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NCBI C++ ToolKit: src/gui/widgets/aln_score/quality_methods.cpp Source File

: m_Space(0), m_Gap(0)

: m_Options(0), m_Space(0), m_Gap(0)

: m_Worst(

.m_Worst),

m_Best(

.m_Best),

m_Options(

.m_Options),

m_Space(

.m_Space),

\

" based on how well a particular residue agrees with the others in a column."

column_size =

.size() - n_space;

vector<double> X(symbols.size(), 0);

(

= 0;

<symbols.size(); ++

) {

(

, c_it, symbols) {

X[

] /= column_size;

quality_score = 0;

(

= 0;

<

.size(); ++

) {

score_sq_sum = 0;

(

= 0;

< symbols.size(); ++

) {

score_sq_sum += score_diff * score_diff;

scores[

] = resid_score;

quality_score += resid_score;

col_score = (

) (quality_score / column_size);

(

= 0;

<

.size(); ++

) {

scores[

] = col_score;

(score < 0.0) score = 0.0;

index = (

) floor(score *

);

DECLARE_EVENT_TABLE()

( wxCommandEvent& event );

m_MatrixChoice(), m_GradPanel()

wxBoxSizer* itemBoxSizer1 =

wxBoxSizer(wxVERTICAL);

this->SetSizer(itemBoxSizer1);

itemBoxSizer1->Add(

, 1, wxGROW|wxALL, 5);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer1->Add(itemBoxSizer2, 0, wxALIGN_RIGHT|wxALL, 5);

itemBoxSizer2->Add(

wxStaticText(

, wxID_STATIC,

(

)),

0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer2->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

(vector<string>, iter, table_names) {

(!matrix_name.empty()) {

wxCheckBox* itemCheckBox1 =

wxCheckBox(

,

,

(

));

itemCheckBox1->SetValidator(wxGenericValidator(&

));

itemBoxSizer1->Add(itemCheckBox1, 0, wxALIGN_LEFT|wxALL, 5);

wxCheckBox* itemCheckBox2 =

wxCheckBox(

,

,

(

));

itemCheckBox2->SetValidator(wxGenericValidator(&

));

itemBoxSizer1->Add(itemCheckBox2, 0, wxALIGN_LEFT|wxALL, 5);

(!matrix_name.empty()) {

;

(

);

;

= {30, 144, 255, 255 };

= { 255, 26, 26, 255 };

m_ConservedOption(

.m_ConservedOption),

m_NotScored(

.m_NotScored)

;

= R

residue_counts[kGap] == 0 && residue_counts[kResidueX] == 0

&& residue_counts[kResidueB] == 0 && residue_counts[kResidueZ] == 0

&& residue_counts[kResidueU] == 0 && residue_counts[kResidueStar] == 0;

* std_prob)

(

= 1;

< counts.size();

++) {

(counts[

] == 0) {

(!(std_prob[

] > 0.0))

;

freq = (double)counts[

] / (

)num_rows;

retval += freq *

(freq / std_prob[

]) /

(2.0);

(

= 1;

< counts.size();

++) {

(counts[

] > 0 && counts[

] < num_rows) {

(counts[

] == num_rows) {

* std_prob)

retval =

;

bit_threshold = 0.0;

: bit_threshold = 1.0;

;

: bit_threshold = 2.0;

;

: bit_threshold = 3.0;

;

: bit_threshold = 4.0;

;

(

& aa :

) {

residue_counts[residue]++;

fill(scores.begin(), scores.end(), col_score);

color_black(

);

index = (

)floor(score *

);

color_white(

);

(opt.second == l_name) {

(

<< name <<

);

DECLARE_EVENT_TABLE()

(wxCommandEvent& event);

m_ConservedOptionChoice(),

wxBoxSizer* itemBoxSizer1 =

wxBoxSizer(wxVERTICAL);

this->SetSizer(itemBoxSizer1);

itemBoxSizer1->Add(

, 1, wxGROW | wxALL, 5);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer1->Add(itemBoxSizer2, 0, wxALIGN_RIGHT | wxALL, 5);

itemBoxSizer2->Add(

wxStaticText(

, wxID_STATIC,

(

)),

0, wxALIGN_CENTER_VERTICAL | wxALL, 5);

s.Replace(

(

),

(

));

s[0] = wxToupper(s[0]);

Declarations of static arrays used to define some NCBI encodings to be used in a toolkit independent ...

Various auxiliary BLAST utility functions.

double * BLAST_GetStandardAaProbabilities(void)

Get the standard amino acid probabilities.

CConservationScoringMethod - implementation of IScoringMethod.

virtual const CRgbaColor & GetColorForScore(TScore score, EColorType type) const

returns a color corresponding to a given score value.

CConservationScoringMethod()

CConservationScoringMethod.

bool x_IsConserved(const vector< int > &counts, int num_rows, const double *std_prob) const

void SetConservedOption(const string &name)

virtual int GetType() const

returns combination of EAlignType flags defining types of alignments that can be colored with this me...

virtual ~CConservationScoringMethod()

virtual wxWindow * CreatePropertiesPanel(wxWindow *parent)

This a factory method that shall produce a CPropertiesPanel representing properties of the method; th...

virtual void CalculateScores(char cons, const string &column, TScore &col_score, TScoreVector &scores)

virtual IUITool * Clone() const

virtual int GetSupportedColorTypes() const

returns a combination of EColorType flags

virtual string GetName() const

returns unique name of the method that is used in UI to identify it

EOptions m_ConservedOption

virtual string GetDescription() const

returns a detailed description of the method that is used in UI

friend class CConservationScoringPanel

CConservationScoringPanel.

