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

hasFGColors = ( hasTR || hasTRF );

(entry.size() != 1) {

(

cbase = entry[0];

(entry.size() != 1) {

(

cbase = entry[0];

(entry.size() != 1) {

(

cbase = entry[0];

(

, base_it, bases) {

cbase = *base_it;

(

= 0;

<

.size();

++) {

= (size_t) score;

DECLARE_EVENT_TABLE()

wxPoint& pos = wxDefaultPosition,

wxSize&

= wxDefaultSize);

( wxKeyEvent& event );

( wxHyperlinkEvent& event );

BEGIN_EVENT_TABLE(

, wxScrolledWindow )

m_Data(

), m_NewID(kIdBase)

Create(parent,

, pos,

, wxScrolledWindowStyle|wxBORDER_SUNKEN|wxTAB_TRAVERSAL);

=

.GetKeyCode();

(wxIsspace(

) || wxIsdigit(

))

wxTextCtrl* textCtrlBase = (wxTextCtrl*)event.GetEventObject();

wxString textBase = textCtrlBase->GetValue().Upper();

wxTextCtrl* textCtrl = (wxTextCtrl*)FindWindow(

);

(textCtrl == 0 || textCtrl == textCtrlBase)

changed =

;

wxString

= textCtrl->GetValue().Upper();

pos =

.find_first_of(textBase);

(pos == wxString::npos)

(changed) textCtrl->ChangeValue(

);

textCtrlBase->ChangeValue(textBase);

textCtrlBase->SetInsertionPointEnd();

wxTextCtrl* textCtrl = (wxTextCtrl*)FindWindow(

);

wxColourPickerCtrl* pickerFG = (wxColourPickerCtrl*)FindWindow(

+ 1);

wxColourPickerCtrl* pickerBG = (wxColourPickerCtrl*)FindWindow(

+ 2);

(textCtrl != 0 && pickerFG != 0 && pickerBG != 0) {

wxFlexGridSizer* itemSizer =

wxFlexGridSizer(4, 0, 0);

this->SetSizer(itemSizer);

itemSizer->AddGrowableCol(0);

itemSizer->Add(

wxStaticText(

,

,

(

)),

1, wxALIGN_CENTER_HORIZONTAL|wxTOP|wxBOTTOM, 5);

itemSizer->Add(

wxStaticText(

,

,

(

)),

0, wxALIGN_LEFT|wxTOP|wxBOTTOM, 5);

itemSizer->Add(

wxStaticText(

,

,

(

)),

0, wxALIGN_LEFT|wxTOP|wxBOTTOM, 5);

itemSizer->Add(

wxStaticText(

,

,

(

)),

0, wxALIGN_LEFT|wxTOP|wxBOTTOM, 5);

(

= 0;

<

.size(); ++

)

wxColourPickerCtrl* pickerFG = (wxColourPickerCtrl*)FindWindow(

+ 1);

wxColourPickerCtrl* pickerBG = (wxColourPickerCtrl*)FindWindow(

+ 2);

(pickerFG != 0 && pickerBG != 0) {

wxColor

= pickerFG->GetColour();

pickerFG->SetColour(pickerBG->GetColour());

pickerBG->SetColour(

);

wxColourPickerCtrl* pickerFG = (wxColourPickerCtrl*)FindWindow(

+ 1);

wxColourPickerCtrl* pickerBG = (wxColourPickerCtrl*)FindWindow(

+ 2);

(pickerFG != 0 && pickerBG != 0) {

wxColourPickerCtrl* pickerFG = (wxColourPickerCtrl*)FindWindow(

+ 1);

wxColourPickerCtrl* pickerBG = (wxColourPickerCtrl*)FindWindow(

+ 2);

