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

: wxVScrolledWindow(parent,

, pos,

, wxFULL_REPAINT_ON_RESIZE|wxWANTS_CHARS), m_Alignment(ah), m_FeatRanges(feat_ranges), m_FeatTypes(feat_types), m_FeatStrand(feat_strand),

m_EnableFeatures(

), m_EnableSubstitute(

)

SetBackgroundStyle(wxBG_STYLE_PAINT);

SetBackgroundColour(*wxWHITE);

m_Font = wxFont(10, wxFONTFAMILY_TELETYPE, wxFONTSTYLE_NORMAL, wxFONTWEIGHT_NORMAL);

(m_TotalLength > 0)

wxGraphicsContext *gc = wxGraphicsContext::Create();

gc->SetFont(m_Font, *wxBLACK);

CalculateFontWidthAndHeight(gc);

m_NumCols = CalculateNumCols();

m_NumRows =

(m_NumAlignRows * (m_TotalLength / m_NumCols));

m_LastRowLength = m_TotalLength % m_NumCols;

(m_LastRowLength > 0)

m_NumRows += m_NumAlignRows;

SetRowCount(m_NumRows);

wxWindow *win = GetParent();

win = win->GetParent();

(CBioseq_Handle::TId::const_iterator it = bsh.

().begin(); it != bsh.

().end(); ++it)

&

= *(it->GetSeqId());

(

.IsGenbank() &&

.GetGenbank().IsSetAccession())

accession =

.GetGenbank().GetAccession();

(

.IsLocal() &&

.GetLocal().IsStr())

=

.GetLocal().GetStr();

(!accession.empty())

(!

.empty())

(start < seq_plus.size())

seq += seq_plus.substr(start,

);

(real_start >= 0 && real_start < seq_minus.size())

seq += seq_minus.substr(real_start,

);

vector<unsigned int> feats_in_row =

(

(

), align_row);

(0, 0,

,

(

), align_row, feats_in_row, feats_with_exons,

);

( seg < num_segs )

res = start + (pos - (total_len -

));

res = start + total_len - 1 - pos;

( seg < num_segs )

res = start +

- 1;

res = start +

- 1;

( seg < num_segs )

start = length - start -

;

pos2 = length - pos - 1;

(start >= 0 && pos2 >= start && pos2 < start +

)

res = total_len + pos2 - start;

(start >= 0 && start > pos2 && left)

(start >= 0 && start +

- 1 < pos2 && !left)

found_len = total_len +

- 1;

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

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

wxSize sz = GetClientSize();

num_rows =

(GetVisibleRowsEnd() - GetVisibleRowsBegin());

uc =

.GetKeyCode();

wxMessageBox (

(

),

(

), wxOK);

=

(GetVisibleRowsBegin());

( y_row < y &&

<= GetVisibleRowsEnd()+1 )

num_groups = col / 12;

pos_in_group = col % 12;

(pos_in_group != 10 && pos_in_group != 11)

(evt.GetModifiers() == wxMOD_SHIFT)

wxMessageBox (

(

),

(

), wxOK);

wxAutoBufferedPaintDC dc(

);

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

gc->SetFont(

, *wxBLACK);

hidden_rows =

(GetVisibleRowsBegin());

= hidden_rows;

client_y = GetClientSize().y;

(

align_row = start_align_row; align_row <

; ++align_row)

seq_pos = start;

(start, y,

,

(align_row), gc, seq_pos);

wxColour backgroundColour = GetBackgroundColour();

(!backgroundColour.Ok())

backgroundColour = wxSystemSettings::GetColour(wxSYS_COLOUR_3DFACE);

wxSize sz = GetClientSize();

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

gc->SetBrush(wxBrush(backgroundColour));

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

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

wxDouble externalLeading;

gc->GetTextExtent(wxString(

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

gc->GetTextExtent(wxString(

.front()), &width, &height, &descent, &externalLeading);

width = ceil(1+width);

height = ceil(2+height);

width =

(GetClientSize().x);

num_groups = line_length / 12;

line_length = 10*num_groups;

orig_pos = seq_pos;

orig_y = y_label;

(orig_pos,x,y_label,

, align_row, feats_in_row, feats_with_exons, gc);

(start,

,

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

(

pos,

x,

&y,

,

align_row,

vector<unsigned int> &feats_in_row,

<

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

<< seq_pos + 1 + (10 - ((col + 1) % 10));

((col +

.Length()) % 10 == 0 )

gc->SetFont(

, wxColour(255,0,255));

gc->DrawText(

,x,y);

gc->SetFont(

,*wxBLACK);

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

( (col +1) % 10 == 0)

( (col +1) % 10 == 5)

(

start,

col,

,

align_row,

seq_pos,

x,

&y,

vector<unsigned int> &feats_in_row,

<

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

gc->SetFont(

,*wxBLACK);

substr =

[align_row][seq_pos];

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

)

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

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

(

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

gc->SetPen( *wxRED_PEN);

wxPen* pen = wxBLACK_PEN;

default : pen = wxBLACK_PEN;

;

wxString id_label(

[align_row]);

(allowed > pos_label.Length() && allowed < pos_label.Length() + id_label.Length())

id_label = id_label.Left(allowed - pos_label.Length());

=

(allowed - pos_label.Length() - id_label.Length());

id_label = wxString(

[align_row]).Left(allowed);

gc->SetFont(

,*wxRED);

gc->SetFont(

,*wxBLACK);

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

wxDouble externalLeading;

gc->GetTextExtent(id_label + wxString(

,

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

gc->SetFont(

,wxColour(255,0,255));

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

gc->SetFont(

,*wxBLACK);

