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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/paint__sequence_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/widgets/edit/paint_sequence.cpp Source File

32 #include <wx/graphics.h> 33 #include <wx/settings.h> 34 #include <wx/clipbrd.h> 35 #include <wx/msgdlg.h> 36 #include <wx/evtloop.h> 65  const

vector<

int

> &feat_frames,

67  const string

&allowed_char_set,

const

vector<

string

> &real_prot,

const

vector<

bool

> &read_only,

70

: wxVScrolledWindow(parent,

id

, pos,

size

, wxFULL_REPAINT_ON_RESIZE|wxWANTS_CHARS), m_Seq(seq), m_SeqLen(seq_len), m_FeatRanges(feat_ranges), m_FeatTypes(feat_types), m_FeatStrand(feat_strand),

71

m_FeatFrames(feat_frames), m_GeneticCode(genetic_code), m_Feat5Partial(feat_partial5),

72

m_AllowedCharSet(allowed_char_set), m_RealProt(real_prot), m_read_only(read_only), m_start(start), m_ProtFeatRanges(prot_feat_ranges),

73

m_EnableTranslation(

true

), m_EnableTranslation1(

true

), m_EnableTranslation2(

true

), m_EnableComplement(

true

), m_EnableFeatures(

true

), m_EnableOnTheFly(

true

), m_EnableMismatch(

true

),

74

m_EnableRevTranslation(

true

), m_EnableRevTranslation1(

true

), m_EnableRevTranslation2(

true

), m_Down(

false

)

76

SetBackgroundStyle(wxBG_STYLE_PAINT);

78

SetBackgroundColour(*wxWHITE);

79

m_Font = wxFont(9, wxFONTFAMILY_TELETYPE, wxFONTSTYLE_NORMAL, wxFONTWEIGHT_NORMAL);

91

m_FeatureStart = pair<int,int>(-1,-1);

92

m_FeatureStop = pair<int,int>(-1,-1);

97

m_EnableTranslation =

false

;

98

m_EnableTranslation1 =

false

;

99

m_EnableTranslation2 =

false

;

100

m_EnableRevTranslation =

false

;

101

m_EnableRevTranslation1 =

false

;

102

m_EnableRevTranslation2 =

false

;

103

m_EnableComplement =

false

;

104

m_EnableFeatures =

false

;

105

m_EnableOnTheFly =

false

;

106

m_EnableMismatch =

false

;

107

m_ShowTripletMismatch = -1;

108

m_ShowTripletTranslation = -4;

111

wxWindow *win = GetParent();

117

win = win->GetParent();

124  if

(!

m_Seq

.empty())

126

wxGraphicsContext *gc = wxGraphicsContext::Create();

127

gc->SetFont(

m_Font

, *wxBLACK);

149  const

vector<pair<string,objects::CSeqFeatData::ESubtype> > &feat_types,

150  const

vector<objects::CBioseq_Handle::EVectorStrand> &feat_strand,

151  const

vector<int> &feat_frames,

153  const

vector<bool> &feat_partial5,

154  const

vector<string> &real_prot,

155  const

unordered_map<

int

, vector<vector<pair<TSeqPos,TSeqPos> > > > &prot_feat_ranges)

260  if

(

m_FeatStrand

[

i

] == objects::CBioseq_Handle::eStrand_Minus)

374  if

(m_CursorSeq < 0 || m_CursorSeq >=

m_Seq

.size() - 1)

376  if

(

m_Seq

.size() == 2)

378

wxMessageBox (

_

(

"Unable to delete the whole sequence"

),

_

(

"Error"

), wxOK|wxICON_ERROR);

410  int

uc =

tolower

(event.GetKeyCode());

411  if

( !event.HasModifiers() && uc != WXK_NONE && uc >= 32 && uc < 255 &&

m_AllowedCharSet

.find(uc) != string::npos)

423

wxSize sz = GetClientSize();

