CVectorTrimPanel Class Reference

Search Toolkit Book for CVectorTrimPanel

#include <gui/widgets/edit/vectortrimpanel.hpp>

Inheritance diagram for CVectorTrimPanel:

Collaboration diagram for CVectorTrimPanel:

Public Types
enum	{ ID_CVECTORTRIMPANEL = wxID_ANY }
	@begin CVectorTrimPanel member variables More...
enum	EInternalTrimType { eTrimToClosestEnd = 0 , eTrimTo5PrimeEnd , eTrimTo3PrimeEnd }

Public Member Functions
	CVectorTrimPanel ()
	Constructors. More...
	CVectorTrimPanel (wxWindow *parent, objects::CSeq_entry_Handle seh, ICommandProccessor *cmdProcessor, wxWindowID id=ID_CVECTORTRIMPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxTAB_TRAVERSAL)
bool	Create (wxWindow *parent, wxWindowID id=ID_CVECTORTRIMPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxTAB_TRAVERSAL)
	Creation. More...
	~CVectorTrimPanel ()
	Destructor. More...
void	Init ()
	Initialises member variables. More...
void	CreateControls ()
	Creates the controls and sizers. More...
virtual bool	TransferDataToWindow ()
virtual bool	TransferDataFromWindow ()
void	OnRunVecscreen (wxCommandEvent &event)
void	OnSort (wxCommandEvent &event)
void	OnSelectAll (wxCommandEvent &event)
void	OnSelectStrongModerate (wxCommandEvent &event)
void	OnUnselectAll (wxCommandEvent &event)
void	OnUnselectInternal (wxCommandEvent &event)
void	OnMakeReport (wxCommandEvent &event)
void	OnTrimSelected (wxCommandEvent &event)
void	OnDismiss (wxCommandEvent &event)
void	OnFindForward (wxCommandEvent &event)
void	OnFindReverse (wxCommandEvent &event)
wxBitmap	GetBitmapResource (const wxString &name)
	Retrieves bitmap resources. More...
wxIcon	GetIconResource (const wxString &name)
	Retrieves icon resources. More...
void	DisplaySummaryBySeqid (const TVecscreenSummaryBySeqid &vecscreen_summary)

Static Public Member Functions
static bool	ShowToolTips ()
	Should we show tooltips? More...

Private Types
typedef vector< SRangeMatch >	TCuts

Private Member Functions
bool	x_TrimSelected ()
void	x_TrimSelected (CRef< CCmdComposite > command, const CSeq_id *seqid, const SVecscreenResult &vecres)
void	x_SetSeqData (const CBioseq_Handle &bsh, CRef< objects::CSeq_inst > inst, const TCuts &sorted_cuts)
void	x_TrimFeatureLocations (CRef< CSeq_feat > feat, const TCuts &sorted_cuts, const CSeq_id *seqid, bool &bFeatureDeleted, bool &bFeatureTrimmed, bool &bProdDeleted, bool &bProdTrimmed)
void	x_SeqLocDelete (CRef< CSeq_loc > loc, TSeqPos from, TSeqPos to, const CSeq_id *seqid, bool &bCompleteCut, bool &bTrimmed)
void	x_SeqIntervalDelete (CRef< CSeq_interval > interval, TSeqPos cut_from, TSeqPos cut_to, const CSeq_id *seqid, bool &bCompleteCut, bool &bTrimmed)
void	x_AdjustInternalCutLocations (TCuts &cuts, TSeqPos seq_length)
void	x_FindCompleteDeletions (const TVecscreenSummaryBySeqid &seqidSummary, TVecscreenSummaryBySeqid &completeDeletions, TVecscreenSummaryBySeqid &trimOnly)
bool	x_IsCompleteCut (const TCuts &sorted_cuts, TSeqPos seq_length)
void	x_MergeCuts (TCuts &sorted_cuts)
void	x_DeleteSelected (CRef< CCmdComposite > command, const CSeq_id *seqid)
void	x_RetranslateCDS (CScope &scope, CRef< CCmdComposite > command, CRef< CSeq_feat > cds)
void	x_AdjustDensegAlignment (CRef< CSeq_align > align, CDense_seg::TDim row, const TCuts &sorted_cuts)
void	x_CutDensegSegment (CRef< CSeq_align > align, CDense_seg::TDim row, TSeqPos pos)
bool	x_FindSegment (const CDense_seg &denseg, CDense_seg::TDim row, TSeqPos pos, CDense_seg::TNumseg &seg, TSeqPos &seg_start) const
void	x_TrimAlignments (CRef< CCmdComposite > command, const TVecscreenSummaryBySeqid &trimOnly)
void	x_GetSortedCuts (TCuts &sorted_cuts, const CSeq_id *seqid)
void	x_TrimSeqGraphs (CRef< CCmdComposite > command, const TVecscreenSummaryBySeqid &trimOnly)
void	x_TrimSeqGraphData (CRef< CSeq_graph > new_graph, const CMappedGraph &orig_graph, const TCuts &sorted_cuts, const CSeq_id *seqid)
void	x_UpdateSeqGraphLoc (CRef< CSeq_graph > new_graph, const TCuts &sorted_cuts, const CSeq_id *seqid)
void	x_GetTrimCoordinates (const TCuts &sorted_cuts, const CSeq_id *seqid, TSeqPos &trim_start, TSeqPos &trim_stop)
CRange< TSeqPos >	x_GetRetainedRange (const TCuts &sorted_cuts, TSeqPos seqLength)

