NCBI C++ ToolKit
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Search Toolkit Book for CGff3FlybaseWriter
#include <objtools/writers/gff3flybase_writer.hpp>
Public Member Functions | |
CGff3FlybaseWriter (objects::CScope &scope, CNcbiOstream &ostr, bool sortAlignments=false) | |
virtual bool | WriteHeader () override |
Protected Attributes | |
map< string, string > | mTaxidMap |
map< string, string > | mDeflineMap |
string | mCurrentIdForAttributes |
Definition at line 41 of file gff3flybase_writer.hpp.
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inline |
Definition at line 45 of file gff3flybase_writer.hpp.
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overridevirtual |
Definition at line 170 of file gff3flybase_writer.cpp.
Referenced by sRunTest(), and sUpdateCase().
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overrideprotectedvirtual |
Definition at line 604 of file gff3flybase_writer.cpp.
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overrideprotectedvirtual |
Definition at line 431 of file gff3flybase_writer.cpp.
References eNa_strand_minus, eNa_strand_plus, CAlnMap::GetSeqStart(), CAlnMap::GetSeqStop(), CGffBaseRecord::SetLocation(), and CAlnMap::StrandSign().
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overrideprotectedvirtual |
Definition at line 447 of file gff3flybase_writer.cpp.
References CAlnMap::GetDenseg(), CScore_Base::GetId(), CDense_seg_Base::GetScores(), CObject_id_Base::GetStr(), CScore_Base::IsSetId(), CDense_seg_Base::IsSetScores(), CObject_id_Base::IsStr(), ncbi::grid::netcache::search::fields::key, CGffBaseRecord::SetScore(), CGffBaseRecord::StrSeqId(), and xIsNeededScore().
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overrideprotectedvirtual |
Definition at line 347 of file gff3flybase_writer.cpp.
References CSeq_id::eContent, eGetId_ForceAcc, GetId(), CSeq_id::GetLabel(), CBioseq_Handle::GetSeq_id_Handle(), CAlnMap::GetSeqId(), CSeq_id_Handle::GetSeqId(), and CGffBaseRecord::SetSeqId().
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overrideprotectedvirtual |
Definition at line 373 of file gff3flybase_writer.cpp.
References CSeq_id::eContent, eGetId_ForceAcc, eNa_strand_minus, eNa_strand_plus, CSeq_id::fAcc_prot, GetId(), CSeq_id::GetLabel(), CAlnMap::GetLen(), CAlnMap::GetNumSegs(), CBioseq_Handle::GetSeq_id_Handle(), CAlnMap::GetSeqId(), CSeq_id_Handle::GetSeqId(), CAlnMap::GetStart(), CSeq_id::IdentifyAccession(), NStr::IntToString(), CGffBaseRecord::SetAttribute(), CAlnMap::StrandSign(), string, and swap().
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overrideprotectedvirtual |
Definition at line 318 of file gff3flybase_writer.cpp.
References CSeq_id_Handle::GetHandle(), CSeq_align_Base::GetScore(), CSeq_align_Base::IsSetScore(), mCurrentIdForAttributes, CGffBaseRecord::SetScore(), CGffBaseRecord::StrSeqId(), xAssignDefline(), xAssignTaxid(), and xIsNeededScore().
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overrideprotectedvirtual |
Definition at line 474 of file gff3flybase_writer.cpp.
References CGffAlignRecord::AddDeletion(), CGffAlignRecord::AddForwardShift(), CGffAlignRecord::AddInsertion(), CGffAlignRecord::AddMatch(), CGffAlignRecord::AddReverseShift(), CSpliced_exon_chunk_Base::e_Diag, CSpliced_exon_chunk_Base::e_Genomic_ins, CSpliced_exon_chunk_Base::e_Match, CSpliced_exon_chunk_Base::e_Mismatch, CSpliced_exon_chunk_Base::e_Product_ins, CGffAlignRecord::FinalizeMatches(), CSpliced_exon_chunk_Base::GetDiag(), CSpliced_exon_chunk_Base::GetGenomic_ins(), CSpliced_exon_chunk_Base::GetMatch(), CSpliced_exon_chunk_Base::GetMismatch(), CSpliced_exon_Base::GetParts(), CSpliced_exon_chunk_Base::GetProduct_ins(), and CSpliced_exon_chunk_Base::Which().