CConservationScoringPanel(CConservationScoringMethod &method, wxWindow *parent, wxWindowID id=wxID_ANY)

void OnApply(wxCommandEvent &event)

CConservationScoringMethod & m_Method

CGradientColorPanel * m_GradPanel

wxChoice * m_ConservedOptionChoice

void GetParams(stParams &params) const

CQualityScoringMethodAA - Quality scoring method for Amino Acids (Protein alignments).

virtual IUITool * Clone() const

const SNCBIPackedScoreMatrix * m_SubstMatrix

SNCBIFullScoreMatrix m_FullSubstMatrix

virtual string GetName() const

returns unique name of the method that is used in UI to identify it

const SNCBIPackedScoreMatrix * GetSubstitutionMatrix()

CQualityScoringMethodAA()

CQualityScoringMethodAA.

virtual ~CQualityScoringMethodAA()

virtual TNCBIScore GetSubstitutionScore(int aa1, int aa2) const

virtual string GetAllowedSymbols() const

void SetSubstitutionMatrix(const SNCBIPackedScoreMatrix *m)

virtual int GetType() const

returns combination of EAlignType flags defining types of alignments that can be colored with this me...

virtual string GetAllowedSymbols() const

CQualityScoringMethodNA()

CQualityScoringMethodNA.

virtual string GetName() const

returns unique name of the method that is used in UI to identify it

virtual TNCBIScore GetSubstitutionScore(int aa1, int aa2) const

virtual IUITool * Clone() const

virtual int GetType() const

returns combination of EAlignType flags defining types of alignments that can be colored with this me...

virtual ~CQualityScoringMethodNA()

CQualityScoringMethod - Like CSimpleScoringMethod, in that it calculate the quality of the alignment ...

virtual ~CQualityScoringMethod()

CQualityScoringMethod()

CQualityScoringMethod.

virtual const CMenuItem * GetMenu()

Returns a pointer to the submenu.

CRgbaGradColorTable m_ColorTable

friend class CQualityScoringPanel

virtual const CRgbaColor & GetColorForNoScore(EColorType type) const

Call for display colors when CanCalculateScores returns false.

virtual bool CanCalculateScores(const IScoringAlignment &aln)

Do we have what it takes to calculate scores? e.g. a master row selected?

virtual TNCBIScore GetSubstitutionScore(int aa1, int aa2) const =0

bool IsScoreWholeColumn() const

virtual string GetDescription() const

returns a detailed description of the method that is used in UI

virtual void SetColorForNoScore(EColorType type, const CRgbaColor &color)

void CreateColorTable(int size)

virtual wxWindow * CreatePropertiesPanel(wxWindow *parent)

This a factory method that shall produce a CPropertiesPanel representing properties of the method; th...

@ fIgnoreGaps

Do not count gaps in the alignment in the score.

@ fScoreWholeColumn

The column's total score is also the score for each residue.

@ fIgnoreEmptySpace

Do not count unaligned regions in score.

virtual bool IsAverageable() const

return "true" if scores could be averaged

virtual const CRgbaColor & GetColorForScore(TScore score, EColorType type) const

returns a color corresponding to a given score value.

virtual void CalculateScores(char cons, const string &column, TScore &col_score, TScoreVector &scores)

virtual string GetAllowedSymbols() const =0

virtual int GetSupportedColorTypes() const

returns a combination of EColorType flags

void SetOptions(int options)

virtual bool HasPropertiesPanel() const

returns true if the method supports properties dialog

void OnApply(wxCommandEvent &event)

CQualityScoringPanel(CQualityScoringMethod &method, wxWindow *parent, wxWindowID id=wxID_ANY)

wxChoice * m_MatrixChoice

CQualityScoringMethod & m_Method

CGradientColorPanel * m_GradPanel

class CRgbaColor provides a simple abstraction for managing colors.

char m_AmbiguousResidue

Ambiguous Residue, typically 'N' for nucleotides, 'X' for proteins.

static const int kAmbiguousResidueScore

vector< TScore > TScoreVector

virtual int GetType() const =0

returns combination of EAlignType flags defining types of alignments that can be colored with this me...

static const int sm_DefGradientSize

default number of colors in gradient

static const Colors colors

static const char * column

const Uint1 AMINOACID_TO_NCBISTDAA[]

Translates between ncbieaa and ncbistdaa.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

void SetSize(size_t size)

void FillGradient(const CRgbaColor &start_c, const CRgbaColor &end_c)

initialize the whole table with gradient colors in [start_c, end_c] range

static const SNCBIPackedScoreMatrix * NameToTable(const string &name)

static vector< string > AllTableNames()

void Set(float r, float g, float b)

set the color from an Fl_Color

static string TableToName(const SNCBIPackedScoreMatrix *)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static string & ToLower(string &str)

Convert string to lower case – string& version.

unsigned int

A callback function used to compare two keys in a database.

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

const struct ncbi::grid::netcache::search::fields::SIZE size

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

static const int kAlphabetSize

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

const string CONSERVATION_METOD_DESCR

static map< CConservationScoringMethod::EOptions, string > sm_ConservationValues

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

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

const SNCBIPackedScoreMatrix NCBISM_Blosum62

#define NCBI_FSM_DIM

Recommended approach: unpack and index directly.

void NCBISM_Unpack(const SNCBIPackedScoreMatrix *psm, SNCBIFullScoreMatrix *fsm)

Expand a packed score matrix into an unpacked one, which callers can proceed to index directly by sta...

int TNCBIScore

data types

static const char * kMaxScore

const char * symbols

order of residues

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

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