Private Attributes
objects::CSeq_entry_Handle	m_TopSeqEntry
ICommandProccessor *	m_CmdProcessor
CVectorScreen	m_vectorscreen
wxBoxSizer *	m_sizerVectorResults
CMatchesListCtrl *	m_listMatches
wxHtmlWindow *	m_viewAlignGraphic
CLocationsListCtrl *	m_listLocations
wxButton *	m_buttonRunVecscreen
wxGauge *	m_gaugeProgressBar
wxTextCtrl *	m_textFind
wxButton *	m_buttonFindForward
wxButton *	m_buttonFindReverse
wxRadioBox *	m_radioBoxSort
wxRadioBox *	m_radioBoxInternalTrimOptions
wxButton *	m_buttonSelectAll
wxButton *	m_buttonUnselectAll
wxButton *	m_buttonUnselectInternal
wxButton *	m_buttonSelectStrongModerate
wxCheckBox *	m_checkboxViewGraphic
wxCheckBox *	m_CitSub
wxButton *	m_buttonMakeReport
wxButton *	m_buttonTrimSelected
wxButton *	m_buttonDismiss
wxWindow *	m_pParentWindow

Detailed Description

CVectorTrimPanel class declaration

Definition at line 90 of file vectortrimpanel.hpp.

Member Typedef Documentation

TCuts

typedef vector<SRangeMatch> CVectorTrimPanel::TCuts

private

Definition at line 171 of file vectortrimpanel.hpp.

Member Enumeration Documentation

anonymous enum

anonymous enum

@begin CVectorTrimPanel member variables

Control identifiers

Enumerator
ID_CVECTORTRIMPANEL

Definition at line 159 of file vectortrimpanel.hpp.

EInternalTrimType

enum CVectorTrimPanel::EInternalTrimType

Enumerator
eTrimToClosestEnd
eTrimTo5PrimeEnd
eTrimTo3PrimeEnd

Definition at line 163 of file vectortrimpanel.hpp.

Constructor & Destructor Documentation

CVectorTrimPanel() [1/2]

CVectorTrimPanel::CVectorTrimPanel

(

)

Constructors.

CVectorTrimPanel type definition

CVectorTrimPanel event table definition

CVectorTrimPanel constructors

Definition at line 152 of file vectortrimpanel.cpp.

References Init(), and NULL.

CVectorTrimPanel() [2/2]

CVectorTrimPanel::CVectorTrimPanel	(	wxWindow *	parent,
		objects::CSeq_entry_Handle	seh,
		ICommandProccessor *	cmdProcessor,
		wxWindowID	id = ID_CVECTORTRIMPANEL,
		const wxPoint &	pos = wxDefaultPosition,
		const wxSize &	size = wxDefaultSize,
		long	style = wxTAB_TRAVERSAL
	)

~CVectorTrimPanel()

CVectorTrimPanel::~CVectorTrimPanel

(

)

Destructor.

CVectorTrimPanel destructor

Definition at line 197 of file vectortrimpanel.cpp.

Member Function Documentation

Create()

bool CVectorTrimPanel::Create	(	wxWindow *	parent,
		wxWindowID	id = ID_CVECTORTRIMPANEL,
		const wxPoint &	pos = wxDefaultPosition,
		const wxSize &	size = wxDefaultSize,
		long	style = wxTAB_TRAVERSAL
	)

Creation.

CVectorTrimPanel creator

Definition at line 175 of file vectortrimpanel.cpp.

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

CreateControls()

void CVectorTrimPanel::CreateControls

(

)

Creates the controls and sizers.

Control creation for CVectorTrimPanel

Definition at line 219 of file vectortrimpanel.cpp.