424  int

num_rows =

static_cast<int>

(GetVisibleRowsEnd() - GetVisibleRowsBegin());

426  int

uc =

event

.GetKeyCode();

435  case

WXK_PAGEUP :

m_CursorRow

=

static_cast<int>

(GetVisibleRowsBegin() - num_rows);

m_CursorSeq

= -1;

break

;

436  case

WXK_PAGEDOWN :

m_CursorRow

=

static_cast<int>

(GetVisibleRowsBegin() + num_rows);

m_CursorSeq

= -1;

break

;

501  int row

=

static_cast<int>

(GetVisibleRowsBegin());

503  while

( y_row < y &&

row

<= GetVisibleRowsEnd()+1 )

545  for

(

unsigned int

k = 0; k < feats_in_row.size(); k++)

547  unsigned int i

= feats_in_row[k];

548  auto

it = feats_with_exons.

find

(

i

);

551  if

(it != feats_with_exons.

end

())

553  for

(

unsigned int

m = 0; m < it->second.size(); m++)

555  unsigned int

j = it->second[m];

596  if

(evt.GetModifiers() == wxMOD_SHIFT)

598

wxPoint p = evt.GetPosition();

628

wxPoint p = evt.GetPosition();

638  int

current = p.y - y_row;

648  if

( current > y && current < y_trial)

714  for

(

size_t

k = 0; k < feats_in_row.size(); k++)

718  unsigned int i

= feats_in_row[k];

723  if

( current > y && current < y_next)

745  if

(

m_Down

&& evt.Dragging())

749

wxPoint p = evt.GetPosition();

792

wxPoint p = evt.GetPosition();

863  if

(IsShownOnScreen())

884

wxAutoBufferedPaintDC dc(

this

);

885

wxGraphicsContext *gc = wxGraphicsContext::Create( dc );

886  if

(gc && !

m_Seq

.empty())

889

gc->SetFont(

m_Font

, *wxBLACK);

900  size_t

hidden_rows = GetVisibleRowsBegin();

902  size_t row

= hidden_rows;

903  int

client_y = GetClientSize().y;

904  size_t

seq_pos = start;

906  while

(start <

m_Seq

.size())

934  while

((*pos) + 1 == pos1)

948  while

((*pos) - 1 == pos2)

990

wxColour backgroundColour = GetBackgroundColour();

991  if

(!backgroundColour.Ok())

992

backgroundColour = wxSystemSettings::GetColour(wxSYS_COLOUR_3DFACE);

993

wxSize sz = GetClientSize();

994

wxRect windowRect(wxPoint(0,0), sz);

995

gc->SetBrush(wxBrush(backgroundColour));

996

gc->SetPen(wxPen(backgroundColour, 1));

997

gc->DrawRectangle(windowRect.GetX(),windowRect.GetY(),windowRect.GetWidth(),windowRect.GetHeight());

1005

wxDouble externalLeading;

1006  if

(

m_Seq

.size() > 1000)

1008

gc->GetTextExtent(wxString(

m_Seq

.substr(0,1000)), &width, &height, &descent, &externalLeading);

1013

gc->GetTextExtent(wxString(

m_Seq

), &width, &height, &descent, &externalLeading);

1014

width /=

m_Seq

.size();

1016

width = ceil(1+width);

1017

height = ceil(2+height);

1024  int

width =

int

(GetClientSize().x);

1028  if

(num_groups == 0)

1040  unsigned int

orig_pos =

static_cast<int>

(seq_pos);

1041  int

orig_y = y_label;

1044  DrawLabelCell

(orig_pos,x,y_label,

row

, feats_in_row, feats_with_exons, gc);

1046  for

(

unsigned int i

=0;

i

<substr.size();

i

++)

1049  DrawTextCell

(wxString(substr[

i

]),

i

,

row

,

static_cast<unsigned int>

(seq_pos),x,y, feats_in_row, feats_with_exons, gc);

