CFarPointerSeq Class Reference

Search Toolkit Book for CFarPointerSeq

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

Inheritance diagram for CFarPointerSeq:

Collaboration diagram for CFarPointerSeq:

Public Member Functions
	CFarPointerSeq ()
	Constructors. More...
	CFarPointerSeq (wxWindow *parent, CSeq_entry_Handle seh, wxWindowID id=wxID_ANY, const wxString &caption=_("Far Pointer Sequences"), 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=wxID_ANY, const wxString &caption=_("Far Pointer Sequences"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)
	Creation. More...
	~CFarPointerSeq ()
	Destructor. More...
void	Init ()
	Initialises member variables. More...
void	CreateControls ()
	Creates the controls and sizers. More...
void	OnCheck (wxCommandEvent &event)
void	OnExport (wxCommandEvent &event)
wxBitmap	GetBitmapResource (const wxString &name)
	Retrieves bitmap resources. More...
wxIcon	GetIconResource (const wxString &name)
	Retrieves icon resources. More...
CRef< CCmdComposite >	GetCommand ()
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...

Private Member Functions
string	GetMessageForId (const CSeq_id &id, string label, bool &check, bool &disable)
CRef< objects::CSeq_align >	RunBlast (const CBioseq_Handle &sh, const CBioseq_Handle &qh)
string	ValidateAlignment (CRef< objects::CSeq_align > align, CBioseq_Handle bsh1, CBioseq_Handle bsh2, bool &check)
void	AddSpaces (string &str, const string &label_max, wxGraphicsContext *gc)
void	ReverseRow (CDense_seg &dense_seg, int offset, size_t row, CSeq_align::TDim num_rows)

Private Attributes
wxCheckListBox *	m_CheckListBox
CSeq_entry_Handle	m_TopSeqEntry
vector< bool >	m_disabled
map< string, string >	m_errors
vector< string >	m_labels
map< string, CBioseq_Handle >	m_label_to_bsh1
map< string, CBioseq_Handle >	m_label_to_bsh2
map< CBioseq_Handle, int >	m_offset
map< CBioseq_Handle, bool >	m_flip_strand

Detailed Description

CFarPointerSeq class declaration

Definition at line 77 of file far_pointer_seq.hpp.

Constructor & Destructor Documentation

CFarPointerSeq() [1/2]

CFarPointerSeq::CFarPointerSeq

(

)

Constructors.

Definition at line 94 of file far_pointer_seq.cpp.

References Init().

CFarPointerSeq() [2/2]

CFarPointerSeq::CFarPointerSeq	(	wxWindow *	parent,
		CSeq_entry_Handle	seh,
		wxWindowID	id = wxID_ANY,
		const wxString &	caption = _("Far Pointer Sequences"),
		const wxPoint &	pos = wxDefaultPosition,
		const wxSize &	size = wxSize(400, 300),
		long	style = wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL
	)

Definition at line 99 of file far_pointer_seq.cpp.

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

~CFarPointerSeq()

CFarPointerSeq::~CFarPointerSeq

(

)

Destructor.

Definition at line 132 of file far_pointer_seq.cpp.

Member Function Documentation

AddSpaces()

void CFarPointerSeq::AddSpaces ( string &  str, const string &  label_max, wxGraphicsContext *  gc  )

private

Definition at line 225 of file far_pointer_seq.cpp.

References _, int, str(), and string.

Referenced by CreateControls().

Create()

bool CFarPointerSeq::Create	(	wxWindow *	parent,
		wxWindowID	id = wxID_ANY,
		const wxString &	caption = _("Far Pointer Sequences"),
		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 111 of file far_pointer_seq.cpp.

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

Referenced by CFarPointerSeq().

CreateControls()

void CFarPointerSeq::CreateControls

(

)

Creates the controls and sizers.

Definition at line 155 of file far_pointer_seq.cpp.

References _, AddSpaces(), check, CSeq_id::eContent, eUnknown, GetMessageForId(), i, ID_FARPOINTERSEQ_CHECKLISTBOX, ID_FARPOINTERSEQ_EXPORT, label, m_CheckListBox, m_disabled, m_errors, m_labels, m_TopSeqEntry, msg(), NCBI_THROW, and row.

Referenced by Create().

GetBitmapResource()

wxBitmap CFarPointerSeq::GetBitmapResource

(

const wxString &

name

)

Retrieves bitmap resources.

Definition at line 388 of file far_pointer_seq.cpp.

GetCommand()

CRef< CCmdComposite > CFarPointerSeq::GetCommand

(

void

)

Definition at line 270 of file far_pointer_seq.cpp.

References CSeq_id::Assign(), CSerialObject::Assign(), cmd, CBioseq_set_Base::eClass_nuc_prot, eGetId_Best, CScope::GetBioseqHandle(), CBioseq_set_Handle::GetClass(), GetId(), CBioseq_Handle::GetParentBioseq_set(), CSeq_entry_Handle::GetScope(), CSeq_id_Handle::GetSeqId(), i, CBioseq_set_Handle::IsSetClass(), label, m_CheckListBox, m_flip_strand, m_label_to_bsh1, m_label_to_bsh2, m_labels, m_offset, m_TopSeqEntry, offset, CSeq_align::OffsetRow(), ReverseRow(), row, and CSeq_align_Base::SetSegs().

Referenced by CSequenceEditingEventHandler::FarPointerSeq().

GetIconResource()

wxIcon CFarPointerSeq::GetIconResource

(

const wxString &

name

)

Retrieves icon resources.