(pickerFG != 0 && pickerBG != 0) {

wxSizer* itemSizer = GetSizer();

wxTextCtrl* itemTextControl1 =

wxTextCtrl(

,

, wxEmptyString,

wxDefaultPosition, wxDLG_UNIT(

, wxSize(48, -1)), wxTE_LEFT);

itemSizer->Add(itemTextControl1, 1, wxGROW|wxALL, 2);

wxColourPickerCtrl* itemColorPicker1 =

wxColourPickerCtrl(

,

+ 1, fgColor);

itemSizer->Add(itemColorPicker1, 0, wxALIGN_CENTER_VERTICAL|wxLEFT|wxRIGHT, 2);

wxColourPickerCtrl* itemColorPicker2 =

wxColourPickerCtrl(

,

+ 2,

);

itemSizer->Add(itemColorPicker2, 0, wxALIGN_CENTER_VERTICAL|wxLEFT|wxRIGHT, 2);

wxHyperlinkCtrl* itemHyperLink =

(

,

+ 3,

(

), wxEmptyString);

itemSizer->Add(itemHyperLink, 0, wxALIGN_CENTER_VERTICAL|wxLEFT|wxRIGHT, 5);

wxWindow* window = FindWindow(

);

wxSizer* sizer = GetSizer();

wxSizerItemList::iterator node = sizer->GetChildren().begin();

( ; node != sizer->GetChildren().end(); ++node, ++index) {

wxSizerItem* item = *node;

(item->IsWindow()&& item->GetWindow() == window)

(node == sizer->GetChildren().end()) {

sizer->GetItem(index)->DeleteWindows();

sizer->GetItem(index-1)->DeleteWindows();

sizer->GetItem(index-2)->DeleteWindows();

sizer->GetItem(index-3)->DeleteWindows();

sizer->Remove(index);

sizer->Remove(index-1);

sizer->Remove(index-2);

sizer->Remove(index-3);

(

, wxColor(255, 255, 255), wxColor(0, 0, 0));

GetClientSize(0, &h);

GetVirtualSize(0, &hv);

(hv > h) Scroll(-1, (hv - h + 5)/5);

DECLARE_EVENT_TABLE()

( wxCommandEvent& event );

( wxCommandEvent& event );

m_Method(method), m_ColorPanel()

(

, base_it, bases) {

cat_found =

;

(cat_it->m_ForeColor == fc && cat_it->m_BackColor == bc) {

cat_it->m_Bases.append(1, *base_it);

.push_back(new_cat);

wxBoxSizer* itemSizer1 =

wxBoxSizer(wxHORIZONTAL);

this->SetSizer(itemSizer1);

wxStaticBox* staticBox =

wxStaticBox(

,

,

(

));

wxStaticBoxSizer* staticSizer =

wxStaticBoxSizer(staticBox, wxVERTICAL);

wxSize clrPanelSize = wxDLG_UNIT(

, wxSize(150, 100));

wxDefaultPosition, clrPanelSize);

staticSizer->Add(

wxButton(

,

,

(

)),

0, wxALIGN_LEFT|wxALL, 2);

itemSizer1->Add(staticSizer, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxBoxSizer* itemSizer2 =

wxBoxSizer(wxVERTICAL);

0, wxALIGN_CENTER_HORIZONTAL|wxALL, 2);

0, wxALIGN_CENTER_HORIZONTAL|wxALL, 2);

0, wxALIGN_CENTER_HORIZONTAL|wxALL, 2);

itemSizer1->Add(itemSizer2, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

(

= 0;

<

.size(); ++

) {

m_MinColor(

),

m_MidColor(

),

m_MaxColor(

),

m_UseConsensus(

),

=

;

=

;

cbase = entry[0];

(

= 0;

<

.size();

++) {

col_score /=

.size();

(

= 0;

<

.size();

++) {

scores[

] = (c_score - col_score);

fudge_factor = 0.75;

normal= ((score - mins) / (mids - mins))/2;

normal = ((score - mids) / (maxs - mids))/2 + 0.5f;

maxnormal = 0.0, minnormal = 1.0;

(normal > maxnormal) {

(

<< maxnormal);

(normal < minnormal) {

(

<< minnormal);

index = (

) (normal *

);

index =

(0, index);

DECLARE_EVENT_TABLE()

( wxCommandEvent& event );

m_Method(method), m_GradPanel(), m_WindowSize(0)

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);

wxTextCtrl* itemTextControl1 =

wxTextCtrl(

,

, wxEmptyString,

wxDefaultPosition, wxDLG_UNIT(

, wxSize(26, -1)), wxTE_RIGHT);

itemTextControl1->SetMaxLength(4);

itemBoxSizer2->Add(itemTextControl1, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxCheckBox* itemCheckBox1 =

wxCheckBox(

,

,

(

));

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

m_CalculateRange(

),

m_MinColor(

),

m_MidColor(

),

m_MaxColor(

),

m_UndefColor(0.8f, 0.8f, 1.0f),

m_UseConsensus(

),

(i < 0 || i > 25)

section =

;

(!reg.

