NCBI C++ ToolKit
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Classes | |
class | CDense_diag_Base |
for (multiway) diagonals More... | |
class | CDense_seg_Base |
Dense-seg: the densist packing for sequence alignments only. More... | |
class | CPacked_seg |
CPacked_seg –. More... | |
class | CPacked_seg_Base |
for (multiway) global or partial alignments More... | |
class | CProduct_pos_Base |
CProduct_pos_Base –. More... | |
class | CProt_pos_Base |
position on protein (1/3 of amino-acid resolution) More... | |
class | CScore_Base |
use of Score is discouraged for external ASN.1 specifications More... | |
class | CScore_Base::C_Value |
C_Value –. More... | |
class | CScore_set |
CScore_set –. More... | |
class | CScore_set_Base |
use of Score-set is encouraged for external ASN.1 specifications More... | |
class | CSeq_align_Base |
CSeq_align_Base –. More... | |
class | CSeq_align_Base::C_Segs |
alignment data More... | |
class | CSeq_align_set_Base |
*** Sequence Alignment ******************************** * More... | |
class | CSparse_align_Base |
CSparse_align_Base –. More... | |
class | CSparse_seg_Base |
========================================================================== More... | |
class | CSparse_seg_ext |
CSparse_seg_ext –. More... | |
class | CSparse_seg_ext_Base |
CSparse_seg_ext_Base –. More... | |
class | CSplice_site |
CSplice_site –. More... | |
class | CSplice_site_Base |
site involved in splice More... | |
class | CSpliced_exon_Base |
complete or partial exon two consecutive Spliced-exons may belong to one exon More... | |
class | CSpliced_exon_chunk |
CSpliced_exon_chunk –. More... | |
class | CSpliced_exon_chunk_Base |
Spliced-exon-chunk: piece of an exon lengths are given in nucleotide bases (1/3 of aminoacid when product is a protein) More... | |
class | CSpliced_seg_Base |
CSpliced_seg_Base –. More... | |
class | CSpliced_seg_modifier |
CSpliced_seg_modifier –. More... | |
class | CSpliced_seg_modifier_Base |
CSpliced_seg_modifier_Base –. More... | |
class | CStd_seg_Base |
CStd_seg_Base –. More... | |
Definition at line 107 of file Spliced_exon_.hpp.
typedef TSeqPos CProt_pos_Base::TAmin |
Definition at line 82 of file Prot_pos_.hpp.
typedef string CSplice_site_Base::TBases |
Definition at line 86 of file Splice_site_.hpp.
typedef list< CRef< CSeq_loc > > CSeq_align_Base::TBounds |
Definition at line 400 of file Seq_align_.hpp.
typedef list< CRef< CScore > > CScore_set_Base::Tdata |
Definition at line 90 of file Score_set_.hpp.
typedef list< CRef< CSeq_align > > CSeq_align_set_Base::Tdata |
Definition at line 91 of file Seq_align_set_.hpp.
typedef list< CRef< CDense_diag > > CSeq_align_Base::C_Segs::TDendiag |
Definition at line 194 of file Seq_align_.hpp.
Definition at line 195 of file Seq_align_.hpp.
Definition at line 148 of file Spliced_exon_chunk_.hpp.
typedef int CDense_diag_Base::TDim |
Definition at line 92 of file Dense_diag_.hpp.
typedef int CDense_seg_Base::TDim |
Definition at line 104 of file Dense_seg_.hpp.
typedef int CPacked_seg_Base::TDim |
Definition at line 92 of file Packed_seg_.hpp.
typedef int CSeq_align_Base::TDim |
Definition at line 397 of file Seq_align_.hpp.
typedef int CStd_seg_Base::TDim |
Definition at line 91 of file Std_seg_.hpp.
Definition at line 198 of file Seq_align_.hpp.
Definition at line 108 of file Spliced_exon_.hpp.
typedef list< CRef< CSpliced_exon > > CSpliced_seg_Base::TExons |
Definition at line 105 of file Spliced_seg_.hpp.
typedef list< CRef< CUser_object > > CSeq_align_Base::TExt |
Definition at line 402 of file Seq_align_.hpp.
typedef vector< CRef< CSparse_seg_ext > > CSparse_seg_Base::TExt |
Definition at line 101 of file Sparse_seg_.hpp.
typedef list< CRef< CUser_object > > CSpliced_exon_Base::TExt |
Definition at line 110 of file Spliced_exon_.hpp.
typedef CSeq_id CSparse_align_Base::TFirst_id |
Definition at line 91 of file Sparse_align_.hpp.
typedef vector< int > CSparse_align_Base::TFirst_starts |
Definition at line 94 of file Sparse_align_.hpp.
typedef TSeqPos CProt_pos_Base::TFrame |
Definition at line 83 of file Prot_pos_.hpp.
Definition at line 100 of file Spliced_exon_.hpp.
Definition at line 102 of file Spliced_exon_.hpp.
Definition at line 101 of file Spliced_seg_.hpp.
Definition at line 150 of file Spliced_exon_chunk_.hpp.
Definition at line 99 of file Spliced_exon_.hpp.
Definition at line 104 of file Spliced_exon_.hpp.
Definition at line 103 of file Spliced_seg_.hpp.
typedef CObject_id CScore_Base::TId |
Definition at line 240 of file Score_.hpp.
typedef list< CRef< CObject_id > > CSeq_align_Base::TId |
Definition at line 401 of file Seq_align_.hpp.
typedef vector< CRef< CSeq_id > > CDense_diag_Base::TIds |
Definition at line 93 of file Dense_diag_.hpp.
typedef vector< CRef< CSeq_id > > CDense_seg_Base::TIds |
Definition at line 106 of file Dense_seg_.hpp.
typedef vector< CRef< CSeq_id > > CPacked_seg_Base::TIds |
Definition at line 94 of file Packed_seg_.hpp.
typedef vector< CRef< CSeq_id > > CStd_seg_Base::TIds |
Definition at line 92 of file Std_seg_.hpp.
typedef int CSparse_seg_ext_Base::TIndex |
Definition at line 81 of file Sparse_seg_ext_.hpp.
typedef int CScore_Base::C_Value::TInt |
Definition at line 163 of file Score_.hpp.
typedef TSeqPos CDense_diag_Base::TLen |
Definition at line 95 of file Dense_diag_.hpp.
typedef vector< TSeqPos > CDense_seg_Base::TLens |
Definition at line 108 of file Dense_seg_.hpp.
typedef vector< TSeqPos > CPacked_seg_Base::TLens |
Definition at line 97 of file Packed_seg_.hpp.
typedef vector< TSeqPos > CSparse_align_Base::TLens |
Definition at line 96 of file Sparse_align_.hpp.
typedef vector< CRef< CSeq_loc > > CStd_seg_Base::TLoc |
Definition at line 93 of file Std_seg_.hpp.
typedef CSeq_id CSparse_seg_Base::TMaster_id |
Definition at line 98 of file Sparse_seg_.hpp.
Definition at line 146 of file Spliced_exon_chunk_.hpp.
Definition at line 109 of file Dense_diag_.hpp.
Definition at line 123 of file Dense_seg_.hpp.
Definition at line 113 of file Packed_seg_.hpp.
Definition at line 91 of file Prot_pos_.hpp.
Definition at line 249 of file Score_.hpp.
Definition at line 415 of file Seq_align_.hpp.
Definition at line 112 of file Sparse_align_.hpp.
Definition at line 111 of file Sparse_seg_.hpp.
Definition at line 88 of file Sparse_seg_ext_.hpp.
Definition at line 93 of file Splice_site_.hpp.
Definition at line 130 of file Spliced_exon_.hpp.
Definition at line 123 of file Spliced_seg_.hpp.
Definition at line 104 of file Std_seg_.hpp.
Definition at line 147 of file Spliced_exon_chunk_.hpp.
typedef list< CRef< CSpliced_seg_modifier > > CSpliced_seg_Base::TModifiers |
Definition at line 108 of file Spliced_seg_.hpp.
typedef TSeqPos CProduct_pos_Base::TNucpos |
Definition at line 144 of file Product_pos_.hpp.
typedef int CDense_seg_Base::TNumseg |
Definition at line 105 of file Dense_seg_.hpp.
typedef int CPacked_seg_Base::TNumseg |
Definition at line 93 of file Packed_seg_.hpp.
typedef int CSparse_align_Base::TNumseg |
Definition at line 93 of file Sparse_align_.hpp.
Definition at line 197 of file Seq_align_.hpp.
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Definition at line 81 of file Dense_diag_.hpp.
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private |
Definition at line 93 of file Dense_seg_.hpp.
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private |
Definition at line 67 of file Packed_seg.hpp.
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private |
Definition at line 81 of file Packed_seg_.hpp.
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private |
Definition at line 74 of file Product_pos_.hpp.
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private |
Definition at line 71 of file Prot_pos_.hpp.
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private |
Definition at line 75 of file Score_.hpp.
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private |
Definition at line 92 of file Score_.hpp.
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private |
Definition at line 67 of file Score_set.hpp.
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private |
Definition at line 79 of file Score_set_.hpp.
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private |
Definition at line 89 of file Seq_align_.hpp.
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private |
Definition at line 119 of file Seq_align_.hpp.
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private |
Definition at line 80 of file Seq_align_set_.hpp.
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private |
Definition at line 80 of file Sparse_align_.hpp.
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private |
Definition at line 87 of file Sparse_seg_.hpp.
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private |
Definition at line 67 of file Sparse_seg_ext.hpp.
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private |
Definition at line 70 of file Sparse_seg_ext_.hpp.
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private |
Definition at line 67 of file Splice_site.hpp.
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private |
Definition at line 75 of file Splice_site_.hpp.
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private |
Definition at line 86 of file Spliced_exon_.hpp.
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private |
Definition at line 67 of file Spliced_exon_chunk.hpp.
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private |
Definition at line 73 of file Spliced_exon_chunk_.hpp.
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private |
Definition at line 81 of file Spliced_seg_.hpp.
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private |
Definition at line 67 of file Spliced_seg_modifier.hpp.
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private |
Definition at line 70 of file Spliced_seg_modifier_.hpp.
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private |
Definition at line 80 of file Std_seg_.hpp.
typedef bool CSpliced_exon_Base::TPartial |
Definition at line 109 of file Spliced_exon_.hpp.
typedef list< CRef< CSpliced_exon_chunk > > CSpliced_exon_Base::TParts |
Definition at line 105 of file Spliced_exon_.hpp.
typedef TSeqPos CSpliced_seg_Base::TPoly_a |
Definition at line 106 of file Spliced_seg_.hpp.
typedef vector< char > CPacked_seg_Base::TPresent |
Definition at line 96 of file Packed_seg_.hpp.
Definition at line 98 of file Spliced_exon_.hpp.
Definition at line 101 of file Spliced_exon_.hpp.
Definition at line 100 of file Spliced_seg_.hpp.
Definition at line 149 of file Spliced_exon_chunk_.hpp.
Definition at line 107 of file Spliced_seg_.hpp.
Definition at line 97 of file Spliced_exon_.hpp.
Definition at line 103 of file Spliced_exon_.hpp.
Definition at line 102 of file Spliced_seg_.hpp.
Definition at line 104 of file Spliced_seg_.hpp.
typedef CProt_pos CProduct_pos_Base::TProtpos |
Definition at line 145 of file Product_pos_.hpp.
typedef double CScore_Base::C_Value::TReal |
Definition at line 162 of file Score_.hpp.
typedef vector< CRef< CScore > > CSparse_seg_Base::TRow_scores |
Definition at line 100 of file Sparse_seg_.hpp.
typedef vector< CRef< CSparse_align > > CSparse_seg_Base::TRows |
Definition at line 99 of file Sparse_seg_.hpp.
typedef vector< CRef< CScore > > CSeq_align_Base::TScore |
Definition at line 398 of file Seq_align_.hpp.
typedef vector< CRef< CScore > > CDense_diag_Base::TScores |
Definition at line 97 of file Dense_diag_.hpp.
typedef vector< CRef< CScore > > CDense_seg_Base::TScores |
Definition at line 110 of file Dense_seg_.hpp.
typedef vector< CRef< CScore > > CPacked_seg_Base::TScores |
Definition at line 99 of file Packed_seg_.hpp.
Definition at line 106 of file Spliced_exon_.hpp.
typedef vector< CRef< CScore > > CStd_seg_Base::TScores |
Definition at line 94 of file Std_seg_.hpp.
Definition at line 92 of file Sparse_align_.hpp.
typedef vector< int > CSparse_align_Base::TSecond_starts |
Definition at line 95 of file Sparse_align_.hpp.
typedef vector< ENa_strand > CSparse_align_Base::TSecond_strands |
Definition at line 97 of file Sparse_align_.hpp.
typedef vector< CRef< CScore > > CSparse_align_Base::TSeg_scores |
Definition at line 98 of file Sparse_align_.hpp.
typedef C_Segs CSeq_align_Base::TSegs |
Definition at line 399 of file Seq_align_.hpp.
Definition at line 200 of file Seq_align_.hpp.
Definition at line 199 of file Seq_align_.hpp.
Definition at line 140 of file Spliced_seg_modifier_.hpp.
typedef vector< TSeqPos > CDense_diag_Base::TStarts |
Definition at line 94 of file Dense_diag_.hpp.
typedef vector< TSignedSeqPos > CDense_seg_Base::TStarts |
Definition at line 107 of file Dense_seg_.hpp.
typedef vector< TSeqPos > CPacked_seg_Base::TStarts |
Definition at line 95 of file Packed_seg_.hpp.
typedef list< CRef< CStd_seg > > CSeq_align_Base::C_Segs::TStd |
Definition at line 196 of file Seq_align_.hpp.
Definition at line 141 of file Spliced_seg_modifier_.hpp.
typedef vector< ENa_strand > CDense_diag_Base::TStrands |
Definition at line 96 of file Dense_diag_.hpp.
typedef vector< ENa_strand > CDense_seg_Base::TStrands |
Definition at line 109 of file Dense_seg_.hpp.
typedef vector< ENa_strand > CPacked_seg_Base::TStrands |
Definition at line 98 of file Packed_seg_.hpp.
typedef EType CSeq_align_Base::TType |
Definition at line 396 of file Seq_align_.hpp.
typedef C_Value CScore_Base::TValue |
Definition at line 241 of file Score_.hpp.
Choice variants.
Enumerator | |
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e_not_set | No variant selected. |
e_Nucpos | |
e_Protpos |
Definition at line 86 of file Product_pos_.hpp.
Choice variants.
Enumerator | |
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e_not_set | No variant selected. |
e_Real | |
e_Int |
Definition at line 104 of file Score_.hpp.
Choice variants.
Enumerator | |
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e_not_set | No variant selected. |
e_Dendiag | |
e_Denseg | |
e_Std | |
e_Packed | |
e_Disc | |
e_Spliced | |
e_Sparse |
Definition at line 131 of file Seq_align_.hpp.
Choice variants.
Definition at line 85 of file Spliced_exon_chunk_.hpp.
Choice variants.
Definition at line 82 of file Spliced_seg_modifier_.hpp.
Maximum+1 value of the choice variant enumerator.
Enumerator | |
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e_MaxChoice | == e_Protpos+1 |
Definition at line 92 of file Product_pos_.hpp.
Maximum+1 value of the choice variant enumerator.
Enumerator | |
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e_MaxChoice | == e_Int+1 |
Definition at line 110 of file Score_.hpp.
Maximum+1 value of the choice variant enumerator.
Enumerator | |
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e_MaxChoice | == e_Sparse+1 |
Definition at line 142 of file Seq_align_.hpp.
Maximum+1 value of the choice variant enumerator.
Enumerator | |
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e_MaxChoice | == e_Genomic_ins+1 |
Definition at line 94 of file Spliced_exon_chunk_.hpp.
Maximum+1 value of the choice variant enumerator.
Enumerator | |
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e_MaxChoice | == e_Stop_codon_found+1 |
Definition at line 88 of file Spliced_seg_modifier_.hpp.
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strong |
Enumerator | |
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e__allMandatory | |
e_dim | |
e_ids | |
e_starts | |
e_len | |
e_strands | |
e_scores |
Definition at line 100 of file Dense_diag_.hpp.
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strong |
Enumerator | |
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e__allMandatory | |
e_dim | |
e_numseg | |
e_ids | |
e_starts | |
e_lens | |
e_strands | |
e_scores |
Definition at line 113 of file Dense_seg_.hpp.
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strong |
Enumerator | |
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e__allMandatory | |
e_dim | |
e_numseg | |
e_ids | |
e_starts | |
e_present | |
e_lens | |
e_strands | |
e_scores |
Definition at line 102 of file Packed_seg_.hpp.
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strong |
Enumerator | |
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e__allMandatory | |
e_amin | |
e_frame |
Definition at line 86 of file Prot_pos_.hpp.
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strong |
Enumerator | |
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e__allMandatory | |
e_id | |
e_value |
Definition at line 244 of file Score_.hpp.
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strong |
Enumerator | |
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e__allMandatory | |
e_type | |
e_dim | |
e_score | |
e_segs | |
e_bounds | |
e_id | |
e_ext |
Definition at line 405 of file Seq_align_.hpp.
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strong |
Enumerator | |
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e__allMandatory | |
e_first_id | |
e_second_id | |
e_numseg | |
e_first_starts | |
e_second_starts | |
e_lens | |
e_second_strands | |
e_seg_scores |
Definition at line 101 of file Sparse_align_.hpp.
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strong |
Enumerator | |
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e__allMandatory | |
e_master_id | |
e_rows | |
e_row_scores | |
e_ext |
Definition at line 104 of file Sparse_seg_.hpp.
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strong |
Enumerator | |
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e__allMandatory | |
e_index |
Definition at line 84 of file Sparse_seg_ext_.hpp.
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strong |
Enumerator | |
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e__allMandatory | |
e_bases |
Definition at line 89 of file Splice_site_.hpp.
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strong |
Definition at line 113 of file Spliced_exon_.hpp.
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strong |
Enumerator | |
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e__allMandatory | |
e_product_id | |
e_genomic_id | |
e_product_strand | |
e_genomic_strand | |
e_product_type | |
e_exons | |
e_poly_a | |
e_product_length | |
e_modifiers |
Definition at line 111 of file Spliced_seg_.hpp.
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strong |
Enumerator | |
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e__allMandatory | |
e_dim | |
e_ids | |
e_loc | |
e_scores |
Definition at line 97 of file Std_seg_.hpp.
Enumerator | |
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eProduct_type_transcript | |
eProduct_type_protein |
Definition at line 91 of file Spliced_seg_.hpp.
enum CSeq_align_Base::EType | ( | void | ) |
Enumerator | |
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eType_not_set | |
eType_global | |
eType_diags | unbroken, but not ordered, diagonals |
eType_partial | mapping pieces together |
eType_disc | discontinuous alignment |
eType_other |
Definition at line 99 of file Seq_align_.hpp.
END_CHOICE_INFO CSeq_align_Base::C_Segs::C_Segs | ( | void | ) |
Definition at line 283 of file Seq_align_.cpp.
END_CHOICE_INFO CScore_Base::C_Value::C_Value | ( | void | ) |
Definition at line 108 of file Score_.cpp.
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Check if it is safe to call Get method.
Definition at line 159 of file Score_set_.hpp.
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Check if it is safe to call Get method.
Definition at line 160 of file Seq_align_set_.hpp.
Referenced by ExtractFirstSeqAlign(), CAlignResultsSet::Insert(), CIgBlastTabularInfo::SetAirrFormatData(), CIgBlastTabularInfo::SetIgAnnotation(), CSeq_align_set::Size(), CSeq_align_set::SwapRows(), and CInversionMergeAligner::x_HandleSingleStrandMerging().
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Check if it is safe to call GetAcceptor_before_exon method.
Definition at line 1030 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::IsSetAcceptor_before_exon().
Referenced by CProteinAlignText::CProteinAlignText(), and CSpliced_exon_Base::GetAcceptor_before_exon().
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Check if it is safe to call GetAmin method.
Definition at line 207 of file Prot_pos_.hpp.
References CProt_pos_Base::IsSetAmin().
Referenced by CProt_pos_Base::GetAmin().
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Check if it is safe to call GetBases method.
Definition at line 168 of file Splice_site_.hpp.
References CSplice_site_Base::IsSetBases().
Referenced by CProteinAlignText::CProteinAlignText(), and CSplice_site_Base::GetBases().
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Check if it is safe to call GetBounds method.
Definition at line 945 of file Seq_align_.hpp.
Referenced by CProteinAlignText::GetGenomicBounds().
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Check if it is safe to call GetDim method.
Definition at line 354 of file Dense_diag_.hpp.
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Check if it is safe to call GetDim method.
Definition at line 402 of file Dense_seg_.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), CPaintAlignment::GetSegments(), CReportTrim::TrimAlignments(), TrimSeqAlign(), TrimSequenceAndAnnotation(), CAlnWriter::WriteAlignDenseSeg(), and CVectorTrimPanel::x_TrimAlignments().
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Check if it is safe to call GetDim method.
Definition at line 426 of file Packed_seg_.hpp.
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Check if it is safe to call GetDim method.
Definition at line 843 of file Seq_align_.hpp.
References CSeq_align_Base::IsSetDim().
Referenced by CSeq_align_Base::GetDim(), and CSeq_align::GetSeqRange().
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Check if it is safe to call GetDim method.
Definition at line 276 of file Std_seg_.hpp.
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Check if it is safe to call GetDonor_after_exon method.
Definition at line 1051 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::IsSetDonor_after_exon().
Referenced by CProteinAlignText::CProteinAlignText(), and CSpliced_exon_Base::GetDonor_after_exon().
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Check if it is safe to call GetExons method.
Definition at line 686 of file Spliced_seg_.hpp.
Referenced by CScore_LastSpliceSite::Get(), CFeatureGenerator::SImplementation::StitchSmallHoles(), and CFeatureGenerator::SImplementation::TrimHolesToCodons().
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Check if it is safe to call GetExt method.
Definition at line 995 of file Seq_align_.hpp.
Referenced by IsGnomonConstructed().
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Check if it is safe to call GetExt method.
Definition at line 353 of file Sparse_seg_.hpp.
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Check if it is safe to call GetExt method.
Definition at line 1119 of file Spliced_exon_.hpp.
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Check if it is safe to call GetFirst_id method.
Definition at line 425 of file Sparse_align_.hpp.
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Check if it is safe to call GetFirst_starts method.
Definition at line 532 of file Sparse_align_.hpp.
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Check if it is safe to call GetFrame method.
Definition at line 254 of file Prot_pos_.hpp.
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Check if it is safe to call GetGenomic_end method.
Definition at line 801 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::IsSetGenomic_end().
Referenced by CSpliced_exon_Base::GetGenomic_end().
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Check if it is safe to call GetGenomic_id method.
Definition at line 869 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::IsSetGenomic_id().
Referenced by CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CSpliced_exon_Base::GetGenomic_id(), and CFeatureGenerator::SImplementation::HasMixedGenomicIds().
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Check if it is safe to call GetGenomic_id method.
Definition at line 524 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::IsSetGenomic_id().
Referenced by CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CSpliced_seg_Base::GetGenomic_id(), CFeatureGenerator::SImplementation::HasMixedGenomicIds(), and s_GetAlignmentContent().
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Check if it is safe to call GetGenomic_start method.
Definition at line 754 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::IsSetGenomic_start().
Referenced by CSpliced_exon_Base::GetGenomic_start().
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Check if it is safe to call GetGenomic_strand method.
Definition at line 937 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::IsSetGenomic_strand().
Referenced by CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), ConvertSplicedToPairwiseAln(), CSpliced_exon_Base::GetGenomic_strand(), and CSpliced_seg::IsConsistentBiologicalOrder().
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Check if it is safe to call GetGenomic_strand method.
Definition at line 592 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::IsSetGenomic_strand().
Referenced by CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), ConvertSplicedToPairwiseAln(), CSpliced_seg_Base::GetGenomic_strand(), CSpliced_seg::GetSeqStrand(), CSpliced_seg::IsConsistentBiologicalOrder(), s_GetAlignmentSpans_Intron(), and CPslRecord::xInitializeStrands().
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Check if it is safe to call GetId method.
Definition at line 438 of file Score_.hpp.
References CScore_Base::IsSetId().
Referenced by CScore_Base::GetId(), and CHitMatrixDataSource::x_UpdateScoreMap().
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Check if it is safe to call GetId method.
Definition at line 970 of file Seq_align_.hpp.
Referenced by GetModelId().
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inline |
Check if it is safe to call GetIds method.
Definition at line 404 of file Dense_diag_.hpp.
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inline |
Check if it is safe to call GetIds method.
Definition at line 499 of file Dense_seg_.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), CPaintAlignment::GetSegments(), CReportTrim::TrimAlignments(), TrimSequenceAndAnnotation(), CAlnWriter::WriteAlignDenseSeg(), and CVectorTrimPanel::x_TrimAlignments().
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inline |
Check if it is safe to call GetIds method.
Definition at line 523 of file Packed_seg_.hpp.
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inline |
Check if it is safe to call GetIds method.
Definition at line 326 of file Std_seg_.hpp.
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inline |
Check if it is safe to call GetIndex method.
Definition at line 164 of file Sparse_seg_ext_.hpp.
References CSparse_seg_ext_Base::IsSetIndex().
Referenced by CSparse_seg_ext_Base::GetIndex().
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inline |
Check if it is safe to call GetLen method.
Definition at line 454 of file Dense_diag_.hpp.
References CDense_diag_Base::IsSetLen().
Referenced by CDense_diag_Base::GetLen().
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Check if it is safe to call GetLens method.
Definition at line 549 of file Dense_seg_.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), CPaintAlignment::GetSegments(), CReportTrim::TrimAlignments(), TrimSequenceAndAnnotation(), CAlnWriter::WriteAlignDenseSeg(), and CVectorTrimPanel::x_TrimAlignments().
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Check if it is safe to call GetLens method.
Definition at line 601 of file Packed_seg_.hpp.
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Check if it is safe to call GetLens method.
Definition at line 582 of file Sparse_align_.hpp.
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Check if it is safe to call GetLoc method.
Definition at line 351 of file Std_seg_.hpp.
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Check if it is safe to call GetMaster_id method.
Definition at line 282 of file Sparse_seg_.hpp.
References CSparse_seg_Base::IsSetMaster_id().
Referenced by CSparse_seg_Base::GetMaster_id().
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Check if it is safe to call GetModifiers method.
Definition at line 805 of file Spliced_seg_.hpp.
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Check if it is safe to call GetNumseg method.
Definition at line 452 of file Dense_seg_.hpp.
References CDense_seg_Base::IsSetNumseg().
Referenced by BOOST_AUTO_TEST_CASE(), CDense_seg_Base::GetNumseg(), CPaintAlignment::GetSegments(), CReportTrim::TrimAlignments(), TrimSequenceAndAnnotation(), CAlnWriter::WriteAlignDenseSeg(), and CVectorTrimPanel::x_TrimAlignments().
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Check if it is safe to call GetNumseg method.
Definition at line 476 of file Packed_seg_.hpp.
References CPacked_seg_Base::IsSetNumseg().
Referenced by CPacked_seg_Base::GetNumseg().
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Check if it is safe to call GetNumseg method.
Definition at line 485 of file Sparse_align_.hpp.
References CSparse_align_Base::IsSetNumseg().
Referenced by CSparse_align_Base::GetNumseg().
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Check if it is safe to call GetPartial method.
Definition at line 1072 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::IsSetPartial().
Referenced by CSpliced_exon_Base::GetPartial().
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Check if it is safe to call GetParts method.
Definition at line 984 of file Spliced_exon_.hpp.
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Check if it is safe to call GetPoly_a method.
Definition at line 711 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::IsSetPoly_a().
Referenced by CSpliced_seg_Base::GetPoly_a(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), and CFeatureGenerator::SImplementation::x_MapFeature().
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Check if it is safe to call GetPresent method.
Definition at line 573 of file Packed_seg_.hpp.
References CPacked_seg_Base::IsSetPresent().
Referenced by CPacked_seg_Base::GetPresent().
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Check if it is safe to call GetProduct_end method.
Definition at line 724 of file Spliced_exon_.hpp.
Referenced by CScore_LastSpliceSite::Get().
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Check if it is safe to call GetProduct_id method.
Definition at line 848 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::IsSetProduct_id().
Referenced by CSpliced_exon_Base::GetProduct_id().
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Check if it is safe to call GetProduct_id method.
Definition at line 503 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::IsSetProduct_id().
Referenced by CSpliced_seg_Base::GetProduct_id(), s_GetAlignmentContent(), and CFeatureGenerator::SImplementation::TrimHolesToCodons().
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Check if it is safe to call GetProduct_length method.
Definition at line 758 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::IsSetProduct_length().
Referenced by CScore_StartStopCodon::Get(), and CSpliced_seg_Base::GetProduct_length().
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Check if it is safe to call GetProduct_start method.
Definition at line 694 of file Spliced_exon_.hpp.
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Check if it is safe to call GetProduct_strand method.
Definition at line 890 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::IsSetProduct_strand().
Referenced by ConvertSplicedToPairwiseAln(), CSpliced_exon_Base::GetProduct_strand(), CSpliced_seg::IsConsistentBiologicalOrder(), and CSpliced_seg::Validate().
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Check if it is safe to call GetProduct_strand method.
Definition at line 545 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::IsSetProduct_strand().
Referenced by ConvertSplicedToPairwiseAln(), CScore_LastSpliceSite::Get(), CSpliced_seg_Base::GetProduct_strand(), CSpliced_seg::GetSeqStrand(), CSpliced_seg::IsConsistentBiologicalOrder(), s_GetAlignmentSpans_Intron(), CSpliced_seg::Validate(), CGff3FlybaseWriter::xAssignAlignmentSplicedLocation(), CGff3Writer::xAssignAlignmentSplicedTarget(), and CPslRecord::xInitializeStrands().
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Check if it is safe to call GetProduct_type method.
Definition at line 639 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::IsSetProduct_type().
Referenced by CScore_LastSpliceSite::Get(), CSpliced_seg_Base::GetProduct_type(), and CPslRecord::xValidateSegment().
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Check if it is safe to call GetRow_scores method.
Definition at line 328 of file Sparse_seg_.hpp.
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Check if it is safe to call GetRows method.
Definition at line 303 of file Sparse_seg_.hpp.
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Check if it is safe to call GetScore method.
Definition at line 890 of file Seq_align_.hpp.
Referenced by CPslWriter::WriteAlign().
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Check if it is safe to call GetScores method.
Definition at line 526 of file Dense_diag_.hpp.
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Check if it is safe to call GetScores method.
Definition at line 599 of file Dense_seg_.hpp.
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Check if it is safe to call GetScores method.
Definition at line 651 of file Packed_seg_.hpp.
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Check if it is safe to call GetScores method.
Definition at line 1009 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::IsSetScores().
Referenced by CSpliced_exon_Base::GetScores().
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Check if it is safe to call GetScores method.
Definition at line 376 of file Std_seg_.hpp.
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Check if it is safe to call GetSecond_id method.
Definition at line 455 of file Sparse_align_.hpp.
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Check if it is safe to call GetSecond_starts method.
Definition at line 557 of file Sparse_align_.hpp.
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Check if it is safe to call GetSecond_strands method.
Definition at line 607 of file Sparse_align_.hpp.
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Check if it is safe to call GetSeg_scores method.
Definition at line 632 of file Sparse_align_.hpp.
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Check if it is safe to call GetSegs method.
Definition at line 915 of file Seq_align_.hpp.
Referenced by CFeatureGenerator::SImplementation::AdjustAlignment(), BOOST_AUTO_TEST_CASE(), CFeatureGenerator::SImplementation::CleanAlignment(), IsProteinAlign(), CTabularFormatter_Cigar::Print(), CTabularFormatter_Traceback::Print(), s_AlignToSeqRanges(), s_CleanSeqAlign(), CReportTrim::TrimAlignments(), TrimSequenceAndAnnotation(), CPrimaryItem::x_CollectSegments(), x_CollectSegments(), CHitMatrixDataSource::x_GetAlignedSeqIds(), CHitMatrixDataSource::x_GetSeqAlignIds(), CVectorTrimPanel::x_TrimAlignments(), and CHitMatrixDataSource::x_UpdateScoreMap().
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Check if it is safe to call GetStarts method.
Definition at line 429 of file Dense_diag_.hpp.
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Check if it is safe to call GetStarts method.
Definition at line 524 of file Dense_seg_.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), CPaintAlignment::GetSegments(), CReportTrim::TrimAlignments(), TrimSequenceAndAnnotation(), CAlnWriter::WriteAlignDenseSeg(), and CVectorTrimPanel::x_TrimAlignments().
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Check if it is safe to call GetStarts method.
Definition at line 548 of file Packed_seg_.hpp.
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Check if it is safe to call GetStrands method.
Definition at line 501 of file Dense_diag_.hpp.
Referenced by CDense_diag::GetSeqStrand().
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Check if it is safe to call GetStrands method.
Definition at line 574 of file Dense_seg_.hpp.
Referenced by CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CDense_seg::GetSeqStart(), CDense_seg::GetSeqStop(), s_CoverageSeqLoc(), CContigAssembly::x_IsAllowedStrands(), CInversionMergeAligner::x_MergeSeqAlignSet(), CMergeAligner::x_MergeSeqAlignSet(), and CInstancedAligner::x_RunCleanup().
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Check if it is safe to call GetStrands method.
Definition at line 626 of file Packed_seg_.hpp.
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Check if it is safe to call GetType method.
Definition at line 796 of file Seq_align_.hpp.
References CSeq_align_Base::IsSetType().
Referenced by CSeq_align_Base::GetType().
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Check if it is safe to call GetValue method.
Definition at line 459 of file Score_.hpp.
References CScore_Base::IsSetValue().
Referenced by CScore_Base::GetValue().
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END_CLASS_INFO CDense_diag_Base::CDense_diag_Base | ( | void | ) |
Definition at line 102 of file Dense_diag_.cpp.
References CDense_diag_Base::m_set_State.
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END_CLASS_INFO CDense_seg_Base::CDense_seg_Base | ( | void | ) |
Definition at line 110 of file Dense_seg_.cpp.
References CDense_seg_Base::m_set_State.
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Verify selection, throw exception if it differs from the expected.
index | Expected selection. |
Definition at line 237 of file Product_pos_.hpp.
References CProduct_pos_Base::m_choice, and CProduct_pos_Base::ThrowInvalidSelection().
Referenced by CProduct_pos_Base::GetNucpos(), and CProduct_pos_Base::GetProtpos().
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Verify selection, throw exception if it differs from the expected.
index | Expected selection. |
Definition at line 355 of file Score_.hpp.
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Verify selection, throw exception if it differs from the expected.
index | Expected selection. |
Definition at line 697 of file Seq_align_.hpp.
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Verify selection, throw exception if it differs from the expected.
index | Expected selection. |
Definition at line 327 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::m_choice, and CSpliced_exon_chunk_Base::ThrowInvalidSelection().
Referenced by CSpliced_exon_chunk_Base::GetDiag(), CSpliced_exon_chunk_Base::GetGenomic_ins(), CSpliced_exon_chunk_Base::GetMatch(), CSpliced_exon_chunk_Base::GetMismatch(), and CSpliced_exon_chunk_Base::GetProduct_ins().
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Verify selection, throw exception if it differs from the expected.
index | Expected selection. |
Definition at line 234 of file Spliced_seg_modifier_.hpp.
References CSpliced_seg_modifier_Base::m_choice, and CSpliced_seg_modifier_Base::ThrowInvalidSelection().
Referenced by CSpliced_seg_modifier_Base::GetStart_codon_found(), and CSpliced_seg_modifier_Base::GetStop_codon_found().
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Definition at line 86 of file Packed_seg.hpp.
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END_CLASS_INFO CPacked_seg_Base::CPacked_seg_Base | ( | void | ) |
Definition at line 118 of file Packed_seg_.cpp.
References CPacked_seg_Base::m_set_State.
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END_CHOICE_INFO CProduct_pos_Base::CProduct_pos_Base | ( | void | ) |
Definition at line 136 of file Product_pos_.cpp.
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END_CLASS_INFO CProt_pos_Base::CProt_pos_Base | ( | void | ) |
Definition at line 68 of file Prot_pos_.cpp.
References CProt_pos_Base::m_set_State.
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END_CLASS_INFO CScore_Base::CScore_Base | ( | void | ) |
Definition at line 167 of file Score_.cpp.
References CScore_Base::m_set_State.
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Definition at line 86 of file Score_set.hpp.
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END_CLASS_INFO CScore_set_Base::CScore_set_Base | ( | void | ) |
Definition at line 68 of file Score_set_.cpp.
References CScore_set_Base::m_set_State.
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END_CLASS_INFO CSeq_align_Base::CSeq_align_Base | ( | void | ) |
Definition at line 361 of file Seq_align_.cpp.
References CObject::IsAllocatedInPool(), CSeq_align_Base::m_set_State, and CSeq_align_Base::ResetSegs().
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END_CLASS_INFO CSeq_align_set_Base::CSeq_align_set_Base | ( | void | ) |
Definition at line 68 of file Seq_align_set_.cpp.
References CSeq_align_set_Base::m_set_State.
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END_CLASS_INFO CSparse_align_Base::CSparse_align_Base | ( | void | ) |
Definition at line 140 of file Sparse_align_.cpp.
References CObject::IsAllocatedInPool(), CSparse_align_Base::m_set_State, CSparse_align_Base::ResetFirst_id(), and CSparse_align_Base::ResetSecond_id().
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END_CLASS_INFO CSparse_seg_Base::CSparse_seg_Base | ( | void | ) |
Definition at line 111 of file Sparse_seg_.cpp.
References CSparse_seg_Base::m_set_State.
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Definition at line 86 of file Sparse_seg_ext.hpp.
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END_CLASS_INFO CSparse_seg_ext_Base::CSparse_seg_ext_Base | ( | void | ) |
Definition at line 66 of file Sparse_seg_ext_.cpp.
References CSparse_seg_ext_Base::m_set_State.
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Definition at line 86 of file Splice_site.hpp.
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END_CLASS_INFO CSplice_site_Base::CSplice_site_Base | ( | void | ) |
Definition at line 72 of file Splice_site_.cpp.
References CSplice_site_Base::m_set_State.
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END_CLASS_INFO CSpliced_exon_Base::CSpliced_exon_Base | ( | void | ) |
Definition at line 223 of file Spliced_exon_.cpp.
References CObject::IsAllocatedInPool(), CSpliced_exon_Base::m_set_State, CSpliced_exon_Base::ResetProduct_end(), and CSpliced_exon_Base::ResetProduct_start().
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Definition at line 86 of file Spliced_exon_chunk.hpp.
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END_CHOICE_INFO CSpliced_exon_chunk_Base::CSpliced_exon_chunk_Base | ( | void | ) |
Definition at line 121 of file Spliced_exon_chunk_.cpp.
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END_CLASS_INFO CSpliced_seg_Base::CSpliced_seg_Base | ( | void | ) |
Definition at line 140 of file Spliced_seg_.cpp.
References CSpliced_seg_Base::m_set_State.
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Definition at line 86 of file Spliced_seg_modifier.hpp.
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END_CHOICE_INFO CSpliced_seg_modifier_Base::CSpliced_seg_modifier_Base | ( | void | ) |
Definition at line 106 of file Spliced_seg_modifier_.cpp.
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END_CLASS_INFO CStd_seg_Base::CStd_seg_Base | ( | void | ) |
Definition at line 93 of file Std_seg_.cpp.
References CStd_seg_Base::m_set_State.
CDense_diag_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CDense_seg_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CPacked_seg_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CProduct_pos_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CProt_pos_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CScore_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CScore_Base::C_Value::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CScore_set_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSeq_align_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSeq_align_Base::C_Segs::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSeq_align_set_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSparse_align_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSparse_seg_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSparse_seg_ext_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSplice_site_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSpliced_exon_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSpliced_exon_chunk_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSpliced_seg_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CSpliced_seg_modifier_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CStd_seg_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
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virtual |
Mark this object as not allocated in heap – do not delete this object.
Reimplemented from CObject.
Definition at line 149 of file Score_.cpp.
References CObject::DoNotDeleteThisObject(), and CScore_Base::m_Value.
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private |
Definition at line 69 of file Product_pos_.cpp.
References CObject::AddReference(), CProduct_pos_Base::e_Nucpos, CProduct_pos_Base::e_Protpos, CProduct_pos_Base::m_choice, CProduct_pos_Base::m_Nucpos, and CProduct_pos_Base::m_object.
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Definition at line 62 of file Score_.cpp.
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private |
Definition at line 102 of file Seq_align_.cpp.
References CObject::AddReference().
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Definition at line 61 of file Spliced_exon_chunk_.cpp.
References 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, CSpliced_exon_chunk_Base::m_choice, CSpliced_exon_chunk_Base::m_Diag, CSpliced_exon_chunk_Base::m_Genomic_ins, CSpliced_exon_chunk_Base::m_Match, CSpliced_exon_chunk_Base::m_Mismatch, and CSpliced_exon_chunk_Base::m_Product_ins.
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Definition at line 61 of file Spliced_seg_modifier_.cpp.
References CSpliced_seg_modifier_Base::e_Start_codon_found, CSpliced_seg_modifier_Base::e_Stop_codon_found, CSpliced_seg_modifier_Base::m_choice, CSpliced_seg_modifier_Base::m_Start_codon_found, and CSpliced_seg_modifier_Base::m_Stop_codon_found.
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Access to EProduct_type's attributes (values, names) as defined in spec.
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static |
Access to EType's attributes (values, names) as defined in spec.
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inline |
Get the member data.
Definition at line 165 of file Score_set_.hpp.
References CScore_set_Base::m_data.
Referenced by CScore_EdgeExonInfo::Get(), s_ExonToDenseg(), CGff3Writer::xAssignAlignmentSplicedScores(), and CGff3FlybaseWriter::xAssignAlignmentSplicedScores().
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inline |
Get the member data.
Definition at line 166 of file Seq_align_set_.hpp.
References CSeq_align_set_Base::m_data.