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overrideprotectedvirtual |
Definition at line 200 of file gff3flybase_writer.cpp.
References CProduct_pos::AsSeqPos(), CSpliced_seg_Base::CanGetProduct_strand(), eNa_strand_minus, eNa_strand_plus, CProt_pos::GetFrame(), CSpliced_exon_Base::GetProduct_end(), CSpliced_exon_Base::GetProduct_start(), CSpliced_seg_Base::GetProduct_strand(), CProduct_pos_Base::GetProtpos(), CProduct_pos_Base::IsProtpos(), CProt_pos_Base::IsSetFrame(), CGffBaseRecord::SetLocation(), and CGffBaseRecord::SetPhase().
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overrideprotectedvirtual |
Definition at line 292 of file gff3flybase_writer.cpp.
References CScore_set_Base::Get(), CScore_Base::GetId(), CSpliced_exon_Base::GetScores(), CObject_id_Base::GetStr(), CScore_Base::IsSetId(), CSpliced_exon_Base::IsSetScores(), CObject_id_Base::IsStr(), ncbi::grid::netcache::search::fields::key, CGffBaseRecord::SetScore(), CGffBaseRecord::StrSeqId(), and xIsNeededScore().
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overrideprotectedvirtual |
Definition at line 276 of file gff3flybase_writer.cpp.
References CSeq_id::eContent, eGetId_Best, GetId(), CSeq_id::GetLabel(), CSpliced_seg_Base::GetProduct_id(), CSeq_id_Handle::GetSeqId(), and CGffBaseRecord::SetSeqId().
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overrideprotectedvirtual |
Definition at line 242 of file gff3flybase_writer.cpp.
References CSeq_id::eContent, eGetId_Best, eNa_strand_minus, CSpliced_exon_Base::GetGenomic_end(), CSpliced_seg_Base::GetGenomic_id(), CSpliced_exon_Base::GetGenomic_start(), CSpliced_seg_Base::GetGenomic_strand(), GetId(), CSeq_id::GetLabel(), CSeq_id_Handle::GetSeqId(), NStr::IntToString(), CSpliced_seg_Base::IsSetGenomic_strand(), and CGffBaseRecord::SetAttribute().
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protected |
Definition at line 149 of file gff3flybase_writer.cpp.
References map_checker< Container >::end(), map_checker< Container >::find(), mDeflineMap, CGffBaseRecord::SetAttribute(), and CGffBaseRecord::StrSeqId().
Referenced by xAssignAlignmentScores().
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Definition at line 97 of file gff3flybase_writer.cpp.
References CObject_id_Base::e_Id, CSeqdesc_Base::e_Source, CObject_id_Base::e_Str, map_checker< Container >::end(), map_checker< Container >::find(), COrg_ref_Base::GetDb(), CBioSource_Base::GetOrg(), NStr::IntToString(), COrg_ref_Base::IsSetDb(), CBioSource_Base::IsSetOrg(), mTaxidMap, CGffBaseRecord::SetAttribute(), CGffBaseRecord::StrSeqId(), and tag.
Referenced by xAssignAlignmentScores().
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protected |
Definition at line 67 of file gff3flybase_writer.cpp.
References ncbi::grid::netcache::search::fields::key.
Referenced by xAssignAlignmentDensegScores(), xAssignAlignmentScores(), and xAssignAlignmentSplicedScores().
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overrideprotectedvirtual |
Definition at line 187 of file gff3flybase_writer.cpp.
References CGff3Writer::xWriteAlignDisc().
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protected |
Definition at line 126 of file gff3flybase_writer.hpp.
Referenced by xAssignAlignmentScores().
Definition at line 125 of file gff3flybase_writer.hpp.
Referenced by xAssignDefline().
Definition at line 124 of file gff3flybase_writer.hpp.
Referenced by xAssignTaxid().