CRemoveSeqFromAlignDlg Class Reference

Search Toolkit Book for CRemoveSeqFromAlignDlg

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

Inheritance diagram for CRemoveSeqFromAlignDlg:

Collaboration diagram for CRemoveSeqFromAlignDlg:

Public Member Functions
	CRemoveSeqFromAlignDlg ()
	Constructors. More...
	CRemoveSeqFromAlignDlg (wxWindow *parent, objects::CSeq_entry_Handle seh, wxWindowID id=12000, const wxString &caption=_("Remove Sequences From Alignments"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)
bool	Create (wxWindow *parent, wxWindowID id=12000, const wxString &caption=_("Remove Sequences From Alignments"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)
	Creation. More...
	~CRemoveSeqFromAlignDlg ()
	Destructor. More...
void	Init ()
	Initialises member variables. More...
void	Init (objects::CSeq_entry_Handle seh)
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...
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...
static void	ApplyToCSeq_entry (objects::CSeq_entry_Handle tse, CCmdComposite *composite, const vector< string > &names)

Private Member Functions
void	GetAlignLabel (const CSeq_align &align)
void	SearchSeq_entry (objects::CSeq_entry_Handle tse, const CSeq_entry &se)

Static Private Member Functions
static bool	RemoveIdLabel (const CSeq_align &align, string name, bool &modified)
static void	ModifyAlign (CRef< CSeq_align > align, const string name)
static bool	GetIdsFromLocs (const CStd_seg::TLoc &locs, set< string > &labels, const string name="", bool detect=false, bool found=false)
static bool	GetIdsFromLoc (const CSeq_loc &loc, set< string > &labels, const string name="", bool detect=false, bool found=false)

Private Attributes
objects::CSeq_entry_Handle	m_TopSeqEntry
set< string >	m_Label
wxListCtrl *	m_ListCtrl

Detailed Description

Definition at line 77 of file remove_sequences_from_alignments.hpp.

Constructor & Destructor Documentation

CRemoveSeqFromAlignDlg() [1/2]

CRemoveSeqFromAlignDlg::CRemoveSeqFromAlignDlg

(

)

Constructors.

Definition at line 102 of file remove_sequences_from_alignments.cpp.

References Init().

CRemoveSeqFromAlignDlg() [2/2]

CRemoveSeqFromAlignDlg::CRemoveSeqFromAlignDlg	(	wxWindow *	parent,
		objects::CSeq_entry_Handle	seh,
		wxWindowID	id = 12000,
		const wxString &	caption = _("Remove Sequences From Alignments"),
		const wxPoint &	pos = wxDefaultPosition,
		const wxSize &	size = wxDefaultSize,
		long	style = wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL
	)

Definition at line 107 of file remove_sequences_from_alignments.cpp.

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

~CRemoveSeqFromAlignDlg()

CRemoveSeqFromAlignDlg::~CRemoveSeqFromAlignDlg

(

)

Destructor.

Definition at line 132 of file remove_sequences_from_alignments.cpp.

Member Function Documentation

ApplyToCSeq_entry()

void CRemoveSeqFromAlignDlg::ApplyToCSeq_entry ( objects::CSeq_entry_Handle  tse, CCmdComposite *  composite, const vector< string > &  names  )

static

Definition at line 519 of file remove_sequences_from_alignments.cpp.

References CCmdComposite::AddCommand(), CSerialObject::Assign(), CSeq_align::CheckNumRows(), cmd, ModifyAlign(), names, and RemoveIdLabel().

Referenced by GetCommand(), and CSequenceEditingEventHandler::WithdrawSequences().

Create()

bool CRemoveSeqFromAlignDlg::Create	(	wxWindow *	parent,
		wxWindowID	id = 12000,
		const wxString &	caption = _("Remove Sequences From Alignments"),
		const wxPoint &	pos = wxDefaultPosition,
		const wxSize &	size = wxDefaultSize,
		long	style = wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL
	)

Creation.

Definition at line 115 of file remove_sequences_from_alignments.cpp.

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

Referenced by CRemoveSeqFromAlignDlg().

CreateControls()

void CRemoveSeqFromAlignDlg::CreateControls

(

)

Creates the controls and sizers.