Referenced by CAlnMix::Add(), CSeqsRange::Add(), CVDBBlastUtil::AddSubjectsToScope(), CContigAssembly::Align(), CAlnGraphic::AlnGraphicDisplay(), BOOST_AUTO_TEST_CASE(), BuildAlignDataSource(), COligoSpecificityTemplate::COligoSpecificityTemplate(), Convert_Seq_align_set_Seq_align(), Convert_Seq_align_set_Seq_loc(), CreateEmptySeq_align_set(), CTableDataAlnSummary::CTableDataAlnSummary(), CDisplaySeqalign::DisplaySeqalign(), ExtractFirstSeqAlign(), CAlignFormatUtil::ExtractQuerySeqAlign(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CSeqAlignFilter::FilterByAccessionType(), CSeqAlignFilter::FilterByGiList(), CSeqAlignFilter::FilterByGiListFromFile(), CSeqAlignFilter::FilterByTaxonomy(), CAlignFormatUtil::FilterSeqalignByEval(), CAlignFormatUtil::FilterSeqalignByPercentIdent(), CAlignFormatUtil::FilterSeqalignBySeqList(), TestUtil::FlattenSeqAlignSet(), CBlastAligner::GenerateAlignments(), CRemoteBlastAligner::GenerateAlignments(), CMergeAligner::GenerateAlignments(), CMergeTreeAligner::GenerateAlignments(), CFileLoadAligner::GenerateAlignments(), CAlignmentCollectionScore::Get(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CAlignFormatUtil::GetDbType(), CShowBlastDeflineTest::GetDeflineInfo(), CAlignFormatUtil::GetMasterCoverage(), CAlignFormatUtil::GetSeqAlignSetCalcParams(), CAlignFormatUtil::GetSeqAlignSetCalcParamsFromASN(), CAlignFormatUtil::GetSeqAlignSetCalcPercentIdent(), CRemoteBlast::GetSeqAlignSets(), CSeq_align::GetSeqStrand(), CAlignFormatUtil::GetSubjectsNumber(), CAlignFormatUtil::GetUniqSeqCoverage(), CAlnGraphic::Init(), CAlnContainer::insert(), CAlignResultsSet::Insert(), CBlastFormatUtil::InsertSubjectScores(), JoinCompartment(), CAlignFormatUtil::LimitSeqalignByHsps(), MakeSubjectScores(), CSortHitByMolecularTypeEx::operator()(), PatchTargetSequence(), CDisplaySeqalign::PrepareBlastUngappedSeqalign(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx(), CBlast_SAM_Formatter::Print(), CIgBlastTabularInfo::PrintHeader(), CBlastTabularInfo::PrintHeader(), CBlastFormat::PrintOneResultSet(), PrintSAM(), PrintTabular(), CAlignFormatUtil::PruneSeqalign(), CAlignFormatUtil::PruneSeqalignAll(), NBestPlacement::Rank(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), CMergeyApp::Run(), CNgAlignApp::Run(), CAlignCleanupApplication::Run(), CFarPointerSeq::RunBlast(), CCreateSeqHistForTpa::RunBlast(), CAdvancedAlignCleanup::RunSplignOnCompartment(), CTestSingleAln_All::RunTest(), s_AlignSet2Annot(), s_AlignToSeqRanges(), s_BlastResults2SeqAlignDatabaseSearch_OMF(), s_BuildArchiveAll(), s_CombineSearchSets(), CPsiBlastTestFixture::s_CountNumberUniqueGIs(), s_CountSegments(), s_ExtractSeqId(), s_Fingerprint_Seq_align_set(), s_GetAlignmentLength(), s_GetAlignmentSpans_Exon(), s_GetAlignmentSpans_Interval(), s_GetAlignmentTooltip(), s_GetCountIdentityMismatch(), s_GetGapCount(), SAlignmentScoringModel::s_GetIdentOdds_disc(), s_GetIndels(), s_GetJoinedAlignment(), s_ProcessAlignSet(), s_Render_PairwiseAlign(), s_RunBlast2NASeq(), s_Seq_align_Seq_loc(), s_SeqAlignSetToXMLHits(), s_SeqAlignSetToXMLHsps(), s_SeqAlignToBlastSeqLoc(), s_SeqAlignToXMLHit(), s_SplitAlignVectorBySubjects(), s_TestCalc(), s_TestStdSegGaps(), CAlignmentCollectionScore::Set(), CIgBlastTabularInfo::SetAirrFormatData(), CIgBlastTabularInfo::SetIgAnnotation(), CSeq_align_set::Size(), CAlignFormatUtil::SortHitByMasterCoverageDescending(), CAlignFormatUtil::SortHitByMasterStartAscending(), CAlignFormatUtil::SortHitByScoreDescending(), CAlignFormatUtil::SortHitByTotalScoreDescending(), CSeq_align::SplitOnLongDiscontinuity(), sRunTest(), sUpdateCase(), testNuclHitList(), testResultAlignments(), CAlignResultsSet::ToBestSeqAlignSet(), CValidError_align::ValidateSeqAlign(), CPslWriter::WriteAlign(), CAlnTableDS::x_AddAlign(), CSeq_annot_Info::x_AddAlignKeys(), CQuerySet::x_AlreadyContains(), CIgBlast::x_AnnotateC(), CIgBlast::x_AnnotateD(), CIgBlast::x_AnnotateDJ(), CIgBlast::x_AnnotateJ(), CMagicBlast::x_BuildResultSet(), CMagicBlast::x_BuildSeqAlignSet(), CTabularFormatter_BiggestGapBases::x_CalcBiggestGap(), CPrimaryItem::x_CollectSegments(), x_CollectSegments(), CQuerySet::x_ContainsAlignment(), CDeltaBlastTestFixture::x_CountNumberUniqueIds(), CCleanupAlignmentsJob::x_CreateProjectItems(), CSplignJob::x_CreateProjectItems(), CIgBlast::x_FindDJ(), CIgBlast::x_FindDJAln(), CTracebackSearchTestFixture::x_FindUsedGis(), CCIGAR_Formatter::x_FormatAlignmentRows(), CProSplignJob::x_GenerateCompartments(), CInstancedAligner::x_GetCleanupInstances(), CInstancedAligner::x_GetDistanceInstances(), CShowBlastDefline::x_GetScoreInfoForTable(), CCommonComponentScorer::x_GetSeqHistCompList(), CIdMapperTestApp::x_HandleAlignments(), CInversionMergeAligner::x_HandleSingleStrandMerging(), CSeq_align_Mapper_Base::x_Init(), CPhyTreeCalc::x_InitAlignDS(), CDisplaySeqalign::x_InitAlignParams(), CSeq_loc_Mapper_Base::x_InitializeAlign(), CTreeAlignMerger::x_MakeMergeableGroups(), CMergeAligner::x_MergeAlignments(), CVecscreen::x_MergeLowerRankSeqalign(), CVecscreen::x_MergeSeqalign(), CInversionMergeAligner::x_MergeSeqAlignSet(), CMergeAligner::x_MergeSeqAlignSet(), CInstancedAligner::x_MinCoverageCheck(), CBlast_SAM_Formatter::x_Print(), CBlastFormat::x_PrintIgTabularReport(), CNgAlignApp::x_PrintNoHitList(), CBlastFormat::x_PrintTabularReport(), CIgBlast::x_ProcessCResult(), CAppHitFilter::x_ReadInputHits(), CTabularFormatter_DiscStrand::x_RecurseStrands(), CInstancedAligner::x_RunAligner(), CInversionMergeAligner::x_RunMerger(), CMultiAligner::x_SetDomainHits(), CMagicBlastResults::x_SetInfo(), COligoSpecificityTemplate::x_SortHit(), CInversionMergeAligner::x_SplitAlignmentsByStrand(), CBlastFormat::x_SplitSeqAlign(), CHitMatrixDataSource::x_TestAndSelectAlign(), CAnnotWriterApp::xProcessInputObject(), and CGff3Writer::xWriteAlignDisc().
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inline |
Get the Acceptor_before_exon member data.
Definition at line 1036 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::CanGetAcceptor_before_exon(), CSpliced_exon_Base::m_Acceptor_before_exon, and CSerialObject::ThrowUnassigned().
Referenced by CProteinAlignText::CProteinAlignText(), CScore_IndelToSplice::Get(), GetExonPartialness(), CAlignGlyph::x_DrawNonConsensusSpliceSites(), CSeq_align_Mapper_Base::x_GetDstExon(), and CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons().
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inline |
Get the Amin member data.
Definition at line 220 of file Prot_pos_.hpp.
References CProt_pos_Base::CanGetAmin(), CProt_pos_Base::m_Amin, and CSerialObject::ThrowUnassigned().
Referenced by CSeqsRange::Add(), CProduct_pos::AsSeqPos(), BOOST_AUTO_TEST_CASE(), variation_ref::CVariationUtil::CheckExonBoundary(), variation::CVariationUtil::CheckExonBoundary(), CFeatureGenerator::SImplementation::MaximizeTranslation(), CProSplign::CImplementation::SeekStartStop(), CAlnSpanVertModel::x_PopulateRowsSpliced(), and CAnnotObject_Info::x_ProcessAlign().
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inline |
Get the Bases member data.
Definition at line 174 of file Splice_site_.hpp.
References CSplice_site_Base::CanGetBases(), CSplice_site_Base::m_Bases, and CSerialObject::ThrowUnassigned().
Referenced by CProteinAlignText::CProteinAlignText(), CScore_IndelToSplice::Get(), GetExonPartialness(), CAlignGlyph::x_DrawNonConsensusSpliceSites(), and CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons().
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Get the Bounds member data.
Definition at line 951 of file Seq_align_.hpp.
References CSeq_align_Base::m_Bounds.
Referenced by CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CSeq_align_Handle::GetBounds(), CSeq_align_Mapper_Base::GetDstAlign(), CProteinAlignText::GetGenomicBounds(), and CSeq_align_Mapper_Base::x_GetDstSpliced().
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Get the variant data.
Definition at line 726 of file Seq_align_.hpp.
Referenced by CSeqsRange::Add(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CRemoveSeqFromAlignDlg::GetAlignLabel(), GetBlockCount(), GetDDSetFromSeqAlign(), GetMasterGIFromSeqAlign(), GetReportableSeqIdForAlignment(), CAlignFormatUtil::GetSeqAlignSetCalcParamsFromASN(), CSeq_align::GetSeqStrand(), CCdCore::Has3DMaster(), CCdCore::HasSeqId(), CDisplaySeqalign::PrepareBlastUngappedSeqalign(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx2(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), s_DivvyUpAlignments_ProcessAnnot_Dendiag(), s_Fingerprint_Seq_align(), s_GetAlnScores(), s_GetSubjectId(), CValidError_align::ValidateSeqAlign(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignFillerBlocks(), CValidError_align::x_GetIds(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitializeAlign(), and CAnnotObject_Info::x_ProcessAlign().
const CSeq_align_Base::C_Segs::TDenseg & CSeq_align_Base::C_Segs::GetDenseg | ( | void | ) | const |
Get the variant data.
Definition at line 153 of file Seq_align_.cpp.
Referenced by CAlnMix::Add(), CSeqsRange::Add(), CAlnVwrApp::AddAlnToMix(), CAlignmentAssistant::AdjustAlign(), CPaintAlignment::AlignPosToSeqPos(), CFeaturePropagator::AlignPosToSeqPos(), BOOST_AUTO_TEST_CASE(), BuildAlignDataSource(), CSeq_align::CheckNumRows(), CDUpdater::ComputePercentIdentity(), CAlignmentAssistant::CreateFeature(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CAlignCleanup::CreatePairwiseFromMultiple(), CFeaturePropagator::CreateRowSeq_loc(), CSeq_align::CreateTranslatedDensegFromNADenseg(), CAlignmentAssistant::DeleteSelection(), Denseg2DenseDiagList(), CDisplaySeqalign::DisplaySeqalign(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CEditSeqEndsWithAlign::FindPosition(), CFeaturePropagator::FindRow(), CSeq_align::GapLengthRange(), CSeq_align::GetAlignedBases(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CAlignFormatUtil::GetAlignmentLength(), CScoreBuilder::GetBlastScoreDenseg(), CAlignmentAssistant::GetFeatures(), GetMasterGIFromSeqAlign(), GetPssmIdFromSeqAlign(), CPaintAlignment::GetSegments(), CSeq_align::GetSeq_id(), CAlignFormatUtil::GetSeqAlignSetCalcParamsFromASN(), CSeq_align::GetSeqRange(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStop(), CSeq_align::GetSeqStrand(), CAlignFormatUtil::GetUniqSeqCoverage(), CScoreUniqSeqCoverage::MakeScore(), CRemoveSeqFromAlignDlg::ModifyAlign(), CAlignmentAssistant::OnPropagateFeatures(), CAlignmentAssistant::OnRemoveSeqFromAlign(), CTabularFormatter_Cigar::Print(), PrintSAM(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), CAlignmentAssistant::ReportUnresolvedBioseqs(), CTestBlastp_All::RunTest(), CTestSingleAln_All::RunTest(), s_AlignToSeqRanges(), s_CheckTraceMateAlign(), s_ComputeTraceback(), s_CoverageSeqLoc(), s_CutDensegSegment(), s_DivvyUpAlignments_ProcessAnnot(), s_DivvyUpAlignments_ProcessAnnot_Denseg(), s_Fingerprint_Seq_align(), s_GetAlignmentContent(), s_GetAlignmentLength(), s_GetAlignmentTooltip(), s_GetAlnScores(), s_GetCigarString(), s_GetCountIdentityMismatch(), s_GetGapCount(), s_GetIndels(), s_GetSubjectId(), s_IsProteinToGenomic(), s_Seq_align_Seq_loc(), s_SeqAlignSetToXMLHsps(), s_SetAirrAlignmentInfo(), s_TestAlignmentFromMSAs(), s_TestCalc(), s_TestResultAlignment(), COverlapScorer::ScoreAlignments(), CClippedScorer::ScoreAlignments(), SeqAlignConvert(), CPaintAlignment::SeqPosToAlignPos(), CFeaturePropagator::SeqPosToAlignPos(), CBlastTabularInfo::SetFields(), CIgBlastTabularInfo::SetIgAnnotation(), CSeq_align::SplitOnLongDiscontinuity(), CAlignmentAssistant::TranslateLocations(), CReportTrim::TrimAlignments(), TrimSeqAlign(), TrimSequenceAndAnnotation(), UpdateDensegAlignment(), CSeq_align::Validate(), CValidError_align::ValidateSeqAlign(), CAlnWriter::WriteAlign(), CPslWriter::WriteAlign(), CVectorTrimPanel::x_AdjustDensegAlignment(), CReportTrim::x_AdjustDensegAlignment(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignFillerBlocks(), CIgBlast::x_AnnotateC(), CIgBlast::x_AnnotateDomain(), CTabularFormatter_BiggestGapBases::x_CalcBiggestGap(), CAlignCleanup::x_Cleanup_AlignVec(), CQuerySet::x_ContainsAlignment(), CInversionMergeAligner::x_CreateDiscAlignment(), CHitMatrixDataSource::x_CreateHit_Denseg(), CTreeBuilderJob::x_CreateProjectItems(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), COligoSpecificityCheck::x_FillGlobalAlignInfo(), CIgBlast::x_FillJDomain(), CMultiAligner::x_FindRPSHits(), CCIGAR_Formatter::x_FormatAlignmentRows(), CApplyRNAITSDlg::x_GetAlignments(), CValidError_align::x_GetIds(), COligoSpecificityCheck::x_GetSlaveRangeGivenMasterRange(), CSeq_align_Mapper_Base::x_Init(), CPhyTreeCalc::x_InitAlignDS(), CUpdateSeqPanel::x_InitDrawingParams(), CSeq_loc_Mapper_Base::x_InitializeAlign(), CUnorderedSplitter::x_MakeAlignmentPairUnique(), COligoSpecificityCheck::x_NW_alignment(), CAnnotObject_Info::x_ProcessAlign(), CApplyRNAITSDlg::x_SeqIdsAlignedWith(), CMultiAligner::x_SetDomainHits(), CApplyRNAITSDlg::x_SetupAlnMgr(), x_TestAlignmentQuerySubjStrandCombinations(), CVectorTrimPanel::x_TrimAlignments(), CValidError_align::x_ValidateAlignPercentIdentity(), CPsiBl2SeqTestFixture::x_ValidatePssmVsGi129295(), CPsiBl2SeqTestFixture::x_ValidatePssmVsGi7450545(), and CGff3Writer::xWriteAlignDenseg().
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Get the variant data.
Definition at line 410 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::CheckSelected(), CSpliced_exon_chunk_Base::e_Diag, and CSpliced_exon_chunk_Base::m_Diag.
Referenced by ChunkSize(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CScore_IndelToSplice::Get(), CSpliced_exon::GetRowSeq_insertions(), CProSplign::CImplementation::HasStartOnNuc(), ProjectExon_oldlogic(), s_ExonToDenseg(), s_GetCountIdentityMismatch(), SBlocks::SBlocks(), CSeq_loc_Mapper_Base::sx_GetExonPartLength(), CSpliced_seg::Validate(), CReportEntry::x_CheckExonGap(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CGff3Writer::xAssignAlignmentSplicedGap(), and CGff3FlybaseWriter::xAssignAlignmentSplicedGap().
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Get the Dim member data.
Definition at line 373 of file Dense_diag_.hpp.
References CDense_diag_Base::m_Dim.
Referenced by CSeqsRange::Add(), CDense_diag::CheckNumRows(), ConvertDendiagToPairwiseAln(), CDense_diag::CreateRowSeq_interval(), CDense_diag::GetSeqStart(), CDense_diag::GetSeqStrand(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), CDense_diag::OffsetRow(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CAnnotObject_Info::x_ProcessAlign(), CValidError_align::x_ValidateDendiag(), and CValidError_align::x_ValidateSeqLength().
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Get the Dim member data.
Definition at line 421 of file Dense_seg_.hpp.
References CDense_seg_Base::m_Dim.
Referenced by CSeqsRange::Add(), CAlnMixMatches::Add(), CAlnMixSequences::Add(), CAlignmentAssistant::AdjustAlign(), CPaintAlignment::AlignPosToSeqPos(), CFeaturePropagator::AlignPosToSeqPos(), BOOST_AUTO_TEST_CASE(), CDense_seg::CheckNumRows(), CDense_seg::CheckNumSegs(), CDense_seg::Compact(), ConvertDensegToPairwiseAln(), ConvertToPairwise(), CreateAlignRow(), CSeq_align::CreateDensegFromDisc(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CAlignCleanup::CreatePairwiseFromMultiple(), CDense_seg::CreateRowSeq_interval(), CFeaturePropagator::CreateRowSeq_loc(), CSeq_align::CreateTranslatedDensegFromNADenseg(), CAlignmentAssistant::DeleteSelection(), Denseg2DenseDiagList(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CDense_seg::ExtractSlice(), CFeaturePropagator::FindRow(), CSeq_align::GapLengthRange(), CSeq_align::GetAlignedBases(), CAlignmentAssistant::GetFeatures(), CPaintAlignment::GetSegments(), CPhyTreeCalc::GetSeqAlign(), CDense_seg::GetSeqStart(), CDense_seg::GetSeqStop(), CValidError_align::IsTpaAlignment(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), CDense_seg::OffsetRow(), CAlignmentAssistant::OnReverseStrand(), CDense_seg::OrderAdjacentGaps(), CDense_seg::CReserveHook::PreReadClassMember(), CAlnAsnReader::Read(), CDenseSegReserveStartsHook::ReadClassMember(), CDenseSegReserveStrandsHook::ReadClassMember(), CDense_seg::RemapToLoc(), CAlignmentAssistant::ReportUnresolvedBioseqs(), CDense_seg::Reverse(), ReverseAlignmentStrand(), s_AlignToSeqRanges(), s_CalculateMatchingColumns(), s_CompressDiscToDenseq(), s_CoverageSeqLoc(), s_CutDensegSegment(), s_DenseSegLength(), s_FindSegment(), s_GetAlignmentLength(), s_GetGapCount(), s_GetIndels(), s_GetNumIdsToUse(), s_Seq_align_Seq_loc(), s_SeqAlignToBlastSeqLoc(), s_TestAlignmentFromMSAs(), COverlapScorer::ScoreAlignments(), CPaintAlignment::SeqPosToAlignPos(), CFeaturePropagator::SeqPosToAlignPos(), CDense_seg::SwapRows(), CAlignmentAssistant::TranslateLocations(), CReportTrim::TrimAlignments(), CDense_seg::TrimEndGaps(), TrimSeqAlign(), CAlnWriter::WriteAlignDenseSeg(), CVectorTrimPanel::x_AdjustDensegAlignment(), CReportTrim::x_AdjustDensegAlignment(), CAlignCleanup::x_Cleanup_AlignVec(), CInversionMergeAligner::x_CreateDiscAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CAppHitFilter::x_DumpOutput(), CAlnMix::x_ExtendDSWithWidths(), CVectorTrimPanel::x_FindSegment(), CReportTrim::x_FindSegment(), CDense_seg::x_FindSegment(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CInversionMergeAligner::x_IsAllGap(), CUnorderedSplitter::x_IsAllGap(), CInversionMergeAligner::x_MergeSeqAlignSet(), CMergeAligner::x_MergeSeqAlignSet(), CInstancedAligner::x_RunCleanup(), x_TestAlignmentQuerySubjStrandCombinations(), CVectorTrimPanel::x_TrimAlignments(), CValidError_align::x_ValidateAlignPercentIdentity(), and CPslRecord::xValidateSegment().
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Get the Dim member data.
Definition at line 445 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_Dim.
Referenced by CSeqsRange::Add(), ConvertPackedsegToPairwiseAln(), CSeq_align_Mapper_Base::x_Init(), and CSeq_loc_Mapper_Base::x_InitAlign().
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Get the Dim member data.
Definition at line 856 of file Seq_align_.hpp.
References CSeq_align_Base::CanGetDim(), CSeq_align_Base::m_Dim, and CSerialObject::ThrowUnassigned().
Referenced by BOOST_AUTO_TEST_CASE(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CDesktopAlignItem::GetDescription(), CSeq_align_Handle::GetDim(), CSeq_align_Mapper_Base::GetDstAlign(), GetPssmIdFromSeqAlign(), GetReportableSeqIdForAlignment(), CSeq_align::GetSeqRange(), CValidError_imp::PostErr(), CDesktopAlignItem::s_ContainsFarPointers(), s_TestCalc(), s_TestResultAlignment(), CLDS2_AnnotType_Hook::SkipObject(), CSeq_align::SplitOnLongDiscontinuity(), and CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile().
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Get the Dim member data.
Definition at line 295 of file Std_seg_.hpp.
References CStd_seg_Base::m_Dim.
Referenced by CStd_seg::CheckNumRows(), CSeq_align::CreateDensegFromStdseg(), CStd_seg::CreateRowSeq_loc(), CStdSegHit::CStdSegHit(), CStd_seg::GetSeqRange(), CStd_seg::GetSeqStart(), CStd_seg::GetSeqStop(), CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()(), CStd_seg::RemapToLoc(), s_GetAlignmentLength(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), and CValidError_align::x_ValidateStd().
const CSeq_align_Base::C_Segs::TDisc & CSeq_align_Base::C_Segs::GetDisc | ( | void | ) | const |
Get the variant data.
Definition at line 197 of file Seq_align_.cpp.
Referenced by CAlnMix::Add(), CSeqsRange::Add(), BuildAlignDataSource(), ExtractFirstSeqAlign(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CAlignFormatUtil::ExtractSeqalignSetFromDiscSegs(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CSeq_align::GetSeqStrand(), CAlnContainer::insert(), PatchTargetSequence(), PrintSAM(), PrintTabular(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), CTestSingleAln_All::RunTest(), s_AlignToSeqRanges(), s_CountSegments(), s_ExtractSeqId(), s_Fingerprint_Seq_align(), s_GetAlignmentLength(), s_GetAlignmentSpans_Exon(), s_GetAlignmentSpans_Interval(), s_GetAlignmentTooltip(), s_GetCountIdentityMismatch(), s_GetGapCount(), SAlignmentScoringModel::s_GetIdentOdds_disc(), s_GetIndels(), s_Render_PairwiseAlign(), s_ScoreAlignments(), s_Seq_align_Seq_loc(), s_SeqAlignToXMLHit(), CSeq_align::SplitOnLongDiscontinuity(), CValidError_align::ValidateSeqAlign(), CPslWriter::WriteAlign(), CAlnTableDS::x_AddAlign(), CSeq_annot_Info::x_AddAlignKeys(), CTabularFormatter_BiggestGapBases::x_CalcBiggestGap(), CPrimaryItem::x_CollectSegments(), x_CollectSegments(), CQuerySet::x_ContainsAlignment(), CCleanupAlignmentsJob::x_CreateProjectItems(), CCIGAR_Formatter::x_FormatAlignmentRows(), CCommonComponentScorer::x_GetSeqHistCompList(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitializeAlign(), CTreeAlignMerger::x_MakeMergeableGroups(), CAnnotObject_Info::x_ProcessAlign(), CAppHitFilter::x_ReadInputHits(), CTabularFormatter_DiscStrand::x_RecurseStrands(), CHitMatrixDataSource::x_TestAndSelectAlign(), and CGff3Writer::xWriteAlignDisc().
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Get the Donor_after_exon member data.
Definition at line 1057 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::CanGetDonor_after_exon(), CSpliced_exon_Base::m_Donor_after_exon, and CSerialObject::ThrowUnassigned().
Referenced by CProteinAlignText::CProteinAlignText(), CScore_IndelToSplice::Get(), GetExonPartialness(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CAlignGlyph::x_DrawNonConsensusSpliceSites(), CSeq_align_Mapper_Base::x_GetDstExon(), and CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons().
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Get the Exons member data.
Definition at line 692 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_Exons.
Referenced by CSeqsRange::Add(), CFeatureGenerator::SImplementation::AdjustAlignment(), CSpliced_seg::AsDiscSeg(), BOOST_AUTO_TEST_CASE(), variation_ref::CVariationUtil::CheckExonBoundary(), variation::CVariationUtil::CheckExonBoundary(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CSeq_align::CreateRowSeq_loc(), CInternalStopFinder::FindStartStopRanges(), CScore_InternalUnaligned::Get(), CScore_ExonCount::Get(), CScore_IndelToSplice::Get(), CScore_LastSpliceSite::Get(), CScore_EdgeExonInfo::Get(), CScoreBuilder::GetBlastScoreSpliced(), CInternalStopFinder::GetCDSNucleotideSequence(), GetExonPartialness(), SAlignmentScoringModel::GetExonsOdds(), CFeatureGenerator::SImplementation::GetExonStructure(), CProteinAlignText::GetGenomicBounds(), SAlignmentScoringModel::GetLongestMatchrunLen(), SAlignmentScoringModel::GetNumGapopensBetweenExons(), CProductStringBuilder::GetProductString(), CSpliced_seg::GetSeqRange(), CSpliced_seg::GetSeqStart(), CSpliced_seg::GetSeqStop(), CSpliced_seg::GetSeqStrand(), SAlignmentScoringModel::GetSplicesOdds(), GetTerminalPartialness(), CFeatureGenerator::SImplementation::HasMixedGenomicIds(), CProSplign::CImplementation::HasStartOnNuc(), CProSplign::CImplementation::HasStopOnNuc(), CSpliced_seg::IsConsistentBiologicalOrder(), CTabularFormatter_MismatchPositions::Print(), CTabularFormatter_ExonIntrons::Print(), PrintSAM(), ProjectExons(), variation::CVariationUtil::s_AddIntronicOffsets(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), s_AlignToSeqRanges(), s_CountSegments(), s_Fingerprint_Spliced_seg(), s_GetAlignmentLength(), s_GetAlignmentMismatches(), s_GetAlignmentSpans_Exon(), s_GetAlignmentSpans_Intron(), s_GetCountIdentityMismatch(), s_GetGapCount(), SAlignmentScoringModel::s_GetIdentOdds_nucSS(), s_SplicedToDisc(), CReportEntry::SetAlignment(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSpliced_seg::Validate(), CAlnWriter::WriteAlignSplicedSeg(), CReportEntry::x_CheckExonGap(), CAdvancedAlignCleanup::x_CleanupProsplignCompartment(), CAlignGlyph::x_DrawNonConsensusSpliceSites(), CSeq_align_Mapper_Base::x_GetDstExon(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitSpliced(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CCDSTranslationPanel::x_SetLocationForProtein(), CPslRecord::xInitializeBlocks(), CPslRecord::xInitializeBlocksStrandNegative(), CPslRecord::xInitializeBlocksStrandPositive(), CPslRecord::xInitializeStats(), CPslRecord::xValidateSegment(), and CGff3Writer::xWriteAlignSpliced().
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Get the Ext member data.
Definition at line 1001 of file Seq_align_.hpp.
References CSeq_align_Base::m_Ext.
Referenced by BOOST_AUTO_TEST_CASE(), CSGAlignmentJob::FilterDuplicatesAndBadReads(), CSeq_align::FindExt(), CSeq_align_Mapper_Base::GetDstAlign(), CProductStringBuilder::GetProductString(), CScoreBuilder::GetTraceback(), IsGnomonConstructed(), CTabularFormatter_BestPlacementGroup::Print(), CTabularFormatter_AssemblyInfo::Print(), CDemoApp::Run(), s_CheckTraceMateAlign(), and s_PopulateExtSet().
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Get the Ext member data.
Definition at line 359 of file Sparse_seg_.hpp.
References CSparse_seg_Base::m_Ext.
Referenced by CRemoveSeqFromAlignDlg::ModifyAlign(), and s_Fingerprint_Sparse_seg().
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Get the Ext member data.
Definition at line 1125 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Ext.
Referenced by CSeq_align_Mapper_Base::x_GetDstExon().
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Get the First_id member data.
Definition at line 431 of file Sparse_align_.hpp.
References CSparse_align_Base::m_First_id, and CSparse_align_Base::ResetFirst_id().
Referenced by CSeqsRange::Add(), ConvertToPairwise(), CreateAlignRow(), GetAlignColl(), CSparse_seg::GetSeq_id(), CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()(), s_Fingerprint_Sparse_align(), CAlnWriter::WriteSparseAlign(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitSparse(), and CAnnotObject_Info::x_ProcessAlign().
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Get the First_starts member data.
Definition at line 538 of file Sparse_align_.hpp.
References CSparse_align_Base::m_First_starts.
Referenced by CSeqsRange::Add(), CSparse_align::CheckNumSegs(), ConvertSparseToPairwiseAln(), CreateAlignRow(), GetAlignColl(), CSparse_seg::GetSeqRange(), CSparse_seg::GetSeqStart(), CSparse_seg::GetSeqStop(), s_Fingerprint_Sparse_align(), CAlnWriter::WriteSparseAlign(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitSparse(), and CAnnotObject_Info::x_ProcessAlign().
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Get the Frame member data.
Definition at line 273 of file Prot_pos_.hpp.
References CProt_pos_Base::m_Frame.
Referenced by CProt_pos::GetFrame().
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Get the Genomic_end member data.
Definition at line 814 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::CanGetGenomic_end(), CSpliced_exon_Base::m_Genomic_end, and CSerialObject::ThrowUnassigned().
Referenced by CSeqsRange::Add(), CFeatureGenerator::SImplementation::AdjustAlignment(), BOOST_AUTO_TEST_CASE(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CSeq_align::ExonLengthRange(), CScore_EdgeExonInfo::Get(), CFeatureGenerator::SImplementation::GetExonStructure(), CSpliced_exon::GetRowSeq_range(), CProSplign::CImplementation::HasStartOnNuc(), CProSplign::CImplementation::HasStopOnNuc(), CSeq_align_Mapper_Base::InitExon(), CSeq_align::IntronLengthRange(), CSpliced_seg::IsConsistentBiologicalOrder(), CTabularFormatter_ExonIntrons::Print(), ProjectExon_newlogic(), variation::CVariationUtil::s_AddIntronicOffsets(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), s_ExonToDenseg(), s_GetAlignmentMismatches(), s_GetAlignmentSpans_Exon(), s_ValidateExon(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExon(), CReportEntry::x_CheckExonGap(), CAlignGlyph::x_DrawNonConsensusSpliceSites(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CSeq_loc_Mapper_Base::x_InitSpliced(), CAnnotObject_Info::x_ProcessAlign(), CGff3Writer::xAssignAlignmentSplicedLocation(), and CGff3FlybaseWriter::xAssignAlignmentSplicedTarget().
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Get the Genomic_id member data.
Definition at line 875 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::CanGetGenomic_id(), CSpliced_exon_Base::m_Genomic_id, and CSerialObject::ThrowUnassigned().
Referenced by CSeqsRange::Add(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CSpliced_exon::CreateRowSeq_interval(), CFeatureGenerator::SImplementation::HasMixedGenomicIds(), CSeq_align_Mapper_Base::InitExon(), ProjectExon_newlogic(), s_ExonToDenseg(), s_Fingerprint_Spliced_exon(), CSeq_loc_Mapper_Base::x_InitSpliced(), and CAnnotObject_Info::x_ProcessAlign().
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Get the Genomic_id member data.
Definition at line 530 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::CanGetGenomic_id(), CSpliced_seg_Base::m_Genomic_id, and CSerialObject::ThrowUnassigned().
Referenced by CSeqsRange::Add(), CFeatureGenerator::SImplementation::AdjustAlignment(), CSpliced_seg::AsDiscSeg(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CSpliced_exon::CreateRowSeq_interval(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CFeatureGenerator::SImplementation::GetExonStructure(), CProteinAlignText::GetGenomicBounds(), CFeatureGenerator::SImplementation::HasMixedGenomicIds(), CProSplign::CImplementation::HasStartOnNuc(), CProSplign::CImplementation::HasStopOnNuc(), CSeq_align_Mapper_Base::InitExon(), CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()(), CProSplignText::Output(), variation_ref::CVariationUtil::Remap(), variation::CVariationUtil::Remap(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), variation::CVariationUtil::s_AddIntronicOffsets(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), s_Fingerprint_Spliced_seg(), s_GetAlignmentContent(), s_SplicedToDisc(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CAlnWriter::WriteAlignSplicedSeg(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CAlnSpanVertModel::x_Init(), CSeq_loc_Mapper_Base::x_InitSpliced(), CGff3Writer::xAssignAlignmentSplicedMethod(), CGff3Writer::xAssignAlignmentSplicedSeqId(), CGff3FlybaseWriter::xAssignAlignmentSplicedTarget(), CGff3Writer::xAssignAlignmentSplicedType(), and CPslRecord::xInitializeSequenceInfo().
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Get the variant data.
Definition at line 464 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::CheckSelected(), CSpliced_exon_chunk_Base::e_Genomic_ins, and CSpliced_exon_chunk_Base::m_Genomic_ins.
Referenced by CScoreBuilderBase::AddSplignScores(), BOOST_AUTO_TEST_CASE(), ChunkSize(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CSpliced_exon::GetRowSeq_insertions(), CFeatureGenerator::SImplementation::MaximizeTranslation(), ProjectExon_oldlogic(), CSplign::s_ComputeStats(), s_ExonToDenseg(), SBlocks::SBlocks(), sExonChunkAppendStats(), CSeq_loc_Mapper_Base::sx_GetExonPartLength(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExonPart(), CReportEntry::x_CheckExonGap(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CGff3Writer::xAssignAlignmentSplicedGap(), and CGff3FlybaseWriter::xAssignAlignmentSplicedGap().
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Get the Genomic_start member data.
Definition at line 767 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::CanGetGenomic_start(), CSpliced_exon_Base::m_Genomic_start, and CSerialObject::ThrowUnassigned().
Referenced by CSeqsRange::Add(), CFeatureGenerator::SImplementation::AdjustAlignment(), BOOST_AUTO_TEST_CASE(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CSeq_align::ExonLengthRange(), CScore_EdgeExonInfo::Get(), CFeatureGenerator::SImplementation::GetExonStructure(), CSpliced_exon::GetRowSeq_range(), CProSplign::CImplementation::HasStartOnNuc(), CProSplign::CImplementation::HasStopOnNuc(), CSeq_align_Mapper_Base::InitExon(), CSeq_align::IntronLengthRange(), CSpliced_seg::IsConsistentBiologicalOrder(), CTabularFormatter_ExonIntrons::Print(), ProjectExon_newlogic(), variation::CVariationUtil::s_AddIntronicOffsets(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), s_ExonToDenseg(), s_GetAlignmentMismatches(), s_GetAlignmentSpans_Exon(), s_ValidateExon(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExon(), CReportEntry::x_CheckExonGap(), CAlignGlyph::x_DrawNonConsensusSpliceSites(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CSeq_loc_Mapper_Base::x_InitSpliced(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CAnnotObject_Info::x_ProcessAlign(), CGff3Writer::xAssignAlignmentSplicedLocation(), and CGff3FlybaseWriter::xAssignAlignmentSplicedTarget().
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Get the Genomic_strand member data.
Definition at line 950 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::CanGetGenomic_strand(), CSpliced_exon_Base::m_Genomic_strand, and CSerialObject::ThrowUnassigned().
Referenced by CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), ConvertSplicedToPairwiseAln(), CSpliced_exon::CreateRowSeq_interval(), CSpliced_exon::GetRowSeq_insertions(), CSeq_align_Mapper_Base::InitExon(), CSpliced_seg::IsConsistentBiologicalOrder(), ProjectExon_newlogic(), s_ExonToDenseg(), s_GetAlignmentMismatches(), CSeq_align_Mapper_Base::x_GetDstExon(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CSeq_loc_Mapper_Base::x_InitSpliced(), CAnnotObject_Info::x_ProcessAlign(), and CGff3Writer::xAssignAlignmentSplicedLocation().
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Get the Genomic_strand member data.
Definition at line 605 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::CanGetGenomic_strand(), CSpliced_seg_Base::m_Genomic_strand, and CSerialObject::ThrowUnassigned().
Referenced by CSpliced_seg::AsDiscSeg(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CSpliced_exon::CreateRowSeq_interval(), CProteinAlignText::GetGenomicBounds(), CSpliced_exon::GetRowSeq_insertions(), CSpliced_seg::GetSeqStrand(), CProSplign::CImplementation::HasStartOnNuc(), CProSplign::CImplementation::HasStopOnNuc(), CSeq_align_Mapper_Base::InitExon(), CSpliced_seg::IsConsistentBiologicalOrder(), CProSplignText::Output(), s_GetAlignmentMismatches(), s_GetAlignmentSpans_Intron(), s_SplicedToDisc(), CReportEntry::SetAlignment(), CAlnWriter::WriteAlignSplicedSeg(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CSeq_loc_Mapper_Base::x_InitSpliced(), CCDSTranslationPanel::x_SetLocationForProtein(), CGff3Writer::xAssignAlignmentSplicedLocation(), CGff3FlybaseWriter::xAssignAlignmentSplicedTarget(), and CPslRecord::xInitializeStrands().
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Get the Id member data.
Definition at line 444 of file Score_.hpp.
References CScore_Base::CanGetId(), CScore_Base::m_Id, and CSerialObject::ThrowUnassigned().
Referenced by s_GetAlignmentTooltip(), s_GetBitScore(), s_GetEvalue(), CGffAlignmentRecord::SetScore(), CGffBaseRecord::SetScore(), sInheritScores(), sPrepareSeqAlign(), testNuclHitList(), CAlnTableDS::x_AdjustColumns(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignFillerBlocks(), CMultiAligner::x_FindRPSHits(), CMultiAligner::x_SetDomainHits(), CHitMatrixDataSource::x_UpdateScoreMap(), CGff3FlybaseWriter::xAssignAlignmentDensegScores(), and CGff3FlybaseWriter::xAssignAlignmentSplicedScores().
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Get the Id member data.
Definition at line 976 of file Seq_align_.hpp.
References CSeq_align_Base::m_Id.
Referenced by ExtractSupportModels(), CSeq_align_Mapper_Base::GetDstAlign(), GetModelId(), CTabularFormatter_AlignId::Print(), RestoreModelFromPublicMrnaFeature(), s_GetAlignID(), and CGff3Writer::xWriteAlign().
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Get the Ids member data.
Definition at line 410 of file Dense_diag_.hpp.
References CDense_diag_Base::m_Ids.
Referenced by CSeqsRange::Add(), CDense_diag::CheckNumRows(), CDense_diag::CreateRowSeq_interval(), GetPendingSeqId(), CCdCore::HasSeqId(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), s_Fingerprint_Dense_diag(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CAnnotObject_Info::x_ProcessAlign(), CValidError_align::x_ValidateDendiag(), and CValidError_align::x_ValidateSeqLength().
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Get the Ids member data.
Definition at line 505 of file Dense_seg_.hpp.
References CDense_seg_Base::m_Ids.
Referenced by CSeqsRange::Add(), CAlnMixSequences::Add(), CAlignmentAssistant::AdjustAlign(), CDense_seg::CheckNumRows(), ConvertToPairwise(), CreateAlignRow(), CAlnVec::CreateConsensus(), CSeq_align::CreateDensegFromDisc(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CAlignCleanup::CreatePairwiseFromMultiple(), CDense_seg::CreateRowSeq_interval(), Denseg2DenseDiagList(), CDense_seg::ExtractRows(), CDense_seg::ExtractSlice(), CDense_seg::FillUnaligned(), GetMasterGIFromSeqAlign(), GetPssmIdFromSeqAlign(), CDense_seg::GetSeq_id(), CPhyTreeCalc::GetSeqIds(), CContigAssembly::IsAtLeastHalfDovetail(), CValidError_align::IsTpaAlignment(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), CRemoveSeqFromAlignDlg::ModifyAlign(), CAlignmentAssistant::OnRemoveSeqFromAlign(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), CTestBlastp_All::RunTest(), s_CheckTraceMateAlign(), s_CoverageSeqLoc(), s_CutDensegSegment(), s_DensegHasAccessionWithZeroVersion(), s_DivvyUpAlignments_ProcessAnnot_Denseg(), s_Fingerprint_Dense_seg(), s_GetAlignmentContent(), s_GetAlignmentTooltip(), s_GetNumIdsToUse(), s_GetSubjectId(), s_Seq_align_Seq_loc(), s_TestAlignmentFromMSAs(), s_TestCalc(), CPhyTreeCalc::SetQuery(), CReportTrim::TrimAlignments(), TrimSeqAlign(), CUpdateAlign::x_ChangeIDsToFarPointers(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CAlnMix::x_ExtendDSWithWidths(), CMultiAligner::x_FindRPSHits(), CApplyRNAITSDlg::x_GetAlignments(), CValidError_align::x_GetIds(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CSeq_loc_Mapper_Base::x_InitializeAlign(), CUpdateAlign::x_MapNonPresentIDs(), CUpdateAlign::x_RemoveIDsFromAlign(), CApplyRNAITSDlg::x_SeqIdsAlignedWith(), CMultiAligner::x_SetDomainHits(), and CVectorTrimPanel::x_TrimAlignments().
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Get the Ids member data.
Definition at line 529 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_Ids.
Referenced by CSeqsRange::Add(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), s_Fingerprint_Packed_seg(), CValidError_align::x_GetIds(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), and CSeq_loc_Mapper_Base::x_InitializeAlign().
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Get the Ids member data.
Definition at line 332 of file Std_seg_.hpp.
References CStd_seg_Base::m_Ids.
Referenced by CStd_seg::CheckNumRows(), CStd_seg::RemapToLoc(), s_Fingerprint_Std_seg(), s_GetStdsegMasterFrame(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CValidError_align::x_ValidateSeqLength(), and CValidError_align::x_ValidateStd().
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Get the Index member data.
Definition at line 177 of file Sparse_seg_ext_.hpp.
References CSparse_seg_ext_Base::CanGetIndex(), CSparse_seg_ext_Base::m_Index, and CSerialObject::ThrowUnassigned().
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Get the variant data.
Definition at line 411 of file Score_.hpp.
Referenced by GetFloatScore(), GetIntScore(), s_CompareValues(), s_GetAlignmentTooltip(), CGffAlignmentRecord::SetScore(), CGffBaseRecord::SetScore(), sPrepareSeqAlign(), testNuclHitList(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignFillerBlocks(), CMultiAligner::x_FindRPSHits(), and CMultiAligner::x_SetDomainHits().
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Get the Len member data.
Definition at line 467 of file Dense_diag_.hpp.
References CDense_diag_Base::CanGetLen(), CDense_diag_Base::m_Len, and CSerialObject::ThrowUnassigned().
Referenced by CSeqsRange::Add(), ConvertDendiagToPairwiseAln(), CDense_diag::CreateRowSeq_interval(), CDense_diag::GetSeqStop(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), s_Fingerprint_Dense_diag(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), and CValidError_align::x_ValidateSeqLength().
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Get the Lens member data.
Definition at line 555 of file Dense_seg_.hpp.
References CDense_seg_Base::m_Lens.