References _, CVectorScreen::IsDbAvailable(), m_buttonDismiss, m_buttonFindForward, m_buttonFindReverse, m_buttonMakeReport, m_buttonRunVecscreen, m_buttonSelectAll, m_buttonSelectStrongModerate, m_buttonTrimSelected, m_buttonUnselectAll, m_buttonUnselectInternal, m_CitSub, m_gaugeProgressBar, m_listLocations, m_listMatches, m_radioBoxInternalTrimOptions, m_radioBoxSort, m_sizerVectorResults, m_textFind, m_viewAlignGraphic, MYID_BUTTON_DISMISS, MYID_BUTTON_FIND_FORWARD, MYID_BUTTON_FIND_REVERSE, MYID_BUTTON_MAKE_REPORT, MYID_BUTTON_RUN_VECSCREEN, MYID_BUTTON_SELECT_ALL, MYID_BUTTON_SELECT_STRONG_MODERATE, MYID_BUTTON_TRIM_SELECTED, MYID_BUTTON_UNSELECT_ALL, MYID_BUTTON_UNSELECT_INTERNAL, MYID_LISTCTRL_LOCATIONS, MYID_LISTCTRL_MATCHES, MYID_RADIOBOX_INTERNAL_TRIM_OPTIONS, MYID_RADIOBOX_SORT, MYID_WEBVIEW_GRAPHIC, CMatchesListCtrl::SetAlignGraphicView(), CMatchesListCtrl::SetRangeView(), and wxID_ANY.

Referenced by Create().

DisplaySummaryBySeqid()

void CVectorTrimPanel::DisplaySummaryBySeqid

(

const TVecscreenSummaryBySeqid &

vecscreen_summary

)

Definition at line 1913 of file vectortrimpanel.cpp.

References m_listMatches, and CMatchesListCtrl::UpdateData().

Referenced by OnRunVecscreen().

GetBitmapResource()

wxBitmap CVectorTrimPanel::GetBitmapResource

(

const wxString &

name

)

Retrieves bitmap resources.

Get bitmap resources

Definition at line 383 of file vectortrimpanel.cpp.

GetIconResource()

wxIcon CVectorTrimPanel::GetIconResource

(

const wxString &

name

)

Retrieves icon resources.

Get icon resources

Definition at line 396 of file vectortrimpanel.cpp.

Init()

void CVectorTrimPanel::Init

(

void

)

Initialises member variables.

Member initialisation

Definition at line 208 of file vectortrimpanel.cpp.

OnDismiss()

void CVectorTrimPanel::OnDismiss

(

wxCommandEvent &

event

)

Definition at line 493 of file vectortrimpanel.cpp.

References m_pParentWindow.

OnFindForward()

void CVectorTrimPanel::OnFindForward

(

wxCommandEvent &

event

)

Definition at line 501 of file vectortrimpanel.cpp.

References CMatchesListCtrl::FindForward(), m_listMatches, and m_textFind.

OnFindReverse()

void CVectorTrimPanel::OnFindReverse

(

wxCommandEvent &

event

)

Definition at line 507 of file vectortrimpanel.cpp.

References CMatchesListCtrl::FindReverse(), m_listMatches, and m_textFind.

OnMakeReport()

void CVectorTrimPanel::OnMakeReport

(

wxCommandEvent &

event

)

Definition at line 467 of file vectortrimpanel.cpp.

References CMatchesListCtrl::GetReport(), m_listMatches, and CVecscreenReport::SetReport().

OnRunVecscreen()

void CVectorTrimPanel::OnRunVecscreen

(

wxCommandEvent &

event

)

Definition at line 406 of file vectortrimpanel.cpp.

References DisplaySummaryBySeqid(), CVectorScreen::GetVecscreenSummaryBySeqid(), m_buttonTrimSelected, m_gaugeProgressBar, m_TopSeqEntry, m_vectorscreen, and CVectorScreen::Run().

OnSelectAll()

void CVectorTrimPanel::OnSelectAll

(

wxCommandEvent &

event

)

Definition at line 442 of file vectortrimpanel.cpp.

References m_listMatches, and CMatchesListCtrl::SelectAll().

OnSelectStrongModerate()

void CVectorTrimPanel::OnSelectStrongModerate

(

wxCommandEvent &

event

)

Definition at line 448 of file vectortrimpanel.cpp.

References m_listMatches, and CMatchesListCtrl::SelectStrongModerate().

OnSort()

void CVectorTrimPanel::OnSort

(

wxCommandEvent &

event

)

Definition at line 414 of file vectortrimpanel.cpp.