(section,

) || (!reg.

(section,

)))

(!reg.

(section,

) || (!reg.

(section,

)))

kBuiltinKey(

);

(reg.

(section, kBuiltinKey)) {

& builtin_name = reg.

(section, kBuiltinKey);

(! builtin_matrix) {

base_cnt = (

) strlen(builtin_matrix->

);

(

= 0;

< base_cnt; ++

) {

(

j = 0; j < base_cnt; ++j) {

list <string> row_names;

section =

;

first_base =

.front().substr(0,1);

list<string> scores;

triangular = scores.size() == 1;

(list<string>, it, row_names) {

list<string> scores;

list<string>::iterator col_it =

.begin();

(list<string>, scores_it, scores) {

(

= 0;

<

.size();

++ ) {

scores[

] = score;

col_score = score_sum/num;

(

= 0;

<

.size();

++ ) {

(col_scores[x] > -1) {

score = scores[col_scores[x]];

(

j = 0; j <

.size(); j++ ) {

score = score_sum/(

.size() + 1);

col_scores[x] = (

)

;

scores[

] = score;

(

= 0;

<

.size();

++) {

avg_score += scores[

];

avg_score /=

.size();

(

= 0;

<

.size();

++) {

scores[

] -= avg_score;

index = (

) (normal *

);

index =

(0, index);

index =

(index,

- 1);

DECLARE_EVENT_TABLE()

( wxCommandEvent& event );

m_Method(method), m_GradPanel(), m_WindowSize(0)

Create(parent,

);

wxBoxSizer* itemBoxSizer1 =

wxBoxSizer(wxVERTICAL);

this->SetSizer(itemBoxSizer1);

itemBoxSizer1->Add(

, 1, wxGROW|wxALL, 5);

wxBoxSizer* itemBoxSizer3 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer3->Add(

wxStaticText(

, wxID_STATIC,

(

)),

0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxColourPickerCtrl* itemColorPicker =

wxColourPickerCtrl(

,

);

itemBoxSizer3->Add(itemColorPicker, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer1->Add(itemBoxSizer3, 0, wxALIGN_RIGHT|wxALL, 0);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxHORIZONTAL);

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

itemBoxSizer2->Add(

wxStaticText(

, wxID_STATIC,

(

)),

0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxTextCtrl* itemTextControl1 =

wxTextCtrl(

,

, wxEmptyString,

wxDefaultPosition, wxDLG_UNIT(

, wxSize(26, -1)), wxTE_RIGHT);

itemTextControl1->SetMaxLength(4);

itemBoxSizer2->Add(itemTextControl1, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxCheckBox* itemCheckBox1 =

wxCheckBox(

,

,

(

), wxDefaultPosition, wxDefaultSize, wxALIGN_RIGHT);

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

static const char * bgColor

CColorPanel(vector< SData > &data, wxWindow *parent, wxWindowID id=wxID_ANY, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize)

void x_AddNewRow(const string &text, wxColor fgColor, wxColor bgColor)

void OnChar(wxKeyEvent &event)

void OnDelete(wxHyperlinkEvent &event)

void x_DeleteRow(wxWindowID id)

void OnTextCtrlUpdated(wxCommandEvent &event)

const string & GetSetBases() const

Which bases have colors specified?

