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CRawSeqToDeltaSeqByLoc Class Reference

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#include <gui/packages/pkg_sequence_edit/raw_seq_to_delta_by_loc.hpp>

+ Inheritance diagram for CRawSeqToDeltaSeqByLoc:
+ Collaboration diagram for CRawSeqToDeltaSeqByLoc:

Public Member Functions

 CRawSeqToDeltaSeqByLoc ()
 Constructors. More...
 
 CRawSeqToDeltaSeqByLoc (wxWindow *parent, objects::CSeq_entry_Handle tse, wxWindowID id=10000, const wxString &caption=_("Convert Raw Sequence to Delta Sequence"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)
 
bool Create (wxWindow *parent, wxWindowID id=10000, const wxString &caption=_("Convert Raw Sequence to Delta Sequence"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)
 Creation. More...
 
 ~CRawSeqToDeltaSeqByLoc ()
 Destructor. More...
 
void Init ()
 Initialises member variables. More...
 
void CreateControls ()
 Creates the controls and sizers. More...
 
wxBitmap GetBitmapResource (const wxString &name)
 Retrieves bitmap resources. More...
 
wxIcon GetIconResource (const wxString &name)
 Retrieves icon resources. More...
 
void OnNewText (wxCommandEvent &event)
 
CRef< CCmdCompositeapply (string title)
 
void UseAlignCoords (objects::CBioseq_Handle bsh, vector< NRawToDeltaSeq::SGap > &gaps)
 
void ComputeAlignCoords (objects::CBioseq_Handle bsh, int before, int after, int &real_before, int &real_after)
 
- Public Member Functions inherited from CReportEditingDialog
virtual bool Show (bool show=1)
 Report opening events in dialogs used in the editing package. More...
 

Static Public Member Functions

static bool ShowToolTips ()
 Should we show tooltips? More...
 
static void UpdateDensegAlignment (const objects::CSeq_entry_Handle &tse, CRef< CCmdComposite > composite, const vector< NRawToDeltaSeq::SGap > &gaps, const bool use_align_coords)
 
static CRef< CCmdCompositeByAssemblyGapFeatures (objects::CSeq_entry_Handle seh)
 

Private Member Functions

CRef< CCmdCompositeapply_impl (string title, map< objects::CObject_id::TId, objects::CObject_id::TId > &old_to_new, bool create_xref_map)
 

Static Private Member Functions

static void x_UpdateRows (size_t num_rows, const vector< NRawToDeltaSeq::SGap > &gaps, const vector< TSignedSeqPos > &orig_starts, const vector< TSeqPos > &lens, const vector< objects::ENa_strand > &strands, const vector< CRef< objects::CScore > > &scores, vector< vector< vector< TSignedSeqPos > > > &all_new_starts, vector< vector< TSeqPos > > &all_new_lens, vector< vector< vector< objects::ENa_strand > > > &all_new_strands, vector< vector< CRef< objects::CScore > > > &all_new_scores, const bool use_align_coords, const objects::CSeq_align &align)
 
static CRef< objects::CSeq_align > x_GetNewAlign (const size_t block, const objects::CSeq_align &align, const size_t num_rows, const vector< vector< vector< TSignedSeqPos > > > &all_new_starts, const vector< vector< TSeqPos > > &all_new_lens, const vector< vector< vector< objects::ENa_strand > > > &all_new_strands, const vector< vector< CRef< objects::CScore > > > &all_new_scores)
 
static CRef< CCmdCompositeByAssemblyGapFeatures_impl (objects::CSeq_entry_Handle seh, map< objects::CObject_id::TId, objects::CObject_id::TId > &old_to_new, bool create_xref_map)
 

Private Attributes

wxBoxSizer * m_ScrollSizer
 
wxRadioButton * m_CoordSeq
 
wxCheckBox * m_AdjustCDS
 
wxTextCtrl * m_LastStart
 
wxTextCtrl * m_LastLength
 
objects::CSeq_entry_Handle m_TopSeqEntry
 

Detailed Description

CRawSeqToDeltaSeqByLoc class declaration

Definition at line 102 of file raw_seq_to_delta_by_loc.hpp.