Referenced by CSeqsRange::Add(), CAlnMixMatches::Add(), CAlignmentAssistant::AdjustAlign(), CPaintAlignment::AlignPosToSeqPos(), CFeaturePropagator::AlignPosToSeqPos(), CContigAssembly::BandedGlobalAlignment(), CContigAssembly::BestLocalSubAlignment(), BOOST_AUTO_TEST_CASE(), CAlignShadow::CAlignShadow(), CDense_seg::CheckNumSegs(), CAlnVecPrinter::ClustalStyle(), CDense_seg::Compact(), ConvertDensegToPairwiseAln(), CreateAlignRow(), CSeq_align::CreateDensegFromDisc(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CAlignCleanup::CreatePairwiseFromMultiple(), CDense_seg::CreateRowSeq_interval(), CFeaturePropagator::CreateRowSeq_loc(), CSeq_align::CreateTranslatedDensegFromNADenseg(), Denseg2DenseDiagList(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CDense_seg::ExtractRows(), CDense_seg::ExtractSlice(), CDense_seg::FillUnaligned(), CEditSeqEndsWithAlign::FindPosition(), CSeq_align::GapLengthRange(), CSeq_align::GetAlignedBases(), CFastaAlignmentBuilder::GetCompletedAlignment(), CPaintAlignment::GetSegments(), CDense_seg::GetSeqStop(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), CAlignmentAssistant::OnReverseStrand(), CAlnVecPrinter::PopsetStyle(), CTabularFormatter_Cigar::Print(), PrintSAM(), CDense_seg::RemapToLoc(), CDense_seg::RemovePureGapSegs(), ReverseAlignmentStrand(), CFarPointerSeq::ReverseRow(), s_AlignToSeqRanges(), s_CoverageSeqLoc(), s_CutDensegSegment(), s_DenseSegLength(), s_FindSegment(), s_Fingerprint_Dense_seg(), s_GetAlignmentLength(), s_GetCigarString(), s_GetGapCount(), s_GetIndels(), s_SeqAlignToBlastSeqLoc(), s_TestAlignmentFromMSAs(), s_TestResultAlignment(), CPaintAlignment::SeqPosToAlignPos(), CFeaturePropagator::SeqPosToAlignPos(), CSeq_align::SplitOnLongDiscontinuity(), CDense_seg::TrimEndGaps(), TrimSeqAlign(), UpdateDensegAlignment(), CDense_seg::Validate(), CAlnWriter::WriteAlignDenseSeg(), CFastaReader::x_AddMultiwayAlignment(), CVectorTrimPanel::x_AdjustDensegAlignment(), CReportTrim::x_AdjustDensegAlignment(), CTabularFormatter_BiggestGapBases::x_CalcBiggestGap(), CAlignCleanup::x_Cleanup_AlignVec(), CQuerySet::x_ContainsAlignment(), CInversionMergeAligner::x_CreateDiscAlignment(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CAlnMix::x_ExtendDSWithWidths(), CVectorTrimPanel::x_FindSegment(), CReportTrim::x_FindSegment(), CDense_seg::x_FindSegment(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CDenseg_CI::x_InitIterator(), CDenseg_CI::x_InitSegment(), x_TestAlignmentQuerySubjStrandCombinations(), and CPslRecord::xInitializeStatsAndBlocks().
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Get the Lens member data.
Definition at line 607 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_Lens.
Referenced by CSeqsRange::Add(), ConvertPackedsegToPairwiseAln(), s_Fingerprint_Packed_seg(), CSeq_align_Mapper_Base::x_Init(), and CSeq_loc_Mapper_Base::x_InitAlign().
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Get the Lens member data.
Definition at line 588 of file Sparse_align_.hpp.
References CSparse_align_Base::m_Lens.
Referenced by CSeqsRange::Add(), CSparse_align::CheckNumSegs(), ConvertSparseToPairwiseAln(), CreateAlignRow(), GetAlignColl(), CSparse_seg::GetSeqRange(), CSparse_seg::GetSeqStop(), s_Fingerprint_Sparse_align(), CAlnWriter::WriteSparseAlign(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitSparse(), and CAnnotObject_Info::x_ProcessAlign().
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Get the Loc member data.
Definition at line 357 of file Std_seg_.hpp.
References CStd_seg_Base::m_Loc.
Referenced by CStd_seg::CheckNumRows(), CSeq_align::CreateDensegFromStdseg(), CStd_seg::CreateRowSeq_loc(), CStdSegHit::CStdSegHit(), CStd_seg::GetSeqRange(), CStd_seg::GetSeqStart(), CStd_seg::GetSeqStop(), CStdSegHit::HasAlignment(), CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()(), s_Fingerprint_Std_seg(), s_GetAlignmentLength(), s_GetAlignmentSpans_Exon(), s_GetGapCount(), s_GetStdsegMasterFrame(), CStd_seg::SwapRows(), CHitMatrixDataSource::x_GoodSeg(), CSeq_loc_Mapper_Base::x_InitAlign(), CValidError_align::x_ValidateSeqLength(), and CValidError_align::x_ValidateStd().
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Get the Master_id member data.
Definition at line 288 of file Sparse_seg_.hpp.
References CSparse_seg_Base::CanGetMaster_id(), CSparse_seg_Base::m_Master_id, and CSerialObject::ThrowUnassigned().
Referenced by ConvertToPairwise(), and s_Fingerprint_Sparse_seg().
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Get the variant data.
Definition at line 356 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::CheckSelected(), CSpliced_exon_chunk_Base::e_Match, and CSpliced_exon_chunk_Base::m_Match.
Referenced by CScoreBuilderBase::AddSplignScores(), BOOST_AUTO_TEST_CASE(), ChunkSize(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CScore_IndelToSplice::Get(), CSpliced_exon::GetRowSeq_insertions(), CProSplign::CImplementation::HasStartOnNuc(), ProjectExon_oldlogic(), CSplign::s_ComputeStats(), s_ExonToDenseg(), s_GetCountIdentityMismatch(), SBlocks::SBlocks(), sExonChunkAppendStats(), CSeq_loc_Mapper_Base::sx_GetExonPartLength(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExonPart(), CReportEntry::x_CheckExonGap(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CGff3Writer::xAssignAlignmentSplicedGap(), and CGff3FlybaseWriter::xAssignAlignmentSplicedGap().
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Get the variant data.
Definition at line 383 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::CheckSelected(), CSpliced_exon_chunk_Base::e_Mismatch, and CSpliced_exon_chunk_Base::m_Mismatch.
Referenced by CScoreBuilderBase::AddSplignScores(), BOOST_AUTO_TEST_CASE(), ChunkSize(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CScore_IndelToSplice::Get(), CSpliced_exon::GetRowSeq_insertions(), CProSplign::CImplementation::HasStartOnNuc(), ProjectExon_oldlogic(), CSplign::s_ComputeStats(), s_ExonToDenseg(), s_GetCountIdentityMismatch(), SBlocks::SBlocks(), sExonChunkAppendStats(), CSeq_loc_Mapper_Base::sx_GetExonPartLength(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExonPart(), CReportEntry::x_CheckExonGap(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CGff3Writer::xAssignAlignmentSplicedGap(), and CGff3FlybaseWriter::xAssignAlignmentSplicedGap().
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Get the Modifiers member data.
Definition at line 811 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_Modifiers.
Referenced by CScore_StartStopCodon::Get(), CProSplign::CImplementation::SeekStartStop(), CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript(), and CCDSTranslationPanel::x_SetLocationForProtein().
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Get the variant data.
Definition at line 266 of file Product_pos_.hpp.
References CProduct_pos_Base::CheckSelected(), CProduct_pos_Base::e_Nucpos, and CProduct_pos_Base::m_Nucpos.
Referenced by CSeqsRange::Add(), CProduct_pos::AsSeqPos(), variation_ref::CVariationUtil::CheckExonBoundary(), variation::CVariationUtil::CheckExonBoundary(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CScore_LastSpliceSite::Get(), CFeatureGenerator::SImplementation::MaximizeTranslation(), CTabularFormatter_ExonIntrons::Print(), ProjectExon_newlogic(), s_ExonToDenseg(), s_ValidateExon(), CProductStringBuilder::x_AddExon(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CAlnSpanVertModel::x_PopulateRowsSpliced(), and CAnnotObject_Info::x_ProcessAlign().
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Get the Numseg member data.
Definition at line 465 of file Dense_seg_.hpp.
References CDense_seg_Base::CanGetNumseg(), CDense_seg_Base::m_Numseg, and CSerialObject::ThrowUnassigned().
Referenced by CSeqsRange::Add(), CAlnMixMatches::Add(), CAlignmentAssistant::AdjustAlign(), CContigAssembly::Align(), CPaintAlignment::AlignPosToSeqPos(), CFeaturePropagator::AlignPosToSeqPos(), CContigAssembly::BandedGlobalAlignment(), BOOST_AUTO_TEST_CASE(), CDense_seg::CheckNumSegs(), CDense_seg::Compact(), ConvertDensegToPairwiseAln(), CreateAlignRow(), CSeq_align::CreateDensegFromDisc(), CSeq_align::CreateDensegFromStdseg(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CAlignCleanup::CreatePairwiseFromMultiple(), CDense_seg::CreateRowSeq_interval(), CFeaturePropagator::CreateRowSeq_loc(), CSeq_align::CreateTranslatedDensegFromNADenseg(), Denseg2DenseDiagList(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CDense_seg::ExtractRows(), CSeq_align::GapLengthRange(), CSeq_align::GetAlignedBases(), CAlignmentAssistant::GetFeatures(), CPaintAlignment::GetSegments(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), CRemoveSeqFromAlignDlg::ModifyAlign(), CDense_seg::OffsetRow(), CAlignmentAssistant::OnRemoveSeqFromAlign(), CAlignmentAssistant::OnReverseStrand(), CDense_seg::OrderAdjacentGaps(), CDense_seg::CReserveHook::PreReadClassMember(), CTabularFormatter_Cigar::Print(), CDenseSegReserveStartsHook::ReadClassMember(), CDenseSegReserveLensHook::ReadClassMember(), CDenseSegReserveStrandsHook::ReadClassMember(), CDense_seg::RemapToLoc(), CAlignmentAssistant::ReportUnresolvedBioseqs(), CDense_seg::Reverse(), ReverseAlignmentStrand(), s_AlignToSeqRanges(), s_CalculateMatchingColumns(), s_ComputeTraceback(), s_CoverageSeqLoc(), s_CutDensegSegment(), s_FindSegment(), s_GetAlignmentLength(), s_GetGapCount(), s_GetIndels(), s_SeqAlignToBlastSeqLoc(), CPaintAlignment::SeqPosToAlignPos(), CFeaturePropagator::SeqPosToAlignPos(), CAlignCompare::SAlignment::Slice(), CSeq_align::SplitOnLongDiscontinuity(), CDense_seg::SwapRows(), CDense_seg::TrimEndGaps(), TrimSeqAlign(), CAlnWriter::WriteAlignDenseSeg(), CVectorTrimPanel::x_AdjustDensegAlignment(), CReportTrim::x_AdjustDensegAlignment(), CTabularFormatter_BiggestGapBases::x_CalcBiggestGap(), CQuerySet::x_ContainsAlignment(), CInversionMergeAligner::x_CreateDiscAlignment(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CAppHitFilter::x_DumpOutput(), CAlnMix::x_ExtendDSWithWidths(), CVectorTrimPanel::x_FindSegment(), CReportTrim::x_FindSegment(), CDense_seg::x_FindSegment(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CDenseg_CI::x_InitIterator(), CInversionMergeAligner::x_IsAllGap(), CUnorderedSplitter::x_IsAllGap(), CInversionMergeAligner::x_MergeSeqAlignSet(), CMergeAligner::x_MergeSeqAlignSet(), CUpdateAlign::x_RemoveIDsFromAlign(), CInstancedAligner::x_RunCleanup(), and CInstancedAligner::x_RunMMGlobal().
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Get the Numseg member data.
Definition at line 489 of file Packed_seg_.hpp.
References CPacked_seg_Base::CanGetNumseg(), CPacked_seg_Base::m_Numseg, and CSerialObject::ThrowUnassigned().
Referenced by CSeqsRange::Add(), ConvertPackedsegToPairwiseAln(), CSeq_align_Mapper_Base::x_Init(), and CSeq_loc_Mapper_Base::x_InitAlign().
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Get the Numseg member data.
Definition at line 498 of file Sparse_align_.hpp.
References CSparse_align_Base::CanGetNumseg(), CSparse_align_Base::m_Numseg, and CSerialObject::ThrowUnassigned().
Referenced by CSeqsRange::Add(), CSparse_align::CheckNumSegs(), ConvertSparseToPairwiseAln(), CreateAlignRow(), GetAlignColl(), CAlnWriter::WriteSparseAlign(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitSparse(), and CAnnotObject_Info::x_ProcessAlign().
const CSeq_align_Base::C_Segs::TPacked & CSeq_align_Base::C_Segs::GetPacked | ( | void | ) | const |
Get the variant data.
Definition at line 175 of file Seq_align_.cpp.
Referenced by CSeqsRange::Add(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), s_Fingerprint_Seq_align(), CValidError_align::ValidateSeqAlign(), CValidError_align::x_GetIds(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitializeAlign(), and CAnnotObject_Info::x_ProcessAlign().
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Get the Partial member data.
Definition at line 1085 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::CanGetPartial(), CSpliced_exon_Base::m_Partial, and CSerialObject::ThrowUnassigned().
Referenced by CReportEntry::SetAlignment().
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Get the Parts member data.
Definition at line 990 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Parts.
Referenced by BOOST_AUTO_TEST_CASE(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CScore_IndelToSplice::Get(), CSpliced_exon::GetRowSeq_insertions(), CProSplign::CImplementation::HasStartOnNuc(), CSeq_align_Mapper_Base::InitExon(), CFeatureGenerator::SImplementation::RecalculateExonIdty(), s_ExonToDenseg(), s_Fingerprint_Spliced_exon(), s_GetAlignmentMismatches(), s_GetCountIdentityMismatch(), s_ValidateExon(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExon(), CReportEntry::x_CheckExonGap(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CSeq_loc_Mapper_Base::x_InitSpliced(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CGff3Writer::xAssignAlignmentSplicedGap(), and CGff3FlybaseWriter::xAssignAlignmentSplicedGap().
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Get the Poly_a member data.
Definition at line 724 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::CanGetPoly_a(), CSpliced_seg_Base::m_Poly_a, and CSerialObject::ThrowUnassigned().
Referenced by CScore_3PrimeUnaligned::Get(), CScore_Polya::Get(), SAlignmentScoringModel::GetPolyA_length(), s_GetPercentCoverage(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSpliced_seg::Validate(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), and CAlnSpanVertModel::x_PopulateRowsSpliced().
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Get the Present member data.
Definition at line 579 of file Packed_seg_.hpp.
References CPacked_seg_Base::CanGetPresent(), CPacked_seg_Base::m_Present, and CSerialObject::ThrowUnassigned().
Referenced by CSeqsRange::Add(), ConvertPackedsegToPairwiseAln(), s_Fingerprint_Packed_seg(), CSeq_align_Mapper_Base::x_Init(), and CSeq_loc_Mapper_Base::x_InitAlign().
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Get the Product_end member data.
Definition at line 730 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Product_end, and CSpliced_exon_Base::ResetProduct_end().
Referenced by CSeqsRange::Add(), AreAbuttingOnProduct(), BOOST_AUTO_TEST_CASE(), variation_ref::CVariationUtil::CheckExonBoundary(), variation::CVariationUtil::CheckExonBoundary(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CScore_LastSpliceSite::Get(), CScore_EdgeExonInfo::Get(), CFeatureGenerator::SImplementation::GetExonStructure(), CSpliced_exon::GetRowSeq_range(), GetTerminalPartialness(), CProSplign::CImplementation::HasStopOnNuc(), CSeq_align_Mapper_Base::InitExon(), CSpliced_seg::IsConsistentBiologicalOrder(), CTabularFormatter_ExonIntrons::Print(), ProjectExon_newlogic(), s_ExonToDenseg(), s_Fingerprint_Spliced_exon(), s_GetAlignmentMismatches(), s_GetAlignmentSpans_Exon(), s_GetCountIdentityMismatch(), s_ValidateExon(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExon(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CSeq_loc_Mapper_Base::x_InitSpliced(), CAnnotObject_Info::x_ProcessAlign(), CGff3FlybaseWriter::xAssignAlignmentSplicedLocation(), and CGff3Writer::xAssignAlignmentSplicedTarget().
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Get the Product_id member data.
Definition at line 854 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::CanGetProduct_id(), CSpliced_exon_Base::m_Product_id, and CSerialObject::ThrowUnassigned().
Referenced by CSeqsRange::Add(), CSpliced_exon::CreateRowSeq_interval(), CSeq_align_Mapper_Base::InitExon(), s_ExonToDenseg(), s_Fingerprint_Spliced_exon(), CSeq_loc_Mapper_Base::x_InitSpliced(), and CAnnotObject_Info::x_ProcessAlign().
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Get the Product_id member data.
Definition at line 509 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::CanGetProduct_id(), CSpliced_seg_Base::m_Product_id, and CSerialObject::ThrowUnassigned().
Referenced by CSeqsRange::Add(), CSpliced_seg::AsDiscSeg(), CProteinAlignText::CProteinAlignText(), CSpliced_exon::CreateRowSeq_interval(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CInternalStopFinder::GetCDSNucleotideSequence(), CSeq_align::GetSeq_id(), CSeq_align_Mapper_Base::InitExon(), CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()(), CProSplignText::Output(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), s_Fingerprint_Spliced_seg(), s_GetAlignmentContent(), s_SplicedToDisc(), CProSplign::CImplementation::SeekStartStop(), CFeatureGenerator::SImplementation::TrimHolesToCodons(), CAlnWriter::WriteAlignSplicedSeg(), CAlnSpanVertModel::x_Init(), CSeq_loc_Mapper_Base::x_InitSpliced(), CGff3Writer::xAssignAlignmentSplicedMethod(), CGff3FlybaseWriter::xAssignAlignmentSplicedSeqId(), CGff3Writer::xAssignAlignmentSplicedTarget(), CGff3Writer::xAssignAlignmentSplicedType(), CPslRecord::xInitializeSequenceInfo(), and CGff3Writer::xSplicedSegHasProteinProd().
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Get the variant data.
Definition at line 437 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::CheckSelected(), CSpliced_exon_chunk_Base::e_Product_ins, and CSpliced_exon_chunk_Base::m_Product_ins.
Referenced by CScoreBuilderBase::AddSplignScores(), BOOST_AUTO_TEST_CASE(), ChunkSize(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CSpliced_exon::GetRowSeq_insertions(), CFeatureGenerator::SImplementation::MaximizeTranslation(), ProjectExon_oldlogic(), CSplign::s_ComputeStats(), s_ExonToDenseg(), s_GetCountIdentityMismatch(), SBlocks::SBlocks(), sExonChunkAppendStats(), CSeq_loc_Mapper_Base::sx_GetExonPartLength(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExonPart(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CGff3Writer::xAssignAlignmentSplicedGap(), and CGff3FlybaseWriter::xAssignAlignmentSplicedGap().
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Get the Product_length member data.
Definition at line 771 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::CanGetProduct_length(), CSpliced_seg_Base::m_Product_length, and CSerialObject::ThrowUnassigned().
Referenced by CFeatureGenerator::SImplementation::AdjustAlignment(), BOOST_AUTO_TEST_CASE(), CProteinAlignText::CProteinAlignText(), CScore_3PrimeUnaligned::Get(), CScore_Polya::Get(), CScore_SequenceLength::Get(), CScore_StartStopCodon::Get(), SAlignmentScoringModel::GetCoverage(), SAlignmentScoringModel::GetPolyA_length(), CProductStringBuilder::GetProductString(), GetUnalignedLength_3p(), GetUnalignedLength_5p(), PrintSAM(), PrintTabular(), s_GetPercentCoverage(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript(), CFeatureGenerator::SImplementation::TrimHolesToCodons(), CSpliced_seg::Validate(), CFeatureGenerator::SImplementation::x_CollectMrnaSequence(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), and CAlnSpanVertModel::x_PopulateRowsSpliced().
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Get the Product_start member data.
Definition at line 700 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Product_start, and CSpliced_exon_Base::ResetProduct_start().
Referenced by CSeqsRange::Add(), AreAbuttingOnProduct(), BOOST_AUTO_TEST_CASE(), variation_ref::CVariationUtil::CheckExonBoundary(), variation::CVariationUtil::CheckExonBoundary(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), ConvertSplicedToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CScore_EdgeExonInfo::Get(), CFeatureGenerator::SImplementation::GetExonStructure(), CSpliced_exon::GetRowSeq_range(), GetTerminalPartialness(), CProSplign::CImplementation::HasStartOnNuc(), CSeq_align_Mapper_Base::InitExon(), CSpliced_seg::IsConsistentBiologicalOrder(), CFeatureGenerator::SImplementation::MaximizeTranslation(), CTabularFormatter_ExonIntrons::Print(), ProjectExon_newlogic(), s_ExonToDenseg(), s_Fingerprint_Spliced_exon(), s_GetAlignmentMismatches(), s_GetAlignmentSpans_Exon(), s_GetCountIdentityMismatch(), s_ValidateExon(), CProSplign::CImplementation::SeekStartStop(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExon(), CSeq_align_Mapper_Base::x_GetDstExon(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CSeq_loc_Mapper_Base::x_InitSpliced(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CAnnotObject_Info::x_ProcessAlign(), CGff3FlybaseWriter::xAssignAlignmentSplicedLocation(), and CGff3Writer::xAssignAlignmentSplicedTarget().
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Get the Product_strand member data.
Definition at line 903 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::CanGetProduct_strand(), CSpliced_exon_Base::m_Product_strand, and CSerialObject::ThrowUnassigned().
Referenced by ConvertSplicedToPairwiseAln(), CSpliced_exon::CreateRowSeq_interval(), CSpliced_exon::GetRowSeq_insertions(), CSeq_align_Mapper_Base::InitExon(), CSpliced_seg::IsConsistentBiologicalOrder(), s_ExonToDenseg(), s_GetAlignmentMismatches(), CSpliced_seg::Validate(), CSeq_loc_Mapper_Base::x_InitSpliced(), and CAnnotObject_Info::x_ProcessAlign().
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Get the Product_strand member data.
Definition at line 558 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::CanGetProduct_strand(), CSpliced_seg_Base::m_Product_strand, and CSerialObject::ThrowUnassigned().
Referenced by CSpliced_seg::AsDiscSeg(), ConvertSplicedToPairwiseAln(), CSpliced_exon::CreateRowSeq_interval(), CScore_InternalUnaligned::Get(), CScore_LastSpliceSite::Get(), CScore_Polya::Get(), CSpliced_exon::GetRowSeq_insertions(), CSpliced_seg::GetSeqStrand(), CSeq_align_Mapper_Base::InitExon(), CSpliced_seg::IsConsistentBiologicalOrder(), s_GetAlignmentMismatches(), s_GetAlignmentSpans_Intron(), s_GetPercentCoverage(), s_SplicedToDisc(), CSpliced_seg::Validate(), CAlnWriter::WriteAlignSplicedSeg(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CSeq_loc_Mapper_Base::x_InitSpliced(), CGff3FlybaseWriter::xAssignAlignmentSplicedLocation(), CGff3Writer::xAssignAlignmentSplicedTarget(), and CPslRecord::xInitializeStrands().
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Get the Product_type member data.
Definition at line 652 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::CanGetProduct_type(), CSpliced_seg_Base::m_Product_type, and CSerialObject::ThrowUnassigned().
Referenced by CFeatureGenerator::SImplementation::AdjustAlignment(), CSpliced_seg::AsDiscSeg(), BOOST_AUTO_TEST_CASE(), CTestSingleAln::CanTest(), ConvertSplicedToPairwiseAln(), CInternalStopFinder::FindStartStopRanges(), CScore_InternalUnaligned::Get(), CScore_LastSpliceSite::Get(), CScore_FrameShifts::Get(), CScore_StartStopCodon::Get(), CScore_TblastnScore::Get(), CScoreBuilder::GetBlastScoreSpliced(), CInternalStopFinder::GetCDSNucleotideSequence(), CProductStringBuilder::GetProductString(), CSpliced_seg::GetSeqRange(), GetTerminalPartialness(), IsProteinAlign(), SAlignmentScoringModel::isProtSS(), CFeatureGenerator::SImplementation::MaximizeTranslation(), CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()(), CTabularFormatter_MismatchPositions::Print(), CTabularFormatter_ExonIntrons::Print(), CFeatureGenerator::SImplementation::RecalculateScores(), s_GetSplicedSegIdentityMismatch(), s_IsProteinToGenomic(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CFeatureGenerator::SImplementation::TrimHolesToCodons(), CSpliced_seg::Validate(), CAlnWriter::WriteAlignSplicedSeg(), CSeq_align_Mapper_Base::x_GetDstExon(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CScoreBuilderBase::x_GetMatrixCounts(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CSeq_loc_Mapper_Base::x_InitSpliced(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CGff3Writer::xAssignAlignmentSplicedType(), CGff3Writer::xSplicedSegHasProteinProd(), and CPslRecord::xValidateSegment().
const CProduct_pos_Base::TProtpos & CProduct_pos_Base::GetProtpos | ( | void | ) | const |
Get the variant data.
Definition at line 100 of file Product_pos_.cpp.
References CProduct_pos_Base::CheckSelected(), CProduct_pos_Base::e_Protpos, and CProduct_pos_Base::m_object.
Referenced by CSeqsRange::Add(), CProduct_pos::AsSeqPos(), BOOST_AUTO_TEST_CASE(), variation_ref::CVariationUtil::CheckExonBoundary(), variation::CVariationUtil::CheckExonBoundary(), CProSplign::CImplementation::HasStartOnNuc(), CProSplign::CImplementation::HasStopOnNuc(), CFeatureGenerator::SImplementation::MaximizeTranslation(), CTabularFormatter_ExonIntrons::Print(), s_Fingerprint_Product_pos(), CProSplign::CImplementation::SeekStartStop(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CAnnotObject_Info::x_ProcessAlign(), and CGff3FlybaseWriter::xAssignAlignmentSplicedLocation().
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Get the variant data.
Definition at line 384 of file Score_.hpp.
Referenced by GetFloatScore(), GetIntScore(), s_CompareValues(), s_GetAlignmentTooltip(), s_GetBitScore(), s_GetEvalue(), CGffAlignmentRecord::SetScore(), CGffBaseRecord::SetScore(), testNuclHitList(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignFillerBlocks(), CMultiAligner::x_FindRPSHits(), and CMultiAligner::x_SetDomainHits().
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Get the Row_scores member data.
Definition at line 334 of file Sparse_seg_.hpp.
References CSparse_seg_Base::m_Row_scores.
Referenced by CSparse_seg::CheckNumRows(), CRemoveSeqFromAlignDlg::ModifyAlign(), and CSeq_align_Mapper_Base::x_Init().
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Get the Rows member data.
Definition at line 309 of file Sparse_seg_.hpp.
References CSparse_seg_Base::m_Rows.
Referenced by CSeqsRange::Add(), CSparse_seg::CheckNumRows(), ConvertSparseToPairwiseAln(), ConvertToPairwise(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CSparse_seg::GetSeq_id(), CSparse_seg::GetSeqRange(), CSparse_seg::GetSeqStart(), CSparse_seg::GetSeqStop(), CSparse_seg::GetSeqStrand(), CRemoveSeqFromAlignDlg::ModifyAlign(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), s_Fingerprint_Sparse_seg(), CSparse_seg::Validate(), CAlnWriter::WriteAlignSparseSeg(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitializeAlign(), CSeq_loc_Mapper_Base::x_InitSparse(), and CAnnotObject_Info::x_ProcessAlign().
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Get the Score member data.
Definition at line 896 of file Seq_align_.hpp.
References CSeq_align_Base::m_Score.
Referenced by CSAM_CIGAR_Formatter::AddRow(), CValidError_align::AlignmentScorePercentIdOk(), BOOST_AUTO_TEST_CASE(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CSeq_align::CreateDensegFromDisc(), CSeq_align::CreateDensegFromStdseg(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CSeq_align_Handle::GetScore(), CAlignFormatUtil::GetSeqAlignSetCalcParamsFromASN(), s_GetAlignmentTooltip(), s_GetAlnScores(), s_PopulateScoreSet(), sInheritScores(), sPrepareSeqAlign(), testNuclHitList(), CPslWriter::WriteAlign(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignFillerBlocks(), CMultiAligner::x_FindRPSHits(), CCIGAR_Formatter::x_FormatAlignmentRows(), CSeq_align::x_GetNamedScore(), CSeq_align_Mapper_Base::x_Init(), CSeqAlignFilter::x_ReadExtraGis(), CMultiAligner::x_SetDomainHits(), CHitMatrixDataSource::x_UpdateScoreMap(), CGff3Writer::xAssignAlignmentScores(), and CGff3FlybaseWriter::xAssignAlignmentScores().
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Get the Scores member data.
Definition at line 532 of file Dense_diag_.hpp.
References CDense_diag_Base::m_Scores.
Referenced by CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignFillerBlocks(), and CSeq_align_Mapper_Base::x_Init().
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Get the Scores member data.
Definition at line 605 of file Dense_seg_.hpp.
References CDense_seg_Base::m_Scores.
Referenced by Denseg2DenseDiagList(), CAlignFormatUtil::GetSeqAlignSetCalcParamsFromASN(), s_GetAlnScores(), CSeq_align_Mapper_Base::x_Init(), CGff3Writer::xAssignAlignmentDensegScores(), and CGff3FlybaseWriter::xAssignAlignmentDensegScores().
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Get the Scores member data.
Definition at line 657 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_Scores.
Referenced by CSeq_align_Mapper_Base::x_Init().
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Get the Scores member data.
Definition at line 1015 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::CanGetScores(), CSpliced_exon_Base::m_Scores, and CSerialObject::ThrowUnassigned().
Referenced by CScore_EdgeExonInfo::Get(), CSeq_align_Mapper_Base::InitExon(), s_ExonToDenseg(), CGff3Writer::xAssignAlignmentSplicedScores(), and CGff3FlybaseWriter::xAssignAlignmentSplicedScores().
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Get the Scores member data.
Definition at line 382 of file Std_seg_.hpp.
References CStd_seg_Base::m_Scores.
Referenced by CSeq_align_Mapper_Base::x_Init().
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Get the Second_id member data.
Definition at line 461 of file Sparse_align_.hpp.
References CSparse_align_Base::m_Second_id, and CSparse_align_Base::ResetSecond_id().
Referenced by CSeqsRange::Add(), ConvertToPairwise(), CreateAlignRow(), GetAlignColl(), CSparse_seg::GetSeq_id(), CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()(), s_Fingerprint_Sparse_align(), CAlnWriter::WriteSparseAlign(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitSparse(), and CAnnotObject_Info::x_ProcessAlign().
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Get the Second_starts member data.
Definition at line 563 of file Sparse_align_.hpp.
References CSparse_align_Base::m_Second_starts.
Referenced by CSeqsRange::Add(), CSparse_align::CheckNumSegs(), ConvertSparseToPairwiseAln(), CreateAlignRow(), GetAlignColl(), CSparse_seg::GetSeqRange(), CSparse_seg::GetSeqStart(), CSparse_seg::GetSeqStop(), s_Fingerprint_Sparse_align(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitSparse(), and CAnnotObject_Info::x_ProcessAlign().
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Get the Second_strands member data.
Definition at line 613 of file Sparse_align_.hpp.
References CSparse_align_Base::m_Second_strands.
Referenced by CSeqsRange::Add(), CSparse_align::CheckNumSegs(), ConvertSparseToPairwiseAln(), CreateAlignRow(), GetAlignColl(), CSparse_seg::GetSeqRange(), CSparse_seg::GetSeqStart(), CSparse_seg::GetSeqStop(), CSparse_seg::GetSeqStrand(), s_Fingerprint_Sparse_align(), CAlnWriter::WriteSparseAlign(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitSparse(), and CAnnotObject_Info::x_ProcessAlign().
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Get the Seg_scores member data.
Definition at line 638 of file Sparse_align_.hpp.
References CSparse_align_Base::m_Seg_scores.
Referenced by CSparse_align::CheckNumSegs(), and CSeq_align_Mapper_Base::x_Init().
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Get the Segs member data.
Definition at line 921 of file Seq_align_.hpp.
References CSeq_align_Base::m_Segs, and CSeq_align_Base::ResetSegs().
Referenced by CAlnMix::Add(), CSeqsRange::Add(), CAlnVwrApp::AddAlnToMix(), CScoreBuilderBase::AddSplignScores(), CFeatureGenerator::SImplementation::AdjustAlignment(), CFeaturePropagator::AlignPosToSeqPos(), BOOST_AUTO_TEST_CASE(), BuildAlignDataSource(), CTestSingleAln::CanTest(), CFeaturePropagator::CFeaturePropagator(), variation_ref::CVariationUtil::CheckExonBoundary(), variation::CVariationUtil::CheckExonBoundary(), CSeq_align::CheckNumRows(), CFeatureGenerator::SImplementation::CleanAlignment(), CDUpdater::ComputePercentIdentity(), CScoreBuilderBase::ComputeScore(), ConvertRawToDeltaByNsCommand_impl(), ConvertRawToDeltaByNsHugeFileCmd_impl(), ConvertSeqAlignToPairwiseAln(), ConvertToPairwise(), CreateAnchoredAlnFromAln(), CreateAnchoredAlnVec(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CSeq_align::CreateDensegFromDisc(), CSeq_align::CreateDensegFromStdseg(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CAlignCleanup::CreatePairwiseFromMultiple(), CFeaturePropagator::CreateRowSeq_loc(), CSeq_align::CreateRowSeq_loc(), CSeq_align::CreateTranslatedDensegFromNADenseg(), Denseg2DenseDiagList(), CDisplaySeqalign::DisplaySeqalign(), CSeq_align::ExonLengthRange(), ExtractFirstSeqAlign(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CProSplign::CImplementation::FindGlobalAlignment_stage2(), CEditSeqEndsWithAlign::FindPosition(), CFeaturePropagator::FindRow(), CInternalStopFinder::FindStartStopRanges(), CSeq_align::GapLengthRange(), CScore_GapCount::Get(), CScore_InternalUnaligned::Get(), CScore_ExonCount::Get(), CScore_IndelToSplice::Get(), CScore_LastSpliceSite::Get(), CScore_FrameShifts::Get(), CScore_3PrimeUnaligned::Get(), CScore_Polya::Get(), CScore_SequenceLength::Get(), CScore_StartStopCodon::Get(), CScore_CdsInternalStops::Get(), CScore_CdsScore::Get(), CScore_TblastnScore::Get(), CScore_EdgeExonInfo::Get(), CSeq_align::GetAlignedBases(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CAlignFormatUtil::GetAlignmentLength(), CScoreBuilder::GetBlastScore(), CScoreBuilder::GetBlastScoreDenseg(), CScoreBuilder::GetBlastScoreSpliced(), GetBlockCount(), CInternalStopFinder::GetCDSNucleotideSequence(), SAlignmentScoringModel::GetCoverage(), GetDDSetFromSeqAlign(), CSeq_align_Mapper_Base::GetDstAlign(), GetExonPartialness(), CFeatureGenerator::SImplementation::GetExons(), SAlignmentScoringModel::GetExonsOdds(), variation::GetFocusLocusIDs(), CProteinAlignText::GetGenomicBounds(), SAlignmentScoringModel::GetIdentOdds(), CSeqUtils::GetLocPlacements(), SAlignmentScoringModel::GetLongestMatchrunLen(), GetMasterGIFromSeqAlign(), SAlignmentScoringModel::GetNumGapopensBetweenExons(), SAlignmentScoringModel::GetPolyA_length(), CProductStringBuilder::GetProductString(), GetPssmIdFromSeqAlign(), GetReportableSeqIdForAlignment(), CSeq_align_Handle::GetSegs(), CSeq_align::GetSeq_id(), CAlignFormatUtil::GetSeqAlignSetCalcParamsFromASN(), CSeq_align::GetSeqRange(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStop(), CSeq_align::GetSeqStrand(), SAlignmentScoringModel::GetSplicesOdds(), GetTerminalPartialness(), GetUnalignedLength_3p(), GetUnalignedLength_5p(), CAlignFormatUtil::GetUniqSeqCoverage(), variation::GetUniquePrimaryTranscriptId(), CCdCore::Has3DMaster(), CFeatureGenerator::SImplementation::HasMixedGenomicIds(), CCdCore::HasSeqId(), CAlnContainer::insert(), CSeq_align::IntronLengthRange(), IsProteinAlign(), SAlignmentScoringModel::isProtSS(), CScoreUniqSeqCoverage::MakeScore(), CRemoveSeqFromAlignDlg::ModifyAlign(), CAlignmentAssistant::OnRemoveSeqFromAlign(), CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()(), CProSplignText::Output(), PatchTargetSequence(), CValidError_imp::PostErr(), CTabularFormatter_MismatchPositions::Print(), CTabularFormatter_ExonIntrons::Print(), CTabularFormatter_Cigar::Print(), CTabularFormatter_Traceback::Print(), PrintSAM(), PrintTabular(), ProjectExons(), CFeatureGenerator::SImplementation::RecalculateScores(), CProSplign::RefineAlignment(), variation_ref::CVariationUtil::Remap(), variation::CVariationUtil::Remap(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), CSeq_align::Reverse(), CTestBlastp_All::RunTest(), CTestSingleAln_All::RunTest(), s_AlignToSeqRanges(), s_CheckTraceMateAlign(), s_CleanSeqAlign(), s_ComputeTraceback(), s_CountSegments(), s_CoverageSeqLoc(), s_CutDensegSegment(), s_ExtractSeqId(), s_Fingerprint_Seq_align(), s_GetAlignmentContent(), s_GetAlignmentLength(), s_GetAlignmentMismatches(), s_GetAlignmentSpans_Exon(), s_GetAlignmentSpans_Interval(), s_GetAlignmentSpans_Intron(), s_GetAlignmentTooltip(), s_GetAlignmentType(), s_GetAlnMapplingLocs(), s_GetAlnScores(), s_GetCigarString(), s_GetCountIdentityMismatch(), s_GetGapCount(), SAlignmentScoringModel::s_GetIdentOdds_disc(), SAlignmentScoringModel::s_GetIdentOdds_nucSS(), s_GetIndels(), s_GetPercentCoverage(), s_GetRnaMappingLocs(), s_GetSplicedSegIdentityMismatch(), s_GetSubjectId(), s_IsProteinToGenomic(), CMacroFunction_RemoveSegGaps::s_RemoveSegGaps(), s_Render_PairwiseAlign(), s_ScoreAlignments(), s_Seq_align_Seq_loc(), s_SeqAlignSetToXMLHsps(), s_SeqAlignToXMLHit(), s_SetAirrAlignmentInfo(), s_SplicedToDisc(), s_TestAlignmentFromMSAs(), s_TestCalc(), s_TestResultAlignment(), s_UpdateSubjectInSeqalign(), COverlapScorer::ScoreAlignments(), CClippedScorer::ScoreAlignments(), CFeaturePropagator::SeqPosToAlignPos(), CReportEntry::SetAlignment(), CBlastTabularInfo::SetFields(), CIgBlastTabularInfo::SetIgAnnotation(), CFeatureGenerator::SImplementation::SMapper::SMapper(), CSeq_align::SplitOnLongDiscontinuity(), sPrepareSeqAlign(), CSeq_align::SwapRows(), testNuclHitList(), CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript(), CReportTrim::TrimAlignments(), TrimSeqAlign(), TrimSequenceAndAnnotation(), UpdateDensegAlignment(), CSeq_align::Validate(), CValidError_align::ValidateSeqAlign(), CAlnWriter::WriteAlign(), CPslWriter::WriteAlign(), CAlnTableDS::x_AddAlign(), CSeq_annot_Info::x_AddAlignKeys(), CAdvancedAlignCleanup::x_AddStandardAlignmentScores(), CVectorTrimPanel::x_AdjustDensegAlignment(), CReportTrim::x_AdjustDensegAlignment(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignFillerBlocks(), CQuerySet::x_AlreadyContains(), CIgBlast::x_AnnotateC(), CIgBlast::x_AnnotateDomain(), CTabularFormatter_BiggestGapBases::x_CalcBiggestGap(), CReportEntry::x_CheckExonGap(), CAlignCleanup::x_Cleanup_AlignVec(), CAdvancedAlignCleanup::x_CleanupProsplignCompartment(), CFeatureGenerator::SImplementation::x_CollectMrnaSequence(), CPrimaryItem::x_CollectSegments(), x_CollectSegments(), CQuerySet::x_ContainsAlignment(), CInversionMergeAligner::x_CreateDiscAlignment(), CHitMatrixDataSource::x_CreateHit(), CHitMatrixDataSource::x_CreateHit_Denseg(), CHitMatrixDataSource::x_CreateHit_Std(), CCleanupAlignmentsJob::x_CreateProjectItems(), CTreeBuilderJob::x_CreateProjectItems(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), COligoSpecificityCheck::x_FillGlobalAlignInfo(), CIgBlast::x_FillJDomain(), CSequenceEditingEventHandler::x_FindRelevantAlignRow(), CMultiAligner::x_FindRPSHits(), CCIGAR_Formatter::x_FormatAlignmentRows(), CAlignFilter::x_FuncCall(), CProSplignJob::x_GenerateCompartments(), CHitMatrixDataSource::x_GetAlignedSeqIds(), CApplyRNAITSDlg::x_GetAlignments(), CDisplaySeqalign::x_GetAlnVecForSeqalign(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CValidError_align::x_GetIds(), CAlnMultiDSBuilder::x_GetLinearAlignments(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CScoreBuilderBase::x_GetMatrixCounts(), CHitMatrixDataSource::x_GetSeqAlignIds(), CCommonComponentScorer::x_GetSeqHistCompList(), COligoSpecificityCheck::x_GetSlaveRangeGivenMasterRange(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CSeq_align_Mapper_Base::x_Init(), CPhyTreeCalc::x_InitAlignDS(), CUpdateSeqPanel::x_InitDrawingParams(), CSeq_loc_Mapper_Base::x_InitializeAlign(), CApplyRNAITSDlg::x_IsThereAlignment(), CAlignFilter::x_IsUnique(), CUnorderedSplitter::x_MakeAlignmentPairUnique(), CTreeAlignMerger::x_MakeMergeableGroups(), CFeatureGenerator::SImplementation::x_MapFeature(), COligoSpecificityCheck::x_NW_alignment(), CAnnotObject_Info::x_ProcessAlign(), CAppHitFilter::x_ReadInputHits(), CIdMapperTestApp::x_RecurseMapSeqAligns(), CTabularFormatter_DiscStrand::x_RecurseStrands(), CApplyRNAITSDlg::x_SeqIdsAlignedWith(), CMultiAligner::x_SetDomainHits(), CCDSTranslationPanel::x_SetLocationForProtein(), CApplyRNAITSDlg::x_SetupAlnMgr(), x_TestAlignmentQuerySubjStrandCombinations(), CHitMatrixDataSource::x_TestAndSelectAlign(), CVectorTrimPanel::x_TrimAlignments(), CSeqAlignFilter::x_UpdateGiInSeqalign(), CModifySeqId::x_UpdateSeqAlign(), CValidError_align::x_ValidateAlignPercentIdentity(), CPsiBl2SeqTestFixture::x_ValidatePssmVsGi129295(), CPsiBl2SeqTestFixture::x_ValidatePssmVsGi7450545(), CEditObjectFeaturePropagate::xInit(), CGff3Writer::xWriteAlign(), CGff3Writer::xWriteAlignDenseg(), CGff3Writer::xWriteAlignDisc(), and CGff3Writer::xWriteAlignSpliced().
const CSeq_align_Base::C_Segs::TSparse & CSeq_align_Base::C_Segs::GetSparse | ( | void | ) | const |
Get the variant data.
Definition at line 241 of file Seq_align_.cpp.