(

,

align_row,

x,

&y,

vector<unsigned int> &feats_in_row,

<

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

(

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

= feats_in_row[k];

gc->DrawText(wxString(

),x,y);

vector<unsigned int> feats_in_row;

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

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

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

feats_in_row.push_back(

(

));

(

,

align_row,

seq_pos,

x,

&y,

vector<unsigned int> &feats_in_row,

<

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

(

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

= feats_in_row[k];

startpoint =

;

endpoint =

;

(

!= feats_with_exons.end())

(

m = 0; m <

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

j =

->second[m];

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

(seq_pos == start)

(seq_pos == stop)

gc->SetBrush(*wxBLACK_BRUSH);

(

[align_row][

] == objects::CBioseq_Handle::eStrand_Plus)

gc->DrawLines(3,lines);

gc->DrawLines(3,lines);

found =

;

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

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

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

vector<pair<TSeqPos,TSeqPos> > feat_whole_range;

vector< vector<TSeqPos> > feat_length_before;

vector<TSeqPos> feat_total_length;

vector<TSeqPos> length_before;

length_before.push_back(length);

feat_whole_range.push_back(pair<TSeqPos,TSeqPos>(start,stop));

feat_total_length.push_back(length);

feat_length_before.push_back(length_before);

vector<unsigned int> ranges;

(

j=0; j<

[align_row][

].size(); j++)

row_end = row_start +

- 1;

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

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

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

ranges.push_back(j);

(

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

= feats_in_row[k];

(!ranges.empty())

feats_with_exons[

] = ranges;

feats_with_exons;

void ReportPos(int pos, const string &label)

void ReportRange(int pos1, int pos2, const string &label)

void GetLabel(string *label, ELabelType type, bool worst=false) const

const CSeq_id & GetSeq_id(TDim row) const

vector< vector< TSeqPos > > m_FeatTotalLength

void CalculateFontWidthAndHeight(wxGraphicsContext *gc)

vector< vector< vector< TSeqPos > > > m_FeatLengthBefore

virtual void OnUpdate()

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

CAlignmentAssistant * m_Parent

int AlignPosToSeqPos(int pos, int row, bool left) const

int FindRowByCoord(int y, int &y_row)

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

vector< CDense_seg::TDim > m_visible_to_row

static string GetSeqTitle(CBioseq_Handle bsh)

virtual void OnEraseBackground(wxEraseEvent &event)

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

void OnMouseDown(wxMouseEvent &evt)

CSeq_align_Handle m_Alignment

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

void DrawTextLine(const unsigned int start, int &y_label, int row, int align_row, wxGraphicsContext *gc, unsigned int &seq_pos)

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

pair< int, int > GetSelection(int row)

void OnMouseDrag(wxMouseEvent &evt)

void SetAlign(CSeq_align_Handle ah)

void DrawFeatureLabels(int row, int align_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

vector< string > m_Labels

void EnableSubstitute(bool enable)

virtual ~CPaintAlignment()

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

void ClearScreen(wxGraphicsContext *gc)

void DrawTopLineNumbers(int align_row, unsigned int seq_pos, int col, int x, int &y, wxGraphicsContext *gc) const

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

int SeqPosToAlignPos(int pos, int row, bool left)

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

void DrawFeatures(int row, int align_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

int LeftMarginWidth() const

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

void EnableFeatures(bool enable)

pair< int, int > GetAlignSelection(void)

void OnResize(wxSizeEvent &)

void NormalizeCursorColRows()

virtual void OnPaint(wxPaintEvent &event)

Painting.

vector< unsigned int > GetFeaturesInRow(int row, int align_row) const

void UpdateFeatures(const vector< vector< vector< pair< TSeqPos, TSeqPos > > > > &feat_ranges, const vector< vector< pair< string, objects::CSeqFeatData::ESubtype > > > &feat_types, const vector< vector< objects::CBioseq_Handle::EVectorStrand > > &feat_strand)

vector< vector< CBioseq_Handle::EVectorStrand > > m_FeatStrand

vector< vector< pair< TSeqPos, TSeqPos > > > m_FeatWholeRange

void OnKeyDown(wxKeyEvent &event)

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

virtual wxCoord OnGetRowHeight(size_t row) const

void DrawTextCell(const unsigned int start, int col, int row, int align_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

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

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.

int TSignedSeqPos

Type for signed sequence position.

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

#define NCBI_THROW(exception_class, err_code, message)

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

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

bool IsNucleotide(void) const

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

CScope & GetScope(void) const

Get scope this handle belongs to.

TSeqPos GetBioseqLength(void) const

const CSeq_align::TSegs & GetSegs(void) const

const TId & GetId(void) const

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static const char label[]

bool CanGetDim(void) const

Check if it is safe to call GetDim method.

const TDenseg & GetDenseg(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetStrands(void) const

Check if a value has been assigned to Strands data member.

const TStarts & GetStarts(void) const

Get the Starts member data.

const TLens & GetLens(void) const

Get the Lens member data.

bool CanGetNumseg(void) const

Check if it is safe to call GetNumseg method.

bool CanGetIds(void) const

Check if it is safe to call GetIds method.

TDim GetDim(void) const

Get the Dim member data.

bool CanGetStarts(void) const

Check if it is safe to call GetStarts method.

TNumseg GetNumseg(void) const

Get the Numseg member data.

const TStrands & GetStrands(void) const

Get the Strands member data.

bool CanGetLens(void) const

Check if it is safe to call GetLens method.

ENa_strand

strand of nucleic acid

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 SLJIT_INLINE sljit_ins lb(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

#define row(bind, expected)

string ToStdString(const wxString &s)

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