Constructor & Destructor Documentation

◆ CRawSeqToDeltaSeqByLoc() [1/2]

CRawSeqToDeltaSeqByLoc::CRawSeqToDeltaSeqByLoc ( )

Constructors.

Definition at line 117 of file raw_seq_to_delta_by_loc.cpp.

References Init().

◆ CRawSeqToDeltaSeqByLoc() [2/2]

CRawSeqToDeltaSeqByLoc::CRawSeqToDeltaSeqByLoc ( wxWindow *  parent,
objects::CSeq_entry_Handle  tse,
wxWindowID  id = 10000,
const wxString &  caption = _("Convert Raw Sequence to Delta Sequence"),
const wxPoint &  pos = wxDefaultPosition,
const wxSize &  size = wxSize(400, 300),
long  style = wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL 
)

◆ ~CRawSeqToDeltaSeqByLoc()

CRawSeqToDeltaSeqByLoc::~CRawSeqToDeltaSeqByLoc ( )

Destructor.

Definition at line 155 of file raw_seq_to_delta_by_loc.cpp.

Member Function Documentation

◆ apply()

CRef< CCmdComposite > CRawSeqToDeltaSeqByLoc::apply ( string  title)

◆ apply_impl()

CRef< CCmdComposite > CRawSeqToDeltaSeqByLoc::apply_impl ( string  title,
map< objects::CObject_id::TId, objects::CObject_id::TId > &  old_to_new,
bool  create_xref_map 
)
private

◆ ByAssemblyGapFeatures()

CRef< CCmdComposite > CRawSeqToDeltaSeqByLoc::ByAssemblyGapFeatures ( objects::CSeq_entry_Handle  seh)
static

◆ ByAssemblyGapFeatures_impl()

CRef< CCmdComposite > CRawSeqToDeltaSeqByLoc::ByAssemblyGapFeatures_impl ( objects::CSeq_entry_Handle  seh,
map< objects::CObject_id::TId, objects::CObject_id::TId > &  old_to_new,
bool  create_xref_map 
)
staticprivate

◆ ComputeAlignCoords()

void CRawSeqToDeltaSeqByLoc::ComputeAlignCoords ( objects::CBioseq_Handle  bsh,
int  before,
int  after,
int real_before,
int real_after 
)

◆ Create()

bool CRawSeqToDeltaSeqByLoc::Create ( wxWindow *  parent,
wxWindowID  id = 10000,
const wxString &  caption = _("Convert Raw Sequence to Delta Sequence"),
const wxPoint &  pos = wxDefaultPosition,
const wxSize &  size = wxSize(400, 300),
long  style = wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL 
)

Creation.

Definition at line 134 of file raw_seq_to_delta_by_loc.cpp.

References CreateControls(), and ncbi::grid::netcache::search::fields::size.

Referenced by CRawSeqToDeltaSeqByLoc().

◆ CreateControls()

void CRawSeqToDeltaSeqByLoc::CreateControls ( )

◆ GetBitmapResource()

wxBitmap CRawSeqToDeltaSeqByLoc::GetBitmapResource ( const wxString &  name)

Retrieves bitmap resources.

Definition at line 334 of file raw_seq_to_delta_by_loc.cpp.

◆ GetIconResource()

wxIcon CRawSeqToDeltaSeqByLoc::GetIconResource ( const wxString &  name)

Retrieves icon resources.

Definition at line 347 of file raw_seq_to_delta_by_loc.cpp.

◆ Init()

void CRawSeqToDeltaSeqByLoc::Init ( void  )

Initialises member variables.

Definition at line 166 of file raw_seq_to_delta_by_loc.cpp.

References m_AdjustCDS, m_CoordSeq, m_ScrollSizer, and NULL.

Referenced by CRawSeqToDeltaSeqByLoc().

◆ OnNewText()

void CRawSeqToDeltaSeqByLoc::OnNewText ( wxCommandEvent &  event)

Definition at line 282 of file raw_seq_to_delta_by_loc.cpp.