Definition at line 155 of file remove_sequences_from_alignments.cpp.

References _, set< Key, Compare >::begin(), set< Key, Compare >::end(), i, ID_LISTCTRL_SEQ_ALIGN, m_Label, m_ListCtrl, and ToWxString().

Referenced by Create().

GetAlignLabel()

void CRemoveSeqFromAlignDlg::GetAlignLabel ( const CSeq_align &  align )

private

Definition at line 283 of file remove_sequences_from_alignments.cpp.

References a, CSeq_align_Base::C_Segs::e_Dendiag, CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_Packed, CSeq_align_Base::C_Segs::e_Sparse, CSeq_align_Base::C_Segs::e_Spliced, CSeq_align_Base::C_Segs::e_Std, CSeq_align_set_Base::Get(), CSeq_align_Base::C_Segs::GetDendiag(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::C_Segs::GetDisc(), CSpliced_seg_Base::GetGenomic_id(), GetIdLabel(), GetIds(), GetIdsFromLocs(), CSeq_align_Base::C_Segs::GetPacked(), CSpliced_seg_Base::GetProduct_id(), CSparse_seg_Base::GetRows(), CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::GetSparse(), CSeq_align_Base::C_Segs::GetSpliced(), CSeq_align_Base::C_Segs::GetStd(), CSpliced_seg_Base::IsSetGenomic_id(), CSpliced_seg_Base::IsSetProduct_id(), CSparse_seg_Base::IsSetRows(), CSeq_align_Base::IsSetSegs(), m_Label, and CSeq_align_Base::C_Segs::Which().

Referenced by SearchSeq_entry().

GetBitmapResource()

wxBitmap CRemoveSeqFromAlignDlg::GetBitmapResource

(

const wxString &

name

)

Retrieves bitmap resources.

Get bitmap resources

Definition at line 200 of file remove_sequences_from_alignments.cpp.

GetCommand()

CRef< CCmdComposite > CRemoveSeqFromAlignDlg::GetCommand

(

void

)

Definition at line 410 of file remove_sequences_from_alignments.cpp.

References ApplyToCSeq_entry(), cmd, m_ListCtrl, m_TopSeqEntry, names, and ToStdString().

Referenced by CSequenceEditingEventHandler::RemoveSequencesFromAlignments().

GetIconResource()

wxIcon CRemoveSeqFromAlignDlg::GetIconResource

(

const wxString &

name

)

Retrieves icon resources.

Get icon resources

Definition at line 211 of file remove_sequences_from_alignments.cpp.

GetIdsFromLoc()

bool CRemoveSeqFromAlignDlg::GetIdsFromLoc ( const CSeq_loc &  loc, set< string > &  labels, const string  name = "", bool  detect = false, bool  found = false  )

staticprivate

Definition at line 249 of file remove_sequences_from_alignments.cpp.

References CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Equiv, CSeq_loc_Base::e_Feat, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, GetIdLabel(), and GetSeqId().

Referenced by GetIdsFromLocs().

GetIdsFromLocs()

bool CRemoveSeqFromAlignDlg::GetIdsFromLocs ( const CStd_seg::TLoc &  locs, set< string > &  labels, const string  name = "", bool  detect = false, bool  found = false  )

staticprivate

Definition at line 242 of file remove_sequences_from_alignments.cpp.

References GetIdsFromLoc(), and l().

Referenced by GetAlignLabel(), and RemoveIdLabel().

Init() [1/2]

void CRemoveSeqFromAlignDlg::Init

(

void

)

Initialises member variables.

Member initialisation

Definition at line 141 of file remove_sequences_from_alignments.cpp.

References m_ListCtrl, and NULL.

Referenced by CRemoveSeqFromAlignDlg().

Init() [2/2]

void CRemoveSeqFromAlignDlg::Init

(

objects::CSeq_entry_Handle

seh

)

Definition at line 146 of file remove_sequences_from_alignments.cpp.

References m_ListCtrl, NULL, and SearchSeq_entry().

ModifyAlign()

void CRemoveSeqFromAlignDlg::ModifyAlign ( CRef< CSeq_align >  align, const string  name  )

staticprivate

Definition at line 428 of file remove_sequences_from_alignments.cpp.

References CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Sparse, CSeq_align_Base::C_Segs::GetDenseg(), CSparse_seg_Base::GetExt(), GetIdLabel(), GetIds(), CDense_seg_Base::GetIds(), CDense_seg_Base::GetNumseg(), CSparse_seg_Base::GetRow_scores(), CSparse_seg_Base::GetRows(), CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::GetSparse(), CDense_seg_Base::GetStarts(), CDense_seg_Base::GetStrands(), i, CSparse_seg_Base::IsSetExt(), CDense_seg_Base::IsSetNumseg(), CSparse_seg_Base::IsSetRow_scores(), CSparse_seg_Base::IsSetRows(), CSeq_align_Base::IsSetSegs(), CDense_seg_Base::IsSetStarts(), CDense_seg_Base::IsSetStrands(), CSeq_align_Base::SetDim(), CSeq_align_Base::SetSegs(), and CSeq_align_Base::C_Segs::Which().

Referenced by ApplyToCSeq_entry().

RemoveIdLabel()

bool CRemoveSeqFromAlignDlg::RemoveIdLabel ( const CSeq_align &  align, string  name, bool &  modified  )

staticprivate

Definition at line 335 of file remove_sequences_from_alignments.cpp.

References a, CSeq_align_Base::C_Segs::e_Dendiag, CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_Packed, CSeq_align_Base::C_Segs::e_Sparse, CSeq_align_Base::C_Segs::e_Spliced, CSeq_align_Base::C_Segs::e_Std, find_id(), CSeq_align_set_Base::Get(), CSeq_align_Base::C_Segs::GetDendiag(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::C_Segs::GetDisc(), CSpliced_seg_Base::GetGenomic_id(), GetIdLabel(), GetIds(), CDense_seg_Base::GetIds(), CPacked_seg_Base::GetIds(), GetIdsFromLocs(), CSeq_align_Base::C_Segs::GetPacked(), CSpliced_seg_Base::GetProduct_id(), CSparse_seg_Base::GetRows(), CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::GetSparse(), CSeq_align_Base::C_Segs::GetSpliced(), CSeq_align_Base::C_Segs::GetStd(), CSpliced_seg_Base::IsSetGenomic_id(), CSpliced_seg_Base::IsSetProduct_id(), CSparse_seg_Base::IsSetRows(), CSeq_align_Base::IsSetSegs(), and CSeq_align_Base::C_Segs::Which().

Referenced by ApplyToCSeq_entry().

SearchSeq_entry()

void CRemoveSeqFromAlignDlg::SearchSeq_entry ( objects::CSeq_entry_Handle  tse, const CSeq_entry &  se  )

private

Definition at line 218 of file remove_sequences_from_alignments.cpp.

References a, CSeq_annot_CI::eSearch_entry, FOR_EACH_SEQENTRY_ON_SEQSET, CSeq_annot_Base::C_Data::GetAlign(), GetAlignLabel(), CSeq_annot_Base::GetData(), CSeq_entry_Handle::GetScope(), CScope::GetSeq_entryHandle(), CSeq_entry_Base::GetSet(), CSeq_annot_Base::C_Data::IsAlign(), CSeq_entry_Base::IsSet(), and CSeq_annot_Base::IsSetData().

Referenced by Init().

ShowToolTips()

bool CRemoveSeqFromAlignDlg::ShowToolTips ( )

static

Should we show tooltips?

Should we show tooltips?

Definition at line 191 of file remove_sequences_from_alignments.cpp.

Member Data Documentation

m_Label

set<string> CRemoveSeqFromAlignDlg::m_Label

private

Definition at line 114 of file remove_sequences_from_alignments.hpp.

Referenced by CreateControls(), and GetAlignLabel().

m_ListCtrl

wxListCtrl* CRemoveSeqFromAlignDlg::m_ListCtrl

private

Definition at line 115 of file remove_sequences_from_alignments.hpp.

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

m_TopSeqEntry

objects::CSeq_entry_Handle CRemoveSeqFromAlignDlg::m_TopSeqEntry

private

Definition at line 113 of file remove_sequences_from_alignments.hpp.

Referenced by GetCommand().

---

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

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