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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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.