References CMatchesListCtrl::eSortAccession, CMatchesListCtrl::eSortInternal5Prime3Prime, CMatchesListCtrl::eSortMarked, CMatchesListCtrl::eSortStrength, m_listMatches, m_radioBoxSort, and CMatchesListCtrl::Sort().

OnTrimSelected()

void CVectorTrimPanel::OnTrimSelected

(

wxCommandEvent &

event

)

Definition at line 477 of file vectortrimpanel.cpp.

References CMatchesListCtrl::AllSelected(), m_buttonTrimSelected, m_listMatches, m_pParentWindow, and x_TrimSelected().

OnUnselectAll()

void CVectorTrimPanel::OnUnselectAll

(

wxCommandEvent &

event

)

Definition at line 454 of file vectortrimpanel.cpp.

References m_listMatches, and CMatchesListCtrl::UnselectAll().

OnUnselectInternal()

void CVectorTrimPanel::OnUnselectInternal

(

wxCommandEvent &

event

)

Definition at line 460 of file vectortrimpanel.cpp.

References m_listMatches, and CMatchesListCtrl::UnselectInternal().

ShowToolTips()

bool CVectorTrimPanel::ShowToolTips ( )

static

Should we show tooltips?

Should we show tooltips?

Definition at line 374 of file vectortrimpanel.cpp.

TransferDataFromWindow()

bool CVectorTrimPanel::TransferDataFromWindow ( )

virtual

Definition at line 360 of file vectortrimpanel.cpp.

TransferDataToWindow()

bool CVectorTrimPanel::TransferDataToWindow ( )

virtual

Definition at line 350 of file vectortrimpanel.cpp.

Referenced by CVectorTrimDlg::CreateControls().

x_AdjustDensegAlignment()

void CVectorTrimPanel::x_AdjustDensegAlignment ( CRef< CSeq_align >  align, CDense_seg::TDim  row, const TCuts &  sorted_cuts  )

private

Definition at line 1185 of file vectortrimpanel.cpp.

References CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CRange_Base::GetFrom(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CSeq_align_Base::GetSegs(), CDense_seg_Base::GetStarts(), CRange_Base::GetTo(), SRangeMatch::m_range, row, CSeq_align_Base::SetSegs(), and x_CutDensegSegment().

Referenced by x_TrimAlignments().

x_AdjustInternalCutLocations()

void CVectorTrimPanel::x_AdjustInternalCutLocations ( TCuts &  cuts, TSeqPos  seq_length  )

private

Definition at line 873 of file vectortrimpanel.cpp.

References eTrimTo5PrimeEnd, eTrimToClosestEnd, CRange_Base::GetFrom(), CRange_Base::GetTo(), m_radioBoxInternalTrimOptions, SRangeMatch::m_range, CRange_Base::SetFrom(), and CRange_Base::SetTo().

Referenced by x_FindCompleteDeletions(), and x_GetSortedCuts().

x_CutDensegSegment()

void CVectorTrimPanel::x_CutDensegSegment ( CRef< CSeq_align >  align, CDense_seg::TDim  row, TSeqPos  pos  )

private

Definition at line 1040 of file vectortrimpanel.cpp.

References eNa_strand_minus, CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CDense_seg_Base::GetIds(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CSeq_align_Base::GetSegs(), CDense_seg_Base::GetStarts(), CDense_seg_Base::GetStrands(), CDense_seg_Base::IsSetStrands(), ITERATE, row, CDense_seg_Base::SetDim(), CDense_seg_Base::SetIds(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CSeq_align_Base::SetSegs(), CDense_seg_Base::SetStarts(), CDense_seg_Base::SetStrands(), si, and x_FindSegment().

Referenced by x_AdjustDensegAlignment().

x_DeleteSelected()

void CVectorTrimPanel::x_DeleteSelected ( CRef< CCmdComposite >  command, const CSeq_id *  seqid  )

private

Definition at line 1783 of file vectortrimpanel.cpp.

References CBioseq_set_Handle::CanGetClass(), command, CBioseq_set_Base::eClass_nuc_prot, CScope::GetBioseqHandle(), CBioseq_set_Handle::GetClass(), CBioseq_Handle::GetParentBioseq_set(), CBioseq_Handle::IsNucleotide(), and m_TopSeqEntry.

Referenced by x_TrimSelected().

x_FindCompleteDeletions()

void CVectorTrimPanel::x_FindCompleteDeletions ( const TVecscreenSummaryBySeqid &  seqidSummary, TVecscreenSummaryBySeqid &  completeDeletions, TVecscreenSummaryBySeqid &  trimOnly  )

private

Definition at line 1735 of file vectortrimpanel.cpp.

