NCBI C++ ToolKit
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#include <ncbi_pch.hpp>
#include <sstream>
#include <corelib/ncbistd.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/biblio/Author.hpp>
#include <objects/biblio/Cit_pat.hpp>
#include <objects/general/Person_id.hpp>
#include <objects/seq/Seq_hist_rec.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/error_codes.hpp>
#include <objtools/format/flat_expt.hpp>
#include <objtools/format/genbank_formatter.hpp>
#include <objtools/format/items/locus_item.hpp>
#include <objtools/format/items/defline_item.hpp>
#include <objtools/format/items/accession_item.hpp>
#include <objtools/format/items/ctrl_items.hpp>
#include <objtools/format/items/version_item.hpp>
#include <objtools/format/items/dbsource_item.hpp>
#include <objtools/format/items/segment_item.hpp>
#include <objtools/format/items/keywords_item.hpp>
#include <objtools/format/items/source_item.hpp>
#include <objtools/format/items/reference_item.hpp>
#include <objtools/format/items/comment_item.hpp>
#include <objtools/format/items/feature_item.hpp>
#include <objtools/format/items/basecount_item.hpp>
#include <objtools/format/items/sequence_item.hpp>
#include <objtools/format/items/wgs_item.hpp>
#include <objtools/format/items/tsa_item.hpp>
#include <objtools/format/items/primary_item.hpp>
#include <objtools/format/items/contig_item.hpp>
#include <objtools/format/items/genome_item.hpp>
#include <objtools/format/items/origin_item.hpp>
#include <objtools/format/items/gap_item.hpp>
#include <objtools/format/items/genome_project_item.hpp>
#include <objtools/format/items/html_anchor_item.hpp>
#include <objtools/format/context.hpp>
#include <objtools/format/ostream_text_ostream.hpp>
#include <objmgr/util/objutil.hpp>
#include <algorithm>
#include <stdio.h>
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Classes | |
class | CGenbankFormatterWrapDest |
Macros | |
#define | NCBI_USE_ERRCODE_X Objtools_Fmt_Genbank |
Variables | |
static const TSeqPos | s_kChunkSize = 10 |
static const TSeqPos | s_kChunkCount = 6 |
static const TSeqPos | s_kFullLineSize = s_kChunkSize*s_kChunkCount |
#define NCBI_USE_ERRCODE_X Objtools_Fmt_Genbank |
Definition at line 79 of file genbank_formatter.cpp.
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Definition at line 1767 of file genbank_formatter.cpp.
References CSeqVector_CI::GetBufferSize(), CSeqVector_CI::GetGapSizeBackward(), CSeqVector_CI::GetPos(), CSeqVector_CI::IsInGap(), s_kFullLineSize, and CSeqVector_CI::SkipGap().
Referenced by CGenbankFormatter::FormatSequence().
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Definition at line 1298 of file genbank_formatter.cpp.
References NStr::eTrunc_End, indent(), l(), NStr::TruncateSpaces(), and NStr::TruncateSpacesInPlace().
Referenced by CGenbankFormatter::FormatComment().
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Definition at line 1811 of file genbank_formatter.cpp.
References IFlatTextOStream::AddLine(), CBioseqContext::Config(), copy(), CFlatFileConfig::DoHTML(), CBioseqContext::GetAccession(), CFlatItem::GetContext(), CFlatItem::GetObject(), i, int, s_FormatSeqPosBack(), s_FormatSeqSpanTag(), s_kChunkCount, s_kChunkSize, s_kFullLineSize, and CFlatFileConfig::ShowSeqSpans().
Referenced by CGenbankFormatter::FormatSequence().
Definition at line 1732 of file genbank_formatter.cpp.
References l().
Referenced by s_FormatRegularSequencePiece().
Definition at line 1746 of file genbank_formatter.cpp.
Referenced by s_FormatRegularSequencePiece().
Definition at line 847 of file genbank_formatter.cpp.
References NStr::FindNoCase(), NPOS, NStr::Replace(), and NStr::ReplaceInPlace().