Referenced by CSeqsRange::Add(), CSeq_align::CheckNumRows(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CSeq_align::GetSeq_id(), CSeq_align::GetSeqRange(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStop(), CSeq_align::GetSeqStrand(), CRemoveSeqFromAlignDlg::ModifyAlign(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), s_Fingerprint_Seq_align(), CSeq_align::Validate(), CAlnWriter::WriteAlign(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitializeAlign(), and CAnnotObject_Info::x_ProcessAlign().
const CSeq_align_Base::C_Segs::TSpliced & CSeq_align_Base::C_Segs::GetSpliced | ( | void | ) | const |
Get the variant data.
Definition at line 219 of file Seq_align_.cpp.
Referenced by CSeqsRange::Add(), CScoreBuilderBase::AddSplignScores(), BOOST_AUTO_TEST_CASE(), CTestSingleAln::CanTest(), CFeaturePropagator::CFeaturePropagator(), variation_ref::CVariationUtil::CheckExonBoundary(), variation::CVariationUtil::CheckExonBoundary(), CSeq_align::CreateRowSeq_loc(), CProSplign::CImplementation::FindGlobalAlignment_stage2(), CInternalStopFinder::FindStartStopRanges(), CScore_InternalUnaligned::Get(), CScore_ExonCount::Get(), CScore_IndelToSplice::Get(), CScore_LastSpliceSite::Get(), CScore_FrameShifts::Get(), CScore_3PrimeUnaligned::Get(), CScore_Polya::Get(), CScore_SequenceLength::Get(), CScore_StartStopCodon::Get(), CScore_TblastnScore::Get(), CScore_EdgeExonInfo::Get(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CScoreBuilder::GetBlastScoreSpliced(), CInternalStopFinder::GetCDSNucleotideSequence(), SAlignmentScoringModel::GetCoverage(), GetExonPartialness(), CFeatureGenerator::SImplementation::GetExons(), SAlignmentScoringModel::GetExonsOdds(), CProteinAlignText::GetGenomicBounds(), SAlignmentScoringModel::GetLongestMatchrunLen(), SAlignmentScoringModel::GetNumGapopensBetweenExons(), SAlignmentScoringModel::GetPolyA_length(), CProductStringBuilder::GetProductString(), CSeq_align::GetSeq_id(), CSeq_align::GetSeqRange(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStop(), CSeq_align::GetSeqStrand(), SAlignmentScoringModel::GetSplicesOdds(), GetTerminalPartialness(), GetUnalignedLength_3p(), GetUnalignedLength_5p(), CFeatureGenerator::SImplementation::HasMixedGenomicIds(), IsProteinAlign(), SAlignmentScoringModel::isProtSS(), CProSplignText::Output(), CTabularFormatter_MismatchPositions::Print(), CTabularFormatter_ExonIntrons::Print(), PrintSAM(), PrintTabular(), ProjectExons(), CFeatureGenerator::SImplementation::RecalculateScores(), CProSplign::RefineAlignment(), variation_ref::CVariationUtil::Remap(), variation::CVariationUtil::Remap(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), s_AlignToSeqRanges(), s_CountSegments(), s_Fingerprint_Seq_align(), s_GetAlignmentContent(), s_GetAlignmentLength(), s_GetAlignmentMismatches(), s_GetAlignmentSpans_Exon(), s_GetAlignmentSpans_Intron(), s_GetCountIdentityMismatch(), s_GetGapCount(), SAlignmentScoringModel::s_GetIdentOdds_nucSS(), s_GetIndels(), s_GetPercentCoverage(), s_GetSplicedSegIdentityMismatch(), s_IsProteinToGenomic(), s_SplicedToDisc(), CReportEntry::SetAlignment(), CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript(), CSeq_align::Validate(), CAlnWriter::WriteAlign(), CPslWriter::WriteAlign(), CReportEntry::x_CheckExonGap(), CAdvancedAlignCleanup::x_CleanupProsplignCompartment(), CFeatureGenerator::SImplementation::x_CollectMrnaSequence(), CCIGAR_Formatter::x_FormatAlignmentRows(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CScoreBuilderBase::x_GetMatrixCounts(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitializeAlign(), CFeatureGenerator::SImplementation::x_MapFeature(), CAnnotObject_Info::x_ProcessAlign(), CCDSTranslationPanel::x_SetLocationForProtein(), and CGff3Writer::xWriteAlignSpliced().
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Get the variant data.
Definition at line 263 of file Spliced_seg_modifier_.hpp.
References CSpliced_seg_modifier_Base::CheckSelected(), CSpliced_seg_modifier_Base::e_Start_codon_found, and CSpliced_seg_modifier_Base::m_Start_codon_found.
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Get the Starts member data.
Definition at line 435 of file Dense_diag_.hpp.
References CDense_diag_Base::m_Starts.
Referenced by CSeqsRange::Add(), CDense_diag::CheckNumRows(), ConvertDendiagToPairwiseAln(), CreateDense_diagFromAnchoredAln(), CDense_diag::CreateRowSeq_interval(), CDense_diag::GetSeqStart(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), CDense_diag::OffsetRow(), s_Fingerprint_Dense_diag(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CAnnotObject_Info::x_ProcessAlign(), CValidError_align::x_ValidateDendiag(), and CValidError_align::x_ValidateSeqLength().
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Get the Starts member data.
Definition at line 530 of file Dense_seg_.hpp.
References CDense_seg_Base::m_Starts.
Referenced by CSeqsRange::Add(), CAlnMixMatches::Add(), CAlignmentAssistant::AdjustAlign(), CPaintAlignment::AlignPosToSeqPos(), CFeaturePropagator::AlignPosToSeqPos(), CContigAssembly::BandedGlobalAlignment(), BOOST_AUTO_TEST_CASE(), CAlignShadow::CAlignShadow(), CDense_seg::CheckNumSegs(), CAlnVecPrinter::ClustalStyle(), CDense_seg::Compact(), CDUpdater::ComputePercentIdentity(), ConvertDensegToPairwiseAln(), CreateAlignRow(), CSeq_align::CreateDensegFromDisc(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CAlignCleanup::CreatePairwiseFromMultiple(), CDense_seg::CreateRowSeq_interval(), CFeaturePropagator::CreateRowSeq_loc(), Denseg2DenseDiagList(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CDense_seg::ExtractRows(), CDense_seg::ExtractSlice(), CDense_seg::FillUnaligned(), CEditSeqEndsWithAlign::FindPosition(), CSeq_align::GapLengthRange(), CSeq_align::GetAlignedBases(), CPaintAlignment::GetSegments(), CDense_seg::GetSeqStart(), CDense_seg::GetSeqStop(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), CRemoveSeqFromAlignDlg::ModifyAlign(), CDense_seg::OffsetRow(), CAlignmentAssistant::OnRemoveSeqFromAlign(), CAlignmentAssistant::OnReverseStrand(), CDense_seg::OrderAdjacentGaps(), CAlnVecPrinter::PopsetStyle(), CTabularFormatter_Cigar::Print(), PrintSAM(), CDense_seg::RemapToLoc(), CDense_seg::RemovePureGapSegs(), CDense_seg::Reverse(), ReverseAlignmentStrand(), CFarPointerSeq::ReverseRow(), s_AlignToSeqRanges(), s_CalculateMatchingColumns(), s_CoverageSeqLoc(), s_CutDensegSegment(), s_DenseSegLength(), s_FindSegment(), s_Fingerprint_Dense_seg(), s_GetAlignmentLength(), s_GetCigarString(), s_GetGapCount(), s_GetIndels(), s_SeqAlignToBlastSeqLoc(), s_TestAlignmentFromMSAs(), s_TestResultAlignment(), CPaintAlignment::SeqPosToAlignPos(), CFeaturePropagator::SeqPosToAlignPos(), CAlignCompare::SAlignment::Slice(), CSeq_align::SplitOnLongDiscontinuity(), CDense_seg::TrimEndGaps(), TrimSeqAlign(), UpdateDensegAlignment(), CDense_seg::Validate(), CAlnWriter::WriteAlignDenseSeg(), CVectorTrimPanel::x_AdjustDensegAlignment(), CReportTrim::x_AdjustDensegAlignment(), CTabularFormatter_BiggestGapBases::x_CalcBiggestGap(), CAlignCleanup::x_Cleanup_AlignVec(), CQuerySet::x_ContainsAlignment(), CInversionMergeAligner::x_CreateDiscAlignment(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CAppHitFilter::x_DumpOutput(), CVectorTrimPanel::x_FindSegment(), CReportTrim::x_FindSegment(), CDense_seg::x_FindSegment(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CDenseg_CI::x_InitIterator(), CDenseg_CI::x_InitSegment(), CInversionMergeAligner::x_IsAllGap(), CUnorderedSplitter::x_IsAllGap(), CUpdateAlign::x_RemoveIDsFromAlign(), CInstancedAligner::x_RunMMGlobal(), x_TestAlignmentQuerySubjStrandCombinations(), and CPslRecord::xInitializeStatsAndBlocks().
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Get the Starts member data.
Definition at line 554 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_Starts.
Referenced by CSeqsRange::Add(), ConvertPackedsegToPairwiseAln(), s_Fingerprint_Packed_seg(), CSeq_align_Mapper_Base::x_Init(), and CSeq_loc_Mapper_Base::x_InitAlign().
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Get the variant data.
Definition at line 752 of file Seq_align_.hpp.
Referenced by CSeqsRange::Add(), BOOST_AUTO_TEST_CASE(), BuildAlignDataSource(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CSeqUtils::GetLocPlacements(), CAlignFormatUtil::GetSeqAlignSetCalcParamsFromASN(), CSeq_align::GetSeqStrand(), CDisplaySeqalign::PrepareBlastUngappedSeqalign(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx2(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), s_Fingerprint_Seq_align(), s_GetAlignmentLength(), s_GetAlignmentSpans_Exon(), s_GetAlignmentSpans_Interval(), s_GetAlnMapplingLocs(), s_GetAlnScores(), s_GetGapCount(), s_GetSubjectId(), testNuclHitList(), CValidError_align::ValidateSeqAlign(), CHitMatrixDataSource::x_CreateHit_Std(), CValidError_align::x_GetIds(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitializeAlign(), CAnnotObject_Info::x_ProcessAlign(), CHitMatrixDataSource::x_TestAndSelectAlign(), and CValidError_align::x_ValidateAlignPercentIdentity().
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Get the variant data.
Definition at line 290 of file Spliced_seg_modifier_.hpp.
References CSpliced_seg_modifier_Base::CheckSelected(), CSpliced_seg_modifier_Base::e_Stop_codon_found, and CSpliced_seg_modifier_Base::m_Stop_codon_found.
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Get the Strands member data.
Definition at line 507 of file Dense_diag_.hpp.
References CDense_diag_Base::m_Strands.
Referenced by ConvertDendiagToPairwiseAln(), CDense_diag::CreateRowSeq_interval(), CDense_diag::GetSeqStrand(), s_Fingerprint_Dense_diag(), CDense_diag::Validate(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CAnnotObject_Info::x_ProcessAlign(), and CValidError_align::x_ValidateDendiag().
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Get the Strands member data.
Definition at line 580 of file Dense_seg_.hpp.
References CDense_seg_Base::m_Strands.
Referenced by CAlnMixMatches::Add(), CAlignmentAssistant::AdjustAlign(), CPaintAlignment::AlignPosToSeqPos(), CFeaturePropagator::AlignPosToSeqPos(), CContigAssembly::BandedGlobalAlignment(), CAlignShadow::CAlignShadow(), CDense_seg::CheckNumSegs(), CDense_seg::Compact(), ConvertDensegToPairwiseAln(), CreateAlignRow(), CSeq_align::CreateDensegFromDisc(), CAlignCleanup::CreatePairwiseFromMultiple(), CDense_seg::CreateRowSeq_interval(), CFeaturePropagator::CreateRowSeq_loc(), Denseg2DenseDiagList(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CDense_seg::ExtractRows(), CDense_seg::ExtractSlice(), CDense_seg::FillUnaligned(), CPaintAlignment::GetSegments(), CDense_seg::GetSeqStart(), CDense_seg::GetSeqStop(), CDense_seg::GetSeqStrand(), CRemoveSeqFromAlignDlg::ModifyAlign(), CAlignmentAssistant::OnRemoveSeqFromAlign(), CAlignmentAssistant::OnReverseStrand(), CDense_seg::OrderAdjacentGaps(), CDense_seg::RemapToLoc(), CDense_seg::RemovePureGapSegs(), ReverseAlignmentStrand(), CFarPointerSeq::ReverseRow(), s_CoverageSeqLoc(), s_CutDensegSegment(), s_Fingerprint_Dense_seg(), s_GetIndels(), s_SeqAlignSetToXMLHsps(), s_SeqAlignToBlastSeqLoc(), CPaintAlignment::SeqPosToAlignPos(), CFeaturePropagator::SeqPosToAlignPos(), CBlastTabularInfo::SetFields(), CDense_seg::TrimEndGaps(), CDense_seg::Validate(), CAlnWriter::WriteAlignDenseSeg(), CAlignCleanup::x_Cleanup_AlignVec(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CContigAssembly::x_IsAllowedStrands(), CInversionMergeAligner::x_MergeSeqAlignSet(), CMergeAligner::x_MergeSeqAlignSet(), CUpdateAlign::x_RemoveIDsFromAlign(), CInstancedAligner::x_RunCleanup(), and x_TestAlignmentQuerySubjStrandCombinations().
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Get the Strands member data.
Definition at line 632 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_Strands.
Referenced by ConvertPackedsegToPairwiseAln(), s_Fingerprint_Packed_seg(), CSeq_align_Mapper_Base::x_Init(), and CSeq_loc_Mapper_Base::x_InitAlign().
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Get the Type member data.
Definition at line 809 of file Seq_align_.hpp.
References CSeq_align_Base::CanGetType(), CSeq_align_Base::m_Type, and CSerialObject::ThrowUnassigned().
Referenced by CTestSingleAln::CanTest(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CAlignCleanup::CreatePairwiseFromMultiple(), CSeq_align_Mapper_Base::GetDstAlign(), GetMasterGIFromSeqAlign(), GetPssmIdFromSeqAlign(), CSeq_align_Handle::GetType(), CValidError_imp::PostErr(), s_TestResultAlignment(), CValidError_align::ValidateSeqAlign(), and CValidError_align::x_ValidateFastaLike().
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Get the Value member data.
Definition at line 465 of file Score_.hpp.
References CScore_Base::CanGetValue(), CScore_Base::m_Value, and CSerialObject::ThrowUnassigned().
Referenced by GetFloatScore(), GetIntScore(), s_GetAlignmentTooltip(), s_GetBitScore(), s_GetEvalue(), CGffAlignmentRecord::SetScore(), CGffBaseRecord::SetScore(), sPrepareSeqAlign(), testNuclHitList(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignFillerBlocks(), CMultiAligner::x_FindRPSHits(), CMultiAligner::x_SetDomainHits(), and CHitMatrixDataSource::x_UpdateScoreMap().
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Check if variant Dendiag is selected.
Dendiag type is defined as 'typedef list< CRef< CDense_diag > > TDendiag'.
Definition at line 720 of file Seq_align_.hpp.
Referenced by CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CAlignFormatUtil::GetAlignmentLength(), GetBlockCount(), GetDDSetFromSeqAlign(), GetMasterGIFromSeqAlign(), GetPssmIdFromSeqAlign(), GetReportableSeqIdForAlignment(), CCdCore::Has3DMaster(), s_DivvyUpAlignments_ProcessAnnot(), s_GetSubjectId(), s_SeqAlignSetToXMLHsps(), CBlastTabularInfo::SetFields(), CAlignFilter::x_FuncCall(), CSeqAlignFilter::x_UpdateGiInSeqalign(), and CModifySeqId::x_UpdateSeqAlign().
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Check if variant Denseg is selected.
Denseg type is defined as 'typedef CDense_seg TDenseg'.
Definition at line 740 of file Seq_align_.hpp.
Referenced by CAlnMix::Add(), CAlnVwrApp::AddAlnToMix(), BOOST_AUTO_TEST_CASE(), BuildAlignDataSource(), CFeaturePropagator::CFeaturePropagator(), ConvertRawToDeltaByNsCommand_impl(), ConvertRawToDeltaByNsHugeFileCmd_impl(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CAlignCleanup::CreatePairwiseFromMultiple(), Denseg2DenseDiagList(), CEditSeqEndsWithAlign::FindPosition(), CScoreBuilder::GetBlastScore(), CScoreBuilder::GetBlastScoreDenseg(), GetMasterGIFromSeqAlign(), GetPssmIdFromSeqAlign(), CTabularFormatter_Cigar::Print(), CTabularFormatter_Traceback::Print(), PrintTabular(), s_CheckTraceMateAlign(), s_CleanSeqAlign(), s_ComputeTraceback(), s_DivvyUpAlignments_ProcessAnnot(), s_GetSubjectId(), s_IsProteinToGenomic(), CMacroFunction_RemoveSegGaps::s_RemoveSegGaps(), s_ScoreAlignments(), s_TestAlignmentFromMSAs(), s_UpdateSubjectInSeqalign(), COverlapScorer::ScoreAlignments(), CClippedScorer::ScoreAlignments(), SeqAlignConvert(), CTabularFormatter_BiggestGapBases::x_CalcBiggestGap(), CAlignCleanup::x_Cleanup_AlignVec(), CPrimaryItem::x_CollectSegments(), x_CollectSegments(), CHitMatrixDataSource::x_CreateHit_Denseg(), CTreeBuilderJob::x_CreateProjectItems(), CCIGAR_Formatter::x_FormatAlignmentRows(), CAlignFilter::x_FuncCall(), CApplyRNAITSDlg::x_GetAlignments(), CUpdateSeqPanel::x_InitDrawingParams(), CApplyRNAITSDlg::x_IsThereAlignment(), CIdMapperTestApp::x_RecurseMapSeqAligns(), CApplyRNAITSDlg::x_SetupAlnMgr(), CSeqAlignFilter::x_UpdateGiInSeqalign(), CModifySeqId::x_UpdateSeqAlign(), CValidError_align::x_ValidateAlignPercentIdentity(), CPsiBl2SeqTestFixture::x_ValidatePssmVsGi129295(), CPsiBl2SeqTestFixture::x_ValidatePssmVsGi7450545(), and CEditObjectFeaturePropagate::xInit().
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Check if variant Diag is selected.
Diag type is defined as 'typedef TSeqPos TDiag'.
Definition at line 404 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::e_Diag, and CSpliced_exon_chunk_Base::m_choice.
Referenced by CProteinAlignText::CProteinAlignText(), CProSplign::CImplementation::HasStartOnNuc(), ProjectExon_oldlogic(), s_ExonToDenseg(), SBlocks::SBlocks(), CReportEntry::x_CheckExonGap(), and CSeq_loc_Mapper_Base::x_IterateExonParts().
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Check if variant Disc is selected.
Disc type is defined as 'typedef CSeq_align_set TDisc'.
Definition at line 772 of file Seq_align_.hpp.
Referenced by CAlnMix::Add(), BuildAlignDataSource(), CFeaturePropagator::CFeaturePropagator(), ExtractFirstSeqAlign(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CAlignFormatUtil::ExtractSeqalignSetFromDiscSegs(), SAlignmentScoringModel::GetIdentOdds(), PatchTargetSequence(), PrintSAM(), PrintTabular(), CTestSingleAln_All::RunTest(), s_CleanSeqAlign(), s_ExtractSeqId(), s_SeqAlignToXMLHit(), CAlnTableDS::x_AddAlign(), CSeq_annot_Info::x_AddAlignKeys(), CTabularFormatter_BiggestGapBases::x_CalcBiggestGap(), CPrimaryItem::x_CollectSegments(), x_CollectSegments(), CQuerySet::x_ContainsAlignment(), CCleanupAlignmentsJob::x_CreateProjectItems(), CAlignFilter::x_FuncCall(), CCommonComponentScorer::x_GetSeqHistCompList(), CTreeAlignMerger::x_MakeMergeableGroups(), CIdMapperTestApp::x_RecurseMapSeqAligns(), and CTabularFormatter_DiscStrand::x_RecurseStrands().
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Check if variant Genomic_ins is selected.
Genomic_ins type is defined as 'typedef TSeqPos TGenomic_ins'.
Definition at line 458 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::e_Genomic_ins, and CSpliced_exon_chunk_Base::m_choice.
Referenced by CProteinAlignText::CProteinAlignText(), CProSplign::CImplementation::HasStartOnNuc(), CSeq_align_Mapper_Base::InitExon(), ProjectExon_oldlogic(), s_ExonToDenseg(), SBlocks::SBlocks(), CReportEntry::x_CheckExonGap(), CSeq_align_Mapper_Base::x_GetDstSpliced(), and CSeq_loc_Mapper_Base::x_IterateExonParts().
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Check if variant Int is selected.
Int type is defined as 'typedef int TInt'.
Definition at line 405 of file Score_.hpp.
Referenced by GetFloatScore(), GetIntScore(), s_CompareValues(), CGffAlignmentRecord::SetScore(), and CGffBaseRecord::SetScore().
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Check if variant Match is selected.
Match type is defined as 'typedef TSeqPos TMatch'.
Definition at line 350 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::e_Match, and CSpliced_exon_chunk_Base::m_choice.
Referenced by CProteinAlignText::CProteinAlignText(), CProSplign::CImplementation::HasStartOnNuc(), ProjectExon_oldlogic(), s_ExonToDenseg(), SBlocks::SBlocks(), CReportEntry::x_CheckExonGap(), and CSeq_loc_Mapper_Base::x_IterateExonParts().
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Check if variant Mismatch is selected.
Mismatch type is defined as 'typedef TSeqPos TMismatch'.
Definition at line 377 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::e_Mismatch, and CSpliced_exon_chunk_Base::m_choice.
Referenced by CProteinAlignText::CProteinAlignText(), CProSplign::CImplementation::HasStartOnNuc(), ProjectExon_oldlogic(), s_ExonToDenseg(), SBlocks::SBlocks(), CReportEntry::x_CheckExonGap(), and CSeq_loc_Mapper_Base::x_IterateExonParts().
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Check if variant Nucpos is selected.
Nucpos type is defined as 'typedef TSeqPos TNucpos'.
Definition at line 260 of file Product_pos_.hpp.
References CProduct_pos_Base::e_Nucpos, and CProduct_pos_Base::m_choice.
Referenced by CSeqsRange::Add(), variation_ref::CVariationUtil::CheckExonBoundary(), variation::CVariationUtil::CheckExonBoundary(), CSpliced_seg::IsConsistentBiologicalOrder(), CProductStringBuilder::x_AddExon(), and CAnnotObject_Info::x_ProcessAlign().
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Check if variant Packed is selected.
Packed type is defined as 'typedef CPacked_seg TPacked'.
Definition at line 766 of file Seq_align_.hpp.
Referenced by CAlignFilter::x_FuncCall().
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Check if variant Product_ins is selected.
Product_ins type is defined as 'typedef TSeqPos TProduct_ins'.
Definition at line 431 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::e_Product_ins, and CSpliced_exon_chunk_Base::m_choice.
Referenced by CProteinAlignText::CProteinAlignText(), CProSplign::CImplementation::HasStartOnNuc(), CSeq_align_Mapper_Base::InitExon(), ProjectExon_oldlogic(), s_ExonToDenseg(), SBlocks::SBlocks(), CReportEntry::x_CheckExonGap(), and CSeq_loc_Mapper_Base::x_IterateExonParts().
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Check if variant Protpos is selected.
Protpos type is defined as 'typedef CProt_pos TProtpos'.
Definition at line 287 of file Product_pos_.hpp.
References CProduct_pos_Base::e_Protpos, and CProduct_pos_Base::m_choice.
Referenced by CSeq_align_Mapper_Base::x_GetDstExon(), CSeq_loc_Mapper_Base::x_InitSpliced(), and CGff3FlybaseWriter::xAssignAlignmentSplicedLocation().
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Check if variant Real is selected.
Real type is defined as 'typedef double TReal'.
Definition at line 378 of file Score_.hpp.
Referenced by s_CompareValues(), s_GetAlignmentTooltip(), s_GetBitScore(), s_GetEvalue(), and CGffBaseRecord::SetScore().
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Check if a value has been assigned to data member.
Data member is mandatory; its type is defined as 'typedef list< CRef< CScore > > Tdata'
Definition at line 153 of file Score_set_.hpp.
References CScore_set_Base::m_set_State.
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Check if a value has been assigned to data member.
Data member is mandatory; its type is defined as 'typedef list< CRef< CSeq_align > > Tdata'
Definition at line 154 of file Seq_align_set_.hpp.
References CSeq_align_set_Base::m_set_State.
Referenced by HitDistributor::addBatch(), CAlignmentCollectionScore::Get(), CBlastFormatUtil::InsertSubjectScores(), CFarPointerSeq::RunBlast(), CCreateSeqHistForTpa::RunBlast(), s_RoundScores(), s_RunBlast2NASeq(), CAlignmentCollectionScore::Set(), CIgBlastTabularInfo::SetAirrFormatData(), CIgBlastTabularInfo::SetIgAnnotation(), CDUpdater::update(), CAutogeneratedCleanup::x_BasicCleanupSeqAlignSet(), CNGAlignJob::x_CreateProjectItems(), and CFindOverlapJob::x_CreateProjectItems().
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splice sites Check if a value has been assigned to Acceptor_before_exon data member.
Data member Acceptor_before_exon is optional; its type is defined as 'typedef CSplice_site TAcceptor_before_exon'
Definition at line 1024 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Acceptor_before_exon.
Referenced by CSpliced_exon_Base::CanGetAcceptor_before_exon(), CScore_IndelToSplice::Get(), GetExonPartialness(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CAlignGlyph::x_DrawNonConsensusSpliceSites(), CSeq_align_Mapper_Base::x_GetDstExon(), and CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons().
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amino-acid position (0-based) Check if a value has been assigned to Amin data member.
Data member Amin is mandatory; its type is defined as 'typedef TSeqPos TAmin'
Definition at line 201 of file Prot_pos_.hpp.
References CProt_pos_Base::m_set_State.
Referenced by CProt_pos_Base::CanGetAmin(), and CProt_pos_Base::SetAmin().
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typically two bases in the intronic region, always in IUPAC format Check if a value has been assigned to Bases data member.
Data member Bases is mandatory; its type is defined as 'typedef string TBases'
Definition at line 162 of file Splice_site_.hpp.
References CSplice_site_Base::m_set_State.
Referenced by CSplice_site_Base::CanGetBases(), and CSplice_site_Base::SetBases().
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regions of sequence over which align was computed Check if a value has been assigned to Bounds data member.
Data member Bounds is optional; its type is defined as 'typedef list< CRef< CSeq_loc > > TBounds'
Definition at line 939 of file Seq_align_.hpp.
References CSeq_align_Base::m_set_State.
Referenced by CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CSeq_align_Mapper_Base::GetDstAlign(), CSeq_align_Handle::IsSetBounds(), CAutogeneratedCleanup::x_BasicCleanupSeqAlign(), and CSeq_align_Mapper_Base::x_GetDstSpliced().
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dimensionality Check if a value has been assigned to Dim data member.
Data member Dim is optional with default 2; its type is defined as 'typedef int TDim'
Definition at line 348 of file Dense_diag_.hpp.
References CDense_diag_Base::m_set_State.
Referenced by CDense_diag_Base::SetDim().
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dimensionality Check if a value has been assigned to Dim data member.
Data member Dim is optional with default 2; its type is defined as 'typedef int TDim'
Definition at line 396 of file Dense_seg_.hpp.
References CDense_seg_Base::m_set_State.
Referenced by BLASTer::CreateNewPairwiseAlignmentsByBlast(), CAlignmentAssistant::GetFeatures(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), CAlignmentAssistant::ReportUnresolvedBioseqs(), CMacroFunction_RemoveSegGaps::s_RemoveSegGaps(), and CDense_seg_Base::SetDim().
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dimensionality Check if a value has been assigned to Dim data member.
Data member Dim is optional with default 2; its type is defined as 'typedef int TDim'
Definition at line 420 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_set_State.
Referenced by CPacked_seg_Base::SetDim().
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dimensionality Check if a value has been assigned to Dim data member.
Data member Dim is optional; its type is defined as 'typedef int TDim'
Definition at line 837 of file Seq_align_.hpp.
References CSeq_align_Base::m_set_State.
Referenced by CSeq_align_Base::CanGetDim(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CDesktopAlignItem::GetDescription(), CSeq_align_Mapper_Base::GetDstAlign(), GetPssmIdFromSeqAlign(), GetReportableSeqIdForAlignment(), CSeq_align_Handle::IsSetDim(), CDesktopAlignItem::s_ContainsFarPointers(), CSeq_align_Base::SetDim(), CLDS2_AnnotType_Hook::SkipObject(), and CSeq_align::SplitOnLongDiscontinuity().
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dimensionality Check if a value has been assigned to Dim data member.
Data member Dim is optional with default 2; its type is defined as 'typedef int TDim'
Definition at line 270 of file Std_seg_.hpp.
References CStd_seg_Base::m_set_State.
Referenced by CStd_seg_Base::SetDim().
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Check if a value has been assigned to Donor_after_exon data member.
Data member Donor_after_exon is optional; its type is defined as 'typedef CSplice_site TDonor_after_exon'
Definition at line 1045 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Donor_after_exon.
Referenced by CSpliced_exon_Base::CanGetDonor_after_exon(), CScore_IndelToSplice::Get(), GetExonPartialness(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CAlignGlyph::x_DrawNonConsensusSpliceSites(), CSeq_align_Mapper_Base::x_GetDstExon(), and CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons().
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set of segments involved each segment corresponds to one exon exons are always in biological order Check if a value has been assigned to Exons data member.
Data member Exons is mandatory; its type is defined as 'typedef list< CRef< CSpliced_exon > > TExons'
Definition at line 680 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_set_State.
Referenced by CFeatureGenerator::SImplementation::AdjustAlignment(), CScore_ExonCount::Get(), CScore_IndelToSplice::Get(), CAlnWriter::WriteAlignSplicedSeg(), and CAutogeneratedCleanup::x_BasicCleanupSplicedSeg().
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extra info Check if a value has been assigned to Ext data member.
Data member Ext is optional; its type is defined as 'typedef list< CRef< CUser_object > > TExt'
Definition at line 989 of file Seq_align_.hpp.
References CSeq_align_Base::m_set_State.
Referenced by CSGAlignmentJob::FilterDuplicatesAndBadReads(), CSeq_align::FindExt(), CSeq_align_Mapper_Base::GetDstAlign(), CProductStringBuilder::GetProductString(), CScoreBuilder::GetTraceback(), CTabularFormatter_BestPlacementGroup::Print(), CTabularFormatter_AssemblyInfo::Print(), s_CheckTraceMateAlign(), and s_PopulateExtSet().
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index of extra items Check if a value has been assigned to Ext data member.
Data member Ext is optional; its type is defined as 'typedef vector< CRef< CSparse_seg_ext > > TExt'
Definition at line 347 of file Sparse_seg_.hpp.
References CSparse_seg_Base::m_set_State.
Referenced by CRemoveSeqFromAlignDlg::ModifyAlign(), and s_Fingerprint_Sparse_seg().
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extra info Check if a value has been assigned to Ext data member.
Data member Ext is optional; its type is defined as 'typedef list< CRef< CUser_object > > TExt'
Definition at line 1113 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_set_State.
Referenced by CFeatureGenerator::SImplementation::StitchSmallHoles(), and CSeq_align_Mapper_Base::x_GetDstExon().
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Check if a value has been assigned to First_id data member.
Data member First_id is mandatory; its type is defined as 'typedef CSeq_id TFirst_id'
Definition at line 419 of file Sparse_align_.hpp.
References CSparse_align_Base::m_First_id.
Referenced by CAutogeneratedCleanup::x_BasicCleanupSparseAlign().
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starts on the first sequence [numseg] Check if a value has been assigned to First_starts data member.
Data member First_starts is mandatory; its type is defined as 'typedef vector< int > TFirst_starts'
Definition at line 526 of file Sparse_align_.hpp.
References CSparse_align_Base::m_set_State.
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position within codon (1-based) 0 = not set (meaning 1) Check if a value has been assigned to Frame data member.
Data member Frame is optional with default 0; its type is defined as 'typedef TSeqPos TFrame'
Definition at line 248 of file Prot_pos_.hpp.
References CProt_pos_Base::m_set_State.
Referenced by CProt_pos_Base::SetFrame(), and CGff3FlybaseWriter::xAssignAlignmentSplicedLocation().
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Check if a value has been assigned to Genomic_end data member.
Data member Genomic_end is mandatory; its type is defined as 'typedef TSeqPos TGenomic_end'
Definition at line 795 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_set_State.
Referenced by CSpliced_exon_Base::CanGetGenomic_end(), CSpliced_exon_Base::SetGenomic_end(), and CReportEntry::x_CheckExonGap().
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Check if a value has been assigned to Genomic_id data member.
Data member Genomic_id is optional; its type is defined as 'typedef CSeq_id TGenomic_id'
Definition at line 863 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Genomic_id.
Referenced by CSeqsRange::Add(), CSpliced_exon_Base::CanGetGenomic_id(), CSpliced_exon::CreateRowSeq_interval(), CSeq_align_Mapper_Base::InitExon(), ProjectExon_newlogic(), s_ExonToDenseg(), s_Fingerprint_Spliced_exon(), CSpliced_seg::Validate(), CAutogeneratedCleanup::x_BasicCleanupSplicedExon(), CSeq_loc_Mapper_Base::x_InitSpliced(), and CAnnotObject_Info::x_ProcessAlign().
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Check if a value has been assigned to Genomic_id data member.
Data member Genomic_id is optional; its type is defined as 'typedef CSeq_id TGenomic_id'
Definition at line 518 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_Genomic_id.
Referenced by CSeqsRange::Add(), CSpliced_seg_Base::CanGetGenomic_id(), CSpliced_exon::CreateRowSeq_interval(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CSeq_align_Mapper_Base::InitExon(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), s_Fingerprint_Spliced_seg(), CSpliced_seg::Validate(), CAlnWriter::WriteAlignSplicedSeg(), CAutogeneratedCleanup::x_BasicCleanupSplicedSeg(), and CSeq_loc_Mapper_Base::x_InitSpliced().
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genomic-end >= genomic-start Check if a value has been assigned to Genomic_start data member.
Data member Genomic_start is mandatory; its type is defined as 'typedef TSeqPos TGenomic_start'
Definition at line 748 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_set_State.
Referenced by CSpliced_exon_Base::CanGetGenomic_start(), CSpliced_exon_Base::SetGenomic_start(), and CReportEntry::x_CheckExonGap().
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genomic-strand represents the strand of translation Check if a value has been assigned to Genomic_strand data member.
Data member Genomic_strand is optional; its type is defined as 'typedef ENa_strand TGenomic_strand'
Definition at line 931 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_set_State.
Referenced by CSpliced_exon_Base::CanGetGenomic_strand(), CSpliced_exon::CreateRowSeq_interval(), CSpliced_exon::GetRowSeq_insertions(), CSeq_align_Mapper_Base::InitExon(), ProjectExon_newlogic(), s_ExonToDenseg(), s_GetAlignmentMismatches(), CSpliced_exon_Base::SetGenomic_strand(), CSeq_align_Mapper_Base::x_GetDstExon(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CSeq_loc_Mapper_Base::x_InitSpliced(), CAnnotObject_Info::x_ProcessAlign(), and CGff3Writer::xAssignAlignmentSplicedLocation().
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Check if a value has been assigned to Genomic_strand data member.
Data member Genomic_strand is optional; its type is defined as 'typedef ENa_strand TGenomic_strand'
Definition at line 586 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_set_State.
Referenced by CSpliced_seg::AsDiscSeg(), CSpliced_seg_Base::CanGetGenomic_strand(), CSpliced_exon::CreateRowSeq_interval(), CSpliced_exon::GetRowSeq_insertions(), CSeq_align_Mapper_Base::InitExon(), s_GetAlignmentMismatches(), CReportEntry::SetAlignment(), CSpliced_seg_Base::SetGenomic_strand(), CAlnWriter::WriteAlignSplicedSeg(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CSeq_loc_Mapper_Base::x_InitSpliced(), CCDSTranslationPanel::x_SetLocationForProtein(), CGff3Writer::xAssignAlignmentSplicedLocation(), and CGff3FlybaseWriter::xAssignAlignmentSplicedTarget().
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Check if a value has been assigned to Id data member.
Data member Id is optional; its type is defined as 'typedef CObject_id TId'
Definition at line 432 of file Score_.hpp.
References CScore_Base::m_Id.
Referenced by CScore_Base::CanGetId(), s_GetAlignmentTooltip(), CGffAlignmentRecord::SetScore(), CGffBaseRecord::SetScore(), CGff3FlybaseWriter::xAssignAlignmentDensegScores(), and CGff3FlybaseWriter::xAssignAlignmentSplicedScores().
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alignment id Check if a value has been assigned to Id data member.
Data member Id is optional; its type is defined as 'typedef list< CRef< CObject_id > > TId'
Definition at line 964 of file Seq_align_.hpp.
References CSeq_align_Base::m_set_State.
Referenced by CSeq_align_Mapper_Base::GetDstAlign(), CTabularFormatter_AlignId::Print(), s_GetAlignID(), and CGff3Writer::xWriteAlign().
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sequences in order Check if a value has been assigned to Ids data member.
Data member Ids is mandatory; its type is defined as 'typedef vector< CRef< CSeq_id > > TIds'
Definition at line 398 of file Dense_diag_.hpp.
References CDense_diag_Base::m_set_State.
Referenced by CAutogeneratedCleanup::x_BasicCleanupDenseDiag().
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sequences in order Check if a value has been assigned to Ids data member.
Data member Ids is mandatory; its type is defined as 'typedef vector< CRef< CSeq_id > > TIds'
Definition at line 493 of file Dense_seg_.hpp.
References CDense_seg_Base::m_set_State.
Referenced by CAlignmentAssistant::GetFeatures(), CDense_seg::GetSeq_id(), CAlignmentAssistant::ReportUnresolvedBioseqs(), s_DensegHasAccessionWithZeroVersion(), s_FixZeroVersions(), s_GetNumIdsToUse(), CMacroFunction_RemoveSegGaps::s_RemoveSegGaps(), CAutogeneratedCleanup::x_BasicCleanupDenseg(), and CApplyRNAITSDlg::x_GetAlignments().
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sequences in order Check if a value has been assigned to Ids data member.
Data member Ids is mandatory; its type is defined as 'typedef vector< CRef< CSeq_id > > TIds'
Definition at line 517 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_set_State.
Referenced by CAutogeneratedCleanup::x_BasicCleanupPackedSeg().
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Check if a value has been assigned to Ids data member.
Data member Ids is optional; its type is defined as 'typedef vector< CRef< CSeq_id > > TIds'
Definition at line 320 of file Std_seg_.hpp.
References CStd_seg_Base::m_set_State.
Referenced by CStd_seg::CheckNumRows(), CStd_seg::RemapToLoc(), CStd_seg::SwapRows(), CAutogeneratedCleanup::x_BasicCleanupStdSeg(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CValidError_align::x_ValidateSeqLength(), and CValidError_align::x_ValidateStd().
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seg-ext SET OF { index INTEGER, data User-field } Check if a value has been assigned to Index data member.
Data member Index is mandatory; its type is defined as 'typedef int TIndex'
Definition at line 158 of file Sparse_seg_ext_.hpp.
References CSparse_seg_ext_Base::m_set_State.
Referenced by CSparse_seg_ext_Base::CanGetIndex(), and CSparse_seg_ext_Base::SetIndex().
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len of aligned segments Check if a value has been assigned to Len data member.
Data member Len is mandatory; its type is defined as 'typedef TSeqPos TLen'
Definition at line 448 of file Dense_diag_.hpp.
References CDense_diag_Base::m_set_State.
Referenced by CDense_diag_Base::CanGetLen(), and CDense_diag_Base::SetLen().
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lengths in ids order within segs Check if a value has been assigned to Lens data member.
Data member Lens is mandatory; its type is defined as 'typedef vector< TSeqPos > TLens'
Definition at line 543 of file Dense_seg_.hpp.
References CDense_seg_Base::m_set_State.
Referenced by CAlignmentAssistant::GetFeatures(), CAlignmentAssistant::ReportUnresolvedBioseqs(), CMacroFunction_RemoveSegGaps::s_RemoveSegGaps(), and CDense_seg::TrimEndGaps().
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length of each segment Check if a value has been assigned to Lens data member.
Data member Lens is mandatory; its type is defined as 'typedef vector< TSeqPos > TLens'
Definition at line 595 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_set_State.
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lengths of segments [numseg] Check if a value has been assigned to Lens data member.
Data member Lens is mandatory; its type is defined as 'typedef vector< TSeqPos > TLens'
Definition at line 576 of file Sparse_align_.hpp.
References CSparse_align_Base::m_set_State.
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Check if a value has been assigned to Loc data member.
Data member Loc is mandatory; its type is defined as 'typedef vector< CRef< CSeq_loc > > TLoc'
Definition at line 345 of file Std_seg_.hpp.
References CStd_seg_Base::m_set_State.
Referenced by CAutogeneratedCleanup::x_BasicCleanupStdSeg().
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Check if a value has been assigned to Master_id data member.
Data member Master_id is optional; its type is defined as 'typedef CSeq_id TMaster_id'
Definition at line 276 of file Sparse_seg_.hpp.
References CSparse_seg_Base::m_Master_id.
Referenced by CSparse_seg_Base::CanGetMaster_id(), and CAutogeneratedCleanup::x_BasicCleaupSparseSeg().
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alignment descriptors / modifiers this provides us a set for extension Check if a value has been assigned to Modifiers data member.
Data member Modifiers is optional; its type is defined as 'typedef list< CRef< CSpliced_seg_modifier > > TModifiers'
Definition at line 799 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_set_State.
Referenced by CProSplign::CImplementation::SeekStartStop().
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number of segments here Check if a value has been assigned to Numseg data member.
Data member Numseg is mandatory; its type is defined as 'typedef int TNumseg'
Definition at line 446 of file Dense_seg_.hpp.
References CDense_seg_Base::m_set_State.
Referenced by CDense_seg_Base::CanGetNumseg(), CAlignmentAssistant::GetFeatures(), CRemoveSeqFromAlignDlg::ModifyAlign(), CAlignmentAssistant::OnRemoveSeqFromAlign(), CAlignmentAssistant::ReportUnresolvedBioseqs(), CMacroFunction_RemoveSegGaps::s_RemoveSegGaps(), CDense_seg_Base::SetNumseg(), and CUpdateAlign::x_RemoveIDsFromAlign().
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number of segments here Check if a value has been assigned to Numseg data member.
Data member Numseg is mandatory; its type is defined as 'typedef int TNumseg'
Definition at line 470 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_set_State.
Referenced by CPacked_seg_Base::CanGetNumseg(), and CPacked_seg_Base::SetNumseg().
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number of segments Check if a value has been assigned to Numseg data member.
Data member Numseg is mandatory; its type is defined as 'typedef int TNumseg'
Definition at line 479 of file Sparse_align_.hpp.
References CSparse_align_Base::m_set_State.
Referenced by CSparse_align_Base::CanGetNumseg(), and CSparse_align_Base::SetNumseg().
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flag: is this exon complete or partial? Check if a value has been assigned to Partial data member.
Data member Partial is optional; its type is defined as 'typedef bool TPartial'
Definition at line 1066 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_set_State.
Referenced by CSpliced_exon_Base::CanGetPartial(), CReportEntry::SetAlignment(), and CSpliced_exon_Base::SetPartial().
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basic seqments always are in biologic order Check if a value has been assigned to Parts data member.
Data member Parts is optional; its type is defined as 'typedef list< CRef< CSpliced_exon_chunk > > TParts'
Definition at line 978 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_set_State.
