NCBI C++ ToolKit
Functions | Variables
gene_model.cpp File Reference
#include <ncbi_pch.hpp>
#include <algo/sequence/gene_model.hpp>
#include <corelib/ncbitime.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/annot_ci.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/align_ci.hpp>
#include <objmgr/seq_loc_mapper.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/util/feature.hpp>
#include <objmgr/seq_vector.hpp>
#include <objtools/alnmgr/score_builder_base.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/User_object.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqalign/Product_pos.hpp>
#include <objects/seqalign/Prot_pos.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Spliced_exon_chunk.hpp>
#include <objects/seqalign/Spliced_exon.hpp>
#include <objects/seqalign/Spliced_seg.hpp>
#include <objects/seqalign/Spliced_seg_modifier.hpp>
#include <objects/seqalign/Splice_site.hpp>
#include <objects/seqfeat/seqfeat__.hpp>
#include <objects/seqfeat/SeqFeatXref.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/Prot_ref.hpp>
#include <objects/seqblock/GB_block.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqloc/Packed_seqint.hpp>
#include <objects/seqloc/Seq_loc_mix.hpp>
#include <objects/seqloc/Seq_loc_equiv.hpp>
#include <objects/seq/seq__.hpp>
#include <objects/seq/seqport_util.hpp>
#include <objects/general/Object_id.hpp>
#include <util/sequtil/sequtil_convert.hpp>
#include <util/range_coll.hpp>
#include <util/value_convert.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include "feature_generator.hpp"
#include <serial/serial.hpp>
+ Include dependency graph for gene_model.cpp:

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Functions

 USING_SCOPE (objects)
 
 USING_SCOPE (sequence)
 
static const CMolInfos_GetMolInfo (const CBioseq_Handle &handle)
 Return the mol-info object for a given sequence. More...
 
static void s_TransformToNucpos (CProduct_pos &pos)
 
string ExtractGnomonModelNum (const CSeq_id &seq_id)
 
bool IsProteinAlign (const CSeq_align &align)
 
void RenameGeneratedBioseqs (const CSeq_id &query_rna_id, CSeq_id &transcribed_rna_id, CRef< CSeq_feat > cds_feat_on_query_mrna, CRef< CSeq_feat > cds_feat_on_genome_with_translated_product)
 
bool IsContinuous (const CSeq_loc &loc)
 
void AddLiteral (CSeq_inst &inst, const string &seq, CSeq_inst::EMol mol_class)
 
void AddCodeBreak (CSeq_feat &feat, CSeq_loc &loc, char ncbieaa)
 
static bool s_Contains (const TSeqRange &range1, const TSeqRange &range2)
 Check whether range1 contains range2. More...
 
static CRef< CSeq_locs_MapSingleAA (TSeqPos pos, CRef< CSeq_id > mapped_protein_id, const CRangeCollection< TSeqPos > &product_ranges, CRef< CSeq_loc_Mapper > to_mrna, CRef< CSeq_loc_Mapper > to_genomic)
 
static string s_Count (unsigned num, const string &item_name)
 
void AddInsertWithGaps (CRef< CSeq_loc > &edited_sequence_seqloc, CSeq_id &genomic_seqid, int &region_begin, int &region_end, int &offset, CRef< CSeq_loc > &insert, const int k_gap_length, const int next_exon_start)
 

Variables

const char * k_except_text_for_gap_filled_gnomon_model
 
const char * k_rna_comment
 
const char * k_cds_comment
 

Function Documentation

◆ AddCodeBreak()

void AddCodeBreak ( CSeq_feat feat,
CSeq_loc loc,
char  ncbieaa 
)

◆ AddInsertWithGaps()

void AddInsertWithGaps ( CRef< CSeq_loc > &  edited_sequence_seqloc,
CSeq_id genomic_seqid,
int region_begin,
int region_end,
int offset,
CRef< CSeq_loc > &  insert,
const int  k_gap_length,
const int  next_exon_start 
)

◆ AddLiteral()

void AddLiteral ( CSeq_inst inst,
const string seq,
CSeq_inst::EMol  mol_class 
)

◆ ExtractGnomonModelNum()

string ExtractGnomonModelNum ( const CSeq_id seq_id)

◆ IsContinuous()

bool IsContinuous ( const CSeq_loc loc)

◆ IsProteinAlign()

bool IsProteinAlign ( const CSeq_align align)

◆ RenameGeneratedBioseqs()

void RenameGeneratedBioseqs ( const CSeq_id query_rna_id,
CSeq_id transcribed_rna_id,
CRef< CSeq_feat cds_feat_on_query_mrna,
CRef< CSeq_feat cds_feat_on_genome_with_translated_product 
)

◆ s_Contains()

static bool s_Contains ( const TSeqRange range1,
const TSeqRange range2 
)
inlinestatic

Check whether range1 contains range2.

Definition at line 2545 of file gene_model.cpp.

References CRange_Base::GetFrom(), and CRange_Base::GetTo().

Referenced by CFeatureGenerator::SImplementation::RecomputePartialFlags().

◆ s_Count()

static string s_Count ( unsigned  num,
const string item_name 
)
static

◆ s_GetMolInfo()

static const CMolInfo* s_GetMolInfo ( const CBioseq_Handle handle)
static

◆ s_MapSingleAA()

static CRef<CSeq_loc> s_MapSingleAA ( TSeqPos  pos,
CRef< CSeq_id mapped_protein_id,
const CRangeCollection< TSeqPos > &  product_ranges,
CRef< CSeq_loc_Mapper to_mrna,
CRef< CSeq_loc_Mapper to_genomic 
)
static

◆ s_TransformToNucpos()

static void s_TransformToNucpos ( CProduct_pos pos)
static

◆ USING_SCOPE() [1/2]

USING_SCOPE ( objects  )

◆ USING_SCOPE() [2/2]

USING_SCOPE ( sequence  )

Variable Documentation

◆ k_cds_comment

const char* k_cds_comment
Initial value:
=
"The sequence of the model RefSeq protein was modified relative "
"to this genomic sequence to represent the inferred CDS"

Definition at line 128 of file gene_model.cpp.

Referenced by CFeatureGenerator::SImplementation::x_SetComment(), and CFeatureGenerator::SImplementation::x_SetCommentForGapFilledModel().

◆ k_except_text_for_gap_filled_gnomon_model

const char* k_except_text_for_gap_filled_gnomon_model
Initial value:
=
"annotated by transcript or proteomic data"

Definition at line 123 of file gene_model.cpp.

Referenced by CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot().

◆ k_rna_comment

const char* k_rna_comment
Initial value:
=
"The sequence of the model RefSeq transcript was modified relative "
"to this genomic sequence to represent the inferred CDS"

Definition at line 125 of file gene_model.cpp.

Referenced by CFeatureGenerator::SImplementation::x_SetComment(), and CFeatureGenerator::SImplementation::x_SetCommentForGapFilledModel().

Modified on Fri Jul 19 17:11:15 2024 by modify_doxy.py rev. 669887