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>

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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< CScope >	TScopeRef

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< TScopeRef >	s_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 1005 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
	)

Definition at line 673 of file alnvec_multi_ds.cpp.

References i, and ncbi::grid::netcache::search::fields::size.

Referenced by CAlnVecMultiDataSource::CreateConsensus().

CollectProteinFrequences()

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

Definition at line 754 of file alnvec_multi_ds.cpp.

References ctll::empty(), and i.

Referenced by CAlnVecMultiDataSource::CreateConsensus().

ON_EVENT()

ON_EVENT	(	CAppJobNotification	,
		CAppJobNotification::eStateChanged	,
		&CAlnVecMultiDataSource::OnAppJobNotification
	)

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

Definition at line 171 of file alnvec_multi_ds.cpp.

References COrg_ref_Base::CanGetCommon(), and COrg_ref_Base::GetCommon().

Referenced by IAlignRowHandle::GetTaxonomy().

s_GetTaxonomyInfoFromService()

static void s_GetTaxonomyInfoFromService ( int  tax_id, string &  taxonomy  )

static

Definition at line 148 of file alnvec_multi_ds.cpp.

References CTaxonCache::GetBlastName(), CTaxonCache::GetCommon(), CTaxonCache::GetInstance(), and CTaxonCache::GetTaxname().

Referenced by IAlignRowHandle::GetTaxonomy().

s_IsGap()

bool s_IsGap

(

char

ch

)

Definition at line 668 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 975 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 CAlnVecMultiDataSource::s_CleanScope(), and s_GetPristineScope().