NCBI C++ ToolKit
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Search Toolkit Book for CFastaOstreamEx
#include <objtools/writers/fasta_writer.hpp>
Public Member Functions | |
CFastaOstreamEx (CNcbiOstream &out) | |
virtual | ~CFastaOstreamEx ()=default |
bool | WriteFeatures (CFeat_CI feat_it, bool translate_cds) |
void | WriteFeature (const CSeq_feat &feat, CScope &scope, bool translate_cds=false) |
void | WriteFeatureTitle (const CSeq_feat &feat, CScope &scope, bool translate_cds=false) |
void | ResetFeatureCount (void) |
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virtual | ~CFeatWriter (void)=default |
bool | WriteFeatures (CFeat_CI &first) |
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CInterruptable () | |
virtual | ~CInterruptable () |
void | SetCanceler (ICanceled *pCanceller) |
bool | IsCanceled () const |
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virtual | ~ICanceled () |
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CFastaOstream (CNcbiOstream &out) | |
virtual | ~CFastaOstream () |
virtual void | Write (const CSeq_entry_Handle &handle, const CSeq_loc *location=0) |
Unspecified locations designate complete sequences; non-empty custom titles override the usual title determination logic. More... | |
virtual void | Write (const CBioseq_Handle &handle, const CSeq_loc *location=0, const string &custom_title=kEmptyStr) |
virtual void | WriteTitle (const CBioseq_Handle &handle, const CSeq_loc *location=0, const string &custom_title=kEmptyStr) |
virtual void | WriteSequence (const CBioseq_Handle &handle, const CSeq_loc *location=0, CSeq_loc::EOpFlags merge_flags=CSeq_loc::fMerge_AbuttingOnly) |
void | Write (const CSeq_entry &entry, const CSeq_loc *location=0, bool no_scope=false) |
These versions may set up a temporary object manager scope In the common case of a raw bioseq, no scope is needed. More... | |
void | Write (const CBioseq &seq, const CSeq_loc *location=0, bool no_scope=false, const string &custom_title=kEmptyStr) |
void | WriteTitle (const CBioseq &seq, const CSeq_loc *location=0, bool no_scope=false, const string &custom_title=kEmptyStr) |
virtual bool | SkipBioseq (const CBioseq &) |
Used only by Write(CSeq_entry[_Handle], ...); permissive by default. More... | |
virtual bool | SkipBioseq (const CBioseq_Handle &handle) |
Delegates to the non-handle version by default for compatibility with older code; newer code should override this version. More... | |
CConstRef< CSeq_loc > | GetMask (EMaskType type) const |
void | SetMask (EMaskType type, CConstRef< CSeq_loc > location) |
TSeqPos | GetWidth (void) const |
Other parameters... More... | |
void | SetWidth (TSeqPos width) |
TFlags | GetAllFlags (void) const |
void | SetAllFlags (TFlags flags) |
void | SetFlag (EFlags flag) |
void | ResetFlag (EFlags flag) |
void | SetGapMode (EGapMode mode) |
EGapMode | GetGapMode (void) const |
Protected Attributes | |
bool | m_TranslateCds |
TSeqPos | m_FeatCount |
CRef< CScope > | m_InternalScope |
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ICanceled * | mpCancelled |
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CNcbiOstream & | m_Out |
unique_ptr< sequence::CDeflineGenerator > | m_Gen |
TFlags | m_Flags |
Additional Inherited Members | |
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enum | EFlags : long { fAssembleParts = 1 << 0 , fInstantiateGaps = 1 << 1 , fSuppressRange = 1 << 2 , fReverseStrand = 1 << 3 , fKeepGTSigns = 1 << 4 , fMapMasksUp = 1 << 5 , fMapMasksDown = 1 << 6 , fNoExpensiveOps = 1 << 7 , fShowModifiers = 1 << 8 , fNoDupCheck = 1 << 9 , fShowGapModifiers = 1 << 10 , fKeepUnknGapNomLen = 1 << 11 , fShowGapsOfSizeZero = 1 << 12 , fEnableGI = 1 << 13 , fHideGenBankPrefix = 1 << 14 , fHTMLEncode = 1 << 15 , fIgnoreOriginalID = 1 << 16 , eAssembleParts = fAssembleParts , eInstantiateGaps = fInstantiateGaps , fUseAutoDef = 1 << 17 , fBaseFirstUnused = 1 << 18 , fDoNotUseAutoDef = 1 << 19 , fShowGnlAndAcc = 1 << 20 } |
enum | EGapMode { eGM_one_dash , eGM_dashes , eGM_letters , eGM_count } |
How to represent gaps with fInstantiateGaps enabled, as it is by default. More... | |
enum | EMaskType { eSoftMask = 1 , eHardMask = 2 } |
Which residues to mask out in subsequent output. More... | |
typedef long | TFlags |
binary OR of EFlags More... | |
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static void | GetGapModText (const CSeq_gap &seq_gap, SGapModText &out_gap_mod_text) |
Given a CSeq_gap object, this outputs the Gap information. More... | |
Definition at line 50 of file fasta_writer.hpp.