Definition at line 401 of file far_pointer_seq.cpp.

GetMessageForId()

string CFarPointerSeq::GetMessageForId ( const CSeq_id &  id, string  label, bool &  check, bool &  disable  )

private

Definition at line 410 of file far_pointer_seq.cpp.

References check, CSeq_id::fParse_Default, CScope::GetBioseqHandle(), CSeq_entry_Handle::GetScope(), kEmptyStr, label, m_label_to_bsh1, m_label_to_bsh2, m_TopSeqEntry, RunBlast(), NStr::StartsWith(), NStr::TrimPrefixInPlace(), and ValidateAlignment().

Referenced by CreateControls().

Init()

void CFarPointerSeq::Init

(

void

)

Initialises member variables.

Definition at line 143 of file far_pointer_seq.cpp.

References m_CheckListBox, and NULL.

Referenced by CFarPointerSeq().

OnCheck()

void CFarPointerSeq::OnCheck

(

wxCommandEvent &

event

)

Definition at line 243 of file far_pointer_seq.cpp.

References i, m_CheckListBox, and m_disabled.

OnExport()

void CFarPointerSeq::OnExport

(

wxCommandEvent &

event

)

Definition at line 255 of file far_pointer_seq.cpp.

References map_checker< Container >::begin(), map_checker< Container >::end(), i, m_errors, msg(), CGenericReportDlgModal::SetText(), and wxT.

ReverseRow()

void CFarPointerSeq::ReverseRow ( CDense_seg &  dense_seg, int  offset, size_t  row, CSeq_align::TDim  num_rows  )

private

Definition at line 347 of file far_pointer_seq.cpp.

References eNa_strand_minus, eNa_strand_plus, CDense_seg_Base::GetLens(), CDense_seg_Base::GetStarts(), CDense_seg_Base::GetStrands(), i, CDense_seg_Base::IsSetStrands(), offset, row, CDense_seg_Base::SetStarts(), CDense_seg_Base::SetStrands(), and ncbi::grid::netcache::search::fields::size.

Referenced by GetCommand().

RunBlast()

CRef< objects::CSeq_align > CFarPointerSeq::RunBlast ( const CBioseq_Handle &  sh, const CBioseq_Handle &  qh  )

private

Definition at line 450 of file far_pointer_seq.cpp.

References eMegablast, CSeq_align_set_Base::Get(), CBioseq_Handle::GetRangeSeq_loc(), CBioseq_Handle::GetScope(), CRef< C, Locker >::IsNull(), CSeq_align_set_Base::IsSet(), and NULL.

Referenced by GetMessageForId().

ShowToolTips()

bool CFarPointerSeq::ShowToolTips ( )

static

Should we show tooltips?

Definition at line 379 of file far_pointer_seq.cpp.

ValidateAlignment()

string CFarPointerSeq::ValidateAlignment ( CRef< objects::CSeq_align >  align, CBioseq_Handle  bsh1, CBioseq_Handle  bsh2, bool &  check  )

private

Definition at line 481 of file far_pointer_seq.cpp.

References a, b, check, eNa_strand_plus, CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetSeqId(), i, len, m_flip_strand, m_offset, n, swap(), tmp, and NStr::ULongToString().

Referenced by GetMessageForId().

Member Data Documentation

m_CheckListBox

wxCheckListBox* CFarPointerSeq::m_CheckListBox

private

Definition at line 125 of file far_pointer_seq.hpp.

Referenced by CreateControls(), GetCommand(), Init(), and OnCheck().

m_disabled

vector<bool> CFarPointerSeq::m_disabled

private

Definition at line 128 of file far_pointer_seq.hpp.

Referenced by CreateControls(), and OnCheck().

m_errors

map<string, string> CFarPointerSeq::m_errors

private

Definition at line 129 of file far_pointer_seq.hpp.

Referenced by CreateControls(), and OnExport().

m_flip_strand

map<CBioseq_Handle, bool> CFarPointerSeq::m_flip_strand

private

Definition at line 134 of file far_pointer_seq.hpp.

Referenced by GetCommand(), and ValidateAlignment().

m_label_to_bsh1

map<string, CBioseq_Handle> CFarPointerSeq::m_label_to_bsh1

private

Definition at line 131 of file far_pointer_seq.hpp.

Referenced by GetCommand(), and GetMessageForId().

m_label_to_bsh2

map<string, CBioseq_Handle> CFarPointerSeq::m_label_to_bsh2

private

Definition at line 132 of file far_pointer_seq.hpp.

Referenced by GetCommand(), and GetMessageForId().

m_labels

vector<string> CFarPointerSeq::m_labels

private

Definition at line 130 of file far_pointer_seq.hpp.

Referenced by CreateControls(), and GetCommand().

m_offset

map<CBioseq_Handle, int> CFarPointerSeq::m_offset

private

Definition at line 133 of file far_pointer_seq.hpp.

Referenced by GetCommand(), and ValidateAlignment().

m_TopSeqEntry

CSeq_entry_Handle CFarPointerSeq::m_TopSeqEntry

private

Definition at line 127 of file far_pointer_seq.hpp.

Referenced by CreateControls(), GetCommand(), and GetMessageForId().

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The documentation for this class was generated from the following files:

• include/gui/packages/pkg_sequence_edit/far_pointer_seq.hpp
• src/gui/packages/pkg_sequence_edit/far_pointer_seq.cpp