Referenced by CFeatureGenerator::SImplementation::AdjustAlignment(), AlignModelToSeqalign(), CScore_IndelToSplice::Get(), CSpliced_exon::GetRowSeq_insertions(), CSeq_align_Mapper_Base::InitExon(), CFeatureGenerator::SImplementation::MaximizeTranslation(), ProjectExon_newlogic(), CFeatureGenerator::SImplementation::RecalculateExonIdty(), s_ExonToDenseg(), s_Fingerprint_Spliced_exon(), s_GetAlignmentMismatches(), s_GetCountIdentityMismatch(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExon(), CReportEntry::x_CheckExonGap(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CSeq_loc_Mapper_Base::x_InitSpliced(), and CAlnSpanVertModel::x_PopulateRowsSpliced().
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start of poly(A) tail on the transcript For sense transcripts: aligned product positions < poly-a <= product-length poly-a == product-length indicates inferred poly(A) tail at transcript's end For antisense transcripts: -1 <= poly-a < aligned product positions poly-a == -1 indicates inferred poly(A) tail at transcript's start Check if a value has been assigned to Poly_a data member.
Data member Poly_a is optional; its type is defined as 'typedef TSeqPos TPoly_a'
Definition at line 705 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_set_State.
Referenced by CSpliced_seg_Base::CanGetPoly_a(), CScore_3PrimeUnaligned::Get(), CScore_Polya::Get(), SAlignmentScoringModel::GetPolyA_length(), GetUnalignedLength_3p(), s_GetPercentCoverage(), CSpliced_seg_Base::SetPoly_a(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSpliced_seg::Validate(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CFeatureGenerator::SImplementation::x_MapFeature(), and CAlnSpanVertModel::x_PopulateRowsSpliced().
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Boolean if each sequence present or absent in each segment Check if a value has been assigned to Present data member.
Data member Present is mandatory; its type is defined as 'typedef vector< char > TPresent'
Definition at line 567 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_set_State.
Referenced by CPacked_seg_Base::CanGetPresent().
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Check if a value has been assigned to Product_end data member.
Data member Product_end is mandatory; its type is defined as 'typedef CProduct_pos TProduct_end'
Definition at line 718 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Product_end.
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product is either protein or transcript (cDNA) Check if a value has been assigned to Product_id data member.
Data member Product_id is optional; its type is defined as 'typedef CSeq_id TProduct_id'
Definition at line 842 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Product_id.
Referenced by CSeqsRange::Add(), CSpliced_exon_Base::CanGetProduct_id(), CSpliced_exon::CreateRowSeq_interval(), CSeq_align_Mapper_Base::InitExon(), s_ExonToDenseg(), s_Fingerprint_Spliced_exon(), CSpliced_seg::Validate(), CAutogeneratedCleanup::x_BasicCleanupSplicedExon(), CSeq_loc_Mapper_Base::x_InitSpliced(), and CAnnotObject_Info::x_ProcessAlign().
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product is either protein or transcript (cDNA) Check if a value has been assigned to Product_id data member.
Data member Product_id is optional; its type is defined as 'typedef CSeq_id TProduct_id'
Definition at line 497 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_Product_id.
Referenced by CSeqsRange::Add(), CSpliced_seg_Base::CanGetProduct_id(), CSpliced_exon::CreateRowSeq_interval(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CSeq_align_Mapper_Base::InitExon(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), s_Fingerprint_Spliced_seg(), CSpliced_seg::Validate(), CAutogeneratedCleanup::x_BasicCleanupSplicedSeg(), CSeq_loc_Mapper_Base::x_InitSpliced(), and CGff3Writer::xAssignAlignmentSplicedMethod().
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length of the product, in bases/residues from this (or from poly-a if present), a 3' unaligned length can be extracted Check if a value has been assigned to Product_length data member.
Data member Product_length is optional; its type is defined as 'typedef TSeqPos TProduct_length'
Definition at line 752 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_set_State.
Referenced by CSpliced_seg_Base::CanGetProduct_length(), CScore_Polya::Get(), SAlignmentScoringModel::GetCoverage(), SAlignmentScoringModel::GetPolyA_length(), CProductStringBuilder::GetProductString(), GetUnalignedLength_3p(), GetUnalignedLength_5p(), PrintTabular(), s_GetPercentCoverage(), CSpliced_seg_Base::SetProduct_length(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSpliced_seg::Validate(), CFeatureGenerator::SImplementation::x_CollectMrnaSequence(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), and CAlnSpanVertModel::x_PopulateRowsSpliced().
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product-end >= product-start Check if a value has been assigned to Product_start data member.
Data member Product_start is mandatory; its type is defined as 'typedef CProduct_pos TProduct_start'
Definition at line 688 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Product_start.
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should be 'plus' or 'minus' Check if a value has been assigned to Product_strand data member.
Data member Product_strand is optional; its type is defined as 'typedef ENa_strand TProduct_strand'
Definition at line 884 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_set_State.
Referenced by CSpliced_exon_Base::CanGetProduct_strand(), CSpliced_exon::CreateRowSeq_interval(), CSpliced_exon::GetRowSeq_insertions(), CSeq_align_Mapper_Base::InitExon(), s_ExonToDenseg(), s_GetAlignmentMismatches(), CSpliced_exon_Base::SetProduct_strand(), CSpliced_seg::Validate(), CSeq_loc_Mapper_Base::x_InitSpliced(), and CAnnotObject_Info::x_ProcessAlign().
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should be 'plus' or 'minus' Check if a value has been assigned to Product_strand data member.
Data member Product_strand is optional; its type is defined as 'typedef ENa_strand TProduct_strand'
Definition at line 539 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_set_State.
Referenced by CSpliced_seg::AsDiscSeg(), CSpliced_seg_Base::CanGetProduct_strand(), CSpliced_exon::CreateRowSeq_interval(), CScore_InternalUnaligned::Get(), CScore_Polya::Get(), CSpliced_exon::GetRowSeq_insertions(), CSeq_align_Mapper_Base::InitExon(), s_GetAlignmentMismatches(), s_GetPercentCoverage(), CSpliced_seg_Base::SetProduct_strand(), CSpliced_seg::Validate(), CAlnWriter::WriteAlignSplicedSeg(), CSeq_align_Mapper_Base::x_GetDstSpliced(), and CSeq_loc_Mapper_Base::x_InitSpliced().
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Check if a value has been assigned to Product_type data member.
Data member Product_type is mandatory; its type is defined as 'typedef EProduct_type TProduct_type'
Definition at line 633 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_set_State.
Referenced by CSpliced_seg_Base::CanGetProduct_type(), CSpliced_seg_Base::SetProduct_type(), CSeq_align_Mapper_Base::x_GetDstExon(), CGff3Writer::xAssignAlignmentSplicedType(), CGff3Writer::xSplicedSegHasProteinProd(), and CGff2Reader::xUpdateSplicedSegment().
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per-row scores Check if a value has been assigned to Row_scores data member.
Data member Row_scores is optional; its type is defined as 'typedef vector< CRef< CScore > > TRow_scores'
Definition at line 322 of file Sparse_seg_.hpp.
References CSparse_seg_Base::m_set_State.
Referenced by CSparse_seg::CheckNumRows(), CRemoveSeqFromAlignDlg::ModifyAlign(), and CSeq_align_Mapper_Base::x_Init().
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pairwise alignments constituting this multiple alignment Check if a value has been assigned to Rows data member.
Data member Rows is mandatory; its type is defined as 'typedef vector< CRef< CSparse_align > > TRows'
Definition at line 297 of file Sparse_seg_.hpp.
References CSparse_seg_Base::m_set_State.
Referenced by CRemoveSeqFromAlignDlg::GetAlignLabel(), CRemoveSeqFromAlignDlg::ModifyAlign(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), and CAutogeneratedCleanup::x_BasicCleaupSparseSeg().
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for whole alignment Check if a value has been assigned to Score data member.
Data member Score is optional; its type is defined as 'typedef vector< CRef< CScore > > TScore'
Definition at line 884 of file Seq_align_.hpp.
References CSeq_align_Base::m_set_State.
Referenced by CGBProjectHelper::AddProjectItemsFromRID(), CSAM_CIGAR_Formatter::AddRow(), CValidError_align::AlignmentScorePercentIdOk(), BOOST_AUTO_TEST_CASE(), CFeatureGenerator::SImplementation::ClearScores(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CSeq_align::CreateDensegFromDisc(), CSeq_align::CreateDensegFromStdseg(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CSeq_align_Handle::IsSetScore(), CFeatureGenerator::SImplementation::RecalculateScores(), CSeq_align::ResetNamedScore(), s_GetAlignmentTooltip(), s_PopulateScoreSet(), sInheritScores(), sPrepareSeqAlign(), CCIGAR_Formatter::x_FormatAlignmentRows(), CSeq_align::x_GetNamedScore(), CSeq_align_Mapper_Base::x_Init(), CSeq_align::x_SetNamedScore(), CGff3Writer::xAssignAlignmentScores(), and CGff3FlybaseWriter::xAssignAlignmentScores().
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Check if a value has been assigned to Scores data member.
Data member Scores is optional; its type is defined as 'typedef vector< CRef< CScore > > TScores'
Definition at line 520 of file Dense_diag_.hpp.
References CDense_diag_Base::m_set_State.
Referenced by CSeq_align_Mapper_Base::x_Init().
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score for each seg Check if a value has been assigned to Scores data member.
Data member Scores is optional; its type is defined as 'typedef vector< CRef< CScore > > TScores'
Definition at line 593 of file Dense_seg_.hpp.
References CDense_seg_Base::m_set_State.
Referenced by CSeq_align_Mapper_Base::x_Init(), CGff3Writer::xAssignAlignmentDensegScores(), and CGff3FlybaseWriter::xAssignAlignmentDensegScores().
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score for each segment Check if a value has been assigned to Scores data member.
Data member Scores is optional; its type is defined as 'typedef vector< CRef< CScore > > TScores'
Definition at line 645 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_set_State.
Referenced by CSeq_align_Mapper_Base::x_Init().
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scores for this exon Check if a value has been assigned to Scores data member.
Data member Scores is optional; its type is defined as 'typedef CScore_set TScores'
Definition at line 1003 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Scores.
Referenced by CSpliced_exon_Base::CanGetScores(), CScore_EdgeExonInfo::Get(), CSeq_align_Mapper_Base::InitExon(), CFeatureGenerator::SImplementation::RecalculateExonIdty(), s_ExonToDenseg(), CGff3Writer::xAssignAlignmentSplicedScores(), and CGff3FlybaseWriter::xAssignAlignmentSplicedScores().
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Check if a value has been assigned to Scores data member.
Data member Scores is optional; its type is defined as 'typedef vector< CRef< CScore > > TScores'
Definition at line 370 of file Std_seg_.hpp.
References CStd_seg_Base::m_set_State.
Referenced by CSeq_align_Mapper_Base::x_Init().
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Check if a value has been assigned to Second_id data member.
Data member Second_id is mandatory; its type is defined as 'typedef CSeq_id TSecond_id'
Definition at line 449 of file Sparse_align_.hpp.
References CSparse_align_Base::m_Second_id.
Referenced by CAutogeneratedCleanup::x_BasicCleanupSparseAlign().
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starts on the second sequence [numseg] Check if a value has been assigned to Second_starts data member.
Data member Second_starts is mandatory; its type is defined as 'typedef vector< int > TSecond_starts'
Definition at line 551 of file Sparse_align_.hpp.
References CSparse_align_Base::m_set_State.
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Check if a value has been assigned to Second_strands data member.
Data member Second_strands is optional; its type is defined as 'typedef vector< ENa_strand > TSecond_strands'
Definition at line 601 of file Sparse_align_.hpp.
References CSparse_align_Base::m_set_State.
Referenced by CSeqsRange::Add(), CSparse_align::CheckNumSegs(), ConvertSparseToPairwiseAln(), CreateAlignRow(), GetAlignColl(), CSparse_seg::GetSeqRange(), CSparse_seg::GetSeqStart(), CSparse_seg::GetSeqStop(), CSparse_seg::GetSeqStrand(), s_Fingerprint_Sparse_align(), CAlnWriter::WriteSparseAlign(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitSparse(), and CAnnotObject_Info::x_ProcessAlign().
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per-segment scores Check if a value has been assigned to Seg_scores data member.
Data member Seg_scores is optional; its type is defined as 'typedef vector< CRef< CScore > > TSeg_scores'
Definition at line 626 of file Sparse_align_.hpp.
References CSparse_align_Base::m_set_State.
Referenced by CSparse_align::CheckNumSegs(), and CSeq_align_Mapper_Base::x_Init().
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Check if a value has been assigned to Segs data member.
Data member Segs is mandatory; its type is defined as 'typedef C_Segs TSegs'
Definition at line 909 of file Seq_align_.hpp.
References CSeq_align_Base::m_Segs.
Referenced by ConvertRawToDeltaByNsCommand_impl(), ConvertRawToDeltaByNsHugeFileCmd_impl(), CEditSeqEndsWithAlign::FindPosition(), CRemoveSeqFromAlignDlg::GetAlignLabel(), GetReportableSeqIdForAlignment(), CRemoveSeqFromAlignDlg::ModifyAlign(), CValidError_imp::PostErr(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), CMacroFunction_RemoveSegGaps::s_RemoveSegGaps(), CValidError_align::ValidateSeqAlign(), CAutogeneratedCleanup::x_BasicCleanupSeqAlign(), CHitMatrixDataSource::x_CreateHit(), CHitMatrixDataSource::x_CreateHits(), CApplyRNAITSDlg::x_GetAlignments(), CApplyRNAITSDlg::x_IsThereAlignment(), CCDSTranslationPanel::x_SetLocationForProtein(), CApplyRNAITSDlg::x_SetupAlnMgr(), CModifySeqId::x_UpdateSeqAlign(), CValidError_align::x_ValidateAlignPercentIdentity(), CPsiBl2SeqTestFixture::x_ValidatePssmVsGi40456275(), CGff3Writer::xWriteAlign(), and CGff3Writer::xWriteAlignSpliced().
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start OFFSETS in ids order Check if a value has been assigned to Starts data member.
Data member Starts is mandatory; its type is defined as 'typedef vector< TSeqPos > TStarts'
Definition at line 423 of file Dense_diag_.hpp.
References CDense_diag_Base::m_set_State.
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start OFFSETS in ids order within segs Check if a value has been assigned to Starts data member.
Data member Starts is mandatory; its type is defined as 'typedef vector< TSignedSeqPos > TStarts'
Definition at line 518 of file Dense_seg_.hpp.
References CDense_seg_Base::m_set_State.
Referenced by CAlignmentAssistant::GetFeatures(), CRemoveSeqFromAlignDlg::ModifyAlign(), CAlignmentAssistant::OnRemoveSeqFromAlign(), CAlignmentAssistant::ReportUnresolvedBioseqs(), CMacroFunction_RemoveSegGaps::s_RemoveSegGaps(), CDense_seg::TrimEndGaps(), and CUpdateAlign::x_RemoveIDsFromAlign().
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start OFFSETS in ids order for whole alignment Check if a value has been assigned to Starts data member.
Data member Starts is mandatory; its type is defined as 'typedef vector< TSeqPos > TStarts'
Definition at line 542 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_set_State.
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Check if a value has been assigned to Strands data member.
Data member Strands is optional; its type is defined as 'typedef vector< ENa_strand > TStrands'
Definition at line 495 of file Dense_diag_.hpp.
References CDense_diag_Base::m_set_State.
Referenced by ConvertDendiagToPairwiseAln(), CDense_diag::CreateRowSeq_interval(), s_Fingerprint_Dense_diag(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CAnnotObject_Info::x_ProcessAlign(), and CValidError_align::x_ValidateDendiag().
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Check if a value has been assigned to Strands data member.
Data member Strands is optional; its type is defined as 'typedef vector< ENa_strand > TStrands'
Definition at line 568 of file Dense_seg_.hpp.
References CDense_seg_Base::m_set_State.
Referenced by CAlignmentAssistant::AdjustAlign(), CPaintAlignment::AlignPosToSeqPos(), CFeaturePropagator::AlignPosToSeqPos(), CDense_seg::Compact(), ConvertDensegToPairwiseAln(), CreateAlignRow(), CreateAlignSetFromPairwiseAln(), CSeq_align::CreateDensegFromDisc(), CreateDensegFromPairwiseAln(), CDense_seg::CreateRowSeq_interval(), CFeaturePropagator::CreateRowSeq_loc(), CDense_seg::ExtractRows(), CDense_seg::ExtractSlice(), CPaintAlignment::GetSegments(), CRemoveSeqFromAlignDlg::ModifyAlign(), CAlignmentAssistant::OnRemoveSeqFromAlign(), CAlignmentAssistant::OnReverseStrand(), CDense_seg::RemovePureGapSegs(), CDense_seg::Reverse(), ReverseAlignmentStrand(), CFarPointerSeq::ReverseRow(), s_CutDensegSegment(), s_Fingerprint_Dense_seg(), s_GetIndels(), s_Seq_align_Seq_loc(), s_SeqAlignSetToXMLHsps(), CPaintAlignment::SeqPosToAlignPos(), CFeaturePropagator::SeqPosToAlignPos(), CBlastTabularInfo::SetFields(), CDense_seg::SwapRows(), CDense_seg::TrimEndGaps(), CAlnWriter::WriteAlignDenseSeg(), CAlignCleanup::x_Cleanup_AlignVec(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), and CUpdateAlign::x_RemoveIDsFromAlign().
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Check if a value has been assigned to Strands data member.
Data member Strands is optional; its type is defined as 'typedef vector< ENa_strand > TStrands'
Definition at line 620 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_set_State.
Referenced by ConvertPackedsegToPairwiseAln(), s_Fingerprint_Packed_seg(), CSeq_align_Mapper_Base::x_Init(), and CSeq_loc_Mapper_Base::x_InitAlign().
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Check if a value has been assigned to Type data member.
Data member Type is mandatory; its type is defined as 'typedef EType TType'
Definition at line 790 of file Seq_align_.hpp.
References CSeq_align_Base::m_set_State.
Referenced by CSeq_align_Base::CanGetType(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CValidError_imp::PostErr(), CSeq_align_Base::SetType(), CValidError_align::ValidateSeqAlign(), and CGff2Reader::xUpdateSplicedAlignment().
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Check if a value has been assigned to Value data member.
Data member Value is mandatory; its type is defined as 'typedef C_Value TValue'
Definition at line 453 of file Score_.hpp.
References CScore_Base::m_set_State.
Referenced by CScore_Base::CanGetValue(), CGffAlignmentRecord::SetScore(), and CGffBaseRecord::SetScore().
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Check if variant Sparse is selected.
Sparse type is defined as 'typedef CSparse_seg TSparse'.
Definition at line 784 of file Seq_align_.hpp.
Referenced by s_CleanSeqAlign(), and CAlignFilter::x_FuncCall().
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Check if variant Spliced is selected.
Spliced type is defined as 'typedef CSpliced_seg TSpliced'.
Definition at line 778 of file Seq_align_.hpp.
Referenced by CFeatureGenerator::SImplementation::AdjustAlignment(), BOOST_AUTO_TEST_CASE(), CTestSingleAln::CanTest(), CFeaturePropagator::CFeaturePropagator(), variation_ref::CVariationUtil::CheckExonBoundary(), variation::CVariationUtil::CheckExonBoundary(), CFeatureGenerator::SImplementation::CleanAlignment(), CScore_GapCount::Get(), CScore_ExonCount::Get(), CScore_IndelToSplice::Get(), CScore_LastSpliceSite::Get(), CScore_FrameShifts::Get(), CScore_3PrimeUnaligned::Get(), CScore_Polya::Get(), CScore_SequenceLength::Get(), CScore_StartStopCodon::Get(), CScore_CdsInternalStops::Get(), CScore_TblastnScore::Get(), CScore_EdgeExonInfo::Get(), CScoreBuilder::GetBlastScore(), CInternalStopFinder::GetCDSNucleotideSequence(), SAlignmentScoringModel::GetCoverage(), SAlignmentScoringModel::GetExonsOdds(), variation::GetFocusLocusIDs(), SAlignmentScoringModel::GetIdentOdds(), SAlignmentScoringModel::GetLongestMatchrunLen(), SAlignmentScoringModel::GetNumGapopensBetweenExons(), SAlignmentScoringModel::GetPolyA_length(), CProductStringBuilder::GetProductString(), SAlignmentScoringModel::GetSplicesOdds(), variation::GetUniquePrimaryTranscriptId(), CFeatureGenerator::SImplementation::HasMixedGenomicIds(), IsProteinAlign(), SAlignmentScoringModel::isProtSS(), CTabularFormatter_MismatchPositions::Print(), CTabularFormatter_ExonIntrons::Print(), PrintTabular(), variation_ref::CVariationUtil::Remap(), variation::CVariationUtil::Remap(), CTestSingleAln_All::RunTest(), s_CleanSeqAlign(), s_GetAlignmentMismatches(), s_GetAlignmentSpans_Intron(), SAlignmentScoringModel::s_GetIdentOdds_nucSS(), s_GetPercentCoverage(), s_GetRnaMappingLocs(), s_IsProteinToGenomic(), CFeatureGenerator::SImplementation::SMapper::SMapper(), CFeatureGenerator::SImplementation::x_CollectMrnaSequence(), CSequenceEditingEventHandler::x_FindRelevantAlignRow(), CAlignFilter::x_FuncCall(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CScoreBuilderBase::x_GetMatrixCounts(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CFeatureGenerator::SImplementation::x_MapFeature(), CIdMapperTestApp::x_RecurseMapSeqAligns(), CCDSTranslationPanel::x_SetLocationForProtein(), and CGff3Writer::xWriteAlignSpliced().
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Check if variant Start_codon_found is selected.
Start_codon_found type is defined as 'typedef bool TStart_codon_found'.
Definition at line 257 of file Spliced_seg_modifier_.hpp.
References CSpliced_seg_modifier_Base::e_Start_codon_found, and CSpliced_seg_modifier_Base::m_choice.
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Check if variant Std is selected.
Std type is defined as 'typedef list< CRef< CStd_seg > > TStd'.
Definition at line 746 of file Seq_align_.hpp.
Referenced by CAlnMix::Add(), BOOST_AUTO_TEST_CASE(), BuildAlignDataSource(), CFeaturePropagator::CFeaturePropagator(), CreateAnchoredAlnFromAln(), CreateAnchoredAlnVec(), CScore_CdsScore::Get(), CAlignFormatUtil::GetAlignmentLength(), CScoreBuilder::GetBlastScore(), CSeqUtils::GetLocPlacements(), GetReportableSeqIdForAlignment(), s_CleanSeqAlign(), s_GetAlnMapplingLocs(), s_GetPercentCoverage(), s_GetSubjectId(), s_SeqAlignSetToXMLHsps(), SeqAlignConvert(), CBlastTabularInfo::SetFields(), testNuclHitList(), CHitMatrixDataSource::x_CreateHit_Std(), CAlignFilter::x_FuncCall(), CProSplignJob::x_GenerateCompartments(), CSeqAlignFilter::x_UpdateGiInSeqalign(), CModifySeqId::x_UpdateSeqAlign(), and CValidError_align::x_ValidateAlignPercentIdentity().
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Check if variant Stop_codon_found is selected.
Stop_codon_found type is defined as 'typedef bool TStop_codon_found'.
Definition at line 284 of file Spliced_seg_modifier_.hpp.
References CSpliced_seg_modifier_Base::e_Stop_codon_found, and CSpliced_seg_modifier_Base::m_choice.
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Conversion operator to 'const Tdata' type.
Definition at line 178 of file Score_set_.hpp.
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Conversion operator to 'const Tdata' type.
Definition at line 179 of file Seq_align_set_.hpp.
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Conversion operator to 'Tdata' type.
Definition at line 184 of file Score_set_.hpp.
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Conversion operator to 'Tdata' type.
Definition at line 185 of file Seq_align_set_.hpp.
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Reset the whole object.
Definition at line 76 of file Dense_diag_.cpp.
References CDense_diag_Base::ResetDim(), CDense_diag_Base::ResetIds(), CDense_diag_Base::ResetLen(), CDense_diag_Base::ResetScores(), CDense_diag_Base::ResetStarts(), and CDense_diag_Base::ResetStrands().
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Reset the whole object.
Definition at line 82 of file Dense_seg_.cpp.
References CDense_seg_Base::ResetDim(), CDense_seg_Base::ResetIds(), CDense_seg_Base::ResetLens(), CDense_seg_Base::ResetNumseg(), CDense_seg_Base::ResetScores(), CDense_seg_Base::ResetStarts(), and CDense_seg_Base::ResetStrands().
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Reset the whole object.
Definition at line 88 of file Packed_seg_.cpp.
References CPacked_seg_Base::ResetDim(), CPacked_seg_Base::ResetIds(), CPacked_seg_Base::ResetLens(), CPacked_seg_Base::ResetNumseg(), CPacked_seg_Base::ResetPresent(), CPacked_seg_Base::ResetScores(), CPacked_seg_Base::ResetStarts(), and CPacked_seg_Base::ResetStrands().
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Reset the whole object.
Definition at line 51 of file Product_pos_.cpp.
References CProduct_pos_Base::e_not_set, CProduct_pos_Base::m_choice, and CProduct_pos_Base::ResetSelection().
Referenced by CProduct_pos_Base::~CProduct_pos_Base().
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Reset the whole object.
Definition at line 50 of file Prot_pos_.cpp.
References CProt_pos_Base::ResetAmin(), and CProt_pos_Base::ResetFrame().
void CScore_Base::C_Value::Reset | ( | void | ) |
Reset the whole object.
Definition at line 51 of file Score_.cpp.
References CScore_Base::C_Value::e_not_set, CScore_Base::C_Value::m_choice, and CScore_Base::C_Value::ResetSelection().
Referenced by CScore_Base::ResetValue().
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Reset the whole object.
Definition at line 143 of file Score_.cpp.
References CScore_Base::ResetId(), and CScore_Base::ResetValue().
Referenced by CScore_Base::C_Value::~C_Value().
void CScore_set_Base::Reset | ( | void | ) |
Reset data member.
Definition at line 51 of file Score_set_.cpp.
References CScore_set_Base::m_data, and CScore_set_Base::m_set_State.
END_ENUM_INFO void CSeq_align_Base::C_Segs::Reset | ( | void | ) |
Reset the whole object.
Definition at line 74 of file Seq_align_.cpp.
References CSeq_align_Base::C_Segs::e_not_set, CSeq_align_Base::C_Segs::m_choice, and CSeq_align_Base::C_Segs::ResetSelection().
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Reset the whole object.
Definition at line 333 of file Seq_align_.cpp.
References CSeq_align_Base::ResetBounds(), CSeq_align_Base::ResetDim(), CSeq_align_Base::ResetExt(), CSeq_align_Base::ResetId(), CSeq_align_Base::ResetScore(), CSeq_align_Base::ResetSegs(), and CSeq_align_Base::ResetType().
Referenced by HitDistributor::distribute(), CSeqEdit_Cmd_ReplaceAnnot_Base::C_Data::C_Align::SetNvalue(), CSeqEdit_Cmd_ReplaceAnnot_Base::C_Data::C_Align::SetOvalue(), BlockModel::toSeqAlign(), and CSeq_align_Base::C_Segs::~C_Segs().
void CSeq_align_set_Base::Reset | ( | void | ) |
Reset data member.
Definition at line 51 of file Seq_align_set_.cpp.
References CSeq_align_set_Base::m_data, and CSeq_align_set_Base::m_set_State.
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Reset the whole object.
Definition at line 110 of file Sparse_align_.cpp.
References CSparse_align_Base::ResetFirst_id(), CSparse_align_Base::ResetFirst_starts(), CSparse_align_Base::ResetLens(), CSparse_align_Base::ResetNumseg(), CSparse_align_Base::ResetSecond_id(), CSparse_align_Base::ResetSecond_starts(), CSparse_align_Base::ResetSecond_strands(), and CSparse_align_Base::ResetSeg_scores().
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Reset the whole object.
Definition at line 89 of file Sparse_seg_.cpp.
References CSparse_seg_Base::ResetExt(), CSparse_seg_Base::ResetMaster_id(), CSparse_seg_Base::ResetRow_scores(), and CSparse_seg_Base::ResetRows().
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Reset the whole object.
Definition at line 50 of file Sparse_seg_ext_.cpp.
References CSparse_seg_ext_Base::ResetIndex().
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Reset the whole object.
Definition at line 56 of file Splice_site_.cpp.
References CSplice_site_Base::ResetBases().
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Reset the whole object.
Definition at line 181 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::ResetAcceptor_before_exon(), CSpliced_exon_Base::ResetDonor_after_exon(), CSpliced_exon_Base::ResetExt(), CSpliced_exon_Base::ResetGenomic_end(), CSpliced_exon_Base::ResetGenomic_id(), CSpliced_exon_Base::ResetGenomic_start(), CSpliced_exon_Base::ResetGenomic_strand(), CSpliced_exon_Base::ResetPartial(), CSpliced_exon_Base::ResetParts(), CSpliced_exon_Base::ResetProduct_end(), CSpliced_exon_Base::ResetProduct_id(), CSpliced_exon_Base::ResetProduct_start(), CSpliced_exon_Base::ResetProduct_strand(), and CSpliced_exon_Base::ResetScores().
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Reset the whole object.
Definition at line 50 of file Spliced_exon_chunk_.cpp.
References CSpliced_exon_chunk_Base::e_not_set, CSpliced_exon_chunk_Base::m_choice, and CSpliced_exon_chunk_Base::ResetSelection().
Referenced by CSpliced_exon_chunk_Base::~CSpliced_exon_chunk_Base().
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Reset the whole object.
Definition at line 108 of file Spliced_seg_.cpp.
References CSpliced_seg_Base::ResetExons(), CSpliced_seg_Base::ResetGenomic_id(), CSpliced_seg_Base::ResetGenomic_strand(), CSpliced_seg_Base::ResetModifiers(), CSpliced_seg_Base::ResetPoly_a(), CSpliced_seg_Base::ResetProduct_id(), CSpliced_seg_Base::ResetProduct_length(), CSpliced_seg_Base::ResetProduct_strand(), and CSpliced_seg_Base::ResetProduct_type().
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Reset the whole object.
Definition at line 50 of file Spliced_seg_modifier_.cpp.
References CSpliced_seg_modifier_Base::e_not_set, CSpliced_seg_modifier_Base::m_choice, and CSpliced_seg_modifier_Base::ResetSelection().
Referenced by CSpliced_seg_modifier_Base::~CSpliced_seg_modifier_Base().
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Reset the whole object.
Definition at line 71 of file Std_seg_.cpp.
References CStd_seg_Base::ResetDim(), CStd_seg_Base::ResetIds(), CStd_seg_Base::ResetLoc(), and CStd_seg_Base::ResetScores().
void CSpliced_exon_Base::ResetAcceptor_before_exon | ( | void | ) |
Reset Acceptor_before_exon data member.
Definition at line 141 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Acceptor_before_exon.
Referenced by CSpliced_exon_Base::Reset(), and CSeq_align_Mapper_Base::x_GetDstExon().
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Reset Amin data member.
Definition at line 213 of file Prot_pos_.hpp.
References CProt_pos_Base::m_Amin, and CProt_pos_Base::m_set_State.
Referenced by CProt_pos_Base::Reset().
void CSplice_site_Base::ResetBases | ( | void | ) |
Reset Bases data member.
Definition at line 50 of file Splice_site_.cpp.
References CSplice_site_Base::m_Bases, and CSplice_site_Base::m_set_State.
Referenced by CSplice_site_Base::Reset().
void CSeq_align_Base::ResetBounds | ( | void | ) |
Reset Bounds data member.
Definition at line 315 of file Seq_align_.cpp.
References CSeq_align_Base::m_Bounds, and CSeq_align_Base::m_set_State.
Referenced by CSeq_align_Base::Reset().
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Reset Dim data member.
Definition at line 360 of file Dense_diag_.hpp.
References CDense_diag_Base::m_Dim, and CDense_diag_Base::m_set_State.
Referenced by CDense_diag_Base::Reset(), and CDense_diag_Base::SetDefaultDim().
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Reset Dim data member.
Definition at line 408 of file Dense_seg_.hpp.
References CDense_seg_Base::m_Dim, and CDense_seg_Base::m_set_State.
Referenced by CDense_seg_Base::Reset(), and CDense_seg_Base::SetDefaultDim().
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Reset Dim data member.
Definition at line 432 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_Dim, and CPacked_seg_Base::m_set_State.
Referenced by CPacked_seg_Base::Reset(), and CPacked_seg_Base::SetDefaultDim().
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Reset Dim data member.
Definition at line 849 of file Seq_align_.hpp.
References CSeq_align_Base::m_Dim, and CSeq_align_Base::m_set_State.
Referenced by CSeq_align_Base::Reset().
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Reset Dim data member.
Definition at line 282 of file Std_seg_.hpp.
References CStd_seg_Base::m_Dim, and CStd_seg_Base::m_set_State.
Referenced by CStd_seg_Base::Reset(), and CStd_seg_Base::SetDefaultDim().
void CSpliced_exon_Base::ResetDonor_after_exon | ( | void | ) |
Reset Donor_after_exon data member.
Definition at line 158 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Donor_after_exon.
Referenced by CSpliced_exon_Base::Reset(), and CSeq_align_Mapper_Base::x_GetDstExon().
void CSpliced_seg_Base::ResetExons | ( | void | ) |
Reset Exons data member.
Definition at line 96 of file Spliced_seg_.cpp.
References CSpliced_seg_Base::m_Exons, and CSpliced_seg_Base::m_set_State.
Referenced by CSpliced_seg_Base::Reset().
void CSeq_align_Base::ResetExt | ( | void | ) |
Reset Ext data member.
Definition at line 327 of file Seq_align_.cpp.
References CSeq_align_Base::m_Ext, and CSeq_align_Base::m_set_State.
Referenced by CSeq_align_Base::Reset(), s_ModifySeqAlnWithFilteredSeqIDs(), and s_UpdateSeqAlnWithFilteredSeqIDs().
void CSparse_seg_Base::ResetExt | ( | void | ) |
Reset Ext data member.
Definition at line 83 of file Sparse_seg_.cpp.
References CSparse_seg_Base::m_Ext, and CSparse_seg_Base::m_set_State.
Referenced by CSparse_seg_Base::Reset().
void CSpliced_exon_Base::ResetExt | ( | void | ) |
Reset Ext data member.
Definition at line 175 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Ext, and CSpliced_exon_Base::m_set_State.
Referenced by CSpliced_exon_Base::Reset().
void CSparse_align_Base::ResetFirst_id | ( | void | ) |
Reset First_id data member.
Definition at line 52 of file Sparse_align_.cpp.
References CSparse_align_Base::m_First_id.
Referenced by CSparse_align_Base::CSparse_align_Base(), CSparse_align_Base::GetFirst_id(), CSparse_align_Base::Reset(), and CSparse_align_Base::SetFirst_id().
void CSparse_align_Base::ResetFirst_starts | ( | void | ) |
Reset First_starts data member.
Definition at line 80 of file Sparse_align_.cpp.
References CSparse_align_Base::m_First_starts, and CSparse_align_Base::m_set_State.
Referenced by CSparse_align_Base::Reset().
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Reset Frame data member.
Definition at line 260 of file Prot_pos_.hpp.
References CProt_pos_Base::m_Frame, and CProt_pos_Base::m_set_State.
Referenced by CProt_pos_Base::Reset(), and CProt_pos_Base::SetDefaultFrame().
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Reset Genomic_end data member.
Definition at line 807 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Genomic_end, and CSpliced_exon_Base::m_set_State.
Referenced by CSpliced_exon_Base::Reset().
void CSpliced_exon_Base::ResetGenomic_id | ( | void | ) |
Reset Genomic_id data member.
Definition at line 101 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Genomic_id.
Referenced by CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), and CSpliced_exon_Base::Reset().
void CSpliced_seg_Base::ResetGenomic_id | ( | void | ) |
Reset Genomic_id data member.
Definition at line 79 of file Spliced_seg_.cpp.
References CSpliced_seg_Base::m_Genomic_id.
Referenced by CSpliced_seg_Base::Reset().
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Reset Genomic_start data member.
Definition at line 760 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Genomic_start, and CSpliced_exon_Base::m_set_State.
Referenced by CSpliced_exon_Base::Reset().
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Reset Genomic_strand data member.
Definition at line 943 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Genomic_strand, and CSpliced_exon_Base::m_set_State.
Referenced by CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), and CSpliced_exon_Base::Reset().
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Reset Genomic_strand data member.
Definition at line 598 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_Genomic_strand, and CSpliced_seg_Base::m_set_State.
Referenced by CSpliced_seg_Base::Reset().
void CScore_Base::ResetId | ( | void | ) |
Reset Id data member.
Definition at line 120 of file Score_.cpp.
References CScore_Base::m_Id.
Referenced by CScore_Base::Reset().
void CSeq_align_Base::ResetId | ( | void | ) |
Reset Id data member.
Definition at line 321 of file Seq_align_.cpp.
References CSeq_align_Base::m_Id, and CSeq_align_Base::m_set_State.
Referenced by CSeq_align_Base::Reset().
void CDense_diag_Base::ResetIds | ( | void | ) |
Reset Ids data member.
Definition at line 52 of file Dense_diag_.cpp.
References CDense_diag_Base::m_Ids, and CDense_diag_Base::m_set_State.
Referenced by CDense_diag_Base::Reset().
void CDense_seg_Base::ResetIds | ( | void | ) |
Reset Ids data member.
Definition at line 52 of file Dense_seg_.cpp.
References CDense_seg_Base::m_Ids, and CDense_seg_Base::m_set_State.
Referenced by CDense_seg_Base::Reset().
void CPacked_seg_Base::ResetIds | ( | void | ) |
Reset Ids data member.
Definition at line 52 of file Packed_seg_.cpp.
References CPacked_seg_Base::m_Ids, and CPacked_seg_Base::m_set_State.
Referenced by CPacked_seg_Base::Reset().
void CStd_seg_Base::ResetIds | ( | void | ) |
Reset Ids data member.
Definition at line 53 of file Std_seg_.cpp.
References CStd_seg_Base::m_Ids, and CStd_seg_Base::m_set_State.
Referenced by CStd_seg_Base::Reset().
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inline |
Reset Index data member.
Definition at line 170 of file Sparse_seg_ext_.hpp.
References CSparse_seg_ext_Base::m_Index, and CSparse_seg_ext_Base::m_set_State.
Referenced by CSparse_seg_ext_Base::Reset().
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inline |
Reset Len data member.
Definition at line 460 of file Dense_diag_.hpp.
References CDense_diag_Base::m_Len, and CDense_diag_Base::m_set_State.
Referenced by CDense_diag_Base::Reset().
void CDense_seg_Base::ResetLens | ( | void | ) |
Reset Lens data member.
Definition at line 64 of file Dense_seg_.cpp.
References CDense_seg_Base::m_Lens, and CDense_seg_Base::m_set_State.
Referenced by ImproveAlignment(), CDense_seg_Base::Reset(), TestCircularTopology(), TestDoNotExtendOverGap(), TestDoNotFuseAbuttingIntervals(), TestExtendOverGap(), TestFuseAbuttingIntervals(), TestPartialWhenCutLastInterval(), TestPartialWhenCutLastIntervalDoNotExtend(), TestPartialWhenCutStart(), TestPartialWhenCutStartDoNotExtend(), TestPartialWhenCutStop(), and TestPartialWhenCutStopDoNotExtend().
void CPacked_seg_Base::ResetLens | ( | void | ) |
Reset Lens data member.
Definition at line 70 of file Packed_seg_.cpp.
References CPacked_seg_Base::m_Lens, and CPacked_seg_Base::m_set_State.
Referenced by CPacked_seg_Base::Reset().
void CSparse_align_Base::ResetLens | ( | void | ) |
Reset Lens data member.
Definition at line 92 of file Sparse_align_.cpp.
References CSparse_align_Base::m_Lens, and CSparse_align_Base::m_set_State.
Referenced by CSparse_align_Base::Reset().
void CStd_seg_Base::ResetLoc | ( | void | ) |
Reset Loc data member.
Definition at line 59 of file Std_seg_.cpp.
References CStd_seg_Base::m_Loc, and CStd_seg_Base::m_set_State.
Referenced by CStd_seg_Base::Reset().
void CSparse_seg_Base::ResetMaster_id | ( | void | ) |
Reset Master_id data member.
Definition at line 54 of file Sparse_seg_.cpp.
References CSparse_seg_Base::m_Master_id.
Referenced by CSparse_seg_Base::Reset().
void CSpliced_seg_Base::ResetModifiers | ( | void | ) |
Reset Modifiers data member.
Definition at line 102 of file Spliced_seg_.cpp.
References CSpliced_seg_Base::m_Modifiers, and CSpliced_seg_Base::m_set_State.
Referenced by CSpliced_seg_Base::Reset(), and CProSplign::CImplementation::SeekStartStop().
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inline |
Reset Numseg data member.
Definition at line 458 of file Dense_seg_.hpp.
References CDense_seg_Base::m_Numseg, and CDense_seg_Base::m_set_State.
Referenced by CDense_seg_Base::Reset().
|
inline |
Reset Numseg data member.
Definition at line 482 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_Numseg, and CPacked_seg_Base::m_set_State.
Referenced by CPacked_seg_Base::Reset().
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inline |
Reset Numseg data member.
Definition at line 491 of file Sparse_align_.hpp.
References CSparse_align_Base::m_Numseg, and CSparse_align_Base::m_set_State.
Referenced by CSparse_align_Base::Reset().
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inline |
Reset Partial data member.
Definition at line 1078 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Partial, and CSpliced_exon_Base::m_set_State.
Referenced by CSpliced_exon_Base::Reset().
void CSpliced_exon_Base::ResetParts | ( | void | ) |
Reset Parts data member.
Definition at line 118 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Parts, and CSpliced_exon_Base::m_set_State.
Referenced by CSpliced_exon_Base::Reset().
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inline |
Reset Poly_a data member.
Definition at line 717 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_Poly_a, and CSpliced_seg_Base::m_set_State.
Referenced by CSpliced_seg_Base::Reset().
void CPacked_seg_Base::ResetPresent | ( | void | ) |
Reset Present data member.
Definition at line 64 of file Packed_seg_.cpp.
References CPacked_seg_Base::m_Present, and CPacked_seg_Base::m_set_State.
Referenced by CPacked_seg_Base::Reset().
void CSpliced_exon_Base::ResetProduct_end | ( | void | ) |
Reset Product_end data member.
Definition at line 70 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Product_end.
Referenced by CSpliced_exon_Base::CSpliced_exon_Base(), CSpliced_exon_Base::GetProduct_end(), CSpliced_exon_Base::Reset(), and CSpliced_exon_Base::SetProduct_end().
void CSpliced_exon_Base::ResetProduct_id | ( | void | ) |
Reset Product_id data member.
Definition at line 84 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Product_id.
Referenced by CSpliced_exon_Base::Reset().
END_ENUM_INFO void CSpliced_seg_Base::ResetProduct_id | ( | void | ) |
Reset Product_id data member.
Definition at line 62 of file Spliced_seg_.cpp.
References CSpliced_seg_Base::m_Product_id.
Referenced by CSpliced_seg_Base::Reset().
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inline |
Reset Product_length data member.
Definition at line 764 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_Product_length, and CSpliced_seg_Base::m_set_State.
Referenced by CSpliced_seg_Base::Reset().
void CSpliced_exon_Base::ResetProduct_start | ( | void | ) |
Reset Product_start data member.
Definition at line 56 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Product_start.