1066 void CPaintSequence::DrawLabelCell

(

unsigned int

pos,

int

x,

int

&y,

int row

,

const

vector<unsigned int> &feats_in_row,

const map

<

unsigned int

, vector<unsigned int> > &feats_with_exons, wxGraphicsContext *gc)

const 1077 void CPaintSequence::DrawTextCell

(

const

wxString &substr,

int

col,

int row

,

unsigned int

seq_pos,

int

x,

int

&y,

const

vector<unsigned int> &feats_in_row,

const map

<

unsigned int

, vector<unsigned int> > &feats_with_exons, wxGraphicsContext *gc)

const 1085

gc->SetFont(

m_Font

, wxColour(255,0,255));

1086

gc->DrawText(

label

,x,y);

1087

gc->SetFont(

m_Font

,*wxBLACK);

1093

gc->SetPen(wxPen(wxColour(255,0,255)));

1105

gc->SetFont(

m_Font

, wxColour(237,222,14));

1109

gc->SetFont(

m_Font

,*wxBLACK);

1115  if

(pos1 >= 0 && pos2 >= 0 && seq_pos >= pos1 && seq_pos <= pos2)

1116

gc->DrawText(substr,x,y, gc->CreateBrush(*wxLIGHT_GREY_BRUSH));

1118

gc->DrawText(substr,x,y);

1119

gc->SetFont(

m_Font

,*wxBLACK);

1122

gc->SetPen( *wxGREY_PEN);

1139  DrawFeatures

(

row

,seq_pos,x,y,y_base,feats_in_row,feats_with_exons,gc);

1147

gc->SetPen( *wxRED_PEN);

1196  if

( seq_pos >=

offset

+1 && (seq_pos - 1 -

offset

) % 3 == 0 )

1198  int

prot_pos = (seq_pos - 1 -

offset

) / 3 ;

1199  if

(gc && prot_pos <

prot

.size() && prot_pos >= 0)

1200

gc->DrawText (wxString(

prot

[prot_pos]),x,y);

1210  if

(

m_FeatStrand

[

i

] == objects::CBioseq_Handle::eStrand_Plus)

1211  for

(

unsigned int

m = 0; m < ranges.size(); m++)

1213  unsigned int

j = ranges[m];

1216  if

(seq_pos >= start && seq_pos <= stop )

1221  if

( prot_pos % 3 == 1)

1223  if

(

i

< translation.size() && prot_pos / 3 < translation[

i

].size())

1224  prot

= translation[

i

][prot_pos / 3];

1226  else if

(prot_pos % 3 == 0)

1228  else if

(prot_pos % 3 == 2)

1234  if

(

m_FeatStrand

[

i

] == objects::CBioseq_Handle::eStrand_Minus)

1235  for

(

int

m =

static_cast<int>

(ranges.size()) - 1; m >= 0; m--)

1237  unsigned int

j = ranges[m];

1240  if

(seq_pos >= start && seq_pos <= stop )

1245  if

( prot_pos % 3 == 1)

1247  if

(

i

< translation.size() && prot_pos / 3 < translation[

i

].size())

1248  prot

= translation[

i

][prot_pos / 3];

1250  else if

(prot_pos % 3 == 0)

1252  else if

(prot_pos % 3 == 2)

1266

gc->SetPen( *wxGREY_PEN);

1272 void CPaintSequence::DrawOnTheFly

(

int

x,

int

&y,

int

y_base,

unsigned int

seq_pos,

int i

,

const map

<

unsigned int

, vector<unsigned int> > &feats_with_exons, wxGraphicsContext *gc)

const 1284

gc->SetFont(

m_Font

, *wxBLUE);

1285

gc->DrawText (wxString(

prot

),x,y);

1286

gc->SetFont(

m_Font

,*wxBLACK);