Referenced by CGenbankFormatter::FormatComment(), and CGenbankFormatter::x_Remark().
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Definition at line 286 of file genbank_formatter.cpp.
Referenced by CGenbankFormatter::EndSection(), and CGenbankFormatter::FormatHtmlAnchor().
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Definition at line 274 of file genbank_formatter.cpp.
Referenced by CGenbankFormatter::x_GetFeatureSpanAndScriptStart().
bool s_GetFeatureKeyLinkLocation | ( | const CMappedFeat & | feat, |
TGi & | iGi, | ||
unsigned int & | iFrom, | ||
unsigned int & | iTo | ||
) |
Definition at line 1427 of file genbank_formatter.cpp.
References eExtreme_Positional, CScope::GetBioseqHandle(), CSeq_id_Handle::GetGi(), CMappedFeat::GetLocation(), CSeq_feat_Handle::GetScope(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_id_Handle::IsGi(), ITERATE, and ZERO_GI.
Referenced by s_GetLinkFeatureKey().
string s_GetLinkCambiaPatentLens | ( | const CReferenceItem & | ref, |
bool | bHtml | ||
) |
Definition at line 758 of file genbank_formatter.cpp.
References CCit_pat_Base::CanGetCountry(), CCit_pat_Base::CanGetNumber(), CCit_pat_Base::GetCountry(), CCit_pat_Base::GetNumber(), CReferenceItem::GetPatent(), CReferenceItem::IsSetPatent(), and string.
Referenced by CGenbankFormatter::x_Remark().
string s_GetLinkFeature | ( | const CReferenceItem & | ref, |
bool | bHtml | ||
) |
Definition at line 794 of file genbank_formatter.cpp.
bool s_GetLinkFeatureKey | ( | const CFeatureItemBase & | item, |
const CFlatFeature & | feat, | ||
const string & | strRawKey, | ||
string & | strLink, | ||
unsigned int | uItemNumber = 0 |
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) |
Definition at line 1457 of file genbank_formatter.cpp.
References CBioseqContext::Config(), IHTMLFormatter::FormatLocation(), CFlatItem::GetContext(), CFeatureItemBase::GetFeat(), CBioseqContext::GetGI(), CFlatFileConfig::GetHTMLFormatter(), CMappedFeat::GetLocation(), GI_TO, s_GetFeatureKeyLinkLocation(), and ZERO_GI.
Referenced by CGenbankFormatter::FormatFeature().
void s_OrphanFixup | ( | list< string > & | wrapped, |
size_t | uMaxSize = 0 |
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) |
Definition at line 1271 of file genbank_formatter.cpp.
References NStr::TruncateSpaces().
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Definition at line 211 of file genbank_formatter.cpp.
References CBioseq_Handle::CanGetInst_Length(), ctx, CSeq_loc_CI::eEmpty_Skip, CInt_fuzz_Base::eLim_tr, eNa_strand_minus, CSeq_loc_CI::eOrder_Biological, CRange_Base::GetFrom(), CSeq_point_Base::GetFuzz(), CBioseq_Handle::GetInst_Length(), CInt_fuzz_Base::GetLim(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), CSeq_loc_CI::GetRange(), CSeq_loc_CI::GetSeq_id_Handle(), CSeq_loc_CI::GetStrand(), CRange_Base::GetTo(), CInt_fuzz_Base::IsLim(), CSeq_loc_Base::IsPnt(), CSeq_point_Base::IsSetFuzz(), CSeq_loc_CI::IsSetStrand(), CBioseq_Handle::IsSynonym(), kMax_UInt, result, string, and swap().
Referenced by CGenbankFormatter::x_GetFeatureSpanAndScriptStart().
Definition at line 1728 of file genbank_formatter.cpp.
Referenced by s_FormatRegularSequencePiece().
Definition at line 1727 of file genbank_formatter.cpp.
Referenced by s_FormatRegularSequencePiece().
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Definition at line 1729 of file genbank_formatter.cpp.
Referenced by s_CalcDistanceUntilNextSignificantGapOrEnd(), and s_FormatRegularSequencePiece().