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Definition at line 67 of file fasta_writer.cpp.
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void CFastaOstreamEx::ResetFeatureCount | ( | void | ) |
Definition at line 76 of file fasta_writer.cpp.
References m_FeatCount.
void CFastaOstreamEx::WriteFeature | ( | const CSeq_feat & | feat, |
CScope & | scope, | ||
bool | translate_cds = false |
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Definition at line 121 of file fasta_writer.cpp.
References ERR_POST, CSeq_loc::fMerge_AbuttingOnly, CScope::GetBioseqHandle(), CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), CSeq_loc::GetId(), CSeq_feat_Base::GetLocation(), CSeqFeatData_Base::IsCdregion(), CSeq_feat_Base::IsSetData(), NCBI_THROW, s_LocationSpansMultipleSeqs(), Warning(), CFastaOstream::WriteSequence(), x_TrimLocation(), x_WriteTranslatedCds(), and xWriteFeatureTitle().
Referenced by CAsn2FastaApp::HandleSeqEntry(), and xWriteFeature().
Definition at line 82 of file fasta_writer.cpp.
References m_TranslateCds, and CFeatWriter::WriteFeatures().
void CFastaOstreamEx::WriteFeatureTitle | ( | const CSeq_feat & | feat, |
CScope & | scope, | ||
bool | translate_cds = false |
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Definition at line 174 of file fasta_writer.cpp.
References xWriteFeatureTitle().
Referenced by CAsn2FastaApp::HandleSeqEntry().
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Definition at line 689 of file fasta_writer.cpp.
References CSeq_feat_Base::GetData(), CDbtag_Base::GetDb(), CSeq_feat_Base::GetDbxref(), CObject_id_Base::GetId(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), CSeqFeatData_Base::IsGene(), CObject_id_Base::IsId(), CSeq_feat_Base::IsSetData(), CDbtag_Base::IsSetDb(), CSeq_feat_Base::IsSetDbxref(), CDbtag_Base::IsSetTag(), s_GetBestGeneForFeat(), and x_AddDeflineAttribute().
Referenced by x_WriteFeatureAttributes().
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Definition at line 548 of file fasta_writer.cpp.
References NStr::IsBlank(), label, and rapidjson::value.
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Definition at line 537 of file fasta_writer.cpp.
References NStr::IsBlank(), label, and rapidjson::value.
Referenced by x_AddDbxrefAttribute(), x_AddExceptionAttribute(), x_AddGBkeyAttribute(), x_AddGeneAttributes(), x_AddLocationAttribute(), x_AddMiscQualifierAttributes(), x_AddncRNAClassAttribute(), x_AddPartialAttribute(), x_AddProteinIdAttribute(), x_AddProteinNameAttribute(), x_AddPseudoAttribute(), x_AddPseudoGeneAttribute(), x_AddReadingFrameAttribute(), x_AddRNAProductAttribute(), x_AddTranscriptIdAttribute(), and x_AddTranslationExceptionAttribute().
