NCBI C++ ToolKit
Classes | Typedefs | Functions | Variables
feature_ds.cpp File Reference
#include <ncbi_pch.hpp>
#include <gui/widgets/seq_graphic/feature_ds.hpp>
#include <gui/widgets/seq_graphic/seqgraphic_job.hpp>
#include <gui/widgets/seq_graphic/cds_glyph.hpp>
#include <gui/widgets/seq_graphic/histogram_glyph.hpp>
#include <gui/widgets/seq_graphic/clone_placement_glyph.hpp>
#include <gui/widgets/seq_graphic/layout_group.hpp>
#include <gui/widgets/seq_graphic/layout_policy.hpp>
#include <gui/widgets/seq_graphic/named_group.hpp>
#include <gui/widgets/seq_graphic/gene_model_config.hpp>
#include <gui/widgets/seq_graphic/gene_model_group.hpp>
#include <gui/widgets/seq_graphic/feature_filter.hpp>
#include <gui/widgets/seq_graphic/comment_glyph.hpp>
#include <gui/widgets/seq_graphic/clone_feature_sorter.hpp>
#include <gui/widgets/seq_graphic/dbvar_feature_sorter.hpp>
#include <gui/widgets/seq_graphic/graph_cache.hpp>
#include <gui/widgets/seq_graphic/bed_coverage_graph.hpp>
#include <gui/widgets/seq_graphic/vcf_heatmap.hpp>
#include <gui/widgets/seq_graphic/intron_glyph.hpp>
#include <gui/widgets/seq_graphic/graph_utils.hpp>
#include <gui/widgets/seq_graphic/seqgraphic_utils.hpp>
#include <objmgr/util/feature.hpp>
#include <objmgr/util/sequence.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/seqalign/Std_seg.hpp>
#include <objects/genesbyloc/GBL_Reply.hpp>
#include <objects/genesbyloc/GBL_Data.hpp>
#include <objects/genesbyloc/GBL_Gene.hpp>
#include <gui/objutils/density_map.hpp>
#include <serial/serial.hpp>
#include <connect/ncbi_types.h>
#include <connect/ncbi_conn_stream.hpp>
#include <serial/objistr.hpp>
+ Include dependency graph for feature_ds.cpp:

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Classes

class  CSGFeatureJob
 CSGFeatureJob: a job class for loading annotated features from a given sequence and visible range. More...
 
struct  CSGFeatureJob::SLandmarkFeat
 
class  CGeneModelFeatJob
 CGeneModelFeatJob: a job class for loading annotated main features, including genes, RNAs, CDSs and exons from a given sequence and a given visible range. More...
 
class  CBatchFeatJob
 CBatchFeatJob: a job class for loading annotated features from a given a set of sequences within the corresponding visible ranges. More...
 
class  CSGCalcFeatHistJob
 CSGCalcFeatHistJob. More...
 
struct  SLandmarkFeatByScore
 CSGFeatureJob implementation. More...
 
struct  SLandmarkFeatBySeqPos
 

Typedefs

typedef map< int, intTId2Wt
 

Functions

 USING_SCOPE (objects)
 
static bool s_HasFeatXref (const CSeq_feat &feat, CSeqFeatData_Base::E_Choice choice)
 
static bool s_HasCDS (const CLinkedFeature &linked_feat)
 
static bool s_IsGnomonModel (const CSeq_feat &feat)
 
static bool s_HasTag (const CSeq_feat &feat, const set< string > &tags)
 
static bool s_IsSelect (const CLinkedFeature &feat)
 
static bool s_IsCCDS (const CLinkedFeature &linked_feat)
 
bool s_GetGeneWeight (TId2Wt &genes, TGi gi, const TSeqRange &r, size_t retmax)
 

Variables

static const int kMaxObjNum = 250000
 
static const size_t kMaxChildNum = 500
 
static const float kSeqZoomLevel = 0.125
 
static const char * kUnsortedGroupName = "--unsorted--"
 
static const float kMinScaleForMapping = 16.
 
static const char * kGeneByLocUrl
 

Typedef Documentation

◆ TId2Wt

typedef map<int, int> TId2Wt

Definition at line 2096 of file feature_ds.cpp.

Function Documentation

◆ s_GetGeneWeight()

bool s_GetGeneWeight ( TId2Wt genes,
TGi  gi,
const TSeqRange r,
size_t  retmax 
)

◆ s_HasCDS()

static bool s_HasCDS ( const CLinkedFeature linked_feat)
static

◆ s_HasFeatXref()

static bool s_HasFeatXref ( const CSeq_feat feat,
CSeqFeatData_Base::E_Choice  choice 
)
static

Definition at line 1670 of file feature_ds.cpp.

References CSeq_feat_Base::GetXref(), and ITERATE.

Referenced by CGeneModelFeatJob::x_CreateGeneModels().

◆ s_HasTag()

static bool s_HasTag ( const CSeq_feat feat,
const set< string > &  tags 
)
static

◆ s_IsCCDS()

static bool s_IsCCDS ( const CLinkedFeature linked_feat)
static

◆ s_IsGnomonModel()

static bool s_IsGnomonModel ( const CSeq_feat feat)
static

◆ s_IsSelect()

static bool s_IsSelect ( const CLinkedFeature feat)
static

◆ USING_SCOPE()

USING_SCOPE ( objects  )

Variable Documentation

◆ kGeneByLocUrl

const char* kGeneByLocUrl
static
Initial value:
=
"http://www.ncbi.nlm.nih.gov/gutils/fgenes_by_loc.fcgi?sort=weight&retmode=asnb"

Definition at line 2098 of file feature_ds.cpp.

Referenced by s_GetGeneWeight().

◆ kMaxChildNum

const size_t kMaxChildNum = 500
static

Definition at line 78 of file feature_ds.cpp.

Referenced by CSGFeatureJob::x_CreateFeature_Recursive().

◆ kMaxObjNum

const int kMaxObjNum = 250000
static

Definition at line 75 of file feature_ds.cpp.

Referenced by CSGFeatureJob::x_Execute().

◆ kMinScaleForMapping

const float kMinScaleForMapping = 16.
static

Definition at line 85 of file feature_ds.cpp.

Referenced by CSGFeatureJob::x_CreateFeature1().

◆ kSeqZoomLevel

const float kSeqZoomLevel = 0.125
static

Definition at line 80 of file feature_ds.cpp.

Referenced by CBatchFeatJob::x_LoadFeatProducts().

◆ kUnsortedGroupName

const char* kUnsortedGroupName = "--unsorted--"
static

Definition at line 82 of file feature_ds.cpp.

Referenced by CSGFeatureJob::x_LinkFeatures(), and CSGFeatureJob::x_SortFeatures().

Modified on Wed Feb 28 07:11:13 2024 by modify_doxy.py rev. 669887