NCBI C++ ToolKit
Classes | Typedefs | Functions | Variables
objcoords.cpp File Reference
#include <ncbi_pch.hpp>
#include <misc/hgvs/objcoords.hpp>
#include <misc/hgvs/sequtils.hpp>
#include <util/checksum.hpp>
#include <util/sequtil/sequtil.hpp>
#include <util/sequtil/sequtil_manip.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/align_ci.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/seq_loc_mapper.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/annot_selector.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/util/feature.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/User_object.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/seq_id_handle.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqloc/Seq_point.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqblock/GB_block.hpp>
#include <objects/seqalign/Spliced_seg.hpp>
#include <objects/seqalign/Spliced_exon_chunk.hpp>
#include <math.h>
+ Include dependency graph for objcoords.cpp:

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Classes

class  CReportEntry
 

Typedefs

typedef vector< CRef< CReportEntry > > TReportEntryList
 

Functions

 USING_SCOPE (ncbi)
 
 USING_SCOPE (objects)
 
static string x_GetSequence (CSeqVector &seq_vec, TSignedSeqPos pos, TSignedSeqPos adjustment=0)
 
static SAnnotSelector x_GetAnnotSelector ()
 
static TReportEntryList s_GetFeaturesForRange (CScope &scope, const CBioseq_Handle &bsh, TSeqRange search_range)
 
static void s_ExtendEntriesFromAlignments (CScope &scope, const CBioseq_Handle &bsh, TSeqRange search_range, TReportEntryList &entries)
 
static bool s_IsRefSeqGene (const CBioseq_Handle &bsh)
 

Variables

static const TSeqPos kSeqFrame = 10
 

Typedef Documentation

◆ TReportEntryList

typedef vector<CRef<CReportEntry> > TReportEntryList

Definition at line 798 of file objcoords.cpp.

Function Documentation

◆ s_ExtendEntriesFromAlignments()

static void s_ExtendEntriesFromAlignments ( CScope scope,
const CBioseq_Handle bsh,
TSeqRange  search_range,
TReportEntryList entries 
)
static

◆ s_GetFeaturesForRange()

static TReportEntryList s_GetFeaturesForRange ( CScope scope,
const CBioseq_Handle bsh,
TSeqRange  search_range 
)
static

◆ s_IsRefSeqGene()

static bool s_IsRefSeqGene ( const CBioseq_Handle bsh)
static

◆ USING_SCOPE() [1/2]

USING_SCOPE ( ncbi  )

◆ USING_SCOPE() [2/2]

USING_SCOPE ( objects  )

◆ x_GetAnnotSelector()

static SAnnotSelector x_GetAnnotSelector ( )
static

◆ x_GetSequence()

static string x_GetSequence ( CSeqVector seq_vec,
TSignedSeqPos  pos,
TSignedSeqPos  adjustment = 0 
)
static

Variable Documentation

◆ kSeqFrame

const TSeqPos kSeqFrame = 10
static

Definition at line 72 of file objcoords.cpp.

Referenced by x_GetSequence().

Modified on Tue Jun 25 13:30:36 2024 by modify_doxy.py rev. 669887