(), and x_GetSegSeqInfoViaCDS().

Referenced by CDeflineGenerator::GenerateDefline().

Definition at line 2696 of file create_defline.cpp.

References CDefLineJoiner::Add(), eHideType, CTempString::empty(), CTempString::find(), ITERATE, CDefLineJoiner::Join(), CDeflineGenerator::m_Breed, CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_Clone, CDeflineGenerator::m_Cultivar, CDeflineGenerator::m_GeneralId, CDeflineGenerator::m_GeneralStr, CDeflineGenerator::m_Genome, CDeflineGenerator::m_Isolate, CDeflineGenerator::m_IsWGS, CDeflineGenerator::m_LinkageGroup, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_Map, CDeflineGenerator::m_Plasmid, CDeflineGenerator::m_SpecimenVoucher, CDeflineGenerator::m_Strain, CDeflineGenerator::m_Substrain, CDeflineGenerator::m_Taxname, CDeflineGenerator::m_Topology, NCBI_GENOME, NCBI_SEQTOPOLOGY, NStr::NumericToString(), s_AddVoucherAndIsolate(), s_EndsWithStrain(), CTempString::substr(), tmp, NStr::TruncateSpacesInPlace(), and CDeflineGenerator::x_DescribeClones().

Referenced by CDeflineGenerator::GenerateDefline().

Definition at line 701 of file seq_trimmer.cpp.

References CInt_fuzz_Base::eLim_unk, CSeq_inst_Base::eRepr_raw, CSeq_inst_Base::eRepr_virtual, CSeqMap::eSeqData, CSeqMap::eSeqGap, eType, CSeqVector::GetCoding(), CBioseq_Handle::GetEditHandle(), CSeqMap_CI::GetEndPosition(), CBioseq_Handle::GetInst(), CSeqMap_CI::GetLength(), CSeqVector::GetPackedSeqData(), CSeqMap_CI::GetPosition(), CSeqMap_CI::GetRefGapLiteral(), CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeqMap(), CSeqMap_CI::GetType(), CSeqMap_CI::IsUnknownLength(), NCBI_USER_THROW_FMT, Ref(), CSeq_inst_Base::ResetExt(), CSeq_inst_Base::ResetSeq_data(), CSeqMap::ResolvedRangeIterator(), CAutoInitRef< T >::Set(), CSeq_inst_Base::SetExt(), CBioseq_EditHandle::SetInst(), CSeq_inst_Base::SetLength(), CSeq_inst_Base::SetRepr(), and CSeq_inst_Base::SetSeq_data().

Referenced by CSequenceAmbigTrimmer::DoTrim().

The bioseq is trimmed to size 0.

Parameters

bioseq_handle The bioseq to trim to nothing.

Returns

Works just like the DoTrim return value.

Definition at line 340 of file seq_trimmer.cpp.

References CSeq_inst_Base::eRepr_virtual, CSequenceAmbigTrimmer::eResult_NoTrimNeeded, CSequenceAmbigTrimmer::eResult_SuccessfullyTrimmed, CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetEditHandle(), CBioseq_Handle::GetInst(), CSeq_inst_Base::ResetExt(), CSeq_inst_Base::ResetSeq_data(), SerialClone(), CBioseq_EditHandle::SetInst(), CSeq_inst_Base::SetLength(), and CSeq_inst_Base::SetRepr().

Referenced by CSequenceAmbigTrimmer::DoTrim().

Definition at line 2875 of file sequence.cpp.

References CFastaOstream::fEnableGI, CFastaOstream::fShowGnlAndAcc, CTextseq_id_Base::GetAccession(), CSeq_id::GetTextseq_Id(), CTextseq_id_Base::GetVersion(), CSeq_id_Base::IsGi(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetVersion(), CFastaOstream::m_Flags, CFastaOstream::m_Out, CConstRef< C, Locker >::NotEmpty(), s_WriteGnlAndAcc(), CSeq_id::WriteAsFasta(), and CFastaOstream::x_GetBestId().

Definition at line 2927 of file sequence.cpp.

References CFastaOstream::fNoDupCheck, CFastaOstream::fSuppressRange, CSeq_id_Handle::GetHandle(), CBioseq_Base::GetId(), set< Key, Compare >::insert(), ITERATE, location, CFastaOstream::m_Flags, CFastaOstream::m_PreviousWholeIds, NCBI_THROW, and NULL.

Referenced by CFastaOstream::Write().

Definition at line 3164 of file sequence.cpp.

References _ASSERT, CTempString::assign(), map_checker< Container >::begin(), count, CTempString::data(), CFastaOstream::eGM_count, CFastaOstream::eGM_dashes, CFastaOstream::eGM_letters, CFastaOstream::eGM_one_dash, CFastaOstream::eHardMask, map_checker< Container >::end(), CSeqMap::eSeqGap, CFastaOstream::eSoftMask, FIELD_IS_SET_AND_IS, CFastaOstream::fInstantiateGaps, CFastaOstream::fKeepUnknGapNomLen, CFastaOstream::fReverseStrand, CFastaOstream::fShowGapModifiers, CFastaOstream::fShowGapsOfSizeZero, AutoPtr< X, Del >::get(), CSeqVector_CI::GetBufferPtr(), CSeqVector_CI::GetBufferSize(), CSeqVector_CI::GetCurrentSeqMap_CI(), CSeqVector::GetGapChar(), CFastaOstream::GetGapModText(), CSeqVector_CI::GetGapSizeForward(), CSeqVector_CI::GetPos(), CSeqMap_CI::GetRefGapLiteral(), CSeqVector_CI::GetStrand(), CSeqMap_CI::GetType(), CSeqVector_CI::HasZeroGapBefore(), CSeqVector::IsProtein(), CSeqMap_CI::IsUnknownLength(), CFastaOstream::m_Dashes, CFastaOstream::m_Flags, CFastaOstream::m_GapMode, CFastaOstream::m_LC_Ns, CFastaOstream::m_LC_Xs, CFastaOstream::m_Out, CFastaOstream::m_UC_Ns, CFastaOstream::m_UC_Xs, CFastaOstream::m_Width, max(), min(), Reverse(), CSeqVector_CI::SetPos(), CSeqVector_CI::SetStrand(), CSeqVector_CI::SkipGap(), NStr::ToLower(), CFastaOstream::SGapModText::WriteAllModsAsFasta(), and CFastaOstream::x_WriteBuffer().