1298 void CPaintSequence::DrawMismatch

(

int

x,

int

&y,

int

y_base,

unsigned int

seq_pos,

int i

,

const map

<

unsigned int

, vector<unsigned int> > &feats_with_exons, wxGraphicsContext *gc)

const 1311  if

(

prot

!= translated_prot)

1312

gc->SetFont(

m_Font

,*wxRED);

1314

gc->SetFont(

m_Font

, *wxBLUE);

1315

gc->DrawText(wxString(

prot

),x,y);

1316

gc->SetFont(

m_Font

,*wxBLACK);

1348  const

wxPen* pen = wxBLACK_PEN;

1352

default : pen = wxBLACK_PEN;

break

;

1363

gc->SetFont(

m_Font

, wxColour(255,0,255));

1364

gc->DrawText(

label

,x,y);

1365

gc->SetFont(

m_Font

,*wxBLACK);

1373  for

(

unsigned int

k = 0; k < feats_in_row.size(); k++)

1375  unsigned int i

= feats_in_row[k];

1382

gc->SetFont(

m_Font

,*wxBLUE);

1383

gc->DrawText(wxString(

label

),x,y);

1384

gc->SetFont(

m_Font

,*wxBLACK);

1396

vector<unsigned int> feats_in_row;

1403  int

row_end = row_start +

m_NumCols

- 1;

1404  if

( (row_start >= start && row_end <= stop) ||

1405

(start >= row_start && start <= row_end) ||

1406

(stop >= row_start && stop <= row_end) )

1408

feats_in_row.push_back(

static_cast<unsigned int>

(

i

));

1412  return

feats_in_row;

1421

gc->DrawText(

_

(

"complement"

),x,y);

1433

gc->SetFont(

m_Font

, *wxBLUE);

1434

gc->DrawText (

_

(

"on-the-fly"

),x,y);

1435

gc->SetFont(

m_Font

, *wxBLACK);

1446

gc->DrawText (

_

(

"frame +1"

),x,y);

1452

gc->DrawText (

_

(

"frame +2"

),x,y);

1458

gc->DrawText (

_

(

"frame +3"

),x,y);

1464

gc->DrawText (

_

(

"frame -1"

),x,y);

1470

gc->DrawText (

_

(

"frame -2"

),x,y);

1476

gc->DrawText (

_

(

"frame -3"

),x,y);

1481 void CPaintSequence::DrawFeatures

(

int row

,

unsigned int

seq_pos,

int

x,

int

&y,

int

y_base,

const

vector<unsigned int> &feats_in_row,

const map

<

unsigned int

, vector<unsigned int> > &feats_with_exons, wxGraphicsContext *gc)

const 1483  for

(

unsigned int

k = 0; k < feats_in_row.size(); k++)

1485  unsigned int i

= feats_in_row[k];

1490  bool

found =

false

;

1491  bool

startpoint =

false

;

1492  bool

endpoint =

false

;

1494  if

(

f

!= feats_with_exons.end())

1496  for

(

unsigned int

m = 0; m <

f

->second.size(); m++)

1498  unsigned int

j =

f

->second[m];

1502  if

(seq_pos >= start && seq_pos <= stop)

1505  if

(seq_pos == start)

1507  if

(seq_pos == stop)

1518

gc->SetBrush(*wxBLACK_BRUSH);

1528  if

(

m_FeatStrand

[

i

] == objects::CBioseq_Handle::eStrand_Plus)

1535

gc->DrawLines(3,lines);

1543

gc->DrawLines(3,lines);

1559  if

(wxTheClipboard->Open())

1567  if

(pos1 >= 0 && pos2 >= 0)

1568

wxTheClipboard->SetData(

new

wxTextDataObject(

m_Seq

.substr(pos1, pos2 - pos1 + 1)) );

1569

wxTheClipboard->Close();

1581  if

(pos1 >= 0 && pos2 >= 0)

1583  if

(pos1 == 0 && pos2 ==

m_Seq

.size() - 2)