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Definition at line 904 of file fasta_writer.cpp.
References CSeq_feat_Base::GetExcept_text(), CSeq_feat_Base::IsSetExcept_text(), and x_AddDeflineAttribute().
Referenced by x_WriteFeatureAttributes().
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Definition at line 652 of file fasta_writer.cpp.
References CSeq_feat_Base::GetData(), CSeqFeatData::GetKey(), NStr::IsBlank(), CSeq_feat_Base::IsSetData(), and x_AddDeflineAttribute().
Referenced by x_WriteFeatureAttributes().
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Definition at line 559 of file fasta_writer.cpp.
References CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetGene(), CSeqFeatData_Base::IsGene(), CSeq_feat_Base::IsSetData(), Ref(), s_GetBestGeneForFeat(), and x_AddDeflineAttribute().
Referenced by x_WriteFeatureAttributes().
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Definition at line 947 of file fasta_writer.cpp.
References CScope::GetBioseqHandle(), CSeq_feat_Base::GetLocation(), CFlatSeqLoc::GetString(), and x_AddDeflineAttribute().
Referenced by x_WriteFeatureAttributes().
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Definition at line 626 of file fasta_writer.cpp.
References CSeq_feat::GetNamedQual(), CSeq_feat_Base::IsSetData(), rapidjson::value, and x_AddDeflineAttribute().
Referenced by x_WriteFeatureAttributes().
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Definition at line 966 of file fasta_writer.cpp.
References CRNA_gen_Base::GetClass(), CSeq_feat_Base::GetData(), CRNA_ref_Base::GetExt(), CRNA_ref_Base::C_Ext::GetGen(), CSeqFeatData_Base::GetRna(), CRNA_ref_Base::C_Ext::IsGen(), CSeqFeatData_Base::IsRna(), CRNA_gen_Base::IsSetClass(), CSeq_feat_Base::IsSetData(), CRNA_ref_Base::IsSetExt(), and x_AddDeflineAttribute().
Referenced by x_WriteFeatureAttributes().
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Definition at line 787 of file fasta_writer.cpp.
References eSeqlocPartial_Nostart, eSeqlocPartial_Nostop, CSeq_feat_Base::GetLocation(), SeqLocPartialCheck(), and x_AddDeflineAttribute().
Referenced by x_WriteFeatureAttributes().
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Definition at line 914 of file fasta_writer.cpp.
References CSeq_feat_Base::GetData(), CSeq_loc::GetId(), CSeq_feat_Base::GetProduct(), CSeqFeatData_Base::IsCdregion(), CSeq_feat_Base::IsSetProduct(), s_GetDeflineIdString(), and x_AddDeflineAttribute().
Referenced by x_WriteFeatureAttributes().
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Definition at line 726 of file fasta_writer.cpp.
References SAnnotSelector::eSortOrder_Normal, CSeqFeatData::eSubtype_prot, CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CSeq_feat_Handle::GetData(), CSeq_loc::GetId(), CProt_ref_Base::GetName(), CSeq_feat_Base::GetProduct(), CSeqFeatData_Base::GetProt(), CSeq_feat::GetProtXref(), CSeqFeatData_Base::IsCdregion(), CSeqFeatData_Base::IsProt(), CSeq_feat_Handle::IsSetData(), CProt_ref_Base::IsSetName(), CSeq_feat_Base::IsSetProduct(), SAnnotSelector::SetExcludeExternal(), SAnnotSelector::SetSortOrder(), and x_AddDeflineAttribute().
Referenced by x_WriteFeatureAttributes().
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Definition at line 594 of file fasta_writer.cpp.
References CSeq_feat_Base::GetPseudo(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetPseudo(), s_GetBestGeneForFeat(), and x_AddDeflineAttribute().
Referenced by x_WriteFeatureAttributes().
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Definition at line 665 of file fasta_writer.cpp.
