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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__AlgoAlignFormat.html below:

NCBI C++ ToolKit: Global Alignment Formatter

Definition at line 74 of file nw_formatter.hpp.

◆ ETextFormatType Enumerator eFormatType1 eFormatType2 eFormatAsn eFormatDenseSeg eFormatFastA eFormatExonTable eFormatExonTableEx

Definition at line 63 of file nw_formatter.hpp.

◆ AsDenseSeg()

Definition at line 150 of file nw_formatter.cpp.

References CSeq_id::Assign(), CNWFormatter::eSAFF_TrimEndGaps, CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, CNWAligner::eTS_Intron, CNWAligner::eTS_SlackDelete, CNWAligner::eTS_SlackInsert, flags, CDense_seg::FromTranscript(), g_msg_NoAlignment, CNWAligner::GetTranscript(), CNWAligner::GetTranscriptString(), CNWAligner::IsSmithWaterman(), CNWFormatter::m_aligner, CNWFormatter::m_Seq1Id, CNWFormatter::m_Seq2Id, NCBI_THROW, CRef< C, Locker >::Reset(), CDense_seg_Base::SetIds(), and CDense_seg::TrimEndGaps().

Referenced by CNWFormatter::AsSeqAlign().

◆ AsSeqAlign()

Definition at line 67 of file nw_formatter.cpp.

References CNWFormatter::AsDenseSeg(), CNWFormatter::eSAFF_DynProgScore, CNWFormatter::eSAFF_Identity, CNWFormatter::eSAFF_TrimEndGaps, CNWAligner::eTS_Match, CNWAligner::eTS_Replace, CSeq_align_Base::eType_global, CSeq_align_Base::eType_partial, flags, CNWAligner::GetScore(), CNWAligner::GetTranscriptString(), CNWAligner::IsSmithWaterman(), ITERATE, CNWFormatter::m_aligner, CSeq_align_Base::SetDim(), CSeq_align_Base::SetScore(), CSeq_align_Base::SetSegs(), and CSeq_align_Base::SetType().

Referenced by s_RunBlast2NWSeq(), and CCreateNeedlemanWunschJob::x_CreateProjectItems().

◆ AsText() ◆ CanExtendLeft() int CNWFormatter::SSegment::CanExtendLeft ( const vector< char > & mrna, const vector< char > & genomic ) const ◆ CanExtendRight() int CNWFormatter::SSegment::CanExtendRight ( const vector< char > & mrna, const vector< char > & genomic ) const ◆ CNWFormatter() ◆ ExtendLeft() void CNWFormatter::SSegment::ExtendLeft ( const vector< char > & mrna, const vector< char > & genomic, Int8 ext_len, const CNWAligner * aligner ) ◆ ExtendRight() void CNWFormatter::SSegment::ExtendRight ( const vector< char > & mrna, const vector< char > & genomic, Int8 ext_len, const CNWAligner * aligner ) ◆ FromBuffer() ◆ GapLength() size_t CNWFormatter::SSegment::GapLength ( ) ◆ GetAcceptor() const char * CNWFormatter::SSegment::GetAcceptor ( void ) const ◆ GetDonor() const char * CNWFormatter::SSegment::GetDonor ( void ) const ◆ ImproveFromLeft() ◆ ImproveFromLeft1() ◆ ImproveFromRight() ◆ ImproveFromRight1() ◆ IsLowComplexityExon() bool CNWFormatter::SSegment::IsLowComplexityExon ( const char * rna_seq ) ◆ MakeSegments() [1/2] void CNWFormatter::MakeSegments ( deque< SSegment > * psegments ) const ◆ MakeSegments() [2/2] void CNWFormatter::MakeSegments ( vector< SSegment > * psegments ) const

Definition at line 872 of file nw_formatter.cpp.

References copy(), CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, CNWAligner::eTS_Intron, CNWAligner::eTS_SlackDelete, CNWAligner::eTS_SlackInsert, g_msg_NoAlignment, CNWAligner::GetEndSpaceFree(), CNWAligner::GetSeq1(), CNWAligner::GetSeq2(), CNWAligner::GetSeqLen2(), CNWAligner::GetTranscript(), CNWFormatter::m_aligner, CNWFormatter::SSegment::m_annot, CNWFormatter::SSegment::m_box, CNWFormatter::SSegment::m_details, CNWFormatter::SSegment::m_exon, CNWFormatter::SSegment::m_idty, CNWFormatter::SSegment::m_len, NCBI_THROW, swap(), toupper(), and CNWFormatter::SSegment::Update().