1585

wxMessageBox (

_

(

"Unable to delete the whole sequence"

),

_

(

"Error"

), wxOK|wxICON_ERROR);

1589  bool

read_only =

false

;

1591  for

(

int i

= pos1;

i

<= pos2;

i

++)

1611

str1 =

m_Seq

.substr(0, pos1);

1613  if

(pos2 + 1 <

m_Seq

.size())

1614

str2 =

m_Seq

.substr(pos2 + 1);

1617  for

(

int i

= pos1;

i

<= pos2;

i

++)

1639  if

(wxTheClipboard->Open())

1646

wxTheClipboard->SetData(

new

wxTextDataObject(

result

) );

1649

wxTheClipboard->Close();

1662  if

(wxTheClipboard->Open())

1664  if

(wxTheClipboard->IsSupported( wxDF_UNICODETEXT ) &&

m_CursorSeq

>= 0)

1666

wxTextDataObject

data

;

1667

wxTheClipboard->GetData(

data

);

1668  string str

=

data

.GetText().ToStdString();

1670  bool

allowed =

true

;

1671  for

(

size_t i

=0;

i

<

str

.size();

i

++)

1677  if

(!

str

.empty() && allowed)

1696

wxTheClipboard->Close();

1702  bool

found =

false

;

1703  if

(wxTheClipboard->Open())

1705  if

(wxTheClipboard->IsSupported( wxDF_UNICODETEXT ))

1707

wxTextDataObject

data

;

1708

wxTheClipboard->GetData(

data

);

1709  string str

=

data

.GetText().ToStdString();

1711  bool

allowed =

true

;

1712  for

(

size_t i

=0;

i

<

str

.size();

i

++)

1718  if

(!

str

.empty() && allowed)

1723

wxTheClipboard->Close();

1730  bool

found =

false

;

1742  return

pair<int,int>(pos1, pos2);

1757  if

(choice ==

"+1"

)

1759  if

(choice ==

"+2"

)

1761  if

(choice ==

"+3"

)

1763  if

(choice ==

"-1"

)

1765  if

(choice ==

"-2"

)

1767  if

(choice ==

"-3"

)

1775  return static_cast<int>

(

m_Seq

.size() - 1);

1799

seq +=

m_Seq

.substr(start, stop-start+1);

1803  if

(

m_FeatStrand

[

i

] == objects::CBioseq_Handle::eStrand_Minus)

1807  swap

(rev_comp,seq);

1821  if

(

m_FeatStrand

[

i

] == objects::CBioseq_Handle::eStrand_Minus)

1828  if

(

m_FeatStrand

[

i

] == objects::CBioseq_Handle::eStrand_Minus)

1870  if

(

offset

< 0 && origin <= start && origin - offset >= stop)

1919

start =

static_cast<int>

(

m_Seq

.size() - 2);

1921

stop =

static_cast<int>

(

m_Seq

.size() - 2);

1940

vector<TSeqPos> length_before;

1947

length_before.push_back(length);

1959

vector<unsigned int> ranges;

1965  int

row_end = row_start +

m_NumCols

- 1;

1966  if

( (row_start >= start && row_end <= stop) ||

1967

(start >= row_start && start <= row_end) ||

1968

(stop >= row_start && stop <= row_end) )

1970

ranges.push_back(j);

1980  for

(

unsigned int

k = 0; k < feats_in_row.size(); k++)

1982  unsigned int i

= feats_in_row[k];

1984  if

(!ranges.empty())

1985

feats_with_exons[

i

] = ranges;