References _, m_LastLength, m_LastStart, m_ScrollSizer, and wxID_ANY.

Referenced by CreateControls().

◆ ShowToolTips()

bool CRawSeqToDeltaSeqByLoc::ShowToolTips ( )
static

Should we show tooltips?

Definition at line 325 of file raw_seq_to_delta_by_loc.cpp.

◆ UpdateDensegAlignment()

void CRawSeqToDeltaSeqByLoc::UpdateDensegAlignment ( const objects::CSeq_entry_Handle &  tse,
CRef< CCmdComposite composite,
const vector< NRawToDeltaSeq::SGap > &  gaps,
const bool  use_align_coords 
)
static

◆ UseAlignCoords()

void CRawSeqToDeltaSeqByLoc::UseAlignCoords ( objects::CBioseq_Handle  bsh,
vector< NRawToDeltaSeq::SGap > &  gaps 
)

Definition at line 503 of file raw_seq_to_delta_by_loc.cpp.

References ComputeAlignCoords(), and i.

Referenced by apply_impl().

◆ x_GetNewAlign()

CRef< CSeq_align > CRawSeqToDeltaSeqByLoc::x_GetNewAlign ( const size_t  block,
const objects::CSeq_align &  align,
const size_t  num_rows,
const vector< vector< vector< TSignedSeqPos > > > &  all_new_starts,
const vector< vector< TSeqPos > > &  all_new_lens,
const vector< vector< vector< objects::ENa_strand > > > &  all_new_strands,
const vector< vector< CRef< objects::CScore > > > &  all_new_scores 
)
staticprivate

◆ x_UpdateRows()

void CRawSeqToDeltaSeqByLoc::x_UpdateRows ( size_t  num_rows,
const vector< NRawToDeltaSeq::SGap > &  gaps,
const vector< TSignedSeqPos > &  orig_starts,
const vector< TSeqPos > &  lens,
const vector< objects::ENa_strand > &  strands,
const vector< CRef< objects::CScore > > &  scores,
vector< vector< vector< TSignedSeqPos > > > &  all_new_starts,
vector< vector< TSeqPos > > &  all_new_lens,
vector< vector< vector< objects::ENa_strand > > > &  all_new_strands,
vector< vector< CRef< objects::CScore > > > &  all_new_scores,
const bool  use_align_coords,
const objects::CSeq_align &  align 
)
staticprivate

Member Data Documentation

◆ m_AdjustCDS

wxCheckBox* CRawSeqToDeltaSeqByLoc::m_AdjustCDS
private

Definition at line 165 of file raw_seq_to_delta_by_loc.hpp.

Referenced by apply_impl(), CreateControls(), and Init().

◆ m_CoordSeq

wxRadioButton* CRawSeqToDeltaSeqByLoc::m_CoordSeq
private

Definition at line 164 of file raw_seq_to_delta_by_loc.hpp.

Referenced by apply_impl(), CreateControls(), and Init().

◆ m_LastLength

wxTextCtrl* CRawSeqToDeltaSeqByLoc::m_LastLength
private

Definition at line 167 of file raw_seq_to_delta_by_loc.hpp.

Referenced by CreateControls(), and OnNewText().

◆ m_LastStart

wxTextCtrl* CRawSeqToDeltaSeqByLoc::m_LastStart
private

Definition at line 166 of file raw_seq_to_delta_by_loc.hpp.

Referenced by CreateControls(), and OnNewText().

◆ m_ScrollSizer

wxBoxSizer* CRawSeqToDeltaSeqByLoc::m_ScrollSizer
private

Definition at line 163 of file raw_seq_to_delta_by_loc.hpp.

Referenced by apply_impl(), CreateControls(), Init(), and OnNewText().

◆ m_TopSeqEntry

objects::CSeq_entry_Handle CRawSeqToDeltaSeqByLoc::m_TopSeqEntry
private

Definition at line 169 of file raw_seq_to_delta_by_loc.hpp.

Referenced by apply_impl(), and CreateControls().


The documentation for this class was generated from the following files:
Modified on Fri Jun 14 16:48:14 2024 by modify_doxy.py rev. 669887