References map_checker< Container >::begin(), CRangeCmp::eAscending, map_checker< Container >::end(), CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), map_checker< Container >::insert(), CBioseq_Handle::IsNucleotide(), SVecscreenResult::m_arrRangeMatch, m_TopSeqEntry, ct::sort(), x_AdjustInternalCutLocations(), x_IsCompleteCut(), and x_MergeCuts().

Referenced by x_TrimSelected().

x_FindSegment()

bool CVectorTrimPanel::x_FindSegment ( const CDense_seg &  denseg, CDense_seg::TDim  row, TSeqPos  pos, CDense_seg::TNumseg &  seg, TSeqPos &  seg_start  ) const

private

Definition at line 1020 of file vectortrimpanel.cpp.

References CDense_seg_Base::GetDim(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CDense_seg_Base::GetStarts(), len, and row.

Referenced by x_CutDensegSegment().

x_GetRetainedRange()

CRange< TSeqPos > CVectorTrimPanel::x_GetRetainedRange ( const TCuts &  sorted_cuts, TSeqPos  seqLength  )

private

Definition at line 1232 of file vectortrimpanel.cpp.

References _ASSERT, and compile_time_bits::range().

Referenced by x_TrimSelected().

x_GetSortedCuts()

void CVectorTrimPanel::x_GetSortedCuts ( TCuts &  sorted_cuts, const CSeq_id *  seqid  )

private

Definition at line 1410 of file vectortrimpanel.cpp.

References CRangeCmp::eAscending, CRangeCmp::eDescending, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), m_TopSeqEntry, ct::sort(), x_AdjustInternalCutLocations(), and x_MergeCuts().

Referenced by x_TrimAlignments(), x_TrimSelected(), and x_TrimSeqGraphs().

x_GetTrimCoordinates()

void CVectorTrimPanel::x_GetTrimCoordinates ( const TCuts &  sorted_cuts, const CSeq_id *  seqid, TSeqPos &  trim_start, TSeqPos &  trim_stop  )

private

Definition at line 1532 of file vectortrimpanel.cpp.

References CScope::GetBioseqHandle(), CRange_Base::GetFrom(), CBioseq_Handle::GetInst(), CSeq_inst_Base::GetLength(), CRange_Base::GetTo(), SRangeMatch::m_range, and m_TopSeqEntry.

Referenced by x_TrimSeqGraphData().

x_IsCompleteCut()

bool CVectorTrimPanel::x_IsCompleteCut ( const TCuts &  sorted_cuts, TSeqPos  seq_length  )

private

Definition at line 1675 of file vectortrimpanel.cpp.

References CRange_Base::GetFrom(), CRange_Base::GetTo(), SRangeMatch::m_range, max(), and min().

Referenced by x_FindCompleteDeletions().

x_MergeCuts()

void CVectorTrimPanel::x_MergeCuts ( TCuts &  sorted_cuts )

private

Definition at line 910 of file vectortrimpanel.cpp.

References CRange_Base::GetFrom(), CRange_Base::GetTo(), SRangeMatch::m_range, and CRange_Base::SetTo().

Referenced by x_FindCompleteDeletions(), and x_GetSortedCuts().

x_RetranslateCDS()

void CVectorTrimPanel::x_RetranslateCDS ( CScope &  scope, CRef< CCmdComposite >  command, CRef< CSeq_feat >  cds  )

private

Definition at line 950 of file vectortrimpanel.cpp.

References CSerialObject::Assign(), CSeq_feat_Base::CanGetLocation(), CSeq_interval_Base::CanGetTo(), command, CSeqFeatData_Base::e_Prot, CAliasBase< TPrim >::Get(), CScope::GetBioseqHandle(), CBioseq_Base::GetInst(), CBioseq_Handle::GetInst(), CSeq_loc_Base::GetInt(), CSeq_data_Base::GetIupacaa(), CBioseq::GetLength(), CSeq_inst_Base::GetLength(), CSeq_feat_Base::GetLocation(), CSeq_data_Base::GetNcbieaa(), CMappedFeat::GetOriginalFeature(), CSeq_feat_Base::GetProduct(), CSeq_inst_Base::GetSeq_data(), CSeq_loc_Base::IsInt(), CSeq_data_Base::IsIupacaa(), CSeq_data_Base::IsNcbieaa(), CBioseq_Handle::IsProtein(), CSeq_inst_Base::IsSetSeq_data(), CSeq_inst_Base::SetLength(), CSeq_feat_Base::SetLocation(), CSeq_inst_Base::SetSeq_data(), and CSeqTranslator::TranslateToProtein().