Referenced by CSpliced_exon_Base::CSpliced_exon_Base(), CSpliced_exon_Base::GetProduct_start(), CSpliced_exon_Base::Reset(), and CSpliced_exon_Base::SetProduct_start().
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inline |
Reset Product_strand data member.
Definition at line 896 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Product_strand, and CSpliced_exon_Base::m_set_State.
Referenced by CSpliced_exon_Base::Reset().
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inline |
Reset Product_strand data member.
Definition at line 551 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_Product_strand, and CSpliced_seg_Base::m_set_State.
Referenced by CSpliced_seg_Base::Reset().
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inline |
Reset Product_type data member.
Definition at line 645 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_Product_type, and CSpliced_seg_Base::m_set_State.
Referenced by CSpliced_seg_Base::Reset().
void CSparse_seg_Base::ResetRow_scores | ( | void | ) |
Reset Row_scores data member.
Definition at line 77 of file Sparse_seg_.cpp.
References CSparse_seg_Base::m_Row_scores, and CSparse_seg_Base::m_set_State.
Referenced by CSparse_seg_Base::Reset().
void CSparse_seg_Base::ResetRows | ( | void | ) |
Reset Rows data member.
Definition at line 71 of file Sparse_seg_.cpp.
References CSparse_seg_Base::m_Rows, and CSparse_seg_Base::m_set_State.
Referenced by CSparse_seg_Base::Reset().
void CSeq_align_Base::ResetScore | ( | void | ) |
Reset Score data member.
Definition at line 295 of file Seq_align_.cpp.
References CSeq_align_Base::m_Score, and CSeq_align_Base::m_set_State.
Referenced by BOOST_AUTO_TEST_CASE(), CFeatureGenerator::SImplementation::ClearScores(), and CSeq_align_Base::Reset().
void CDense_diag_Base::ResetScores | ( | void | ) |
Reset Scores data member.
Definition at line 70 of file Dense_diag_.cpp.
References CDense_diag_Base::m_Scores, and CDense_diag_Base::m_set_State.
Referenced by CDense_diag_Base::Reset().
void CDense_seg_Base::ResetScores | ( | void | ) |
Reset Scores data member.
Definition at line 76 of file Dense_seg_.cpp.
References CDense_seg_Base::m_Scores, and CDense_seg_Base::m_set_State.
Referenced by CDense_seg_Base::Reset().
void CPacked_seg_Base::ResetScores | ( | void | ) |
Reset Scores data member.
Definition at line 82 of file Packed_seg_.cpp.
References CPacked_seg_Base::m_Scores, and CPacked_seg_Base::m_set_State.
Referenced by CPacked_seg_Base::Reset().
void CSpliced_exon_Base::ResetScores | ( | void | ) |
Reset Scores data member.
Definition at line 124 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Scores.
Referenced by CSpliced_exon_Base::Reset().
void CStd_seg_Base::ResetScores | ( | void | ) |
Reset Scores data member.
Definition at line 65 of file Std_seg_.cpp.
References CStd_seg_Base::m_Scores, and CStd_seg_Base::m_set_State.
Referenced by CStd_seg_Base::Reset().
void CSparse_align_Base::ResetSecond_id | ( | void | ) |
Reset Second_id data member.
Definition at line 66 of file Sparse_align_.cpp.
References CSparse_align_Base::m_Second_id.
Referenced by CSparse_align_Base::CSparse_align_Base(), CSparse_align_Base::GetSecond_id(), CSparse_align_Base::Reset(), and CSparse_align_Base::SetSecond_id().
void CSparse_align_Base::ResetSecond_starts | ( | void | ) |
Reset Second_starts data member.
Definition at line 86 of file Sparse_align_.cpp.
References CSparse_align_Base::m_Second_starts, and CSparse_align_Base::m_set_State.
Referenced by CSparse_align_Base::Reset().
void CSparse_align_Base::ResetSecond_strands | ( | void | ) |
Reset Second_strands data member.
Definition at line 98 of file Sparse_align_.cpp.
References CSparse_align_Base::m_Second_strands, and CSparse_align_Base::m_set_State.
Referenced by CSparse_align_Base::Reset().
void CSparse_align_Base::ResetSeg_scores | ( | void | ) |
Reset Seg_scores data member.
Definition at line 104 of file Sparse_align_.cpp.
References CSparse_align_Base::m_Seg_scores, and CSparse_align_Base::m_set_State.
Referenced by CSparse_align_Base::Reset().
void CSeq_align_Base::ResetSegs | ( | void | ) |
Reset Segs data member.
Definition at line 301 of file Seq_align_.cpp.
References CSeq_align_Base::m_Segs.
Referenced by CAlignmentAssistant::AdjustAlign(), BOOST_FIXTURE_TEST_CASE(), CSeq_align_Base::CSeq_align_Base(), CSeq_align_Base::GetSegs(), CSeq_align_Base::Reset(), s_DivvyUpAlignments_ProcessAnnot_Dendiag(), and CSeq_align_Base::SetSegs().
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virtual |
Reset the selection (set it to e_not_set).
Definition at line 57 of file Product_pos_.cpp.
References CProduct_pos_Base::e_not_set, CProduct_pos_Base::e_Protpos, CProduct_pos_Base::m_choice, and CProduct_pos_Base::m_object.
Referenced by CProduct_pos_Base::Reset(), and CProduct_pos_Base::SetProtpos().
void CScore_Base::C_Value::ResetSelection | ( | void | ) |
Reset the selection (set it to e_not_set).
Definition at line 57 of file Score_.cpp.
References e_not_set.
Referenced by CScore_Base::C_Value::Reset().
void CSeq_align_Base::C_Segs::ResetSelection | ( | void | ) |
Reset the selection (set it to e_not_set).
Definition at line 80 of file Seq_align_.cpp.
References e_not_set.
Referenced by CSeq_align_Base::C_Segs::Reset().
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virtual |
Reset the selection (set it to e_not_set).
Definition at line 56 of file Spliced_exon_chunk_.cpp.
References CSpliced_exon_chunk_Base::e_not_set, and CSpliced_exon_chunk_Base::m_choice.
Referenced by CSpliced_exon_chunk_Base::Reset().
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virtual |
Reset the selection (set it to e_not_set).
Definition at line 56 of file Spliced_seg_modifier_.cpp.
References CSpliced_seg_modifier_Base::e_not_set, and CSpliced_seg_modifier_Base::m_choice.
Referenced by CSpliced_seg_modifier_Base::Reset().
void CDense_diag_Base::ResetStarts | ( | void | ) |
Reset Starts data member.
Definition at line 58 of file Dense_diag_.cpp.
References CDense_diag_Base::m_set_State, and CDense_diag_Base::m_Starts.
Referenced by CDense_diag_Base::Reset().
void CDense_seg_Base::ResetStarts | ( | void | ) |
Reset Starts data member.
Definition at line 58 of file Dense_seg_.cpp.
References CDense_seg_Base::m_set_State, and CDense_seg_Base::m_Starts.
Referenced by ImproveAlignment(), CDense_seg_Base::Reset(), TestCircularTopology(), TestDoNotExtendOverGap(), TestDoNotFuseAbuttingIntervals(), TestExtendOverGap(), TestFuseAbuttingIntervals(), TestPartialWhenCutLastInterval(), TestPartialWhenCutLastIntervalDoNotExtend(), TestPartialWhenCutStart(), TestPartialWhenCutStartDoNotExtend(), TestPartialWhenCutStop(), and TestPartialWhenCutStopDoNotExtend().
void CPacked_seg_Base::ResetStarts | ( | void | ) |
Reset Starts data member.
Definition at line 58 of file Packed_seg_.cpp.
References CPacked_seg_Base::m_set_State, and CPacked_seg_Base::m_Starts.
Referenced by CPacked_seg_Base::Reset().
void CDense_diag_Base::ResetStrands | ( | void | ) |
Reset Strands data member.
Definition at line 64 of file Dense_diag_.cpp.
References CDense_diag_Base::m_set_State, and CDense_diag_Base::m_Strands.
Referenced by CDense_diag_Base::Reset().
void CDense_seg_Base::ResetStrands | ( | void | ) |
Reset Strands data member.
Definition at line 70 of file Dense_seg_.cpp.
References CDense_seg_Base::m_set_State, and CDense_seg_Base::m_Strands.
Referenced by CDense_seg_Base::Reset(), CCleanupAlignmentsJob::x_CreateProjectItems(), and CAppHitFilter::x_DumpOutput().
void CPacked_seg_Base::ResetStrands | ( | void | ) |
Reset Strands data member.
Definition at line 76 of file Packed_seg_.cpp.
References CPacked_seg_Base::m_set_State, and CPacked_seg_Base::m_Strands.
Referenced by CPacked_seg_Base::Reset().
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inline |
Reset Type data member.
Definition at line 802 of file Seq_align_.hpp.
References CSeq_align_Base::m_set_State, and CSeq_align_Base::m_Type.
Referenced by CSeq_align_Base::Reset().
void CScore_Base::ResetValue | ( | void | ) |
Reset Value data member.
Definition at line 137 of file Score_.cpp.
References CScore_Base::m_set_State, CScore_Base::m_Value, and CScore_Base::C_Value::Reset().
Referenced by CScore_Base::Reset().
void CProduct_pos_Base::Select | ( | E_Choice | index, |
EResetVariant | reset, | ||
CObjectMemoryPool * | pool | ||
) |
Select the requested variant if needed, allocating CObject variants from memory pool.
void CScore_Base::C_Value::Select | ( | E_Choice | index, |
EResetVariant | reset, | ||
CObjectMemoryPool * | pool | ||
) |
Select the requested variant if needed, allocating CObject variants from memory pool.
void CSeq_align_Base::C_Segs::Select | ( | E_Choice | index, |
EResetVariant | reset, | ||
CObjectMemoryPool * | pool | ||
) |
Select the requested variant if needed, allocating CObject variants from memory pool.
void CSpliced_exon_chunk_Base::Select | ( | E_Choice | index, |
EResetVariant | reset, | ||
CObjectMemoryPool * | pool | ||
) |
Select the requested variant if needed, allocating CObject variants from memory pool.
void CSpliced_seg_modifier_Base::Select | ( | E_Choice | index, |
EResetVariant | reset, | ||
CObjectMemoryPool * | pool | ||
) |
Select the requested variant if needed, allocating CObject variants from memory pool.
void CProduct_pos_Base::Select | ( | E_Choice | index, |
EResetVariant | reset = eDoResetVariant |
||
) |
Select the requested variant if needed.
index | New selection state. |
reset | Flag that defines the resetting of the variant data. The data will be reset if either the current selection differs from the new one, or the flag is set to eDoResetVariant. |
Referenced by CProduct_pos_Base::SetNucpos(), and CProduct_pos_Base::SetProtpos().
void CScore_Base::C_Value::Select | ( | E_Choice | index, |
EResetVariant | reset = eDoResetVariant |
||
) |
Select the requested variant if needed.
index | New selection state. |
reset | Flag that defines the resetting of the variant data. The data will be reset if either the current selection differs from the new one, or the flag is set to eDoResetVariant. |
void CSeq_align_Base::C_Segs::Select | ( | E_Choice | index, |
EResetVariant | reset = eDoResetVariant |
||
) |
Select the requested variant if needed.
index | New selection state. |
reset | Flag that defines the resetting of the variant data. The data will be reset if either the current selection differs from the new one, or the flag is set to eDoResetVariant. |
void CSpliced_exon_chunk_Base::Select | ( | E_Choice | index, |
EResetVariant | reset = eDoResetVariant |
||
) |
Select the requested variant if needed.
index | New selection state. |
reset | Flag that defines the resetting of the variant data. The data will be reset if either the current selection differs from the new one, or the flag is set to eDoResetVariant. |
Referenced by CSpliced_exon_chunk_Base::SetDiag(), CSpliced_exon_chunk_Base::SetGenomic_ins(), CSpliced_exon_chunk_Base::SetMatch(), CSpliced_exon_chunk_Base::SetMismatch(), and CSpliced_exon_chunk_Base::SetProduct_ins().
void CSpliced_seg_modifier_Base::Select | ( | E_Choice | index, |
EResetVariant | reset = eDoResetVariant |
||
) |
Select the requested variant if needed.
index | New selection state. |
reset | Flag that defines the resetting of the variant data. The data will be reset if either the current selection differs from the new one, or the flag is set to eDoResetVariant. |
Referenced by CSpliced_seg_modifier_Base::SetStart_codon_found(), and CSpliced_seg_modifier_Base::SetStop_codon_found().
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static |
Retrieve selection name (for diagnostic purposes).
index | One of possible selection states. |
Definition at line 90 of file Product_pos_.cpp.
References CProduct_pos_Base::sm_SelectionNames.
|
static |
Retrieve selection name (for diagnostic purposes).
index | One of possible selection states. |
Definition at line 83 of file Score_.cpp.
|
static |
Retrieve selection name (for diagnostic purposes).
index | One of possible selection states. |
Definition at line 143 of file Seq_align_.cpp.
Referenced by CScoreBuilder::GetBlastScore(), and CValidError_imp::PostErr().
|
static |
Retrieve selection name (for diagnostic purposes).
index | One of possible selection states. |
Definition at line 94 of file Spliced_exon_chunk_.cpp.
References CSpliced_exon_chunk_Base::sm_SelectionNames.
Referenced by CScoreBuilderBase::AddSplignScores(), CSplign::s_ComputeStats(), and CSeq_loc_Mapper_Base::sx_GetExonPartLength().
|
static |
Retrieve selection name (for diagnostic purposes).
index | One of possible selection states. |
Definition at line 82 of file Spliced_seg_modifier_.cpp.
References CSpliced_seg_modifier_Base::sm_SelectionNames.
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inline |
Assign a value to data member.
Definition at line 171 of file Score_set_.hpp.
References CScore_set_Base::m_data, and CScore_set_Base::m_set_State.
Referenced by CSplign::s_ComputeStats().
|
inline |
Assign a value to data member.
Definition at line 172 of file Seq_align_set_.hpp.
References CSeq_align_set_Base::m_data, and CSeq_align_set_Base::m_set_State.
Referenced by HitDistributor::addBatch(), CGBProjectHelper::AddProjectItemsFromRID(), CContigAssembly::Align(), CSplignFormatter::AsSeqAlignSet(), CCompartmentAccessor< THit >::AsSeqAlignSet(), CAdvancedAlignCleanup::BestPlacement(), BlastHitList2SeqAlign_OMF(), BOOST_AUTO_TEST_CASE(), CreateAlignSetFromAnchoredAln(), CreateAlignSetFromPairwiseAln(), CreateEmptySeq_align_set(), ConsensusMaker::degapAlignment(), CAlignFormatUtil::ExtractQuerySeqAlign(), CAlignFormatUtil::ExtractSeqalignSetFromDiscSegs(), CSeqAlignFilter::FilterByAccessionType(), CSeqAlignFilter::FilterByGiList(), CSeqAlignFilter::FilterByGiListFromFile(), CSeqAlignFilter::FilterByTaxonomy(), CAlignFormatUtil::FilterSeqalignByEval(), CAlignFormatUtil::FilterSeqalignByPercentIdent(), CAlignFormatUtil::FilterSeqalignBySeqList(), FindCompartments(), TestUtil::FlattenSeqAlignSet(), CVecscreenRun::CFormatter::FormatResults(), fta_parse_tpa_tsa_block(), CSplitSeqAlignMerger::GenerateAlignments(), CBlastAligner::GenerateAlignments(), CRemoteBlastAligner::GenerateAlignments(), CMergeTreeAligner::GenerateAlignments(), CFileLoadAligner::GenerateAlignments(), CLDS2_DataLoader::GetChunk(), CShowBlastDeflineTest::GetDeflineInfo(), CMagicBlastResultSet::GetFlatResults(), CShowBlastDefline::GetFormattingInfo(), CRemoteBlast::GetSeqAlignSets(), CAlignFormatUtil::GetUniqSeqCoverage(), CAlignFormatUtil::HitListToHspList(), CAlignFormatUtil::HspListToHitList(), CAlignFormatUtil::HspListToHitMap(), CBlastFormatUtil::InsertSubjectScores(), JoinCompartment(), CAlignFormatUtil::LimitSeqalignByHsps(), MakeSubjectScores(), CDisplaySeqalign::PrepareBlastUngappedSeqalign(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx2(), CBlast_SAM_Formatter::Print(), PrintASN1(), CAlignFormatUtil::PruneSeqalign(), CAlignFormatUtil::PruneSeqalignAll(), NBestPlacement::Rank(), CDUpdater::retrieveAllSequences(), CNgAlignApp::Run(), CIgBlast::s_AppendResults(), s_BLAST_OneSubjectResults2CSeqAlign(), s_BuildArchiveAll(), s_CalcAlnPercentIdent(), s_CombineSearchSets(), s_GetIndels(), s_RestoreHspPos(), s_RoundScores(), s_SeqAlignSetToXMLHits(), s_SetBlastXMlHitList(), CIgBlast::s_SortResultsByEvalue(), s_SplitAlignVectorBySubjects(), CMagicBlastResults::SortAlignments(), CAlignFormatUtil::SortHitByMasterStartAscending(), CAlignFormatUtil::SortHitByScoreDescending(), CAlignFormatUtil::SortOneSeqalignForSortableFormat(), CSeq_align::SplitOnLongDiscontinuity(), CSeq_align_set::SwapRows(), TestSimpleAlignment(), CDUpdater::update(), CVecscreenTest::VecscreenDisplay(), CAutogeneratedCleanup::x_BasicCleanupSeqAlignSet(), CMagicBlast::x_BuildResultSet(), CMagicBlast::x_BuildSeqAlignSet(), CIgBlast::x_ConvertResultType(), CInversionMergeAligner::x_CreateDiscAlignment(), CPssmCddInputTest::x_CreateDuplicateNonOverlappingHit(), CPssmCddInputTest::x_CreateDuplicateOverlappingHit(), CSeqAlignFilter::x_CreateOusputSeqaligns(), CBLASTSeqToolJob::x_CreateProjectItems(), CNGAlignJob::x_CreateProjectItems(), CFindOverlapJob::x_CreateProjectItems(), CSplignJob::x_CreateProjectItems(), CMagicBlast::x_CreateSeqAlignSet(), CQuerySet::x_FilterStrictSubAligns(), CIgBlast::x_FindDJAln(), CInstancedAligner::x_GetCleanupInstances(), CIdMapperTestApp::x_HandleAlignments(), CInversionMergeAligner::x_HandleSingleStrandMerging(), CShowBlastDefline::x_InitDeflineTable(), CMergeAligner::x_MergeAlignments(), CVecscreen::x_MergeInclusiveSeqalign(), CVecscreen::x_MergeLowerRankSeqalign(), CBlast_SAM_Formatter::x_Print(), CIgBlast::x_ProcessCResult(), CIgBlast::x_ProcessDGeneResult(), CSplignApp::x_ProcessPair(), CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile(), CBlastFormat::x_ReverseQuery(), CInstancedAligner::x_RunAligner(), CInversionMergeAligner::x_RunMerger(), CInversionMergeAligner::x_SortAlignSet(), CMergeAligner::x_SortAlignSet(), COligoSpecificityTemplate::x_SortHit(), CAdvancedAlignCleanup::x_SplignCompartmentsToGenomicFormat(), CInversionMergeAligner::x_SplitAlignmentsByStrand(), and CBlastFormat::x_SplitSeqAlign().
void CSpliced_exon_Base::SetAcceptor_before_exon | ( | CSpliced_exon_Base::TAcceptor_before_exon & | value | ) |
Assign a value to Acceptor_before_exon data member.
value | Reference to value. |
Definition at line 146 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Acceptor_before_exon, and value.
CSpliced_exon_Base::TAcceptor_before_exon & CSpliced_exon_Base::SetAcceptor_before_exon | ( | void | ) |
Assign a value to Acceptor_before_exon data member.
Definition at line 151 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Acceptor_before_exon.
|
inline |
Assign a value to Amin data member.
value | Value to assign |
Definition at line 229 of file Prot_pos_.hpp.
References CProt_pos_Base::m_Amin, CProt_pos_Base::m_set_State, and value.
Referenced by NucPosToProtPos(), and NultriposToProduct_pos().
|
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Assign a value to Amin data member.
Definition at line 236 of file Prot_pos_.hpp.
References CProt_pos_Base::IsSetAmin(), CProt_pos_Base::m_Amin, CProt_pos_Base::m_set_State, and CSerialObject::UnassignedByte().
Assign a value to Bases data member.
value | Value to assign |
Definition at line 183 of file Splice_site_.hpp.
References CSplice_site_Base::m_Bases, CSplice_site_Base::m_set_State, and value.
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Definition at line 190 of file Splice_site_.hpp.
References CSplice_site_Base::m_Bases, CSplice_site_Base::m_set_State, and value.
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Assign a value to Bases data member.
Definition at line 197 of file Splice_site_.hpp.
References CSplice_site_Base::IsSetBases(), CSplice_site_Base::m_Bases, CSplice_site_Base::m_set_State, and CSerialObject::UnassignedString().
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Assign a value to Bounds data member.
Definition at line 957 of file Seq_align_.hpp.
References CSeq_align_Base::m_Bounds, and CSeq_align_Base::m_set_State.
Referenced by CCompartmentAccessor< THit >::AsSeqAlignSet(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CSeq_align_Mapper_Base::GetDstAlign(), CAliToSeq_align::MakeSeq_align(), s_CleanSeqAlign(), CReadBlastApp::StoreBlast(), CAutogeneratedCleanup::x_BasicCleanupSeqAlign(), and CSeq_align_Mapper_Base::x_GetDstSpliced().
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Assign default value to Dim data member.
Definition at line 367 of file Dense_diag_.hpp.
References CDense_diag_Base::ResetDim().
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Assign default value to Dim data member.
Definition at line 415 of file Dense_seg_.hpp.
References CDense_seg_Base::ResetDim().
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Assign default value to Dim data member.
Definition at line 439 of file Packed_seg_.hpp.
References CPacked_seg_Base::ResetDim().
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Assign default value to Dim data member.
Definition at line 289 of file Std_seg_.hpp.
References CStd_seg_Base::ResetDim().
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Assign default value to Frame data member.
Definition at line 267 of file Prot_pos_.hpp.
References CProt_pos_Base::ResetFrame().
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Select the variant.
Definition at line 733 of file Seq_align_.hpp.
References eDoNotResetVariant.
Referenced by CAutogeneratedCleanup::x_BasicCleanupAlignSegs().
void CSeq_align_Base::C_Segs::SetDenseg | ( | TDenseg & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 165 of file Seq_align_.cpp.
References CObject::AddReference(), and value.
CSeq_align_Base::C_Segs::TDenseg & CSeq_align_Base::C_Segs::SetDenseg | ( | void | ) |
Select the variant.
Definition at line 159 of file Seq_align_.cpp.
References eDoNotResetVariant.
Referenced by CDUpdater::modifySeqAlignSeqEntry(), CSeq_align::OffsetRow(), CSeq_align::RemapToLoc(), CSeq_align::Reverse(), CSeq_align::SwapRows(), CDUpdater::update(), CAutogeneratedCleanup::x_BasicCleanupAlignSegs(), and CGff2Reader::xAlignmentSetDenseg().
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Select the variant and set its data.
value | Variant data. |
Definition at line 424 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::e_Diag, eDoNotResetVariant, CSpliced_exon_chunk_Base::m_Diag, CSpliced_exon_chunk_Base::Select(), and value.
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Select the variant.
Definition at line 417 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::e_Diag, eDoNotResetVariant, CSpliced_exon_chunk_Base::m_Diag, and CSpliced_exon_chunk_Base::Select().
Referenced by CFeatureGenerator::SImplementation::MaximizeTranslation(), and SetPartLength().
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Assign a value to Dim data member.
value | Value to assign |
Definition at line 379 of file Dense_diag_.hpp.
References CDense_diag_Base::m_Dim, CDense_diag_Base::m_set_State, and value.
Referenced by CreateDense_diagFromAnchoredAln(), and CreatePairwiseSeqAlignFromMultipleRow().
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Assign a value to Dim data member.
value | Value to assign |
Definition at line 427 of file Dense_seg_.hpp.
References CDense_seg_Base::m_Dim, CDense_seg_Base::m_set_State, and value.
Referenced by CAlignmentAssistant::AdjustAlign(), BOOST_AUTO_TEST_CASE(), CAlnMap::CreateAlignFromRange(), CreateAlignSetFromAnchoredAln(), CreateAlignSetFromPairwiseAln(), CAlnVec::CreateConsensus(), CreateDensegFromAnchoredAln(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CSeq_align::CreateDensegFromDisc(), CreateDensegFromPairwiseAln(), CSeq_align::CreateDensegFromStdseg(), CAlignCleanup::CreatePairwiseFromMultiple(), CDense_seg::ExtractRows(), CDense_seg::ExtractSlice(), CDense_seg::FillUnaligned(), CAlnReader::GetSeqAlign(), CUpdateSeq_Input::s_Align2IdenticalSeq(), s_CompressDiscToDenseq(), s_CreateDenseg(), s_CutDensegSegment(), CFastaReader::x_AddMultiwayAlignment(), CPssmCddInputTest::x_CreateAlignment(), CAlnMixMerger::x_CreateDenseg(), CPhrap_Contig::x_CreateSeq_align(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CSeq_align_Mapper_Base::x_GetDstDenseg(), CSeq_align_Mapper_Base::x_GetPartialDenseg(), CMultiAligner::x_GetSeqalign(), CTreeAlignMerger::x_MakeSeqAlign(), CUpdateAlign::x_RemoveIDsFromAlign(), CGff2Reader::xAlignmentSetDenseg(), and CFastaReader::xCreateAlignment().
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Assign a value to Dim data member.
value | Value to assign |
Definition at line 451 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_Dim, CPacked_seg_Base::m_set_State, and value.
Referenced by CSeq_align_Mapper_Base::x_GetDstPacked().
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Assign a value to Dim data member.
value | Value to assign |
Definition at line 865 of file Seq_align_.hpp.
References CSeq_align_Base::m_Dim, CSeq_align_Base::m_set_State, and value.
Referenced by CNWFormatter::AsSeqAlign(), CSplignFormatter::AsSeqAlignSet(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildGoodAlign(), BuildGoodEcoSetWithAlign(), CSeqAnnotFromFasta::BuildMasterSlaveSeqAlign(), BuildSetAlign(), BuildSetDendiagAlign(), CFeatureGenerator::ConvertLocToAnnot(), CAlnMap::CreateAlignFromRange(), CreateAlignSetFromAnchoredAln(), CreateAlignSetFromPairwiseAln(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CreatePairwiseSeqAlignFromMultipleRow(), CreateSeqAlignFromAnchoredAln(), CreateSeqAlignFromEachPairwiseAln(), CreateSeqAlignFromPairwiseAln(), fta_parse_tpa_tsa_block(), CFastaAlignmentBuilder::GetCompletedAlignment(), CSeq_align_Mapper_Base::GetDstAlign(), CPhyTreeCalc::GetSeqAlign(), CAliToSeq_align::MakeSeq_align(), CRemoveSeqFromAlignDlg::ModifyAlign(), CAlignmentAssistant::OnRemoveSeqFromAlign(), SCigarAlignment::operator()(), CAlnAsnReader::Read(), CUpdateSeq_Input::s_Align2IdenticalSeq(), s_BlastHSP2SeqAlign(), s_CreateSeqAlign(), s_GetJoinedAlignment(), s_OOFBlastHSP2SeqAlign(), s_SplitAlignVectorBySubjects(), CAlignCompare::SAlignment::Slice(), TestFeatInsideGap(), BlockModel::toSeqAlign(), CFastaReader::x_AddMultiwayAlignment(), CGff2Reader::x_CreateAlignment(), CPssmCddInputTest::x_CreateAlignment(), CAlnMixMerger::x_CreateDenseg(), CPhrap_Contig::x_CreateSeq_align(), CMagicBlast::x_CreateSeqAlignSet(), CSeq_align::x_CreateSubsegAlignment(), CMultiAligner::x_GetSeqalign(), CGff2Reader::x_MergeAlignments(), CGFFReader::x_ParseAlignRecord(), CGff2Reader::x_UpdateAnnotAlignment(), and CFastaReader::xCreateAlignment().
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Assign a value to Dim data member.
value | Value to assign |
Definition at line 301 of file Std_seg_.hpp.
References CStd_seg_Base::m_Dim, CStd_seg_Base::m_set_State, and value.
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Assign a value to Dim data member.
Definition at line 386 of file Dense_diag_.hpp.
References CDense_diag_Base::IsSetDim(), CDense_diag_Base::m_Dim, CDense_diag_Base::m_set_State, and CSerialObject::UnassignedByte().
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Assign a value to Dim data member.
Definition at line 434 of file Dense_seg_.hpp.
References CDense_seg_Base::IsSetDim(), CDense_seg_Base::m_Dim, CDense_seg_Base::m_set_State, and CSerialObject::UnassignedByte().
Referenced by CDense_seg::FromTranscript().
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Assign a value to Dim data member.
Definition at line 458 of file Packed_seg_.hpp.
References CPacked_seg_Base::IsSetDim(), CPacked_seg_Base::m_Dim, CPacked_seg_Base::m_set_State, and CSerialObject::UnassignedByte().
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Assign a value to Dim data member.
Definition at line 872 of file Seq_align_.hpp.
References CSeq_align_Base::IsSetDim(), CSeq_align_Base::m_Dim, CSeq_align_Base::m_set_State, and CSerialObject::UnassignedByte().
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Assign a value to Dim data member.
Definition at line 308 of file Std_seg_.hpp.
References CStd_seg_Base::IsSetDim(), CStd_seg_Base::m_Dim, CStd_seg_Base::m_set_State, and CSerialObject::UnassignedByte().
void CSeq_align_Base::C_Segs::SetDisc | ( | TDisc & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 209 of file Seq_align_.cpp.
References CObject::AddReference(), and value.
CSeq_align_Base::C_Segs::TDisc & CSeq_align_Base::C_Segs::SetDisc | ( | void | ) |
Select the variant.
Definition at line 203 of file Seq_align_.cpp.
References eDoNotResetVariant.
Referenced by s_GetIndels(), CSeq_align::SwapRows(), and CAutogeneratedCleanup::x_BasicCleanupAlignSegs().
void CSpliced_exon_Base::SetDonor_after_exon | ( | CSpliced_exon_Base::TDonor_after_exon & | value | ) |
Assign a value to Donor_after_exon data member.
value | Reference to value. |
Definition at line 163 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Donor_after_exon, and value.
CSpliced_exon_Base::TDonor_after_exon & CSpliced_exon_Base::SetDonor_after_exon | ( | void | ) |
Assign a value to Donor_after_exon data member.
Definition at line 168 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Donor_after_exon.
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Assign a value to Exons data member.
Definition at line 698 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_Exons, and CSpliced_seg_Base::m_set_State.
Referenced by CFeatureGenerator::SImplementation::AdjustAlignment(), AlignModelToSeqalign(), CSplignFormatter::AsSeqAlignSet(), BOOST_AUTO_TEST_CASE(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), variation::CreateSplicedSeqAlignFromFeat(), InitSplicedsegFromPairwiseAln(), CAliToSeq_align::MakeSeq_align(), MakeSplicedSeg(), CFeatureGenerator::SImplementation::MaximizeTranslation(), CProSplign::CImplementation::SeekStartStop(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CFeatureGenerator::SImplementation::TrimHolesToCodons(), CAutogeneratedCleanup::x_BasicCleanupSplicedSeg(), CSeq_align_Mapper_Base::x_GetDstExon(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CIdMapperTestApp::x_RecurseMapSeqAligns(), and CGff2Reader::xUpdateSplicedSegment().
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Assign a value to Ext data member.
Definition at line 1007 of file Seq_align_.hpp.
References CSeq_align_Base::m_Ext, and CSeq_align_Base::m_set_State.
Referenced by CScoreBuilder::AddTracebacks(), AlignModelToSeqalign(), CSplignFormatter::AsSeqAlignSet(), CSeq_align::FindExt(), CSeq_align_Mapper_Base::GetDstAlign(), CBamAlignIterator::GetMatchAlign(), CCSraAlignIterator::GetMatchAlign(), CAnnotationASN1::CImplementationData::model2spliced_seq_align(), CDemoSeqQaApp::Run(), s_AddUserObjectToSeqAlign(), s_CleanSeqAlign(), s_CreateSeqAlign(), s_ModifySeqAlnWithFilteredSeqIDs(), and s_UpdateSeqAlnWithFilteredSeqIDs().
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Assign a value to Ext data member.
Definition at line 365 of file Sparse_seg_.hpp.
References CSparse_seg_Base::m_Ext, and CSparse_seg_Base::m_set_State.
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Assign a value to Ext data member.
Definition at line 1131 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Ext, and CSpliced_exon_Base::m_set_State.
Referenced by CFeatureGenerator::SImplementation::StitchSmallHoles().
void CSparse_align_Base::SetFirst_id | ( | CSparse_align_Base::TFirst_id & | value | ) |
Assign a value to First_id data member.
value | Reference to value. |
Definition at line 61 of file Sparse_align_.cpp.
References CSparse_align_Base::m_First_id, and value.
Referenced by CAutogeneratedCleanup::x_BasicCleanupSparseAlign().
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Assign a value to First_id data member.
Definition at line 440 of file Sparse_align_.hpp.
References CSparse_align_Base::m_First_id, and CSparse_align_Base::ResetFirst_id().
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Assign a value to First_starts data member.
Definition at line 544 of file Sparse_align_.hpp.
References CSparse_align_Base::m_First_starts, and CSparse_align_Base::m_set_State.
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Assign a value to Frame data member.
value | Value to assign |
Definition at line 279 of file Prot_pos_.hpp.
References CProt_pos_Base::m_Frame, CProt_pos_Base::m_set_State, and value.
Referenced by NucPosToProtPos(), and NultriposToProduct_pos().
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Assign a value to Frame data member.
Definition at line 286 of file Prot_pos_.hpp.
References CProt_pos_Base::IsSetFrame(), CProt_pos_Base::m_Frame, CProt_pos_Base::m_set_State, and CSerialObject::UnassignedByte().
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Assign a value to Genomic_end data member.
value | Value to assign |
Definition at line 823 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Genomic_end, CSpliced_exon_Base::m_set_State, and value.
Referenced by CFeatureGenerator::SImplementation::AdjustAlignment(), BOOST_AUTO_TEST_CASE(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), and CFeatureGenerator::SImplementation::StitchSmallHoles().
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Assign a value to Genomic_end data member.
Definition at line 830 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::IsSetGenomic_end(), CSpliced_exon_Base::m_Genomic_end, CSpliced_exon_Base::m_set_State, and CSerialObject::UnassignedByte().
void CSpliced_exon_Base::SetGenomic_id | ( | CSpliced_exon_Base::TGenomic_id & | value | ) |
Assign a value to Genomic_id data member.
value | Reference to value. |
Definition at line 106 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Genomic_id, and value.
Referenced by CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), and CAutogeneratedCleanup::x_BasicCleanupSplicedExon().
void CSpliced_seg_Base::SetGenomic_id | ( | CSpliced_seg_Base::TGenomic_id & | value | ) |
Assign a value to Genomic_id data member.
value | Reference to value. |
Definition at line 84 of file Spliced_seg_.cpp.
References CSpliced_seg_Base::m_Genomic_id, and value.
Referenced by AlignModelToSeqalign(), CSplignFormatter::AsSeqAlignSet(), BOOST_AUTO_TEST_CASE(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), variation::CreateSplicedSeqAlignFromFeat(), InitSplicedsegFromPairwiseAln(), CAliToSeq_align::MakeSeq_align(), MakeSplicedSeg(), CAutogeneratedCleanup::x_BasicCleanupSplicedSeg(), and CSeq_align_Mapper_Base::x_GetDstSpliced().
CSpliced_exon_Base::TGenomic_id & CSpliced_exon_Base::SetGenomic_id | ( | void | ) |
Assign a value to Genomic_id data member.
Definition at line 111 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Genomic_id.
CSpliced_seg_Base::TGenomic_id & CSpliced_seg_Base::SetGenomic_id | ( | void | ) |
Assign a value to Genomic_id data member.
Definition at line 89 of file Spliced_seg_.cpp.
References CSpliced_seg_Base::m_Genomic_id.
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Select the variant and set its data.
value | Variant data. |
Definition at line 478 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::e_Genomic_ins, eDoNotResetVariant, CSpliced_exon_chunk_Base::m_Genomic_ins, CSpliced_exon_chunk_Base::Select(), and value.
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Select the variant.
Definition at line 471 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::e_Genomic_ins, eDoNotResetVariant, CSpliced_exon_chunk_Base::m_Genomic_ins, and CSpliced_exon_chunk_Base::Select().
Referenced by CFeatureGenerator::SImplementation::MaximizeTranslation(), and SetPartLength().
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Assign a value to Genomic_start data member.
value | Value to assign |
Definition at line 776 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Genomic_start, CSpliced_exon_Base::m_set_State, and value.
Referenced by CFeatureGenerator::SImplementation::AdjustAlignment(), BOOST_AUTO_TEST_CASE(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), and CFeatureGenerator::SImplementation::StitchSmallHoles().
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Assign a value to Genomic_start data member.
Definition at line 783 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::IsSetGenomic_start(), CSpliced_exon_Base::m_Genomic_start, CSpliced_exon_Base::m_set_State, and CSerialObject::UnassignedByte().
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Assign a value to Genomic_strand data member.
value | Value to assign |
Definition at line 959 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Genomic_strand, CSpliced_exon_Base::m_set_State, and value.
Referenced by BOOST_AUTO_TEST_CASE().
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Assign a value to Genomic_strand data member.
value | Value to assign |
Definition at line 614 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_Genomic_strand, CSpliced_seg_Base::m_set_State, and value.
Referenced by AlignModelToSeqalign(), CSplignFormatter::AsSeqAlignSet(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), variation::CreateSplicedSeqAlignFromFeat(), CAliToSeq_align::MakeSeq_align(), and CSeq_align_Mapper_Base::x_GetDstSpliced().
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Assign a value to Genomic_strand data member.
Definition at line 966 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::IsSetGenomic_strand(), CSpliced_exon_Base::m_Genomic_strand, CSpliced_exon_Base::m_set_State, and CSerialObject::UnassignedByte().
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Assign a value to Genomic_strand data member.
Definition at line 621 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::IsSetGenomic_strand(), CSpliced_seg_Base::m_Genomic_strand, CSpliced_seg_Base::m_set_State, and CSerialObject::UnassignedByte().
void CScore_Base::SetId | ( | CScore_Base::TId & | value | ) |
Assign a value to Id data member.
value | Reference to value. |
Definition at line 125 of file Score_.cpp.
References CScore_Base::m_Id, and value.
Referenced by CReadBlastApp::StoreBlast().
CScore_Base::TId & CScore_Base::SetId | ( | void | ) |
Assign a value to Id data member.
Definition at line 130 of file Score_.cpp.
References CScore_Base::m_Id.
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Assign a value to Id data member.
Definition at line 982 of file Seq_align_.hpp.
References CSeq_align_Base::m_Id, and CSeq_align_Base::m_set_State.
Referenced by AlignModelToSeqalign(), CSeq_align_Mapper_Base::GetDstAlign(), and s_CleanSeqAlign().
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Assign a value to Ids data member.
Definition at line 416 of file Dense_diag_.hpp.
References CDense_diag_Base::m_Ids, and CDense_diag_Base::m_set_State.
Referenced by CreateDense_diagFromAnchoredAln(), CreatePairwiseSeqAlignFromMultipleRow(), and CAutogeneratedCleanup::x_BasicCleanupDenseDiag().
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Assign a value to Ids data member.
Definition at line 511 of file Dense_seg_.hpp.
References CDense_seg_Base::m_Ids, and CDense_seg_Base::m_set_State.
Referenced by CAlignmentAssistant::AdjustAlign(), CNWFormatter::AsDenseSeg(), CCompartmentAccessor< THit >::AsSeqAlignSet(), CContigAssembly::BandedGlobalAlignment(), BOOST_AUTO_TEST_CASE(), CAlnMap::CreateAlignFromRange(), CreateAlignSetFromAnchoredAln(), CreateAlignSetFromPairwiseAln(), CAlnVec::CreateConsensus(), CreateDensegFromAnchoredAln(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CSeq_align::CreateDensegFromDisc(), CreateDensegFromPairwiseAln(), CSeq_align::CreateDensegFromStdseg(), CAlignCleanup::CreatePairwiseFromMultiple(), CPslData::ExportToSeqAlign(), CDense_seg::ExtractRows(), CDense_seg::ExtractSlice(), CDense_seg::FillUnaligned(), CBamAlignIterator::GetMatchAlign(), CCSraAlignIterator::GetMatchAlign(), CUpdateSeq_Input::s_Align2IdenticalSeq(), s_CompressDiscToDenseq(), s_CreateDenseg(), s_CutDensegSegment(), s_DoNWalign(), s_ExonToDenseg(), s_FixZeroVersions(), CClippedScorer::ScoreAlignments(), CDense_seg::SwapRows(), CFastaReader::x_AddMultiwayAlignment(), CAlnReader::x_AssignDensegIds(), CAutogeneratedCleanup::x_BasicCleanupDenseg(), CUpdateAlign::x_ChangeIDsToFarPointers(), CPssmCddInputTest::x_CreateAlignment(), CAlnMixMerger::x_CreateDenseg(), CCleanupAlignmentsJob::x_CreateProjectItems(), CPhrap_Contig::x_CreateSeq_align(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CAppHitFilter::x_DumpOutput(), CUnorderedSplitter::x_FixAlignment(), CSeq_align_Mapper_Base::x_GetDstDenseg(), CSequenceUpdater::x_GetNewAlign_Replace(), CSeq_align_Mapper_Base::x_GetPartialDenseg(), CScore_BlastRatio::x_GetPerfectScore(), CMultiAligner::x_GetSeqalign(), CTreeAlignMerger::x_MakeSeqAlign(), CUpdateAlign::x_MapNonPresentIDs(), CGFFReader::x_ParseAlignRecord(), CIdMapperTestApp::x_RecurseMapSeqAligns(), CUpdateAlign::x_RemoveIDsFromAlign(), and CFastaReader::xCreateAlignment().
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Assign a value to Ids data member.
Definition at line 535 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_Ids, and CPacked_seg_Base::m_set_State.
Referenced by CAutogeneratedCleanup::x_BasicCleanupPackedSeg(), and CSeq_align_Mapper_Base::x_GetDstPacked().
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Assign a value to Ids data member.
Definition at line 338 of file Std_seg_.hpp.
References CStd_seg_Base::m_Ids, and CStd_seg_Base::m_set_State.
Referenced by CStd_seg::SwapRows(), and CAutogeneratedCleanup::x_BasicCleanupStdSeg().
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Assign a value to Index data member.
value | Value to assign |
Definition at line 186 of file Sparse_seg_ext_.hpp.
References CSparse_seg_ext_Base::m_Index, CSparse_seg_ext_Base::m_set_State, and value.
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Assign a value to Index data member.
Definition at line 193 of file Sparse_seg_ext_.hpp.
References CSparse_seg_ext_Base::IsSetIndex(), CSparse_seg_ext_Base::m_Index, CSparse_seg_ext_Base::m_set_State, and CSerialObject::UnassignedByte().
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Select the variant and set its data.
value | Variant data. |
Definition at line 425 of file Score_.hpp.
References eDoNotResetVariant, and value.
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Select the variant.
Definition at line 418 of file Score_.hpp.
References eDoNotResetVariant.
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Assign a value to Len data member.
value | Value to assign |
Definition at line 476 of file Dense_diag_.hpp.
References CDense_diag_Base::m_Len, CDense_diag_Base::m_set_State, and value.
Referenced by CreatePairwiseSeqAlignFromMultipleRow().