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

returns a color corresponding to a given score value.

virtual bool HasPropertiesPanel() const

returns true if the method supports properties dialog

virtual ~CColorTableMethod()

virtual int GetSupportedColorTypes() const

returns a combination of EColorType flags

virtual wxWindow * CreatePropertiesPanel(wxWindow *parent)

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

string m_SetBases

> Foreground color when nothing specified for a base.

virtual const CMenuItem * GetMenu()

Returns a pointer to the submenu.

virtual IScoringMethod * Clone() const

CRgbaColor GetColor(char cbase, EColorType type) const

virtual void CalculateScores(IAlnExplorer::TNumrow row, const IScoringAlignment &aln_vec, TScoreColl &scores)

void AddSetBase(char cbase)

CRgbaColor m_DefaultForeColor

> Background color when nothing specified for a base.

virtual const CRgbaColor & GetColorForNoScore(EColorType type) const

Call for display colors when CanCalculateScores returns false.

CRgbaColor m_DefaultBackColor

> foreground or text colors

vector< CRgbaColor > m_Colors

virtual bool Load(CNcbiRegistry &reg)

vector< CRgbaColor > m_ForeColors

> background colors

bool Save(CNcbiRegistry &reg)

Opposite of Load().

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

void SetColor(char cbase, const CRgbaColor &color, EColorType type=fForeground)

CColorTableScoringPanel - Properties Panel for CColorTableMethod.

void OnSwapColors(wxCommandEvent &event)

void OnContrastBG(wxCommandEvent &event)

void OnApply(wxCommandEvent &event)

CColorTableMethod & m_Method

CColorTableScoringPanel(CColorTableMethod &method, wxWindow *parent, wxWindowID id=wxID_ANY)

CColorPanel * m_ColorPanel

void OnContrastFG(wxCommandEvent &event)

vector< CColorPanel::SData > m_Data

void OnAddRow(wxCommandEvent &event)

void SetColorForNoScore(EColorType type, const CRgbaColor &color)

vector< TScore > m_vScore

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

returns a color corresponding to a given score value.

void x_CalculateNonConsensusScores(const string &column, TScore &col_score, TScoreVector &scores)

virtual bool Load(CNcbiRegistry &reg)

virtual ~CColumnScoringMethod()

virtual int GetSupportedColorTypes() const

returns a combination of EColorType flags

size_t m_WindowSize

relative, not absolute scores.

size_t GetWindowSize() const

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

virtual IScoringMethod * Clone() const

CRgbaGradColorTable m_ColorTable

TScore m_MinScore

weight matrix

bool CanCalculateScores(const IScoringAlignment &aln)

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

virtual wxWindow * CreatePropertiesPanel(wxWindow *parent)

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

TScore m_MaxScore

possible range of scores.

virtual const CMenuItem * GetMenu()

Returns a pointer to the submenu.

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

CColumnScoringMethod()

CColumnScoringMethod.

const CRgbaColor & GetColorForNoScore(EColorType type) const

Call for display colors when CanCalculateScores returns false.

virtual void CreateColorTable(int size)

friend class CColumnScoringPanel

virtual bool HasPropertiesPanel() const

returns true if the method supports properties dialog

CColumnScoringPanel(CColumnScoringMethod &method, wxWindow *parent, wxWindowID id=wxID_ANY)

void OnApply(wxCommandEvent &event)

CGradientColorPanel * m_GradPanel

CColumnScoringMethod & m_Method

void GetParams(stParams &params) const

CHyperlink is wrapper class for wxHyperlinkCtrl On OSX platform it posts URL click instead of sending...

virtual wxWindow * CreatePropertiesPanel(wxWindow *parent)

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

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 ~CMatrixScoringMethod()

void x_CalculateNonConsensusRange()

TScore m_NonConsensusMaxScore

const CRgbaColor & GetColorForNoScore(EColorType type) const

Call for display colors when CanCalculateScores returns false.

virtual bool HasPropertiesPanel() const

returns true if the method supports properties dialog

TScore m_NonConsensusMinScore

static int x_BaseToIndex(char c)

virtual int GetSupportedColorTypes() const

returns a combination of EColorType flags

virtual IScoringMethod * Clone() const

virtual bool Load(CNcbiRegistry &reg)

virtual const CMenuItem * GetMenu()

Returns a pointer to the submenu.

unsigned char m_CalculateRange

void x_CalculateConsensusRange()

void SetColorForNoScore(EColorType type, const CRgbaColor &color)

bool CanCalculateScores(const IScoringAlignment &aln)