Referenced by x_TrimSelected().

x_SeqIntervalDelete()

void CVectorTrimPanel::x_SeqIntervalDelete ( CRef< CSeq_interval >  interval, TSeqPos  cut_from, TSeqPos  cut_to, const CSeq_id *  seqid, bool &  bCompleteCut, bool &  bTrimmed  )

private

Definition at line 648 of file vectortrimpanel.cpp.

References CSeq_interval_Base::CanGetFrom(), CSeq_interval_Base::CanGetTo(), CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetTo(), CSeq_interval_Base::SetFrom(), and CSeq_interval_Base::SetTo().

Referenced by x_SeqLocDelete().

x_SeqLocDelete()

void CVectorTrimPanel::x_SeqLocDelete ( CRef< CSeq_loc >  loc, TSeqPos  from, TSeqPos  to, const CSeq_id *  seqid, bool &  bCompleteCut, bool &  bTrimmed  )

private

Definition at line 725 of file vectortrimpanel.cpp.

References CSerialObject::Assign(), CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc_Base::Which(), and x_SeqIntervalDelete().

Referenced by x_TrimFeatureLocations(), and x_UpdateSeqGraphLoc().

x_SetSeqData()

void CVectorTrimPanel::x_SetSeqData ( const CBioseq_Handle &  bsh, CRef< objects::CSeq_inst >  inst, const TCuts &  sorted_cuts  )

private

Definition at line 552 of file vectortrimpanel.cpp.

References CScope::AddBioseq(), CSerialObject::Assign(), CBioseq_Handle::eCoding_Iupac, CInt_fuzz_Base::eLim_unk, CSeq_inst_Base::eRepr_raw, CSeqMap::eSeqData, CSeqMap::eSeqGap, CBioseq_Handle::GetCompleteBioseq(), CSeqMap_CI::GetEndPosition(), CSeq_inst_Base::GetLength(), CSeqMap_CI::GetLength(), CSeqMap_CI::GetPosition(), CSeqMap_CI::GetRefGapLiteral(), CBioseq_Handle::GetScope(), CSeq_entry_Handle::GetScope(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqMap(), CBioseq_Handle::GetTopLevelEntry(), CSeqMap_CI::GetType(), CBioseq_Handle::IsNucleotide(), CSeqMap_CI::IsUnknownLength(), CSeqportUtil::Pack(), Ref(), CScope::RemoveBioseq(), CSeq_inst_Base::ResetExt(), CSeq_inst_Base::ResetSeq_data(), CSeqMap::ResolvedRangeIterator(), CAutoInitRef< T >::Set(), CSeq_inst_Base::SetExt(), CSeq_data_Base::SetIupacna(), CSeq_inst_Base::SetLength(), CSeq_inst_Base::SetRepr(), and CSeq_inst_Base::SetSeq_data().

Referenced by x_TrimSelected().

x_TrimAlignments()

void CVectorTrimPanel::x_TrimAlignments ( CRef< CCmdComposite >  command, const TVecscreenSummaryBySeqid &  trimOnly  )

private

Definition at line 1441 of file vectortrimpanel.cpp.

References CSerialObject::Assign(), map_checker< Container >::begin(), CDense_seg_Base::CanGetDim(), CDense_seg_Base::CanGetIds(), CDense_seg_Base::CanGetLens(), CDense_seg_Base::CanGetNumseg(), CSeq_align_Base::CanGetSegs(), CDense_seg_Base::CanGetStarts(), command, CSeq_annot_Base::C_Data::e_Align, CSeq_align_Base::C_Segs::e_Denseg, map_checker< Container >::end(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CDense_seg_Base::GetIds(), CAlign_CI::GetOriginalSeq_align(), CSeq_align_Base::GetSegs(), CAlign_CI::GetSeq_align_Handle(), m_TopSeqEntry, result, row, CSeq_align_Base::C_Segs::Which(), x_AdjustDensegAlignment(), and x_GetSortedCuts().

Referenced by x_TrimSelected().

x_TrimFeatureLocations()

void CVectorTrimPanel::x_TrimFeatureLocations ( CRef< CSeq_feat >  feat, const TCuts &  sorted_cuts, const CSeq_id *  seqid, bool &  bFeatureDeleted, bool &  bFeatureTrimmed, bool &  bProdDeleted, bool &  bProdTrimmed  )

private

Definition at line 832 of file vectortrimpanel.cpp.