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Assign a value to Len data member.
Definition at line 483 of file Dense_diag_.hpp.
References CDense_diag_Base::IsSetLen(), CDense_diag_Base::m_Len, CDense_diag_Base::m_set_State, and CSerialObject::UnassignedByte().
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Assign a value to Lens data member.
Definition at line 561 of file Dense_seg_.hpp.
References CDense_seg_Base::m_Lens, and CDense_seg_Base::m_set_State.
Referenced by CFastaAlignmentBuilder::AddData(), CAlignmentAssistant::AdjustAlign(), CContigAssembly::BandedGlobalAlignment(), BOOST_AUTO_TEST_CASE(), CDense_seg::Compact(), CAlnMap::CreateAlignFromRange(), CreateAlignSetFromAnchoredAln(), CreateAlignSetFromPairwiseAln(), CAlnVec::CreateConsensus(), CreateDensegFromAnchoredAln(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CSeq_align::CreateDensegFromDisc(), CreateDensegFromPairwiseAln(), CSeq_align::CreateDensegFromStdseg(), CAlignCleanup::CreatePairwiseFromMultiple(), CSeq_align::CreateTranslatedDensegFromNADenseg(), CPslData::ExportToSeqAlign(), CDense_seg::ExtractRows(), CDense_seg::ExtractSlice(), CDense_seg::FillUnaligned(), CDense_seg::FromTranscript(), CBamAlignIterator::GetMatchAlign(), CCSraAlignIterator::GetMatchAlign(), CAlnReader::GetSeqAlign(), ImproveAlignment(), CDense_seg::OrderAdjacentGaps(), CDense_seg::CReserveHook::PreReadClassMember(), CDenseSegReserveLensHook::ReadClassMember(), CDense_seg::RemapToLoc(), CDense_seg::RemovePureGapSegs(), CDense_seg::Reverse(), CUpdateSeq_Input::s_Align2IdenticalSeq(), s_CompressDiscToDenseq(), s_CreateDenseg(), s_CutDensegSegment(), s_ExonToDenseg(), TestCircularTopology(), TestDoNotExtendOverGap(), TestDoNotFuseAbuttingIntervals(), TestExtendOverGap(), TestFuseAbuttingIntervals(), TestPartialWhenCutLastInterval(), TestPartialWhenCutLastIntervalDoNotExtend(), TestPartialWhenCutStart(), TestPartialWhenCutStartDoNotExtend(), TestPartialWhenCutStop(), TestPartialWhenCutStopDoNotExtend(), CDense_seg::TrimEndGaps(), CFastaReader::x_AddMultiwayAlignment(), CPssmCddInputTest::x_CreateAlignment(), CAlnMixMerger::x_CreateDenseg(), CPhrap_Contig::x_CreateSeq_align(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CAlnMix::x_ExtendDSWithWidths(), CSeq_align_Mapper_Base::x_GetDstDenseg(), CSeq_align_Mapper_Base::x_GetPartialDenseg(), CScore_BlastRatio::x_GetPerfectScore(), CMultiAligner::x_GetSeqalign(), CTreeAlignMerger::x_MakeSeqAlign(), CGFFReader::x_ParseAlignRecord(), CUnorderedSplitter::x_TrimRows(), and CFastaReader::xCreateAlignment().
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Assign a value to Lens data member.
Definition at line 613 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_Lens, and CPacked_seg_Base::m_set_State.
Referenced by CSeq_align_Mapper_Base::x_GetDstPacked().
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Assign a value to Lens data member.
Definition at line 594 of file Sparse_align_.hpp.
References CSparse_align_Base::m_Lens, and CSparse_align_Base::m_set_State.
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Assign a value to Loc data member.
Definition at line 363 of file Std_seg_.hpp.
References CStd_seg_Base::m_Loc, and CStd_seg_Base::m_set_State.
Referenced by CStd_seg::OffsetRow(), CStd_seg::RemapToLoc(), CStd_seg::SwapRows(), and CAutogeneratedCleanup::x_BasicCleanupStdSeg().
void CSparse_seg_Base::SetMaster_id | ( | CSparse_seg_Base::TMaster_id & | value | ) |
Assign a value to Master_id data member.
value | Reference to value. |
Definition at line 59 of file Sparse_seg_.cpp.
References CSparse_seg_Base::m_Master_id, and value.
Referenced by CAutogeneratedCleanup::x_BasicCleaupSparseSeg().
CSparse_seg_Base::TMaster_id & CSparse_seg_Base::SetMaster_id | ( | void | ) |
Assign a value to Master_id data member.
Definition at line 64 of file Sparse_seg_.cpp.
References CSparse_seg_Base::m_Master_id.
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Select the variant and set its data.
value | Variant data. |
Definition at line 370 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::e_Match, eDoNotResetVariant, CSpliced_exon_chunk_Base::m_Match, CSpliced_exon_chunk_Base::Select(), and value.
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Select the variant.
Definition at line 363 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::e_Match, eDoNotResetVariant, CSpliced_exon_chunk_Base::m_Match, and CSpliced_exon_chunk_Base::Select().
Referenced by SetPartLength().
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Select the variant and set its data.
value | Variant data. |
Definition at line 397 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::e_Mismatch, eDoNotResetVariant, CSpliced_exon_chunk_Base::m_Mismatch, CSpliced_exon_chunk_Base::Select(), and value.
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Select the variant.
Definition at line 390 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::e_Mismatch, eDoNotResetVariant, CSpliced_exon_chunk_Base::m_Mismatch, and CSpliced_exon_chunk_Base::Select().
Referenced by SetPartLength().
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Assign a value to Modifiers data member.
Definition at line 817 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_Modifiers, and CSpliced_seg_Base::m_set_State.
Referenced by CAlignModel::MakeSeqAlign(), CProSplign::CImplementation::SeekStartStop(), and CSeq_align_Mapper_Base::x_GetDstSpliced().
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Select the variant and set its data.
value | Variant data. |
Definition at line 280 of file Product_pos_.hpp.
References CProduct_pos_Base::e_Nucpos, eDoNotResetVariant, CProduct_pos_Base::m_Nucpos, CProduct_pos_Base::Select(), and value.
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Select the variant.
Definition at line 273 of file Product_pos_.hpp.
References CProduct_pos_Base::e_Nucpos, eDoNotResetVariant, CProduct_pos_Base::m_Nucpos, and CProduct_pos_Base::Select().
Referenced by s_TransformToNucpos().
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Assign a value to Numseg data member.
value | Value to assign |
Definition at line 474 of file Dense_seg_.hpp.
References CDense_seg_Base::m_Numseg, CDense_seg_Base::m_set_State, and value.
Referenced by CAlignmentAssistant::AdjustAlign(), CContigAssembly::BandedGlobalAlignment(), BOOST_AUTO_TEST_CASE(), CAlnMap::CreateAlignFromRange(), CreateAlignSetFromAnchoredAln(), CreateAlignSetFromPairwiseAln(), CAlnVec::CreateConsensus(), CreateDensegFromAnchoredAln(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CSeq_align::CreateDensegFromDisc(), CreateDensegFromPairwiseAln(), CSeq_align::CreateDensegFromStdseg(), CAlignCleanup::CreatePairwiseFromMultiple(), CPslData::ExportToSeqAlign(), CDense_seg::ExtractRows(), CDense_seg::ExtractSlice(), CDense_seg::FillUnaligned(), CFastaAlignmentBuilder::GetCompletedAlignment(), CBamAlignIterator::GetMatchAlign(), CCSraAlignIterator::GetMatchAlign(), CAlnReader::GetSeqAlign(), ImproveAlignment(), CUpdateSeq_Input::s_Align2IdenticalSeq(), s_CompressDiscToDenseq(), s_CreateDenseg(), s_CutDensegSegment(), s_ExonToDenseg(), TestCircularTopology(), TestDoNotExtendOverGap(), TestDoNotFuseAbuttingIntervals(), TestExtendOverGap(), TestFuseAbuttingIntervals(), TestPartialWhenCutLastInterval(), TestPartialWhenCutLastIntervalDoNotExtend(), TestPartialWhenCutStart(), TestPartialWhenCutStartDoNotExtend(), TestPartialWhenCutStop(), TestPartialWhenCutStopDoNotExtend(), CFastaReader::x_AddMultiwayAlignment(), CPssmCddInputTest::x_CreateAlignment(), CAlnMixMerger::x_CreateDenseg(), CPhrap_Contig::x_CreateSeq_align(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CSeq_align_Mapper_Base::x_GetDstDenseg(), CSeq_align_Mapper_Base::x_GetPartialDenseg(), CScore_BlastRatio::x_GetPerfectScore(), CMultiAligner::x_GetSeqalign(), CTreeAlignMerger::x_MakeSeqAlign(), CGFFReader::x_ParseAlignRecord(), CUnorderedSplitter::x_TrimRows(), and CFastaReader::xCreateAlignment().
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Assign a value to Numseg data member.
value | Value to assign |
Definition at line 498 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_Numseg, CPacked_seg_Base::m_set_State, and value.
Referenced by CSeq_align_Mapper_Base::x_GetDstPacked().
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Assign a value to Numseg data member.
value | Value to assign |
Definition at line 507 of file Sparse_align_.hpp.
References CSparse_align_Base::m_Numseg, CSparse_align_Base::m_set_State, and value.
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Assign a value to Numseg data member.
Definition at line 481 of file Dense_seg_.hpp.
References CDense_seg_Base::IsSetNumseg(), CDense_seg_Base::m_Numseg, CDense_seg_Base::m_set_State, and CSerialObject::UnassignedByte().
Referenced by CDense_seg::Compact(), CDense_seg::FromTranscript(), CDense_seg::RemapToLoc(), CDense_seg::RemovePureGapSegs(), and CDense_seg::TrimEndGaps().
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Assign a value to Numseg data member.
Definition at line 505 of file Packed_seg_.hpp.
References CPacked_seg_Base::IsSetNumseg(), CPacked_seg_Base::m_Numseg, CPacked_seg_Base::m_set_State, and CSerialObject::UnassignedByte().
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Assign a value to Numseg data member.
Definition at line 514 of file Sparse_align_.hpp.
References CSparse_align_Base::IsSetNumseg(), CSparse_align_Base::m_Numseg, CSparse_align_Base::m_set_State, and CSerialObject::UnassignedByte().
void CSeq_align_Base::C_Segs::SetPacked | ( | TPacked & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 187 of file Seq_align_.cpp.
References CObject::AddReference(), and value.
CSeq_align_Base::C_Segs::TPacked & CSeq_align_Base::C_Segs::SetPacked | ( | void | ) |
Select the variant.
Definition at line 181 of file Seq_align_.cpp.
References eDoNotResetVariant.
Referenced by CAutogeneratedCleanup::x_BasicCleanupAlignSegs().
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Assign a value to Partial data member.
value | Value to assign |
Definition at line 1094 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Partial, CSpliced_exon_Base::m_set_State, and value.
Referenced by CFeatureGenerator::SImplementation::StitchSmallHoles(), and CSeq_align_Mapper_Base::x_GetDstExon().
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Assign a value to Partial data member.
Definition at line 1101 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::IsSetPartial(), CSpliced_exon_Base::m_Partial, CSpliced_exon_Base::m_set_State, and CSerialObject::UnassignedByte().
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Assign a value to Parts data member.
Definition at line 996 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Parts, and CSpliced_exon_Base::m_set_State.
Referenced by CFeatureGenerator::SImplementation::AdjustAlignment(), AlignModelToSeqalign(), CFeatureGenerator::SImplementation::MaximizeTranslation(), CProSplign::CImplementation::SeekStartStop(), CFeatureGenerator::SImplementation::StitchSmallHoles(), and CSeq_align_Mapper_Base::x_PushExonPart().
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Assign a value to Poly_a data member.
value | Value to assign |
Definition at line 733 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_Poly_a, CSpliced_seg_Base::m_set_State, and value.
Referenced by AlignModelToSeqalign(), CSplignFormatter::AsSeqAlignSet(), and CSeq_align_Mapper_Base::x_GetDstSpliced().
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Assign a value to Poly_a data member.
Definition at line 740 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::IsSetPoly_a(), CSpliced_seg_Base::m_Poly_a, CSpliced_seg_Base::m_set_State, and CSerialObject::UnassignedByte().
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Assign a value to Present data member.
Definition at line 588 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_Present, and CPacked_seg_Base::m_set_State.
Referenced by CSeq_align_Mapper_Base::x_GetDstPacked().
void CSpliced_exon_Base::SetProduct_end | ( | CSpliced_exon_Base::TProduct_end & | value | ) |
Assign a value to Product_end data member.
value | Reference to value. |
Definition at line 79 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Product_end, and value.
Referenced by CFeatureGenerator::SImplementation::AdjustAlignment(), BOOST_AUTO_TEST_CASE(), CFeatureGenerator::SImplementation::MaximizeTranslation(), and CFeatureGenerator::SImplementation::StitchSmallHoles().
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Assign a value to Product_end data member.
Definition at line 739 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Product_end, and CSpliced_exon_Base::ResetProduct_end().
void CSpliced_exon_Base::SetProduct_id | ( | CSpliced_exon_Base::TProduct_id & | value | ) |
Assign a value to Product_id data member.
value | Reference to value. |
Definition at line 89 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Product_id, and value.
Referenced by CAutogeneratedCleanup::x_BasicCleanupSplicedExon().
void CSpliced_seg_Base::SetProduct_id | ( | CSpliced_seg_Base::TProduct_id & | value | ) |
Assign a value to Product_id data member.
value | Reference to value. |
Definition at line 67 of file Spliced_seg_.cpp.
References CSpliced_seg_Base::m_Product_id, and value.
Referenced by AlignModelToSeqalign(), CSplignFormatter::AsSeqAlignSet(), BOOST_AUTO_TEST_CASE(), variation::CreateSplicedSeqAlignFromFeat(), InitSplicedsegFromPairwiseAln(), CAliToSeq_align::MakeSeq_align(), MakeSplicedSeg(), CAutogeneratedCleanup::x_BasicCleanupSplicedSeg(), and CSeq_align_Mapper_Base::x_GetDstSpliced().
CSpliced_exon_Base::TProduct_id & CSpliced_exon_Base::SetProduct_id | ( | void | ) |
Assign a value to Product_id data member.
Definition at line 94 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Product_id.
CSpliced_seg_Base::TProduct_id & CSpliced_seg_Base::SetProduct_id | ( | void | ) |
Assign a value to Product_id data member.
Definition at line 72 of file Spliced_seg_.cpp.
References CSpliced_seg_Base::m_Product_id.
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Select the variant and set its data.
value | Variant data. |
Definition at line 451 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::e_Product_ins, eDoNotResetVariant, CSpliced_exon_chunk_Base::m_Product_ins, CSpliced_exon_chunk_Base::Select(), and value.
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Select the variant.
Definition at line 444 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::e_Product_ins, eDoNotResetVariant, CSpliced_exon_chunk_Base::m_Product_ins, and CSpliced_exon_chunk_Base::Select().
Referenced by CFeatureGenerator::SImplementation::MaximizeTranslation(), and SetPartLength().
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Assign a value to Product_length data member.
value | Value to assign |
Definition at line 780 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_Product_length, CSpliced_seg_Base::m_set_State, and value.
Referenced by CFeatureGenerator::SImplementation::AdjustAlignment(), AlignModelToSeqalign(), CSplignFormatter::AsSeqAlignSet(), BOOST_AUTO_TEST_CASE(), CAliToSeq_align::MakeSeq_align(), MakeSplicedSeg(), CFeatureGenerator::SImplementation::MaximizeTranslation(), and CSeq_align_Mapper_Base::x_GetDstSpliced().
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Assign a value to Product_length data member.
Definition at line 787 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::IsSetProduct_length(), CSpliced_seg_Base::m_Product_length, CSpliced_seg_Base::m_set_State, and CSerialObject::UnassignedByte().
void CSpliced_exon_Base::SetProduct_start | ( | CSpliced_exon_Base::TProduct_start & | value | ) |
Assign a value to Product_start data member.
value | Reference to value. |
Definition at line 65 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Product_start, and value.
Referenced by CFeatureGenerator::SImplementation::AdjustAlignment(), BOOST_AUTO_TEST_CASE(), CFeatureGenerator::SImplementation::MaximizeTranslation(), and CFeatureGenerator::SImplementation::StitchSmallHoles().
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Assign a value to Product_start data member.
Definition at line 709 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Product_start, and CSpliced_exon_Base::ResetProduct_start().
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Assign a value to Product_strand data member.
value | Value to assign |
Definition at line 912 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::m_Product_strand, CSpliced_exon_Base::m_set_State, and value.
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Assign a value to Product_strand data member.
value | Value to assign |
Definition at line 567 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_Product_strand, CSpliced_seg_Base::m_set_State, and value.
Referenced by AlignModelToSeqalign(), CSplignFormatter::AsSeqAlignSet(), variation::CreateSplicedSeqAlignFromFeat(), and CSeq_align_Mapper_Base::x_GetDstSpliced().
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Assign a value to Product_strand data member.
Definition at line 919 of file Spliced_exon_.hpp.
References CSpliced_exon_Base::IsSetProduct_strand(), CSpliced_exon_Base::m_Product_strand, CSpliced_exon_Base::m_set_State, and CSerialObject::UnassignedByte().
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Assign a value to Product_strand data member.
Definition at line 574 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::IsSetProduct_strand(), CSpliced_seg_Base::m_Product_strand, CSpliced_seg_Base::m_set_State, and CSerialObject::UnassignedByte().
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Assign a value to Product_type data member.
value | Value to assign |
Definition at line 661 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::m_Product_type, CSpliced_seg_Base::m_set_State, and value.
Referenced by AlignModelToSeqalign(), CSplignFormatter::AsSeqAlignSet(), BOOST_AUTO_TEST_CASE(), variation::CreateSplicedSeqAlignFromFeat(), InitSplicedsegFromPairwiseAln(), CAliToSeq_align::MakeSeq_align(), MakeSplicedSeg(), CSeq_align_Mapper_Base::x_GetDstExon(), and CGff2Reader::xUpdateSplicedSegment().
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Assign a value to Product_type data member.
Definition at line 668 of file Spliced_seg_.hpp.
References CSpliced_seg_Base::IsSetProduct_type(), CSpliced_seg_Base::m_Product_type, CSpliced_seg_Base::m_set_State, and CSerialObject::UnassignedByte().
void CProduct_pos_Base::SetProtpos | ( | CProduct_pos_Base::TProtpos & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 112 of file Product_pos_.cpp.
References CObject::AddReference(), CProduct_pos_Base::e_Protpos, CProduct_pos_Base::m_choice, CProduct_pos_Base::m_object, CProduct_pos_Base::ResetSelection(), and value.
CProduct_pos_Base::TProtpos & CProduct_pos_Base::SetProtpos | ( | void | ) |
Select the variant.
Definition at line 106 of file Product_pos_.cpp.
References CProduct_pos_Base::e_Protpos, eDoNotResetVariant, CProduct_pos_Base::m_object, and CProduct_pos_Base::Select().
Referenced by NucPosToProtPos(), and NultriposToProduct_pos().
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Select the variant and set its data.
value | Variant data. |
Definition at line 398 of file Score_.hpp.
References eDoNotResetVariant, and value.
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Select the variant.
Definition at line 391 of file Score_.hpp.
References eDoNotResetVariant.
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Assign a value to Row_scores data member.
Definition at line 340 of file Sparse_seg_.hpp.
References CSparse_seg_Base::m_Row_scores, and CSparse_seg_Base::m_set_State.
Referenced by CSeq_align_Mapper_Base::x_GetDstSparse().
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Assign a value to Rows data member.
Definition at line 315 of file Sparse_seg_.hpp.
References CSparse_seg_Base::m_Rows, and CSparse_seg_Base::m_set_State.
Referenced by CAutogeneratedCleanup::x_BasicCleaupSparseSeg(), and CSeq_align_Mapper_Base::x_GetDstSparse().
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Assign a value to Score data member.
Definition at line 902 of file Seq_align_.hpp.
References CSeq_align_Base::m_Score, and CSeq_align_Base::m_set_State.
Referenced by CScoreBuilderBase::AddSplignScores(), CNWFormatter::AsSeqAlign(), CFeatureGenerator::SImplementation::ClearScores(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CSeq_align::CreateDensegFromDisc(), CSeq_align::CreateDensegFromStdseg(), CSeq_align_Mapper_Base::GetDstAlign(), CDisplaySeqalign::PrepareBlastUngappedSeqalign(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx2(), CBlast_SAM_Formatter::Print(), CSeq_align::ResetNamedScore(), s_AddScoresToSeqAlign(), s_CleanSeqAlign(), s_GetUseThisGiEntries(), CClippedScorer::ScoreAlignments(), sInheritScores(), CAlignCompare::SAlignment::Slice(), sPrepareSeqAlign(), CReadBlastApp::StoreBlast(), CSeqAlignFilter::x_AddUseGiEntryInSeqalign(), CAppHitFilter::x_DumpOutput(), CUnorderedSplitter::x_FixAlignment(), CCIGAR_Formatter::x_FormatAlignmentRows(), CGff2Reader::x_MergeAlignments(), CGFFReader::x_ParseAlignRecord(), CSeqAlignFilter::x_RemoveExtraGis(), and CSeq_align::x_SetNamedScore().
void CSpliced_exon_Base::SetScores | ( | CSpliced_exon_Base::TScores & | value | ) |
Assign a value to Scores data member.
value | Reference to value. |
Definition at line 129 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Scores, and value.
Referenced by CFeatureGenerator::SImplementation::RecalculateExonIdty().
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Assign a value to Scores data member.
Definition at line 538 of file Dense_diag_.hpp.
References CDense_diag_Base::m_Scores, and CDense_diag_Base::m_set_State.
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Assign a value to Scores data member.
Definition at line 611 of file Dense_seg_.hpp.
References CDense_seg_Base::m_Scores, and CDense_seg_Base::m_set_State.
Referenced by CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CPslData::ExportToSeqAlign(), s_ExonToDenseg(), CCleanupAlignmentsJob::x_CreateProjectItems(), and CSeq_align_Mapper_Base::x_GetDstDenseg().
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Assign a value to Scores data member.
Definition at line 663 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_Scores, and CPacked_seg_Base::m_set_State.
Referenced by CSeq_align_Mapper_Base::x_GetDstPacked().
CSpliced_exon_Base::TScores & CSpliced_exon_Base::SetScores | ( | void | ) |
Assign a value to Scores data member.
Definition at line 134 of file Spliced_exon_.cpp.
References CSpliced_exon_Base::m_Scores.
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Assign a value to Scores data member.
Definition at line 388 of file Std_seg_.hpp.
References CStd_seg_Base::m_Scores, and CStd_seg_Base::m_set_State.
void CSparse_align_Base::SetSecond_id | ( | CSparse_align_Base::TSecond_id & | value | ) |
Assign a value to Second_id data member.
value | Reference to value. |
Definition at line 75 of file Sparse_align_.cpp.
References CSparse_align_Base::m_Second_id, and value.
Referenced by CAutogeneratedCleanup::x_BasicCleanupSparseAlign().
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Assign a value to Second_id data member.
Definition at line 470 of file Sparse_align_.hpp.
References CSparse_align_Base::m_Second_id, and CSparse_align_Base::ResetSecond_id().
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Assign a value to Second_starts data member.
Definition at line 569 of file Sparse_align_.hpp.
References CSparse_align_Base::m_Second_starts, and CSparse_align_Base::m_set_State.
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Assign a value to Second_strands data member.
Definition at line 619 of file Sparse_align_.hpp.
References CSparse_align_Base::m_Second_strands, and CSparse_align_Base::m_set_State.
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Assign a value to Seg_scores data member.
Definition at line 644 of file Sparse_align_.hpp.
References CSparse_align_Base::m_Seg_scores, and CSparse_align_Base::m_set_State.
void CSeq_align_Base::SetSegs | ( | CSeq_align_Base::TSegs & | value | ) |
Assign a value to Segs data member.
value | Reference to value. |
Definition at line 310 of file Seq_align_.cpp.
References CSeq_align_Base::m_Segs, and value.
Referenced by CAlignmentAssistant::AdjustAlign(), CFeatureGenerator::SImplementation::AdjustAlignment(), CContigAssembly::Align(), AlignModelToSeqalign(), CEditSelectedGaps::apply_impl(), CSpliced_seg::AsDiscSeg(), CNWFormatter::AsSeqAlign(), CSplignFormatter::AsSeqAlignSet(), CCompartmentAccessor< THit >::AsSeqAlignSet(), BLASTUngappedHspListToSeqAlign(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildGoodAlign(), BuildGoodEcoSetWithAlign(), CSeqAnnotFromFasta::BuildMasterSlaveSeqAlign(), BuildSetAlign(), BuildSetDendiagAlign(), ChangeSeqIdInSeqAlign(), CFeatureGenerator::SImplementation::ClearScores(), CUnorderedSplitter::CombineAlignments(), Convert_Dense_seg_Seq_align(), CFeatureGenerator::ConvertLocToAnnot(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CAlnMap::CreateAlignFromRange(), CreateAlignSetFromAnchoredAln(), CreateAlignSetFromPairwiseAln(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CSeq_align::CreateDensegFromDisc(), CSeq_align::CreateDensegFromStdseg(), CAlignCleanup::CreatePairwiseFromMultiple(), CreatePairwiseSeqAlignFromMultipleRow(), CreateSeqAlignFromAnchoredAln(), CreateSeqAlignFromEachPairwiseAln(), CreateSeqAlignFromPairwiseAln(), variation::CreateSplicedSeqAlignFromFeat(), CSeq_align::CreateTranslatedDensegFromNADenseg(), Denseg2DenseDiagList(), CPslData::ExportToSeqAlign(), CSeqAlignFilter::FilterByGiList(), CSeqAlignFilter::FilterByGiListFromFile(), CVecscreenRun::CFormatter::FormatResults(), fta_parse_tpa_tsa_block(), CScoreBuilder::GetBlastScoreSpliced(), CFarPointerSeq::GetCommand(), CFastaAlignmentBuilder::GetCompletedAlignment(), CCreateSeqHistForTpa::GetCreateSeqHistFromTpaCommand(), GetDDSetFromSeqAlign(), CBamAlignIterator::GetMatchAlign(), CCSraAlignIterator::GetMatchAlign(), GetPendingSeqId(), CPhyTreeCalc::GetSeqAlign(), ImproveAlignment(), JoinCompartment(), MakeCompartment(), CAliToSeq_align::MakeSeq_align(), CAlignModel::MakeSeqAlign(), CFeatureGenerator::SImplementation::MaximizeTranslation(), CRemoveSeqFromAlignDlg::ModifyAlign(), CDUpdater::modifySeqAlignSeqEntry(), CAlignmentAssistant::OnRemoveSeqFromAlign(), CAlignmentAssistant::OnReverseStrand(), SCigarAlignment::operator()(), CDUpdater::pickBioseq(), CDisplaySeqalign::PrepareBlastUngappedSeqalign(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx2(), CBlast_SAM_Formatter::Print(), CSAM_Formatter::Print(), CAlnAsnReader::Read(), CFeatureGenerator::SImplementation::RecalculateScores(), CTestCompartApplication::Run(), CUpdateSeq_Input::s_Align2IdenticalSeq(), s_BlastHSP2SeqAlign(), s_CleanSeqAlign(), s_CreateSeqAlign(), s_CutDensegSegment(), s_DivvyUpAlignments_ProcessAnnot_Dendiag(), s_DivvyUpAlignments_ProcessAnnot_Denseg(), s_GetIndels(), s_GetJoinedAlignment(), s_OOFBlastHSP2SeqAlign(), CMacroFunction_RemoveSegGaps::s_RemoveSegGaps(), s_RunBlast2NWSeq(), s_SeqAlignSetToXMLHits(), s_SetBlastXMlHitList(), s_SplicedToDisc(), s_SplitAlignVectorBySubjects(), s_UpdateSubjectInSeqalign(), SCompartmentData::SCompartmentData(), CClippedScorer::ScoreAlignments(), CProSplign::CImplementation::SeekStartStop(), CAlignCompare::SAlignment::Slice(), sPrepareSeqAlign(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CReadBlastApp::StoreBlast(), TestCircularTopology(), TestDoNotExtendOverGap(), TestDoNotFuseAbuttingIntervals(), TestExtendOverGap(), TestFeatInsideGap(), TestFuseAbuttingIntervals(), TestPartialWhenCutLastInterval(), TestPartialWhenCutLastIntervalDoNotExtend(), TestPartialWhenCutStart(), TestPartialWhenCutStartDoNotExtend(), TestPartialWhenCutStop(), TestPartialWhenCutStopDoNotExtend(), BlockModel::toSeqAlign(), CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript(), CFeatureGenerator::SImplementation::TrimHolesToCodons(), TrimSeqAlign(), CDUpdater::update(), CFastaReader::x_AddMultiwayAlignment(), CVectorTrimPanel::x_AdjustDensegAlignment(), CReportTrim::x_AdjustDensegAlignment(), CAutogeneratedCleanup::x_BasicCleanupSeqAlign(), CSeq_align_Mapper_Base::x_ConvToDstDisc(), CPssmCddInputTest::x_CreateAlignment(), CAlnMixMerger::x_CreateDenseg(), CInversionMergeAligner::x_CreateDiscAlignment(), CCleanupAlignmentsJob::x_CreateProjectItems(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CPhrap_Contig::x_CreateSeq_align(), CMagicBlast::x_CreateSeqAlignSet(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CAppHitFilter::x_DumpOutput(), COligoSpecificityCheck::x_FillGlobalAlignInfo(), CUnorderedSplitter::x_FixAlignment(), CSeq_align_Mapper_Base::x_GetDstDendiag(), CSeq_align_Mapper_Base::x_GetDstDenseg(), CSeq_align_Mapper_Base::x_GetDstDisc(), CSeq_align_Mapper_Base::x_GetDstPacked(), CSeq_align_Mapper_Base::x_GetDstSparse(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CSeq_align_Mapper_Base::x_GetDstStd(), CRawSeqToDeltaSeqByLoc::x_GetNewAlign(), CSequenceUpdater::x_GetNewAlign_Replace(), CSeq_align_Mapper_Base::x_GetPartialDenseg(), CScore_BlastRatio::x_GetPerfectScore(), CMultiAligner::x_GetSeqalign(), CUnorderedSplitter::x_MakeAlignmentPairUnique(), CTreeAlignMerger::x_MakeSeqAlign(), CGff2Reader::x_MergeAlignments(), CInversionMergeAligner::x_MergeSeqAlignSet(), CMergeAligner::x_MergeSeqAlignSet(), CGFFReader::x_ParseAlignRecord(), CIdMapperTestApp::x_RecurseMapSeqAligns(), CInstancedAligner::x_RunAligner(), CSeqAlignFilter::x_UpdateGiInSeqalign(), CModifySeqId::x_UpdateSeqAlign(), CGff2Reader::xAlignmentSetDenseg(), CGff2Reader::xAlignmentSetSpliced_seg(), CFastaReader::xCreateAlignment(), and CGff2Reader::xUpdateSplicedAlignment().
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Assign a value to Segs data member.
Definition at line 930 of file Seq_align_.hpp.
References CSeq_align_Base::m_Segs, and CSeq_align_Base::ResetSegs().
Referenced by CSeq_align::OffsetRow(), CSeq_align::RemapToLoc(), CSeq_align::Reverse(), s_GetIndels(), and CSeq_align::SwapRows().
void CSeq_align_Base::C_Segs::SetSparse | ( | TSparse & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 253 of file Seq_align_.cpp.
References CObject::AddReference(), and value.
CSeq_align_Base::C_Segs::TSparse & CSeq_align_Base::C_Segs::SetSparse | ( | void | ) |
Select the variant.
Definition at line 247 of file Seq_align_.cpp.
References eDoNotResetVariant.
Referenced by CAutogeneratedCleanup::x_BasicCleanupAlignSegs().
void CSeq_align_Base::C_Segs::SetSpliced | ( | TSpliced & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 231 of file Seq_align_.cpp.
References CObject::AddReference(), and value.
CSeq_align_Base::C_Segs::TSpliced & CSeq_align_Base::C_Segs::SetSpliced | ( | void | ) |
Select the variant.
Definition at line 225 of file Seq_align_.cpp.
References eDoNotResetVariant.
Referenced by CAutogeneratedCleanup::x_BasicCleanupAlignSegs(), and CGff2Reader::xAlignmentSetSpliced_seg().
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Select the variant and set its data.
value | Variant data. |
Definition at line 277 of file Spliced_seg_modifier_.hpp.
References CSpliced_seg_modifier_Base::e_Start_codon_found, eDoNotResetVariant, CSpliced_seg_modifier_Base::m_Start_codon_found, CSpliced_seg_modifier_Base::Select(), and value.
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Select the variant.
Definition at line 270 of file Spliced_seg_modifier_.hpp.
References CSpliced_seg_modifier_Base::e_Start_codon_found, eDoNotResetVariant, CSpliced_seg_modifier_Base::m_Start_codon_found, and CSpliced_seg_modifier_Base::Select().
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Assign a value to Starts data member.
Definition at line 441 of file Dense_diag_.hpp.
References CDense_diag_Base::m_set_State, and CDense_diag_Base::m_Starts.
Referenced by CreateDense_diagFromAnchoredAln(), CreatePairwiseSeqAlignFromMultipleRow(), and CDense_diag::OffsetRow().
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Assign a value to Starts data member.
Definition at line 536 of file Dense_seg_.hpp.
References CDense_seg_Base::m_set_State, and CDense_seg_Base::m_Starts.
Referenced by CFastaAlignmentBuilder::AddData(), CAlignmentAssistant::AdjustAlign(), CContigAssembly::BandedGlobalAlignment(), BOOST_AUTO_TEST_CASE(), CDense_seg::Compact(), CAlnMap::CreateAlignFromRange(), CreateAlignSetFromAnchoredAln(), CreateAlignSetFromPairwiseAln(), CAlnVec::CreateConsensus(), CreateDensegFromAnchoredAln(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CSeq_align::CreateDensegFromDisc(), CreateDensegFromPairwiseAln(), CSeq_align::CreateDensegFromStdseg(), CAlignCleanup::CreatePairwiseFromMultiple(), CPslData::ExportToSeqAlign(), CDense_seg::ExtractRows(), CDense_seg::ExtractSlice(), CDense_seg::FillUnaligned(), CDense_seg::FromTranscript(), CBamAlignIterator::GetMatchAlign(), CCSraAlignIterator::GetMatchAlign(), CAlnReader::GetSeqAlign(), ImproveAlignment(), CDense_seg::OffsetRow(), CAlignmentAssistant::OnReverseStrand(), CDense_seg::OrderAdjacentGaps(), CDense_seg::CReserveHook::PreReadClassMember(), CDenseSegReserveStartsHook::ReadClassMember(), CDense_seg::RemapToLoc(), CDense_seg::RemovePureGapSegs(), CDense_seg::Reverse(), ReverseAlignmentStrand(), CFarPointerSeq::ReverseRow(), CUpdateSeq_Input::s_Align2IdenticalSeq(), s_CompressDiscToDenseq(), s_CreateDenseg(), s_CutDensegSegment(), s_ExonToDenseg(), CDense_seg::SwapRows(), TestCircularTopology(), TestDoNotExtendOverGap(), TestDoNotFuseAbuttingIntervals(), TestExtendOverGap(), TestFuseAbuttingIntervals(), TestPartialWhenCutLastInterval(), TestPartialWhenCutLastIntervalDoNotExtend(), TestPartialWhenCutStart(), TestPartialWhenCutStartDoNotExtend(), TestPartialWhenCutStop(), TestPartialWhenCutStopDoNotExtend(), CDense_seg::TrimEndGaps(), CFastaReader::x_AddMultiwayAlignment(), CPssmCddInputTest::x_CreateAlignment(), CAlnMixMerger::x_CreateDenseg(), CInversionMergeAligner::x_CreateDiscAlignment(), CPhrap_Contig::x_CreateSeq_align(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CSeq_align_Mapper_Base::x_GetDstDenseg(), CSeq_align_Mapper_Base::x_GetPartialDenseg(), CScore_BlastRatio::x_GetPerfectScore(), CMultiAligner::x_GetSeqalign(), CTreeAlignMerger::x_MakeSeqAlign(), CGFFReader::x_ParseAlignRecord(), CUpdateAlign::x_RemoveIDsFromAlign(), CUnorderedSplitter::x_TrimRows(), and CFastaReader::xCreateAlignment().
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Assign a value to Starts data member.
Definition at line 560 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_set_State, and CPacked_seg_Base::m_Starts.
Referenced by CSeq_align_Mapper_Base::x_GetDstPacked().
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Select the variant.
Definition at line 759 of file Seq_align_.hpp.
References eDoNotResetVariant.
Referenced by CAutogeneratedCleanup::x_BasicCleanupAlignSegs().
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Select the variant and set its data.
value | Variant data. |
Definition at line 304 of file Spliced_seg_modifier_.hpp.
References CSpliced_seg_modifier_Base::e_Stop_codon_found, eDoNotResetVariant, CSpliced_seg_modifier_Base::m_Stop_codon_found, CSpliced_seg_modifier_Base::Select(), and value.
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Select the variant.
Definition at line 297 of file Spliced_seg_modifier_.hpp.
References CSpliced_seg_modifier_Base::e_Stop_codon_found, eDoNotResetVariant, CSpliced_seg_modifier_Base::m_Stop_codon_found, and CSpliced_seg_modifier_Base::Select().
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Assign a value to Strands data member.
Definition at line 513 of file Dense_diag_.hpp.
References CDense_diag_Base::m_set_State, and CDense_diag_Base::m_Strands.
Referenced by CreateDense_diagFromAnchoredAln().
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Assign a value to Strands data member.
Definition at line 586 of file Dense_seg_.hpp.
References CDense_seg_Base::m_set_State, and CDense_seg_Base::m_Strands.
Referenced by CAlignmentAssistant::AdjustAlign(), CContigAssembly::BandedGlobalAlignment(), CDense_seg::Compact(), CAlnMap::CreateAlignFromRange(), CreateAlignSetFromAnchoredAln(), CreateAlignSetFromPairwiseAln(), CAlnVec::CreateConsensus(), CreateDensegFromAnchoredAln(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CSeq_align::CreateDensegFromDisc(), CreateDensegFromPairwiseAln(), CSeq_align::CreateDensegFromStdseg(), CAlignCleanup::CreatePairwiseFromMultiple(), CPslData::ExportToSeqAlign(), CDense_seg::ExtractRows(), CDense_seg::ExtractSlice(), CDense_seg::FillUnaligned(), CDense_seg::FromTranscript(), CBamAlignIterator::GetMatchAlign(), CCSraAlignIterator::GetMatchAlign(), CAlignmentAssistant::OnReverseStrand(), CDense_seg::OrderAdjacentGaps(), CDense_seg::CReserveHook::PreReadClassMember(), CDenseSegReserveStrandsHook::ReadClassMember(), CDense_seg::RemapToLoc(), CDense_seg::RemovePureGapSegs(), CDense_seg::Reverse(), ReverseAlignmentStrand(), CFarPointerSeq::ReverseRow(), s_CompressDiscToDenseq(), s_CreateDenseg(), s_CutDensegSegment(), s_ExonToDenseg(), CDense_seg::SwapRows(), CDense_seg::TrimEndGaps(), CAlnMixMerger::x_CreateDenseg(), CPhrap_Contig::x_CreateSeq_align(), CSeq_align::x_CreateSubsegAlignment(), CVectorTrimPanel::x_CutDensegSegment(), CReportTrim::x_CutDensegSegment(), CSeq_align_Mapper_Base::x_GetDstDenseg(), CSeq_align_Mapper_Base::x_GetPartialDenseg(), CTreeAlignMerger::x_MakeSeqAlign(), CInversionMergeAligner::x_MergeSeqAlignSet(), CMergeAligner::x_MergeSeqAlignSet(), CGFFReader::x_ParseAlignRecord(), CUpdateAlign::x_RemoveIDsFromAlign(), CInstancedAligner::x_RunCleanup(), CUnorderedSplitter::x_TrimRows(), and CFastaReader::xCreateAlignment().
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Assign a value to Strands data member.
Definition at line 638 of file Packed_seg_.hpp.
References CPacked_seg_Base::m_set_State, and CPacked_seg_Base::m_Strands.
Referenced by CSeq_align_Mapper_Base::x_GetDstPacked().
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Assign a value to Type data member.
value | Value to assign |
Definition at line 818 of file Seq_align_.hpp.
References CSeq_align_Base::m_set_State, CSeq_align_Base::m_Type, and value.
Referenced by CContigAssembly::Align(), AlignModelToSeqalign(), CSpliced_seg::AsDiscSeg(), CNWFormatter::AsSeqAlign(), CSplignFormatter::AsSeqAlignSet(), CCompartmentAccessor< THit >::AsSeqAlignSet(), BLASTUngappedHspListToSeqAlign(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildGoodAlign(), BuildGoodEcoSetWithAlign(), CSeqAnnotFromFasta::BuildMasterSlaveSeqAlign(), BuildSetAlign(), BuildSetDendiagAlign(), CUnorderedSplitter::CombineAlignments(), Convert_Dense_seg_Seq_align(), CFeatureGenerator::ConvertLocToAnnot(), CAlnMap::CreateAlignFromRange(), CreateAlignSetFromAnchoredAln(), CreateAlignSetFromPairwiseAln(), CAlignFormatUtil::CreateDensegFromDendiag(), CreateDensegFromDendiag(), CSeq_align::CreateDensegFromDisc(), CSeq_align::CreateDensegFromStdseg(), CAlignCleanup::CreatePairwiseFromMultiple(), CreatePairwiseSeqAlignFromMultipleRow(), CreateSeqAlignFromAnchoredAln(), CreateSeqAlignFromEachPairwiseAln(), CreateSeqAlignFromPairwiseAln(), variation::CreateSplicedSeqAlignFromFeat(), CSeq_align::CreateTranslatedDensegFromNADenseg(), CPslData::ExportToSeqAlign(), CProSplign::CImplementation::FindGlobalAlignment_stage2(), fta_parse_tpa_tsa_block(), CFastaAlignmentBuilder::GetCompletedAlignment(), CSeq_align_Mapper_Base::GetDstAlign(), CBamAlignIterator::GetMatchAlign(), CCSraAlignIterator::GetMatchAlign(), CPhyTreeCalc::GetSeqAlign(), JoinCompartment(), MakeCompartment(), CAliToSeq_align::MakeSeq_align(), SCigarAlignment::operator()(), CDisplaySeqalign::PrepareBlastUngappedSeqalign(), CSAM_Formatter::Print(), CAlnAsnReader::Read(), CProSplign::RefineAlignment(), CUpdateSeq_Input::s_Align2IdenticalSeq(), s_BlastHSP2SeqAlign(), s_CreateSeqAlign(), s_GetIndels(), s_GetJoinedAlignment(), s_OOFBlastHSP2SeqAlign(), s_SplicedToDisc(), s_SplitAlignVectorBySubjects(), CAlignCompare::SAlignment::Slice(), CReadBlastApp::StoreBlast(), TestFeatInsideGap(), BlockModel::toSeqAlign(), CFastaReader::x_AddMultiwayAlignment(), CGff2Reader::x_CreateAlignment(), CAlnMixMerger::x_CreateDenseg(), CInversionMergeAligner::x_CreateDiscAlignment(), CCleanupAlignmentsJob::x_CreateProjectItems(), CPhrap_Contig::x_CreateSeq_align(), CMagicBlast::x_CreateSeqAlignSet(), CSeq_align::x_CreateSubsegAlignment(), CAppHitFilter::x_DumpOutput(), COligoSpecificityCheck::x_FillGlobalAlignInfo(), CSeq_align_Mapper_Base::x_GetPartialDenseg(), CMultiAligner::x_GetSeqalign(), CTreeAlignMerger::x_MakeSeqAlign(), CGff2Reader::x_MergeAlignments(), CGFFReader::x_ParseAlignRecord(), CInstancedAligner::x_RunAligner(), CGff2Reader::x_UpdateAnnotAlignment(), CFastaReader::xCreateAlignment(), and CGff2Reader::xUpdateSplicedAlignment().