Referenced by CFastaOstream::Write(), and CFastaOstream::WriteSequence().

Definition at line 359 of file sequence.hpp.

Do-nothing destructor just to allow inheritance.

Definition at line 1348 of file sequence.hpp.

Definition at line 1205 of file sequence.hpp.

subsource fields

Definition at line 330 of file create_defline.hpp.

Referenced by CDeflineGenerator::x_GetModifiers(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetBioSrcIdx(), CDeflineGenerator::x_SetFlags(), CDeflineGenerator::x_SetFlagsIdx(), CDeflineGenerator::x_SetSuffix(), CDeflineGenerator::x_SetTitleFromBioSrc(), CDeflineGenerator::x_SetTitleFromGPipe(), CDeflineGenerator::x_SetTitleFromMap(), CDeflineGenerator::x_SetTitleFromNC(), and CDeflineGenerator::x_SetTitleFromWGS().

This holds the current interpretation for "ambiguous".

For example, it indicates whether just 'N' is ambiguous or if any non-ACGT letter is ambiguous. Works for amino acids, too (e.g. 'X' for completely unknown, etc.)

Definition at line 1380 of file sequence.hpp.

Referenced by CSequenceAmbigTrimmer::CSequenceAmbigTrimmer().

Definition at line 895 of file sequence.hpp.

Definition at line 319 of file create_defline.hpp.

Referenced by CDeflineGenerator::x_AdjustProteinTitleSuffix(), CDeflineGenerator::x_AdjustProteinTitleSuffixIdx(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetBioSrcIdx(), CDeflineGenerator::x_SetFlags(), CDeflineGenerator::x_SetFlagsIdx(), CDeflineGenerator::x_SetSuffix(), CDeflineGenerator::x_SetTitleFromNC(), CDeflineGenerator::x_SetTitleFromProtein(), CDeflineGenerator::x_SetTitleFromProteinIdx(), and CDeflineGenerator::x_SetTitleFromWGS().

Definition at line 276 of file create_defline.hpp.

Referenced by CDeflineGenerator::GenerateDefline(), CDeflineGenerator::x_AdjustProteinTitleSuffix(), CDeflineGenerator::x_AdjustProteinTitleSuffixIdx(), CDeflineGenerator::x_GetModifiers(), CDeflineGenerator::x_SetFlags(), CDeflineGenerator::x_SetFlagsIdx(), CDeflineGenerator::x_SetPrefix(), CDeflineGenerator::x_SetSuffix(), CDeflineGenerator::x_SetTitleFromBioSrc(), CDeflineGenerator::x_SetTitleFromGPipe(), CDeflineGenerator::x_SetTitleFromMap(), CDeflineGenerator::x_SetTitleFromNC(), CDeflineGenerator::x_SetTitleFromNM(), CDeflineGenerator::x_SetTitleFromNR(), CDeflineGenerator::x_SetTitleFromPatent(), CDeflineGenerator::x_SetTitleFromPDB(), CDeflineGenerator::x_SetTitleFromProtein(), CDeflineGenerator::x_SetTitleFromProteinIdx(), CDeflineGenerator::x_SetTitleFromSegSeq(), and CDeflineGenerator::x_SetTitleFromWGS().

Definition at line 335 of file create_defline.hpp.

Referenced by CDeflineGenerator::x_GetModifiers(), CDeflineGenerator::x_OrganelleName(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetBioSrcIdx(), CDeflineGenerator::x_SetFlags(), CDeflineGenerator::x_SetFlagsIdx(), CDeflineGenerator::x_SetTitleFromBioSrc(), CDeflineGenerator::x_SetTitleFromGPipe(), CDeflineGenerator::x_SetTitleFromMap(), CDeflineGenerator::x_SetTitleFromNC(), and CDeflineGenerator::x_SetTitleFromWGS().

Definition at line 315 of file create_defline.hpp.

Referenced by CDeflineGenerator::x_AdjustProteinTitleSuffix(), CDeflineGenerator::x_AdjustProteinTitleSuffixIdx(), CDeflineGenerator::x_OrganelleName(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetBioSrcIdx(), CDeflineGenerator::x_SetFlags(), CDeflineGenerator::x_SetFlagsIdx(), CDeflineGenerator::x_SetTitleFromBioSrc(), CDeflineGenerator::x_SetTitleFromGPipe(), CDeflineGenerator::x_SetTitleFromMap(), CDeflineGenerator::x_SetTitleFromNC(), CDeflineGenerator::x_SetTitleFromNM(), CDeflineGenerator::x_SetTitleFromNR(), CDeflineGenerator::x_SetTitleFromProtein(), CDeflineGenerator::x_SetTitleFromProteinIdx(), CDeflineGenerator::x_SetTitleFromSegSeq(), and CDeflineGenerator::x_SetTitleFromWGS().

how many gaps we've seen so far on this sequence.

For example, 2 would mean we're currently on the second relevant gap on this sequence.

Definition at line 1650 of file sequence.hpp.

Referenced by CBioseqGaps_CI::x_Next().

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