NCBI C++ ToolKit
Classes | Macros | Functions | Variables
quality_methods.cpp File Reference
#include <ncbi_pch.hpp>
#include <gui/widgets/aln_score/quality_methods.hpp>
#include <gui/widgets/aln_score/gradient_color_panel.hpp>
#include <gui/utils/table_names.hpp>
#include <gui/widgets/wx/wx_utils.hpp>
#include <algo/blast/core/blast_encoding.h>
#include <algo/blast/core/blast_util.h>
#include "wx/valgen.h"
#include "wx/choice.h"
#include "wx/checkbox.h"
+ Include dependency graph for quality_methods.cpp:

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Classes

class  CQualityScoringPanel
 CQualityScoringPanel. More...
 
class  CConservationScoringPanel
 CConservationScoringPanel. More...
 

Macros

#define QUALITY_DESCR
 

Functions

static bool s_IsResidueOnlyColumn (const vector< int > &residue_counts)
 
static double s_GetInfoContent (const vector< int > &counts, int num_rows, const double *std_prob)
 
static bool s_IsIdentity (const vector< int > &counts, int num_rows)
 

Variables

const string CONSERVATION_METOD_DESCR
 
static const int kAlphabetSize = 28
 
static map< CConservationScoringMethod::EOptions, stringsm_ConservationValues
 

Macro Definition Documentation

◆ QUALITY_DESCR

#define QUALITY_DESCR
Value:
"This scheme assigns scores to residues" \
" based on how well a particular residue agrees with the others in a column."

Definition at line 121 of file quality_methods.cpp.

Function Documentation

◆ s_GetInfoContent()

static double s_GetInfoContent ( const vector< int > &  counts,
int  num_rows,
const double *  std_prob 
)
static

Definition at line 618 of file quality_methods.cpp.

References _ASSERT, i, kAlphabetSize, and log.

Referenced by CConservationScoringMethod::x_IsConserved().

◆ s_IsIdentity()

static bool s_IsIdentity ( const vector< int > &  counts,
int  num_rows 
)
static

Definition at line 640 of file quality_methods.cpp.

References i.

Referenced by CConservationScoringMethod::x_IsConserved().

◆ s_IsResidueOnlyColumn()

static bool s_IsResidueOnlyColumn ( const vector< int > &  residue_counts)
static

Definition at line 601 of file quality_methods.cpp.

References AMINOACID_TO_NCBISTDAA, and int.

Referenced by CConservationScoringMethod::CalculateScores().

Variable Documentation

◆ CONSERVATION_METOD_DESCR

const string CONSERVATION_METOD_DESCR
Initial value:
= R"foo(This is a column-based method that highlights highly conserved and less conserved columns based on residues's relative entropy threshold.
Alignment columns with no gaps are colored in blue or red.
The red color indicates highly conserved columns and blue indicates less conserved ones.)foo"

Definition at line 574 of file quality_methods.cpp.

Referenced by CConservationScoringMethod::GetDescription().

◆ kAlphabetSize

const int kAlphabetSize = 28
static

◆ sm_ConservationValues

map<CConservationScoringMethod::EOptions, string> sm_ConservationValues
static
Modified on Mon May 27 04:37:59 2024 by modify_doxy.py rev. 669887