Referenced by CNWFormatter::MakeSegments(), and CSplign::x_Run().

◆ s_IsConsensusSplice() bool CNWFormatter::SSegment::s_IsConsensusSplice ( const char * donor, const char * acceptor, bool semi_as_cons = false ) static ◆ SetSeqIds() void CNWFormatter::SetSeqIds ( CConstRef< objects::CSeq_id > id1, CConstRef< objects::CSeq_id > id2 ) ◆ SetToGap() void CNWFormatter::SSegment::SetToGap ( )

Definition at line 211 of file nw_formatter.cpp.

References CNWFormatter::SSegment::m_annot, CNWFormatter::SSegment::m_box, CNWFormatter::SSegment::m_details, CNWFormatter::SSegment::m_exon, CNWFormatter::SSegment::m_idty, CNWFormatter::SSegment::m_len, CNWFormatter::SSegment::m_score, and s_kGap.

Referenced by CSplignTrim::CutFromLeft(), CSplignTrim::CutFromRight(), CSplignTrim::CutToMatchLeft(), CSplignTrim::CutToMatchRight(), CSplignTrim::ThrowAway20_28_90(), CSplignTrim::ThrowAwayShortExon(), CSplignTrim::Update(), CSplign::x_ProcessTermSegm(), CSplign::x_Run(), and CSplign::x_RunOnCompartment().

◆ ToBuffer() ◆ Update() ◆ x_ApplyTranscript() size_t CNWFormatter::x_ApplyTranscript ( vector< char > * seq1_transformed, vector< char > * seq2_transformed ) const private

Definition at line 1229 of file nw_formatter.cpp.

◆ m_aligner ◆ m_annot string CNWFormatter::SSegment::m_annot ◆ m_box size_t CNWFormatter::SSegment::m_box[4]

Definition at line 113 of file nw_formatter.hpp.

Referenced by CSplignTrim::AdjustGaps(), CSplignFormatter::AsExonTable(), CSplignFormatter::AsSeqAlignSet(), CSplignTrim::CutFromLeft(), CSplignTrim::CutFromRight(), CSplign::SAlignedCompartment::GetBox(), CSplignTrim::JoinExons(), CNWFormatter::MakeSegments(), CNWFormatter::SSegment::SetToGap(), CSplignTrim::ThrowAwayShortExon(), CSplignTrim::UpdateAnnot(), CSplign::x_ProcessTermSegm(), CSplign::x_Run(), and CSplign::x_RunOnCompartment().

◆ m_details string CNWFormatter::SSegment::m_details

Definition at line 115 of file nw_formatter.hpp.

Referenced by CSplignFormatter::AsExonTable(), CSplignFormatter::AsSeqAlignSet(), CSplignTrim::Cut50FromLeft(), CSplignTrim::Cut50FromRight(), CSplignTrim::CutFromLeft(), CSplignTrim::CutFromRight(), CSplignTrim::CutToMatchLeft(), CSplignTrim::CutToMatchRight(), CSplign::SAlignedCompartment::GetIdentity(), CSplignTrim::ImproveFromLeft(), CSplignTrim::ImproveFromRight(), CSplignTrim::JoinExons(), CNWFormatter::MakeSegments(), CNWFormatter::SSegment::SetToGap(), CSplign::x_Run(), and CSplign::x_RunOnCompartment().

◆ m_exon bool CNWFormatter::SSegment::m_exon ◆ m_idty double CNWFormatter::SSegment::m_idty ◆ m_len size_t CNWFormatter::SSegment::m_len ◆ m_score float CNWFormatter::SSegment::m_score ◆ m_Seq1Id CConstRef<objects::CSeq_id> CNWFormatter::m_Seq1Id private ◆ m_Seq2Id CConstRef<objects::CSeq_id> CNWFormatter::m_Seq2Id private

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