References CSeq_feat_Base::CanGetLocation(), CSeq_feat_Base::CanGetProduct(), CRange_Base::GetFrom(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetProduct(), CRange_Base::GetTo(), SRangeMatch::m_range, CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetProduct(), and x_SeqLocDelete().

Referenced by x_TrimSelected().

x_TrimSelected() [1/2]

bool CVectorTrimPanel::x_TrimSelected ( )

private

Definition at line 1814 of file vectortrimpanel.cpp.

References _, CSeq_id::AsFastaString(), map_checker< Container >::begin(), command, map_checker< Container >::empty(), map_checker< Container >::end(), ICommandProccessor::Execute(), CMatchesListCtrl::GetSelectedLocations(), CMatchesListCtrl::GetSelectedVecscreenSummaryBySeqid(), m_CmdProcessor, m_listMatches, m_radioBoxInternalTrimOptions, result, CListReportDlg::SetFooter(), CListReportDlg::SetHeader(), CListReportDlg::SetList(), CVecscreenReport::SetReport(), map_checker< Container >::size(), wxCLOSE_BOX, wxID_ANY, x_DeleteSelected(), x_FindCompleteDeletions(), x_TrimAlignments(), and x_TrimSeqGraphs().

Referenced by OnTrimSelected().

x_TrimSelected() [2/2]

void CVectorTrimPanel::x_TrimSelected ( CRef< CCmdComposite >  command, const CSeq_id *  seqid, const SVecscreenResult &  vecres  )

private

Definition at line 1258 of file vectortrimpanel.cpp.

References CSeq_id::Assign(), CSerialObject::Assign(), CBioseq_set_Handle::CanGetClass(), command, CSeqFeatData_Base::e_Cdregion, CSeq_annot_Base::C_Data::e_Ftable, CBioseq_set_Base::eClass_nuc_prot, CScope::GetBioseqHandle(), CBioseq_set_Handle::GetClass(), CSeq_feat_Base::GetData(), CSeq_feat_Handle::GetData(), CBioseq_Handle::GetEditHandle(), CBioseq_Handle::GetInst(), CMappedFeat::GetOriginalFeature(), CBioseq_Handle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), CMappedFeat::GetProduct(), CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeq_entry_Handle(), CBioseq_Handle::IsNucleotide(), CBioseq_Handle::IsProtein(), CSeq_feat_Base::IsSetData(), CSeq_feat_Handle::IsSetData(), CSeq_feat_Base::IsSetProduct(), CSeq_feat_Handle::IsSetProduct(), SVecscreenResult::m_arrRangeMatch, m_CitSub, SVecscreenResult::m_SeqLen, m_TopSeqEntry, msg(), CCitSubUpdater::s_GetCitSubForTrimmedSequence(), CSeq_feat_Base::SetData(), CBioseq_EditHandle::SetInst(), CSeq_loc::SetWhole(), CSeqFeatData_Base::Which(), x_GetRetainedRange(), x_GetSortedCuts(), x_RetranslateCDS(), x_SetSeqData(), and x_TrimFeatureLocations().

x_TrimSeqGraphData()

void CVectorTrimPanel::x_TrimSeqGraphData ( CRef< CSeq_graph >  new_graph, const CMappedGraph &  orig_graph, const TCuts &  sorted_cuts, const CSeq_id *  seqid  )

private

Definition at line 1569 of file vectortrimpanel.cpp.

References CSeq_graph_Base::C_Graph::e_Byte, eExtreme_Positional, CByte_graph_Base::GetAxis(), CSeq_graph_Base::C_Graph::GetByte(), CMappedGraph::GetGraph(), CSeq_graph_Base::GetLoc(), CByte_graph_Base::GetMax(), CByte_graph_Base::GetMin(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CByte_graph_Base::GetValues(), CSeq_graph_Base::C_Graph::Reset(), CByte_graph_Base::SetAxis(), CSeq_graph_Base::C_Graph::SetByte(), CSeq_graph_Base::SetGraph(), CByte_graph_Base::SetMax(), CByte_graph_Base::SetMin(), CSeq_graph_Base::SetNumval(), CByte_graph_Base::SetValues(), CSeq_graph_Base::C_Graph::Which(), x_GetTrimCoordinates(), and x_UpdateSeqGraphLoc().

Referenced by x_TrimSeqGraphs().

x_TrimSeqGraphs()

void CVectorTrimPanel::x_TrimSeqGraphs ( CRef< CCmdComposite >  command, const TVecscreenSummaryBySeqid &  trimOnly  )

private

Definition at line 1629 of file vectortrimpanel.cpp.