References CSeqFeatData::eQual_pseudogene, CSeq_feat_Base::GetData(), CSeq_feat::GetNamedQual(), CSeqFeatData::IsLegalQualifier(), CSeq_feat_Base::IsSetData(), s_GetBestGeneForFeat(), and x_AddDeflineAttribute().
Referenced by x_WriteFeatureAttributes().
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Definition at line 770 of file fasta_writer.cpp.
References CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), CSeqFeatData_Base::IsCdregion(), CSeq_feat_Base::IsSetData(), CCdregion_Base::IsSetFrame(), and x_AddDeflineAttribute().
Referenced by x_WriteFeatureAttributes().
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Definition at line 1015 of file fasta_writer.cpp.
References CRNA_ref_Base::eType_tRNA, CRNA_ref_Base::eType_unknown, CSeq_feat_Base::GetData(), CSeq_feat::GetNamedQual(), CSeqFeatData_Base::GetRna(), CWriteUtil::GetTrnaProductName(), CSeqFeatData_Base::IsRna(), CSeq_feat_Base::IsSetData(), rna, and x_AddDeflineAttribute().
Referenced by x_WriteFeatureAttributes().
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Definition at line 928 of file fasta_writer.cpp.
References CSeq_feat_Base::GetData(), CSeq_loc::GetId(), CSeq_feat::GetNamedQual(), CSeq_feat_Base::GetProduct(), CSeqFeatData_Base::IsRna(), CSeq_feat_Base::IsSetProduct(), s_GetDeflineIdString(), and x_AddDeflineAttribute().
Referenced by x_WriteFeatureAttributes().
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Definition at line 876 of file fasta_writer.cpp.
References CSeqFeatData_Base::GetCdregion(), CCdregion_Base::GetCode_break(), CSeq_feat_Base::GetData(), CSeqFeatData_Base::IsCdregion(), CCdregion_Base::IsSetCode_break(), CSeq_feat_Base::IsSetData(), x_AddDeflineAttribute(), and x_GetCodeBreak().
Referenced by x_WriteFeatureAttributes().
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Definition at line 402 of file fasta_writer.cpp.
References CSeq_feat_Base::GetLocation(), NStr::IsBlank(), s_GetDeflineIdString(), and s_GetProductIdOrLocusTag().
Referenced by xWriteFeatureTitle().
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Definition at line 808 of file fasta_writer.cpp.
References CSeq_loc_Base::e_Int, eExtreme_Positional, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, eOffset_FromStart, CWriteUtil::GetAaName(), CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), CSeq_interval_Base::GetFrom(), CSeq_loc_Base::GetInt(), CCode_break_Base::GetLoc(), CSeq_feat_Base::GetLocation(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_interval_Base::GetTo(), NStr::IntToString(), CSeqFeatData_Base::IsCdregion(), CCdregion_Base::IsSetFrame(), CCode_break_Base::IsSetLoc(), LocationOffset(), NCBI_THROW, offset, and CSeq_loc_Base::Which().
Referenced by x_AddTranslationExceptionAttribute().
Definition at line 524 of file fasta_writer.cpp.
References CSeq_feat_Base::GetLocation(), and s_GetDeflineIdString().
Referenced by xWriteFeatureTitle().
Definition at line 422 of file fasta_writer.cpp.
References CSeqFeatData_Base::e_Imp, CSeqFeatData_Base::e_Region, CSeq_inst_Base::eMol_aa, CSeq_feat_Base::GetData(), CSeq_loc::GetId(), CSeq_feat_Base::GetLocation(), CScope::GetSequenceType(), ncbi::grid::netcache::search::fields::key, NStr::ReplaceInPlace(), s_GetDeflineIdString(), and CSeqFeatData_Base::Which().
Referenced by xWriteFeatureTitle().
Definition at line 506 of file fasta_writer.cpp.
References prot, and s_GetDeflineIdString().
Definition at line 463 of file fasta_writer.cpp.