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Assign a value to Type data member.
Definition at line 825 of file Seq_align_.hpp.
References CSeq_align_Base::IsSetType(), CSeq_align_Base::m_set_State, CSeq_align_Base::m_Type, and CSerialObject::UnassignedByte().
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Assign a value to Value data member.
Definition at line 474 of file Score_.hpp.
References CScore_Base::m_set_State, and CScore_Base::m_Value.
void CProduct_pos_Base::ThrowInvalidSelection | ( | E_Choice | index | ) | const |
Throw 'InvalidSelection' exception.
index | Expected selection. |
Definition at line 95 of file Product_pos_.cpp.
References DIAG_COMPILE_INFO, CProduct_pos_Base::m_choice, and CProduct_pos_Base::sm_SelectionNames.
Referenced by CProduct_pos_Base::CheckSelected().
void CScore_Base::C_Value::ThrowInvalidSelection | ( | E_Choice | index | ) | const |
Throw 'InvalidSelection' exception.
index | Expected selection. |
Definition at line 88 of file Score_.cpp.
References DIAG_COMPILE_INFO.
void CSeq_align_Base::C_Segs::ThrowInvalidSelection | ( | E_Choice | index | ) | const |
Throw 'InvalidSelection' exception.
index | Expected selection. |
Definition at line 148 of file Seq_align_.cpp.
References DIAG_COMPILE_INFO.
void CSpliced_exon_chunk_Base::ThrowInvalidSelection | ( | E_Choice | index | ) | const |
Throw 'InvalidSelection' exception.
index | Expected selection. |
Definition at line 99 of file Spliced_exon_chunk_.cpp.
References DIAG_COMPILE_INFO, CSpliced_exon_chunk_Base::m_choice, and CSpliced_exon_chunk_Base::sm_SelectionNames.
Referenced by CSpliced_exon_chunk_Base::CheckSelected().
void CSpliced_seg_modifier_Base::ThrowInvalidSelection | ( | E_Choice | index | ) | const |
Throw 'InvalidSelection' exception.
index | Expected selection. |
Definition at line 87 of file Spliced_seg_modifier_.cpp.
References DIAG_COMPILE_INFO, CSpliced_seg_modifier_Base::m_choice, and CSpliced_seg_modifier_Base::sm_SelectionNames.
Referenced by CSpliced_seg_modifier_Base::CheckSelected().
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Which variant is currently selected.
Definition at line 231 of file Product_pos_.hpp.
References CProduct_pos_Base::m_choice.
Referenced by CProduct_pos::AsSeqPos(), s_Fingerprint_Product_pos(), and s_ProductLength().
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Which variant is currently selected.
Definition at line 349 of file Score_.hpp.
References CScore_Base::C_Value::m_choice.
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Which variant is currently selected.
Definition at line 691 of file Seq_align_.hpp.
References CSeq_align_Base::C_Segs::m_choice.
Referenced by CSeqsRange::Add(), BOOST_AUTO_TEST_CASE(), CScoreBuilderBase::ComputeScore(), CScore_InternalUnaligned::Get(), CRemoveSeqFromAlignDlg::GetAlignLabel(), CScoreBuilder::GetBlastScore(), CSeq_align_Mapper_Base::GetDstAlign(), CAlignmentAssistant::GetFeatures(), CPaintAlignment::GetSegments(), CAlignFormatUtil::GetSeqAlignSetCalcParamsFromASN(), CAlnContainer::insert(), CRemoveSeqFromAlignDlg::ModifyAlign(), CValidError_imp::PostErr(), CDisplaySeqalign::PrepareBlastUngappedSeqalign(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx2(), PrintSAM(), CRemoveSeqFromAlignDlg::RemoveIdLabel(), CAlignmentAssistant::ReportUnresolvedBioseqs(), s_AlignToSeqRanges(), s_CountSegments(), s_Fingerprint_Seq_align(), s_GetAlignmentContent(), s_GetAlignmentLength(), s_GetAlignmentSpans_Exon(), s_GetAlignmentSpans_Interval(), s_GetAlignmentTooltip(), s_GetAlignmentType(), s_GetAlnScores(), s_GetCigarString(), s_GetCountIdentityMismatch(), s_GetGapCount(), s_GetIndels(), s_Render_PairwiseAlign(), s_ScoreAlignments(), s_Seq_align_Seq_loc(), SeqAlignConvert(), CReportEntry::SetAlignment(), sPrepareSeqAlign(), CReportTrim::TrimAlignments(), TrimSequenceAndAnnotation(), CValidError_align::ValidateSeqAlign(), CAlnWriter::WriteAlign(), CPslWriter::WriteAlign(), CAdvancedAlignCleanup::x_AddStandardAlignmentScores(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignFillerBlocks(), CQuerySet::x_AlreadyContains(), CAutogeneratedCleanup::x_BasicCleanupAlignSegs(), CInversionMergeAligner::x_CreateDiscAlignment(), CHitMatrixDataSource::x_CreateHit(), CCIGAR_Formatter::x_FormatAlignmentRows(), CHitMatrixDataSource::x_GetAlignedSeqIds(), CDisplaySeqalign::x_GetAlnVecForSeqalign(), CValidError_align::x_GetIds(), CHitMatrixDataSource::x_GetSeqAlignIds(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitializeAlign(), CAnnotObject_Info::x_ProcessAlign(), CHitMatrixDataSource::x_TestAndSelectAlign(), CVectorTrimPanel::x_TrimAlignments(), and CGff3Writer::xWriteAlign().
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Which variant is currently selected.
Definition at line 321 of file Spliced_exon_chunk_.hpp.
References CSpliced_exon_chunk_Base::m_choice.
Referenced by CScoreBuilderBase::AddSplignScores(), BOOST_AUTO_TEST_CASE(), ChunkSize(), ConvertSplicedToPairwiseAln(), CScore_IndelToSplice::Get(), CSpliced_exon::GetRowSeq_insertions(), CSeq_align_Mapper_Base::InitExon(), CFeatureGenerator::SImplementation::MaximizeTranslation(), CSplign::s_ComputeStats(), s_Fingerprint_Spliced_exon_chunk(), s_GetCountIdentityMismatch(), sExonChunkAppendStats(), CSeq_loc_Mapper_Base::sx_GetExonPartLength(), CSpliced_seg::Validate(), CProductStringBuilder::x_AddExonPart(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CGff3Writer::xAssignAlignmentSplicedGap(), and CGff3FlybaseWriter::xAssignAlignmentSplicedGap().
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Which variant is currently selected.
Definition at line 228 of file Spliced_seg_modifier_.hpp.
References CSpliced_seg_modifier_Base::m_choice.
CSeq_align_Base::C_Segs::~C_Segs | ( | void | ) |
Definition at line 289 of file Seq_align_.cpp.
References CSeq_align_Base::Reset().
CScore_Base::C_Value::~C_Value | ( | void | ) |
Definition at line 114 of file Score_.cpp.
References CScore_Base::Reset().
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Definition at line 109 of file Dense_diag_.cpp.
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Definition at line 117 of file Dense_seg_.cpp.
CPacked_seg::~CPacked_seg | ( | void | ) |
Definition at line 50 of file Packed_seg.cpp.
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Definition at line 125 of file Packed_seg_.cpp.
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Definition at line 142 of file Product_pos_.cpp.
References CProduct_pos_Base::Reset().
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Definition at line 75 of file Prot_pos_.cpp.
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Definition at line 173 of file Score_.cpp.
CScore_set::~CScore_set | ( | void | ) |
Definition at line 50 of file Score_set.cpp.
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Definition at line 74 of file Score_set_.cpp.
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Definition at line 371 of file Seq_align_.cpp.
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Definition at line 74 of file Seq_align_set_.cpp.
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Definition at line 151 of file Sparse_align_.cpp.
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Definition at line 117 of file Sparse_seg_.cpp.
CSparse_seg_ext::~CSparse_seg_ext | ( | void | ) |
Definition at line 50 of file Sparse_seg_ext.cpp.
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Definition at line 73 of file Sparse_seg_ext_.cpp.
CSplice_site::~CSplice_site | ( | void | ) |
Definition at line 50 of file Splice_site.cpp.
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Definition at line 78 of file Splice_site_.cpp.
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Definition at line 234 of file Spliced_exon_.cpp.
CSpliced_exon_chunk::~CSpliced_exon_chunk | ( | void | ) |
Definition at line 50 of file Spliced_exon_chunk.cpp.
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Definition at line 127 of file Spliced_exon_chunk_.cpp.
References CSpliced_exon_chunk_Base::Reset().
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Definition at line 147 of file Spliced_seg_.cpp.
CSpliced_seg_modifier::~CSpliced_seg_modifier | ( | void | ) |
Definition at line 50 of file Spliced_seg_modifier.cpp.
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Definition at line 112 of file Spliced_seg_modifier_.cpp.
References CSpliced_seg_modifier_Base::Reset().
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Definition at line 100 of file Std_seg_.cpp.
union { ... } |
union { ... } |
union { ... } |
union { ... } |
union { ... } |
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Definition at line 672 of file Spliced_exon_.hpp.
Referenced by CSpliced_exon_Base::GetAcceptor_before_exon(), CSpliced_exon_Base::IsSetAcceptor_before_exon(), CSpliced_exon_Base::ResetAcceptor_before_exon(), and CSpliced_exon_Base::SetAcceptor_before_exon().
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Definition at line 187 of file Prot_pos_.hpp.
Referenced by CProt_pos_Base::GetAmin(), CProt_pos_Base::ResetAmin(), and CProt_pos_Base::SetAmin().
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Definition at line 149 of file Splice_site_.hpp.
Referenced by CSplice_site_Base::GetBases(), CSplice_site_Base::ResetBases(), and CSplice_site_Base::SetBases().
Definition at line 676 of file Seq_align_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CSeq_align_Base::GetBounds(), CSeq_align_Base::ResetBounds(), and CSeq_align_Base::SetBounds().
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Definition at line 209 of file Product_pos_.hpp.
Referenced by CProduct_pos_Base::CheckSelected(), CProduct_pos_Base::DoSelect(), CProduct_pos_Base::IsNucpos(), CProduct_pos_Base::IsProtpos(), CProduct_pos_Base::Reset(), CProduct_pos_Base::ResetSelection(), CProduct_pos_Base::SetProtpos(), CProduct_pos_Base::ThrowInvalidSelection(), and CProduct_pos_Base::Which().
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Definition at line 228 of file Score_.hpp.
Referenced by CScore_Base::C_Value::Reset(), and CScore_Base::C_Value::Which().
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Definition at line 383 of file Seq_align_.hpp.
Referenced by CSeq_align_Base::C_Segs::Reset(), and CSeq_align_Base::C_Segs::Which().
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Definition at line 296 of file Spliced_exon_chunk_.hpp.
Referenced by CSpliced_exon_chunk_Base::CheckSelected(), CSpliced_exon_chunk_Base::DoSelect(), CSpliced_exon_chunk_Base::IsDiag(), CSpliced_exon_chunk_Base::IsGenomic_ins(), CSpliced_exon_chunk_Base::IsMatch(), CSpliced_exon_chunk_Base::IsMismatch(), CSpliced_exon_chunk_Base::IsProduct_ins(), CSpliced_exon_chunk_Base::Reset(), CSpliced_exon_chunk_Base::ResetSelection(), CSpliced_exon_chunk_Base::ThrowInvalidSelection(), and CSpliced_exon_chunk_Base::Which().
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Definition at line 206 of file Spliced_seg_modifier_.hpp.
Referenced by CSpliced_seg_modifier_Base::CheckSelected(), CSpliced_seg_modifier_Base::DoSelect(), CSpliced_seg_modifier_Base::IsStart_codon_found(), CSpliced_seg_modifier_Base::IsStop_codon_found(), CSpliced_seg_modifier_Base::Reset(), CSpliced_seg_modifier_Base::ResetSelection(), CSpliced_seg_modifier_Base::ThrowInvalidSelection(), and CSpliced_seg_modifier_Base::Which().
Definition at line 140 of file Score_set_.hpp.
Referenced by CScore_set_Base::Get(), CScore_set_Base::Reset(), and CScore_set_Base::Set().
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Definition at line 141 of file Seq_align_set_.hpp.
Referenced by CSeq_align_set_Base::Get(), CSeq_align_set_Base::Reset(), and CSeq_align_set_Base::Set().
NCBI_NS_NCBI::CUnionBuffer<TDendiag> { ... } ::m_Dendiag |
Definition at line 390 of file Seq_align_.hpp.
NCBI_NS_NCBI::CUnionBuffer<TDendiag> CSeq_align_Base::C_Segs::m_Dendiag |
Definition at line 390 of file Seq_align_.hpp.
TDiag CSpliced_exon_chunk_Base::m_Diag |
Definition at line 305 of file Spliced_exon_chunk_.hpp.
Referenced by CSpliced_exon_chunk_Base::DoSelect(), CSpliced_exon_chunk_Base::GetDiag(), and CSpliced_exon_chunk_Base::SetDiag().
TDiag { ... } ::m_Diag |
Definition at line 305 of file Spliced_exon_chunk_.hpp.
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Definition at line 330 of file Dense_diag_.hpp.
Referenced by CDense_diag_Base::GetDim(), CDense_diag_Base::ResetDim(), and CDense_diag_Base::SetDim().
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Definition at line 377 of file Dense_seg_.hpp.
Referenced by CDense_seg_Base::GetDim(), CDense_seg_Base::ResetDim(), and CDense_seg_Base::SetDim().
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Definition at line 400 of file Packed_seg_.hpp.
Referenced by CPacked_seg_Base::GetDim(), CPacked_seg_Base::ResetDim(), and CPacked_seg_Base::SetDim().
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Definition at line 673 of file Seq_align_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CSeq_align_Base::GetDim(), CSeq_align_Base::ResetDim(), and CSeq_align_Base::SetDim().
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Definition at line 254 of file Std_seg_.hpp.
Referenced by CStd_seg_Base::GetDim(), CStd_seg_Base::ResetDim(), and CStd_seg_Base::SetDim().
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Definition at line 673 of file Spliced_exon_.hpp.
Referenced by CSpliced_exon_Base::GetDonor_after_exon(), CSpliced_exon_Base::IsSetDonor_after_exon(), CSpliced_exon_Base::ResetDonor_after_exon(), and CSpliced_exon_Base::SetDonor_after_exon().
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Definition at line 481 of file Spliced_seg_.hpp.
Referenced by CSpliced_seg_Base::GetExons(), CSpliced_seg_Base::ResetExons(), and CSpliced_seg_Base::SetExons().
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Definition at line 678 of file Seq_align_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CSeq_align_Base::GetExt(), CSeq_align_Base::ResetExt(), and CSeq_align_Base::SetExt().
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Definition at line 263 of file Sparse_seg_.hpp.
Referenced by CSparse_seg_Base::GetExt(), CSparse_seg_Base::ResetExt(), and CSparse_seg_Base::SetExt().
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Definition at line 675 of file Spliced_exon_.hpp.
Referenced by CSpliced_exon_Base::GetExt(), CSpliced_exon_Base::ResetExt(), and CSpliced_exon_Base::SetExt().
Definition at line 399 of file Sparse_align_.hpp.
Referenced by CSparse_align_Base::GetFirst_id(), CSparse_align_Base::IsSetFirst_id(), CSparse_align_Base::ResetFirst_id(), and CSparse_align_Base::SetFirst_id().
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Definition at line 402 of file Sparse_align_.hpp.
Referenced by CSparse_align_Base::GetFirst_starts(), CSparse_align_Base::ResetFirst_starts(), and CSparse_align_Base::SetFirst_starts().
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Definition at line 188 of file Prot_pos_.hpp.
Referenced by CProt_pos_Base::GetFrame(), CProt_pos_Base::ResetFrame(), and CProt_pos_Base::SetFrame().
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Definition at line 665 of file Spliced_exon_.hpp.
Referenced by CSpliced_exon_Base::GetGenomic_end(), CSpliced_exon_Base::ResetGenomic_end(), and CSpliced_exon_Base::SetGenomic_end().
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Definition at line 667 of file Spliced_exon_.hpp.
Referenced by CSpliced_exon_Base::GetGenomic_id(), CSpliced_exon_Base::IsSetGenomic_id(), CSpliced_exon_Base::ResetGenomic_id(), and CSpliced_exon_Base::SetGenomic_id().
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Definition at line 477 of file Spliced_seg_.hpp.
Referenced by CSpliced_seg_Base::GetGenomic_id(), CSpliced_seg_Base::IsSetGenomic_id(), CSpliced_seg_Base::ResetGenomic_id(), and CSpliced_seg_Base::SetGenomic_id().
TGenomic_ins CSpliced_exon_chunk_Base::m_Genomic_ins |
Definition at line 307 of file Spliced_exon_chunk_.hpp.
Referenced by CSpliced_exon_chunk_Base::DoSelect(), CSpliced_exon_chunk_Base::GetGenomic_ins(), and CSpliced_exon_chunk_Base::SetGenomic_ins().
TGenomic_ins { ... } ::m_Genomic_ins |
Definition at line 307 of file Spliced_exon_chunk_.hpp.
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Definition at line 664 of file Spliced_exon_.hpp.
Referenced by CSpliced_exon_Base::GetGenomic_start(), CSpliced_exon_Base::ResetGenomic_start(), and CSpliced_exon_Base::SetGenomic_start().
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Definition at line 669 of file Spliced_exon_.hpp.
Referenced by CSpliced_exon_Base::GetGenomic_strand(), CSpliced_exon_Base::ResetGenomic_strand(), and CSpliced_exon_Base::SetGenomic_strand().
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Definition at line 479 of file Spliced_seg_.hpp.
Referenced by CSpliced_seg_Base::GetGenomic_strand(), CSpliced_seg_Base::ResetGenomic_strand(), and CSpliced_seg_Base::SetGenomic_strand().
Definition at line 335 of file Score_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CScore_Base::GetId(), CScore_Base::IsSetId(), CScore_Base::ResetId(), and CScore_Base::SetId().
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Definition at line 677 of file Seq_align_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CSeq_align_Base::GetId(), CSeq_align_Base::ResetId(), and CSeq_align_Base::SetId().
Definition at line 331 of file Dense_diag_.hpp.
Referenced by CDense_diag_Base::GetIds(), CDense_diag_Base::ResetIds(), and CDense_diag_Base::SetIds().
Definition at line 379 of file Dense_seg_.hpp.
Referenced by CDense_seg_Base::GetIds(), CDense_seg_Base::ResetIds(), and CDense_seg_Base::SetIds().
Definition at line 402 of file Packed_seg_.hpp.
Referenced by CPacked_seg_Base::GetIds(), CPacked_seg_Base::ResetIds(), and CPacked_seg_Base::SetIds().
Definition at line 255 of file Std_seg_.hpp.
Referenced by CStd_seg_Base::GetIds(), CStd_seg_Base::ResetIds(), and CStd_seg_Base::SetIds().
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Definition at line 145 of file Sparse_seg_ext_.hpp.
Referenced by CSparse_seg_ext_Base::GetIndex(), CSparse_seg_ext_Base::ResetIndex(), and CSparse_seg_ext_Base::SetIndex().
TInt CScore_Base::C_Value::m_Int |
Definition at line 236 of file Score_.hpp.
TInt { ... } ::m_Int |
Definition at line 236 of file Score_.hpp.
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Definition at line 333 of file Dense_diag_.hpp.
Referenced by CDense_diag_Base::GetLen(), CDense_diag_Base::ResetLen(), and CDense_diag_Base::SetLen().
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Definition at line 381 of file Dense_seg_.hpp.
Referenced by CDense_seg_Base::GetLens(), CDense_seg_Base::ResetLens(), and CDense_seg_Base::SetLens().
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Definition at line 405 of file Packed_seg_.hpp.
Referenced by CPacked_seg_Base::GetLens(), CPacked_seg_Base::ResetLens(), and CPacked_seg_Base::SetLens().
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Definition at line 404 of file Sparse_align_.hpp.
Referenced by CSparse_align_Base::GetLens(), CSparse_align_Base::ResetLens(), and CSparse_align_Base::SetLens().
Definition at line 256 of file Std_seg_.hpp.
Referenced by CStd_seg_Base::GetLoc(), CStd_seg_Base::ResetLoc(), and CStd_seg_Base::SetLoc().
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Definition at line 260 of file Sparse_seg_.hpp.
Referenced by CSparse_seg_Base::GetMaster_id(), CSparse_seg_Base::IsSetMaster_id(), CSparse_seg_Base::ResetMaster_id(), and CSparse_seg_Base::SetMaster_id().
TMatch CSpliced_exon_chunk_Base::m_Match |
Definition at line 303 of file Spliced_exon_chunk_.hpp.
Referenced by CSpliced_exon_chunk_Base::DoSelect(), CSpliced_exon_chunk_Base::GetMatch(), and CSpliced_exon_chunk_Base::SetMatch().
TMatch { ... } ::m_Match |
Definition at line 303 of file Spliced_exon_chunk_.hpp.
TMismatch CSpliced_exon_chunk_Base::m_Mismatch |
Definition at line 304 of file Spliced_exon_chunk_.hpp.
Referenced by CSpliced_exon_chunk_Base::DoSelect(), CSpliced_exon_chunk_Base::GetMismatch(), and CSpliced_exon_chunk_Base::SetMismatch().
TMismatch { ... } ::m_Mismatch |
Definition at line 304 of file Spliced_exon_chunk_.hpp.
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Definition at line 484 of file Spliced_seg_.hpp.
Referenced by CSpliced_seg_Base::GetModifiers(), CSpliced_seg_Base::ResetModifiers(), and CSpliced_seg_Base::SetModifiers().
TNucpos CProduct_pos_Base::m_Nucpos |
Definition at line 216 of file Product_pos_.hpp.
Referenced by CProduct_pos_Base::DoSelect(), CProduct_pos_Base::GetNucpos(), and CProduct_pos_Base::SetNucpos().
TNucpos { ... } ::m_Nucpos |
Definition at line 216 of file Product_pos_.hpp.
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Definition at line 378 of file Dense_seg_.hpp.
Referenced by CDense_seg_Base::GetNumseg(), CDense_seg_Base::ResetNumseg(), and CDense_seg_Base::SetNumseg().
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Definition at line 401 of file Packed_seg_.hpp.
Referenced by CPacked_seg_Base::GetNumseg(), CPacked_seg_Base::ResetNumseg(), and CPacked_seg_Base::SetNumseg().
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Definition at line 401 of file Sparse_align_.hpp.
Referenced by CSparse_align_Base::GetNumseg(), CSparse_align_Base::ResetNumseg(), and CSparse_align_Base::SetNumseg().
NCBI_NS_NCBI::CSerialObject* CProduct_pos_Base::m_object |
Definition at line 217 of file Product_pos_.hpp.
Referenced by CProduct_pos_Base::DoSelect(), CProduct_pos_Base::GetProtpos(), CProduct_pos_Base::ResetSelection(), and CProduct_pos_Base::SetProtpos().
NCBI_NS_NCBI::CSerialObject* { ... } ::m_object |
Definition at line 217 of file Product_pos_.hpp.
NCBI_NS_NCBI::CSerialObject* CSeq_align_Base::C_Segs::m_object |
Definition at line 392 of file Seq_align_.hpp.
NCBI_NS_NCBI::CSerialObject* { ... } ::m_object |
Definition at line 392 of file Seq_align_.hpp.
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Definition at line 674 of file Spliced_exon_.hpp.
Referenced by CSpliced_exon_Base::GetPartial(), CSpliced_exon_Base::ResetPartial(), and CSpliced_exon_Base::SetPartial().
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Definition at line 670 of file Spliced_exon_.hpp.
Referenced by CSpliced_exon_Base::GetParts(), CSpliced_exon_Base::ResetParts(), and CSpliced_exon_Base::SetParts().
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Definition at line 482 of file Spliced_seg_.hpp.
Referenced by CSpliced_seg_Base::GetPoly_a(), CSpliced_seg_Base::ResetPoly_a(), and CSpliced_seg_Base::SetPoly_a().
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Definition at line 404 of file Packed_seg_.hpp.
Referenced by CPacked_seg_Base::GetPresent(), CPacked_seg_Base::ResetPresent(), and CPacked_seg_Base::SetPresent().
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Definition at line 663 of file Spliced_exon_.hpp.
Referenced by CSpliced_exon_Base::GetProduct_end(), CSpliced_exon_Base::IsSetProduct_end(), CSpliced_exon_Base::ResetProduct_end(), and CSpliced_exon_Base::SetProduct_end().
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Definition at line 666 of file Spliced_exon_.hpp.
Referenced by CSpliced_exon_Base::GetProduct_id(), CSpliced_exon_Base::IsSetProduct_id(), CSpliced_exon_Base::ResetProduct_id(), and CSpliced_exon_Base::SetProduct_id().
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Definition at line 476 of file Spliced_seg_.hpp.
Referenced by CSpliced_seg_Base::GetProduct_id(), CSpliced_seg_Base::IsSetProduct_id(), CSpliced_seg_Base::ResetProduct_id(), and CSpliced_seg_Base::SetProduct_id().
TProduct_ins CSpliced_exon_chunk_Base::m_Product_ins |
Definition at line 306 of file Spliced_exon_chunk_.hpp.
Referenced by CSpliced_exon_chunk_Base::DoSelect(), CSpliced_exon_chunk_Base::GetProduct_ins(), and CSpliced_exon_chunk_Base::SetProduct_ins().
TProduct_ins { ... } ::m_Product_ins |
Definition at line 306 of file Spliced_exon_chunk_.hpp.
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Definition at line 483 of file Spliced_seg_.hpp.
Referenced by CSpliced_seg_Base::GetProduct_length(), CSpliced_seg_Base::ResetProduct_length(), and CSpliced_seg_Base::SetProduct_length().
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Definition at line 662 of file Spliced_exon_.hpp.
Referenced by CSpliced_exon_Base::GetProduct_start(), CSpliced_exon_Base::IsSetProduct_start(), CSpliced_exon_Base::ResetProduct_start(), and CSpliced_exon_Base::SetProduct_start().
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Definition at line 668 of file Spliced_exon_.hpp.
Referenced by CSpliced_exon_Base::GetProduct_strand(), CSpliced_exon_Base::ResetProduct_strand(), and CSpliced_exon_Base::SetProduct_strand().
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Definition at line 478 of file Spliced_seg_.hpp.
Referenced by CSpliced_seg_Base::GetProduct_strand(), CSpliced_seg_Base::ResetProduct_strand(), and CSpliced_seg_Base::SetProduct_strand().
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Definition at line 480 of file Spliced_seg_.hpp.
Referenced by CSpliced_seg_Base::GetProduct_type(), CSpliced_seg_Base::ResetProduct_type(), and CSpliced_seg_Base::SetProduct_type().
TReal CScore_Base::C_Value::m_Real |
Definition at line 235 of file Score_.hpp.
TReal { ... } ::m_Real |
Definition at line 235 of file Score_.hpp.
Definition at line 262 of file Sparse_seg_.hpp.
Referenced by CSparse_seg_Base::GetRow_scores(), CSparse_seg_Base::ResetRow_scores(), and CSparse_seg_Base::SetRow_scores().
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Definition at line 261 of file Sparse_seg_.hpp.
Referenced by CSparse_seg_Base::GetRows(), CSparse_seg_Base::ResetRows(), and CSparse_seg_Base::SetRows().
Definition at line 674 of file Seq_align_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CSeq_align_Base::GetScore(), CSeq_align_Base::ResetScore(), and CSeq_align_Base::SetScore().
Definition at line 335 of file Dense_diag_.hpp.
Referenced by CDense_diag_Base::GetScores(), CDense_diag_Base::ResetScores(), and CDense_diag_Base::SetScores().
Definition at line 383 of file Dense_seg_.hpp.
Referenced by CDense_seg_Base::GetScores(), CDense_seg_Base::ResetScores(), and CDense_seg_Base::SetScores().
Definition at line 407 of file Packed_seg_.hpp.
Referenced by CPacked_seg_Base::GetScores(), CPacked_seg_Base::ResetScores(), and CPacked_seg_Base::SetScores().
Definition at line 671 of file Spliced_exon_.hpp.
Referenced by CSpliced_exon_Base::GetScores(), CSpliced_exon_Base::IsSetScores(), CSpliced_exon_Base::ResetScores(), and CSpliced_exon_Base::SetScores().
Definition at line 257 of file Std_seg_.hpp.
Referenced by CStd_seg_Base::GetScores(), CStd_seg_Base::ResetScores(), and CStd_seg_Base::SetScores().
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Definition at line 400 of file Sparse_align_.hpp.
Referenced by CSparse_align_Base::GetSecond_id(), CSparse_align_Base::IsSetSecond_id(), CSparse_align_Base::ResetSecond_id(), and CSparse_align_Base::SetSecond_id().
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Definition at line 403 of file Sparse_align_.hpp.
Referenced by CSparse_align_Base::GetSecond_starts(), CSparse_align_Base::ResetSecond_starts(), and CSparse_align_Base::SetSecond_starts().
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Definition at line 405 of file Sparse_align_.hpp.
Referenced by CSparse_align_Base::GetSecond_strands(), CSparse_align_Base::ResetSecond_strands(), and CSparse_align_Base::SetSecond_strands().
Definition at line 406 of file Sparse_align_.hpp.
Referenced by CSparse_align_Base::GetSeg_scores(), CSparse_align_Base::ResetSeg_scores(), and CSparse_align_Base::SetSeg_scores().
Definition at line 675 of file Seq_align_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CSeq_align_Base::GetSegs(), CSeq_align_Base::IsSetSegs(), CSeq_align_Base::ResetSegs(), and CSeq_align_Base::SetSegs().
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Definition at line 329 of file Dense_diag_.hpp.
Referenced by CDense_diag_Base::CDense_diag_Base(), CDense_diag_Base::IsSetDim(), CDense_diag_Base::IsSetIds(), CDense_diag_Base::IsSetLen(), CDense_diag_Base::IsSetScores(), CDense_diag_Base::IsSetStarts(), CDense_diag_Base::IsSetStrands(), CDense_diag_Base::ResetDim(), CDense_diag_Base::ResetIds(), CDense_diag_Base::ResetLen(), CDense_diag_Base::ResetScores(), CDense_diag_Base::ResetStarts(), CDense_diag_Base::ResetStrands(), CDense_diag_Base::SetDim(), CDense_diag_Base::SetIds(), CDense_diag_Base::SetLen(), CDense_diag_Base::SetScores(), CDense_diag_Base::SetStarts(), and CDense_diag_Base::SetStrands().
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Definition at line 376 of file Dense_seg_.hpp.
Referenced by CDense_seg_Base::CDense_seg_Base(), CDense_seg_Base::IsSetDim(), CDense_seg_Base::IsSetIds(), CDense_seg_Base::IsSetLens(), CDense_seg_Base::IsSetNumseg(), CDense_seg_Base::IsSetScores(), CDense_seg_Base::IsSetStarts(), CDense_seg_Base::IsSetStrands(), CDense_seg_Base::ResetDim(), CDense_seg_Base::ResetIds(), CDense_seg_Base::ResetLens(), CDense_seg_Base::ResetNumseg(), CDense_seg_Base::ResetScores(), CDense_seg_Base::ResetStarts(), CDense_seg_Base::ResetStrands(), CDense_seg_Base::SetDim(), CDense_seg_Base::SetIds(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CDense_seg_Base::SetScores(), CDense_seg_Base::SetStarts(), and CDense_seg_Base::SetStrands().
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Definition at line 399 of file Packed_seg_.hpp.
Referenced by CPacked_seg_Base::CPacked_seg_Base(), CPacked_seg_Base::IsSetDim(), CPacked_seg_Base::IsSetIds(), CPacked_seg_Base::IsSetLens(), CPacked_seg_Base::IsSetNumseg(), CPacked_seg_Base::IsSetPresent(), CPacked_seg_Base::IsSetScores(), CPacked_seg_Base::IsSetStarts(), CPacked_seg_Base::IsSetStrands(), CPacked_seg_Base::ResetDim(), CPacked_seg_Base::ResetIds(), CPacked_seg_Base::ResetLens(), CPacked_seg_Base::ResetNumseg(), CPacked_seg_Base::ResetPresent(), CPacked_seg_Base::ResetScores(), CPacked_seg_Base::ResetStarts(), CPacked_seg_Base::ResetStrands(), CPacked_seg_Base::SetDim(), CPacked_seg_Base::SetIds(), CPacked_seg_Base::SetLens(), CPacked_seg_Base::SetNumseg(), CPacked_seg_Base::SetPresent(), CPacked_seg_Base::SetScores(), CPacked_seg_Base::SetStarts(), and CPacked_seg_Base::SetStrands().
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Definition at line 186 of file Prot_pos_.hpp.
Referenced by CProt_pos_Base::CProt_pos_Base(), CProt_pos_Base::IsSetAmin(), CProt_pos_Base::IsSetFrame(), CProt_pos_Base::ResetAmin(), CProt_pos_Base::ResetFrame(), CProt_pos_Base::SetAmin(), and CProt_pos_Base::SetFrame().
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Definition at line 334 of file Score_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CScore_Base::CScore_Base(), CScore_Base::IsSetValue(), CScore_Base::ResetValue(), and CScore_Base::SetValue().
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Definition at line 139 of file Score_set_.hpp.
Referenced by CScore_set_Base::CScore_set_Base(), CScore_set_Base::IsSet(), CScore_set_Base::Reset(), and CScore_set_Base::Set().
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Definition at line 671 of file Seq_align_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CSeq_align_Base::CSeq_align_Base(), CSeq_align_Base::IsSetBounds(), CSeq_align_Base::IsSetDim(), CSeq_align_Base::IsSetExt(), CSeq_align_Base::IsSetId(), CSeq_align_Base::IsSetScore(), CSeq_align_Base::IsSetType(), CSeq_align_Base::ResetBounds(), CSeq_align_Base::ResetDim(), CSeq_align_Base::ResetExt(), CSeq_align_Base::ResetId(), CSeq_align_Base::ResetScore(), CSeq_align_Base::ResetType(), CSeq_align_Base::SetBounds(), CSeq_align_Base::SetDim(), CSeq_align_Base::SetExt(), CSeq_align_Base::SetId(), CSeq_align_Base::SetScore(), and CSeq_align_Base::SetType().
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Definition at line 140 of file Seq_align_set_.hpp.
Referenced by CSeq_align_set_Base::CSeq_align_set_Base(), CSeq_align_set_Base::IsSet(), CSeq_align_set_Base::Reset(), and CSeq_align_set_Base::Set().
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Definition at line 398 of file Sparse_align_.hpp.
Referenced by CSparse_align_Base::CSparse_align_Base(), CSparse_align_Base::IsSetFirst_starts(), CSparse_align_Base::IsSetLens(), CSparse_align_Base::IsSetNumseg(), CSparse_align_Base::IsSetSecond_starts(), CSparse_align_Base::IsSetSecond_strands(), CSparse_align_Base::IsSetSeg_scores(), CSparse_align_Base::ResetFirst_starts(), CSparse_align_Base::ResetLens(), CSparse_align_Base::ResetNumseg(), CSparse_align_Base::ResetSecond_starts(), CSparse_align_Base::ResetSecond_strands(), CSparse_align_Base::ResetSeg_scores(), CSparse_align_Base::SetFirst_starts(), CSparse_align_Base::SetLens(), CSparse_align_Base::SetNumseg(), CSparse_align_Base::SetSecond_starts(), CSparse_align_Base::SetSecond_strands(), and CSparse_align_Base::SetSeg_scores().
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Definition at line 259 of file Sparse_seg_.hpp.
Referenced by CSparse_seg_Base::CSparse_seg_Base(), CSparse_seg_Base::IsSetExt(), CSparse_seg_Base::IsSetRow_scores(), CSparse_seg_Base::IsSetRows(), CSparse_seg_Base::ResetExt(), CSparse_seg_Base::ResetRow_scores(), CSparse_seg_Base::ResetRows(), CSparse_seg_Base::SetExt(), CSparse_seg_Base::SetRow_scores(), and CSparse_seg_Base::SetRows().
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Definition at line 144 of file Sparse_seg_ext_.hpp.
Referenced by CSparse_seg_ext_Base::CSparse_seg_ext_Base(), CSparse_seg_ext_Base::IsSetIndex(), CSparse_seg_ext_Base::ResetIndex(), and CSparse_seg_ext_Base::SetIndex().
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Definition at line 148 of file Splice_site_.hpp.
Referenced by CSplice_site_Base::CSplice_site_Base(), CSplice_site_Base::IsSetBases(), CSplice_site_Base::ResetBases(), and CSplice_site_Base::SetBases().
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Definition at line 661 of file Spliced_exon_.hpp.
Referenced by CSpliced_exon_Base::CSpliced_exon_Base(), CSpliced_exon_Base::IsSetExt(), CSpliced_exon_Base::IsSetGenomic_end(), CSpliced_exon_Base::IsSetGenomic_start(), CSpliced_exon_Base::IsSetGenomic_strand(), CSpliced_exon_Base::IsSetPartial(), CSpliced_exon_Base::IsSetParts(), CSpliced_exon_Base::IsSetProduct_strand(), CSpliced_exon_Base::ResetExt(), CSpliced_exon_Base::ResetGenomic_end(), CSpliced_exon_Base::ResetGenomic_start(), CSpliced_exon_Base::ResetGenomic_strand(), CSpliced_exon_Base::ResetPartial(), CSpliced_exon_Base::ResetParts(), CSpliced_exon_Base::ResetProduct_strand(), CSpliced_exon_Base::SetExt(), CSpliced_exon_Base::SetGenomic_end(), CSpliced_exon_Base::SetGenomic_start(), CSpliced_exon_Base::SetGenomic_strand(), CSpliced_exon_Base::SetPartial(), CSpliced_exon_Base::SetParts(), and CSpliced_exon_Base::SetProduct_strand().
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Definition at line 475 of file Spliced_seg_.hpp.
Referenced by CSpliced_seg_Base::CSpliced_seg_Base(), CSpliced_seg_Base::IsSetExons(), CSpliced_seg_Base::IsSetGenomic_strand(), CSpliced_seg_Base::IsSetModifiers(), CSpliced_seg_Base::IsSetPoly_a(), CSpliced_seg_Base::IsSetProduct_length(), CSpliced_seg_Base::IsSetProduct_strand(), CSpliced_seg_Base::IsSetProduct_type(), CSpliced_seg_Base::ResetExons(), CSpliced_seg_Base::ResetGenomic_strand(), CSpliced_seg_Base::ResetModifiers(), CSpliced_seg_Base::ResetPoly_a(), CSpliced_seg_Base::ResetProduct_length(), CSpliced_seg_Base::ResetProduct_strand(), CSpliced_seg_Base::ResetProduct_type(), CSpliced_seg_Base::SetExons(), CSpliced_seg_Base::SetGenomic_strand(), CSpliced_seg_Base::SetModifiers(), CSpliced_seg_Base::SetPoly_a(), CSpliced_seg_Base::SetProduct_length(), CSpliced_seg_Base::SetProduct_strand(), and CSpliced_seg_Base::SetProduct_type().
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Definition at line 253 of file Std_seg_.hpp.
Referenced by CStd_seg_Base::CStd_seg_Base(), CStd_seg_Base::IsSetDim(), CStd_seg_Base::IsSetIds(), CStd_seg_Base::IsSetLoc(), CStd_seg_Base::IsSetScores(), CStd_seg_Base::ResetDim(), CStd_seg_Base::ResetIds(), CStd_seg_Base::ResetLoc(), CStd_seg_Base::ResetScores(), CStd_seg_Base::SetDim(), CStd_seg_Base::SetIds(), CStd_seg_Base::SetLoc(), and CStd_seg_Base::SetScores().
TStart_codon_found { ... } ::m_Start_codon_found |
Definition at line 213 of file Spliced_seg_modifier_.hpp.
TStart_codon_found CSpliced_seg_modifier_Base::m_Start_codon_found |
Definition at line 213 of file Spliced_seg_modifier_.hpp.
Referenced by CSpliced_seg_modifier_Base::DoSelect(), CSpliced_seg_modifier_Base::GetStart_codon_found(), and CSpliced_seg_modifier_Base::SetStart_codon_found().
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Definition at line 332 of file Dense_diag_.hpp.
Referenced by CDense_diag_Base::GetStarts(), CDense_diag_Base::ResetStarts(), and CDense_diag_Base::SetStarts().
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Definition at line 380 of file Dense_seg_.hpp.
Referenced by CDense_seg_Base::GetStarts(), CDense_seg_Base::ResetStarts(), and CDense_seg_Base::SetStarts().
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Definition at line 403 of file Packed_seg_.hpp.
Referenced by CPacked_seg_Base::GetStarts(), CPacked_seg_Base::ResetStarts(), and CPacked_seg_Base::SetStarts().
NCBI_NS_NCBI::CUnionBuffer<TStd> { ... } ::m_Std |
Definition at line 391 of file Seq_align_.hpp.
NCBI_NS_NCBI::CUnionBuffer<TStd> CSeq_align_Base::C_Segs::m_Std |
Definition at line 391 of file Seq_align_.hpp.
TStop_codon_found { ... } ::m_Stop_codon_found |
Definition at line 214 of file Spliced_seg_modifier_.hpp.
TStop_codon_found CSpliced_seg_modifier_Base::m_Stop_codon_found |
Definition at line 214 of file Spliced_seg_modifier_.hpp.
Referenced by CSpliced_seg_modifier_Base::DoSelect(), CSpliced_seg_modifier_Base::GetStop_codon_found(), and CSpliced_seg_modifier_Base::SetStop_codon_found().
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Definition at line 334 of file Dense_diag_.hpp.
Referenced by CDense_diag_Base::GetStrands(), CDense_diag_Base::ResetStrands(), and CDense_diag_Base::SetStrands().
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Definition at line 382 of file Dense_seg_.hpp.
Referenced by CDense_seg_Base::GetStrands(), CDense_seg_Base::ResetStrands(), and CDense_seg_Base::SetStrands().
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Definition at line 406 of file Packed_seg_.hpp.
Referenced by CPacked_seg_Base::GetStrands(), CPacked_seg_Base::ResetStrands(), and CPacked_seg_Base::SetStrands().
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Definition at line 672 of file Seq_align_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CSeq_align_Base::GetType(), CDensegSegment::Init(), CSeq_align_Base::ResetType(), and CSeq_align_Base::SetType().
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Definition at line 336 of file Score_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CScore_Base::DoNotDeleteThisObject(), CScore_Base::GetValue(), CScore_Base::ResetValue(), and CScore_Base::SetValue().
Definition at line 213 of file Product_pos_.hpp.
Referenced by CProduct_pos_Base::SelectionName(), and CProduct_pos_Base::ThrowInvalidSelection().
Definition at line 232 of file Score_.hpp.
Definition at line 387 of file Seq_align_.hpp.
Definition at line 300 of file Spliced_exon_chunk_.hpp.
Referenced by CSpliced_exon_chunk_Base::SelectionName(), and CSpliced_exon_chunk_Base::ThrowInvalidSelection().
Definition at line 210 of file Spliced_seg_modifier_.hpp.
Referenced by CSpliced_seg_modifier_Base::SelectionName(), and CSpliced_seg_modifier_Base::ThrowInvalidSelection().