NCBI C++ ToolKit
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#include <ncbi_pch.hpp>
#include <corelib/ncbifile.hpp>
#include <objmgr/feat_ci.hpp>
#include <gui/packages/pkg_alignment/align_tab_export_job.hpp>
#include <objmgr/align_ci.hpp>
#include <objmgr/util/sequence.hpp>
#include <objects/seqalign/Spliced_seg.hpp>
#include <algo/align/util/score_builder.hpp>
#include <gui/objutils/utils.hpp>
#include <gui/widgets/wx/csv_exporter.hpp>
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Functions | |
USING_SCOPE (ncbi::objects) | |
static CSeq_align::TDim | sFindAnchorRow (CBioseq_Handle handle, const CSeq_align &align) |
static size_t | s_CountSegments (const CSeq_align &align) |
static void | s_GetDefline (CBioseq_Handle bsh, string &defline) |
static string | s_ShortenIdLabel (const string &label) |
static string | s_RemovePanfsBasePath (const string &label) |
static map< string, string > | sGenerateFields (CBioseq_Handle handle, const CSeq_align &align, CSeq_align::TDim anchorRow) |
Variables | |
static CFastMutex | s_DFLock |
static sequence::CDeflineGenerator | s_DefGen |
This class seems to be non-thread safe even as a stack var. More... | |
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Definition at line 104 of file align_tab_export_job.cpp.
References CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_Spliced, CSeq_align_set_Base::Get(), CSeq_align_Base::C_Segs::GetDisc(), CSpliced_seg_Base::GetExons(), CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::GetSpliced(), and CSeq_align_Base::C_Segs::Which().
Referenced by sGenerateFields().
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inlinestatic |
Definition at line 122 of file align_tab_export_job.cpp.
References s_DefGen, and s_DFLock.
Referenced by sGenerateFields().
Definition at line 151 of file align_tab_export_job.cpp.
References label.
Referenced by sGenerateFields().
Definition at line 129 of file align_tab_export_job.cpp.
References label.
Referenced by sGenerateFields().
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Definition at line 57 of file align_tab_export_job.cpp.
References _ASSERT, CSeq_align::CheckNumRows(), CBioseq_Handle::ContainsSegment(), eGetId_Best, eGetId_Canonical, eUnknown, GetId(), CBioseq_Handle::GetScope(), CSeq_align::GetSeq_id(), CBioseq_Handle::IsSynonym(), NCBI_THROW, and row.
Referenced by CAlignTabExportJob::Run().
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Definition at line 165 of file align_tab_export_job.cpp.
References buf, CSeq_align::CheckNumRows(), CSeq_id::eContent, eGetId_Best, eNa_strand_plus, CSeq_align::eScore_IdentityCount, CSeq_align::eScore_MismatchCount, CSeq_align::eScore_PercentCoverage, CSeq_align::eScore_PercentIdentity, NStr::fWithCommas, CScoreBuilderBase::GetAlignLength(), CScope::GetBioseqHandle(), CScoreBuilderBase::GetGapCount(), CSeq_id_Handle::GetHandle(), GetId(), CSeq_id::GetLabel(), CScoreBuilderBase::GetMismatchCount(), CSeq_align::GetNamedScore(), CScoreBuilderBase::GetPercentCoverage(), CBioseq_Handle::GetScope(), CSeq_align::GetSeq_id(), CSeq_id_Handle::GetSeqId(), CSeq_id_Handle::GetSeqIdOrNull(), CSeq_align::GetSeqRange(), CSeq_align::GetSeqStrand(), i, NStr::IntToString(), CBioseq_Handle::IsProtein(), label, NStr::NumericToString(), compile_time_bits::range(), s_CountSegments(), s_GetDefline(), s_RemovePanfsBasePath(), s_ShortenIdLabel(), and NStr::SizetToString().
Referenced by CAlignTabExportJob::Run().
USING_SCOPE | ( | ncbi::objects | ) |
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This class seems to be non-thread safe even as a stack var.
Definition at line 119 of file align_tab_export_job.cpp.
Referenced by s_GetDefline().
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Definition at line 118 of file align_tab_export_job.cpp.
Referenced by s_GetDefline().