1987  return

feats_with_exons;

void ReportRange(int pos1, int pos2)

void ShowReadOnlyWarning()

void EnableCommit(bool enable)

set< int > & SetHighlights()

vector< vector< pair< TSeqPos, TSeqPos > > > m_FeatRanges

virtual wxCoord OnGetRowHeight(size_t row) const

int m_ShowTripletMismatch

vector< CRef< objects::CGenetic_code > > m_GeneticCode

void EnableRevTranslation1(bool enable)

virtual ~CPaintSequence()

void DrawOnTheFlyLabel(int x, int &y, bool is_exon_present, wxGraphicsContext *gc) const

void EnableOnTheFly(bool enable)

vector< pair< TSeqPos, TSeqPos > > m_FeatWholeRange

void DrawLineNumber(unsigned int seq_pos, int x, int &y, wxGraphicsContext *gc) const

const wxPen * GetColorForFeature(objects::CSeqFeatData::ESubtype subtype) const

bool m_EnableTranslation2

void DrawLabelCell(unsigned int pos, int x, int &y, int row, const vector< unsigned int > &feats_in_row, const map< unsigned int, vector< unsigned int > > &feats_with_exons, wxGraphicsContext *gc) const

vector< bool > m_Feat5Partial

vector< string > m_RealProt

vector< int > m_FeatFrames

void AdjustFeatStartStop(int origin, int offset, int &start, int &stop)

void DrawOffsetTranslation(int x, int y, unsigned int seq_pos, int offset, const string &prot, wxGraphicsContext *gc) const

vector< string > m_Translated

void OnChar(wxKeyEvent &event)

vector< unsigned int > GetFeaturesInRow(int row) const

void ClearScreen(wxGraphicsContext *gc)

void OnCut(wxCommandEvent &event)

vector< bool > m_read_only

virtual void OnEraseBackground(wxEraseEvent &event)

vector< int > & GetSeqLen()

pair< int, int > m_FeatureStart

string * GetFindString(bool is_nuc, bool is_revcomp, const string &choice)

bool m_EnableRevTranslation1

pair< int, int > GetSelection()

void DrawMismatch(int x, int &y, int y_base, unsigned int seq_pos, int i, const map< unsigned int, vector< unsigned int > > &feats_with_exons, wxGraphicsContext *gc) const

void DrawOnTheFly(int x, int &y, int y_base, unsigned int seq_pos, int i, const map< unsigned int, vector< unsigned int > > &feats_with_exons, wxGraphicsContext *gc) const

void DrawTranslation(int x, int &y, unsigned int seq_pos, wxGraphicsContext *gc) const

void EnableMismatch(bool enable)

void DrawMismatchLabel(int x, int &y, bool is_exon_present, wxGraphicsContext *gc) const

void DrawCursor(int col, int row, int x, int &y, wxGraphicsContext *gc) const

void EnableComplement(bool enable)

void DrawTranslationLabels(int row, int x, int &y, wxGraphicsContext *gc) const

void OnMouseDrag(wxMouseEvent &evt)

int FindRowByCoord(int y, int &y_row)

void UpdateFeatures(const vector< vector< pair< TSeqPos, TSeqPos > > > &feat_ranges, const vector< pair< string, objects::CSeqFeatData::ESubtype > > &feat_types, const vector< objects::CBioseq_Handle::EVectorStrand > &feat_strand, const vector< int > &feat_frames, const vector< CRef< objects::CGenetic_code > > &genetic_code, const vector< bool > &feat_partial5, const vector< string > &real_prot, const unordered_map< int, vector< vector< pair< TSeqPos, TSeqPos > > > > &prot_feat_ranges)

void OnPaste(wxCommandEvent &event)

void DrawFeatures(int row, unsigned int seq_pos, int x, int &y, int y_base, const vector< unsigned int > &feats_in_row, const map< unsigned int, vector< unsigned int > > &feats_with_exons, wxGraphicsContext *gc) const

int m_ShowTripletTranslation

void OnKeyDown(wxKeyEvent &event)

void EnableTranslation1(bool enable)

void SetRange(int pos1, int pos2)

void DrawComplement(int x, int &y, unsigned int seq_pos, wxGraphicsContext *gc) const