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

CNcbiMatrix< TScore > m_vScore

TScore m_ConsensusMinScore

TScore m_ConsensusMaxScore

size_t GetWindowSize() const

virtual void CreateColorTable(int size)

friend class CMatrixScoringPanel

CRgbaGradColorTable m_ColorTable

CGradientColorPanel * m_GradPanel

CMatrixScoringMethod & m_Method

CMatrixScoringPanel(CMatrixScoringMethod &method, wxWindow *parent, wxWindowID id=wxID_ANY)

void OnApply(wxCommandEvent &event)

void Resize(size_t i, size_t j, T val=T())

resize this matrix, filling the empty cells with a known value

size_t GetRows() const

get the number of rows in this matrix

size_t GetCols() const

get the number of columns in this matrix

class CRgbaColor provides a simple abstraction for managing colors.

virtual bool SaveInfo(CNcbiRegistry &reg)

saves only descriptive information

EColorGradType m_ColorGradType

CRgbaColor x_GetColor(CNcbiRegistry &reg, const string &key, const string def_value)

virtual bool LoadInfo(CNcbiRegistry &reg)

loads only descriptive information

virtual TSeqPos GetAlnStart() const =0

virtual TSeqPos GetBaseWidth(IAlnExplorer::TNumrow) const =0

virtual TSeqPos GetAlnStop() const =0

virtual string & GetAlnSeqString(IAlnExplorer::TNumrow row, string &buffer, const IAlnExplorer::TSignedRange &aln_range) const =0

IScoringMethod represents an abstract algorithm for calculating alignment scores and assigning colors...

vector< TScore > TScoreVector

static const int sm_DefGradientSize

default number of colors in gradient

CRgbaColor & GetColor(CSeqFeatData::ESubtype subtype)

static const char * str(char *buf, int n)

static const char * column

static const column_t columns[]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define ERR_POST(message)

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

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

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

void SetFrom(TSeqPos start)

string ToString(bool printAlpha=true, bool uchars=true) const

Return a string representation of the current color.

static CRgbaColor GetColor(const string &color_type)

return a color based on a string.

void push_back(const attr_type &attr)

virtual bool GetBool(const string &section, const string &name, bool default_value, TFlags flags=0, EErrAction err_action=eThrow) const

Get boolean value of specified parameter name.

virtual const string & Get(const string &section, const string &name, TFlags flags=0) const

Get the parameter value.

virtual double GetDouble(const string &section, const string &name, double default_value, TFlags flags=0, EErrAction err_action=eThrow) const

Get double value of specified parameter name.

virtual bool HasEntry(const string &section, const string &name=kEmptyStr, TFlags flags=0) const

virtual void EnumerateEntries(const string &section, list< string > *entries, TFlags flags=fAllLayers) const

Enumerate parameter names for a specified section.

virtual string GetString(const string &section, const string &name, const string &default_value, TFlags flags=0) const

Get the parameter string value.

bool Set(const string &section, const string &name, const string &value, TFlags flags=0, const string &comment=kEmptyStr)

Set the configuration parameter value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static double StringToDouble(const CTempStringEx str, TStringToNumFlags flags=0)

Convert string to double.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

TFrom GetFrom(void) const

Get the From member data.

unsigned int

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

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

static void text(MDB_val *v)

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

const struct ncbi::grid::netcache::search::fields::KEY key

Process information in the NCBI Registry, including working with configuration files.

const SNCBIPackedScoreMatrix NCBISM_Pam30

const SNCBIPackedScoreMatrix NCBISM_Blosum62

const SNCBIPackedScoreMatrix NCBISM_Pam250

const SNCBIPackedScoreMatrix NCBISM_Blosum80

const SNCBIPackedScoreMatrix NCBISM_Pam70

const SNCBIPackedScoreMatrix NCBISM_Blosum45

The standard matrices.

#define row(bind, expected)

const TNCBIScore * scores

strlen(symbols) x strlen(symbols)

const char * symbols

order of residues

static const string kTablerowB

static const string kTablerowF

static const string kTablerow

const unsigned int kMatrixSize

CMatrixScoringMethod.

static const string kDefaultColorStr

CColorTableMethod.

static wxAcceleratorEntry entries[3]

wxColour ConvertColor(const CRgbaColor &color)

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

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