References CRNA_ref_Base::eType_mRNA, CRNA_ref_Base::eType_ncRNA, CRNA_ref_Base::eType_premsg, CRNA_ref_Base::eType_rRNA, CRNA_ref_Base::eType_scRNA, CRNA_ref_Base::eType_snoRNA, CRNA_ref_Base::eType_snRNA, CRNA_ref_Base::eType_tmRNA, CRNA_ref_Base::eType_tRNA, CRNA_ref_Base::eType_unknown, CSeq_feat_Base::GetData(), CSeq_feat_Base::GetLocation(), CSeqFeatData_Base::GetRna(), NStr::IsBlank(), CSeqFeatData_Base::IsRna(), CSeq_feat_Base::IsSetData(), rna, s_GetDeflineIdString(), and s_GetProductIdOrLocusTag().
Referenced by xWriteFeatureTitle().
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Definition at line 218 of file fasta_writer.cpp.
References eExtreme_Biological, eNa_strand_minus, CSeq_loc::fMerge_AbuttingOnly, CSeq_loc::GetId(), CSeq_loc::GetStart(), NCBI_THROW, Ref(), and Seq_loc_Subtract().
Referenced by WriteFeature().
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Reimplemented from CFastaOstream.
Definition at line 1188 of file fasta_writer.cpp.
References count, CInterruptable::IsCanceled(), NCBI_THROW, and CFastaOstream::x_WriteBuffer().
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Definition at line 290 of file fasta_writer.cpp.
References CSeq_feat_Base::IsSetData(), CFastaOstream::m_Out, x_AddDbxrefAttribute(), x_AddExceptionAttribute(), x_AddGBkeyAttribute(), x_AddGeneAttributes(), x_AddLocationAttribute(), x_AddMiscQualifierAttributes(), x_AddncRNAClassAttribute(), x_AddPartialAttribute(), x_AddProteinIdAttribute(), x_AddProteinNameAttribute(), x_AddPseudoAttribute(), x_AddPseudoGeneAttribute(), x_AddReadingFrameAttribute(), x_AddRNAProductAttribute(), x_AddTranscriptIdAttribute(), and x_AddTranslationExceptionAttribute().
Referenced by xWriteFeatureTitle().
Definition at line 254 of file fasta_writer.cpp.
References CScope::AddBioseq(), CRef< C, Locker >::Empty(), CSeq_loc::fMerge_AbuttingOnly, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), GetLength(), CSeq_feat_Base::GetLocation(), CException::GetMsg(), CRef< C, Locker >::GetObject(), CCdregion_Base::IsSetFrame(), m_InternalScope, NCBI_THROW, CSeqTranslator::TranslateToProtein(), CFastaOstream::WriteSequence(), and xWriteFeatureTitle().
Referenced by WriteFeature().
Reimplemented from CFeatWriter.
Definition at line 92 of file fasta_writer.cpp.
References CSeq_feat_Handle::GetScope(), CMappedFeat::GetSeq_feat(), m_TranslateCds, and WriteFeature().
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Definition at line 183 of file fasta_writer.cpp.
References CSeq_feat_Base::GetData(), CSeqFeatData_Base::IsCdregion(), CSeqFeatData_Base::IsGene(), CSeqFeatData_Base::IsRna(), CSeq_feat_Base::IsSetData(), m_FeatCount, CFastaOstream::m_Out, x_GetCDSIdString(), x_GetGeneIdString(), x_GetOtherIdString(), x_GetRNAIdString(), and x_WriteFeatureAttributes().
Referenced by WriteFeature(), WriteFeatureTitle(), and x_WriteTranslatedCds().
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Definition at line 180 of file fasta_writer.hpp.
Referenced by ResetFeatureCount(), and xWriteFeatureTitle().
Definition at line 181 of file fasta_writer.hpp.
Referenced by x_WriteTranslatedCds().
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Definition at line 179 of file fasta_writer.hpp.
Referenced by WriteFeatures(), and xWriteFeature().