void OnMouseClick(wxMouseEvent &evt)

void OnCopy(wxCommandEvent &event)

void DrawFeatureLabels(int row, int x, int &y, const vector< unsigned int > &feats_in_row, const map< unsigned int, vector< unsigned int > > &feats_with_exons, wxGraphicsContext *gc) const

void EnableRevTranslation(bool enable)

void MouseToFeature(wxPoint p, int row, int y0)

bool MouseToSeqPos(wxPoint p, int &row, int &y_row)

void DrawTextLine(const string &substr, int &y_label, int row, wxGraphicsContext *gc, size_t &seq_pos)

void NormalizeCursorColRows()

void EnableTranslation2(bool enable)

virtual void OnUpdate()

Notification for the derived class that moment is good for doing its update and drawing stuff.

void AdjustProtFeatRange(int origin, int offset, int i)

void OnResize(wxSizeEvent &)

void EnableTranslation(bool enable)

void AdjustFeatureRange(int origin, int offset)

bool m_EnableRevTranslation2

char TranslateOnTheFly(unsigned int seq_pos, int i, const vector< unsigned int > &ranges, const vector< string > &translation, bool &left, bool &right) const

void Search(const string &val)

bool m_EnableTranslation1

virtual void OnPaint(wxPaintEvent &event)

Painting.

void EnableRevTranslation2(bool enable)

vector< pair< string, objects::CSeqFeatData::ESubtype > > m_FeatTypes

void DrawTextCell(const wxString &substr, int col, int row, unsigned int seq_pos, int x, int &y, const vector< unsigned int > &feats_in_row, const map< unsigned int, vector< unsigned int > > &feats_with_exons, wxGraphicsContext *gc) const

void SetClean(bool clean)

vector< TSeqPos > m_FeatTotalLength

TSeqPos GetFeatureStop(int i, int j)

vector< vector< TSeqPos > > m_FeatLengthBefore

vector< unsigned int > IsExonPresent(int i, int row) const

pair< int, int > m_FeatureStop

unsigned int PosToSegment()

void EnableFeatures(bool enable)

void CalculateFontWidthAndHeight(wxGraphicsContext *gc)

unordered_map< int, vector< vector< pair< TSeqPos, TSeqPos > > > > m_ProtFeatRanges

map< unsigned int, vector< unsigned int > > GetFeatsWithExons(int row, const vector< unsigned int > &feats_in_row) const

vector< objects::CBioseq_Handle::EVectorStrand > m_FeatStrand

void OnMouseDown(wxMouseEvent &evt)

void DrawTripletMismatch(int x, int y, int y_base, int i, wxGraphicsContext *gc) const

bool m_EnableRevTranslation

TSeqPos GetFeatureStart(int i, int j)

void DrawComplementLabel(int row, int x, int &y, wxGraphicsContext *gc) const

static SIZE_TYPE ReverseComplement(const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)

static SIZE_TYPE Complement(const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)

const_iterator end() const

const_iterator find(const key_type &key) const

const_iterator begin() const

const_iterator find(const key_type &key) const

const_iterator end() const

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

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

unsigned int TSeqPos

Type for sequence locations and lengths.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

static void Translate(const string &seq, string &prot, const CGenetic_code *code, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=NULL, bool is_5prime_complete=true, bool is_3prime_complete=true)

Translate a string using a specified genetic code.

@ fIs5PrimePartial

= 0x4 Translate first codon even if not start codon (because sequence is 5' partial)

@ fRemoveTrailingX

= 0x2 Remove trailing Xs from protein

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

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

Truncate whitespace in a string.

static string & ToLower(string &str)

Convert string to lower case – string& version.

static const char label[]

unsigned int

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

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

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

static const GLdouble origin[]

static const int chars_per_group

static const int space_between_groups

BOOL UpdateData(HWND hDlg, CProjBulderApp *pApp, BOOL bGet)

#define row(bind, expected)

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