NCBI C++ ToolKit
Macros | Typedefs | Functions | Variables
alnvec_multi_ds.cpp File Reference
#include <ncbi_pch.hpp>
#include <gui/widgets/aln_multiple/alnvec_multi_ds.hpp>
#include <gui/objutils/utils.hpp>
#include <gui/utils/event_translator.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objmgr/align_ci.hpp>
#include <gui/objutils/taxon_cache.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seq/Seq_descr.hpp>
+ Include dependency graph for alnvec_multi_ds.cpp:

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Macros

#define ADD_BASE_TO_GRAPH(b)    { if (graphs[b].size() == 0) graphs[b].resize(ref_len, 0); graphs[b][curr_pos] += 1; }
 

Typedefs

typedef CRef< CScopeTScopeRef
 

Functions

 USING_SCOPE (ncbi::objects)
 
template<class T >
void TlsValCleanup (T *oldVal, void *)
 
static objects::CScope & s_GetPristineScope (const objects::CBioseq_Handle &bio_handle)
 
static void s_GetTaxonomyInfoFromService (int tax_id, string &taxonomy)
 
static void s_GetTaxonomyInfoFromBiosrc (const objects::CBioSource &biosrc, std::string &taxonomy)
 
 ON_EVENT (CAppJobNotification, CAppJobNotification::eStateChanged, &CAlnVecMultiDataSource::OnAppJobNotification) ON_EVENT(CAppJobNotification
 
bool s_IsGap (char ch)
 
void CollectNucleotideFrequences (const vector< string > &rows, int col, int base_count[], int numBases)
 
void CollectProteinFrequences (const vector< string > &rows, int col, int base_count[], int numBases)
 
static void s_TranslateAndExpand (string &seq, int gen_code)
 

Variables

static CStaticTls< TScopeRefs_ScopeTls
 

Macro Definition Documentation

◆ ADD_BASE_TO_GRAPH

#define ADD_BASE_TO_GRAPH (   b)     { if (graphs[b].size() == 0) graphs[b].resize(ref_len, 0); graphs[b][curr_pos] += 1; }

Definition at line 985 of file alnvec_multi_ds.cpp.

Typedef Documentation

◆ TScopeRef

typedef CRef<CScope> TScopeRef

Definition at line 60 of file alnvec_multi_ds.cpp.

Function Documentation

◆ CollectNucleotideFrequences()

void CollectNucleotideFrequences ( const vector< string > &  rows,
int  col,
int  base_count[],
int  numBases 
)

◆ CollectProteinFrequences()

void CollectProteinFrequences ( const vector< string > &  rows,
int  col,
int  base_count[],
int  numBases 
)

Definition at line 755 of file alnvec_multi_ds.cpp.

References ctll::empty(), and i.

Referenced by CAlnVecMultiDataSource::CreateConsensus().

◆ ON_EVENT()

◆ s_GetPristineScope()

static objects::CScope& s_GetPristineScope ( const objects::CBioseq_Handle &  bio_handle)
static

Definition at line 75 of file alnvec_multi_ds.cpp.

References s_ScopeTls.

Referenced by IAlignRowHandle::GetOrgLabel(), and IAlignRowHandle::GetTaxId().

◆ s_GetTaxonomyInfoFromBiosrc()

static void s_GetTaxonomyInfoFromBiosrc ( const objects::CBioSource &  biosrc,
std::string taxonomy 
)
static

◆ s_GetTaxonomyInfoFromService()

static void s_GetTaxonomyInfoFromService ( int  tax_id,
string taxonomy 
)
static

◆ s_IsGap()

bool s_IsGap ( char  ch)

Definition at line 669 of file alnvec_multi_ds.cpp.

Referenced by IAlnMultiDataSource::CollectAlignStats().

◆ s_TranslateAndExpand()

static void s_TranslateAndExpand ( string seq,
int  gen_code 
)
static

Definition at line 955 of file alnvec_multi_ds.cpp.

References i, and CAlnVec::TranslateNAToAA().

Referenced by IAlnMultiDataSource::CollectAlignStats().

◆ TlsValCleanup()

template<class T >
void TlsValCleanup ( T oldVal,
void *   
)

Definition at line 65 of file alnvec_multi_ds.cpp.

◆ USING_SCOPE()

USING_SCOPE ( ncbi::objects  )

Variable Documentation

◆ s_ScopeTls

CStaticTls<TScopeRef> s_ScopeTls
static

Definition at line 62 of file alnvec_multi_ds.cpp.

Referenced by s_GetPristineScope().

Modified on Sat Feb 24 07:48:56 2024 by modify_doxy.py rev. 669887