NCBI C++ ToolKit
Classes | Functions
score_lookup.cpp File Reference
#include <ncbi_pch.hpp>
#include <algo/sequence/gene_model.hpp>
#include <algo/sequence/internal_stops.hpp>
#include <algo/align/util/algo_align_util_exceptions.hpp>
#include <algo/align/util/score_lookup.hpp>
#include <algo/sequence/util.hpp>
#include <algo/blast/core/blast_seg.h>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqalign/Score.hpp>
#include <objects/seqalign/Score_set.hpp>
#include <objects/seqalign/Spliced_seg.hpp>
#include <objects/seqalign/Spliced_seg_modifier.hpp>
#include <objects/seqalign/Spliced_exon.hpp>
#include <objects/seqalign/Spliced_exon_chunk.hpp>
#include <objects/seqalign/Product_pos.hpp>
#include <objects/seqalign/Prot_pos.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/Genetic_code_table.hpp>
#include <objects/seqfeat/Genetic_code.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/taxon1/taxon1.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/alnmgr/alntext.hpp>
#include <objtools/alnmgr/pairwise_aln.hpp>
#include <objtools/alnmgr/aln_converters.hpp>
+ Include dependency graph for score_lookup.cpp:

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Classes

class  CScore_AlignLength
 
class  CScore_GapCount
 
class  CScore_FrameShifts
 
class  CScore_LongestGapLength
 
class  CScore_3PrimeUnaligned
 
class  CScore_Polya
 
class  CScore_InternalUnaligned
 
class  CScore_AlignStartStop
 
class  CScore_AlignLengthRatio
 
class  CScore_SequenceLength
 
class  CScore_SymmetricOverlap
 
class  CScore_MinExonLength
 
class  CScore_MaxIntronLength
 
class  CScore_ExonCount
 
class  CScore_IndelToSplice
 
class  CScore_StartStopCodon
 
class  CScore_CdsInternalStops
 
class  CScore_CdsScore
 
class  CScore_Coverage
 
class  CScore_Taxid
 
class  CScore_LastSpliceSite
 
class  CScore_Overlap
 
class  CScore_OverlapBoth
 
class  CScore_OrdinalPos
 
class  CScore_TblastnScore
 
class  CScore_BlastRatio
 
class  CScore_EdgeExonInfo
 
class  CScore_GeneID
 
class  CScore_TieBreaker
 
class  CScore_Partial
 
class  CScore_RibosomalSlippage
 
class  CScore_SegPct
 
class  CScore_Entropy
 

Functions

 USING_SCOPE (objects)
 
static TSeqPos s_GetNaLength (CBioseq_Handle bsh)
 Get sequence's length in nucleic acids. More...
 
static const CGenetic_codes_GetGeneticCode (const CSeq_id &seq_id, CScope *scope)
 

Function Documentation

◆ s_GetGeneticCode()

static const CGenetic_code* s_GetGeneticCode ( const CSeq_id seq_id,
CScope scope 
)
static

◆ s_GetNaLength()

static TSeqPos s_GetNaLength ( CBioseq_Handle  bsh)
inlinestatic

◆ USING_SCOPE()

USING_SCOPE ( objects  )
Modified on Sun Mar 03 03:13:12 2024 by modify_doxy.py rev. 669887