References CSerialObject::Assign(), map_checker< Container >::begin(), command, NStr::CompareNocase(), CSeq_annot_Base::C_Data::e_Graph, map_checker< Container >::end(), CMappedGraph::GetLoc(), CMappedGraph::GetOriginalGraph(), CMappedGraph::GetSeq_graph_Handle(), CMappedGraph::GetTitle(), CMappedGraph::IsSetTitle(), m_TopSeqEntry, result, x_GetSortedCuts(), and x_TrimSeqGraphData().

Referenced by x_TrimSelected().

x_UpdateSeqGraphLoc()

void CVectorTrimPanel::x_UpdateSeqGraphLoc ( CRef< CSeq_graph >  new_graph, const TCuts &  sorted_cuts, const CSeq_id *  seqid  )

private

Definition at line 1509 of file vectortrimpanel.cpp.

References CSeq_graph_Base::CanGetLoc(), CRange_Base::GetFrom(), CSeq_graph_Base::GetLoc(), CRange_Base::GetTo(), SRangeMatch::m_range, CSeq_graph_Base::SetLoc(), and x_SeqLocDelete().

Referenced by x_TrimSeqGraphData().

Member Data Documentation

m_buttonDismiss

wxButton* CVectorTrimPanel::m_buttonDismiss

private

Definition at line 282 of file vectortrimpanel.hpp.

Referenced by CreateControls().

m_buttonFindForward

wxButton* CVectorTrimPanel::m_buttonFindForward

private

Definition at line 261 of file vectortrimpanel.hpp.

Referenced by CreateControls().

m_buttonFindReverse

wxButton* CVectorTrimPanel::m_buttonFindReverse

private

Definition at line 262 of file vectortrimpanel.hpp.

Referenced by CreateControls().

m_buttonMakeReport

wxButton* CVectorTrimPanel::m_buttonMakeReport

private

Definition at line 280 of file vectortrimpanel.hpp.

Referenced by CreateControls().

m_buttonRunVecscreen

wxButton* CVectorTrimPanel::m_buttonRunVecscreen

private

Definition at line 256 of file vectortrimpanel.hpp.

Referenced by CreateControls().

m_buttonSelectAll

wxButton* CVectorTrimPanel::m_buttonSelectAll

private

Definition at line 271 of file vectortrimpanel.hpp.

Referenced by CreateControls().

m_buttonSelectStrongModerate

wxButton* CVectorTrimPanel::m_buttonSelectStrongModerate

private

Definition at line 274 of file vectortrimpanel.hpp.

Referenced by CreateControls().

m_buttonTrimSelected

wxButton* CVectorTrimPanel::m_buttonTrimSelected

private

Definition at line 281 of file vectortrimpanel.hpp.

Referenced by CreateControls(), OnRunVecscreen(), and OnTrimSelected().

m_buttonUnselectAll

wxButton* CVectorTrimPanel::m_buttonUnselectAll

private

Definition at line 272 of file vectortrimpanel.hpp.

Referenced by CreateControls().

m_buttonUnselectInternal

wxButton* CVectorTrimPanel::m_buttonUnselectInternal

private

Definition at line 273 of file vectortrimpanel.hpp.

Referenced by CreateControls().

m_checkboxViewGraphic

wxCheckBox* CVectorTrimPanel::m_checkboxViewGraphic

private

Definition at line 275 of file vectortrimpanel.hpp.

m_CitSub

wxCheckBox* CVectorTrimPanel::m_CitSub

private

Definition at line 277 of file vectortrimpanel.hpp.

Referenced by CreateControls(), and x_TrimSelected().

m_CmdProcessor

ICommandProccessor* CVectorTrimPanel::m_CmdProcessor

private

Definition at line 240 of file vectortrimpanel.hpp.

Referenced by x_TrimSelected().

m_gaugeProgressBar

wxGauge* CVectorTrimPanel::m_gaugeProgressBar

private

Definition at line 257 of file vectortrimpanel.hpp.

Referenced by CreateControls(), and OnRunVecscreen().

m_listLocations

CLocationsListCtrl* CVectorTrimPanel::m_listLocations

private

Definition at line 253 of file vectortrimpanel.hpp.

Referenced by CreateControls().

m_listMatches

CMatchesListCtrl* CVectorTrimPanel::m_listMatches

private

Definition at line 249 of file vectortrimpanel.hpp.

Referenced by CreateControls(), DisplaySummaryBySeqid(), OnFindForward(), OnFindReverse(), OnMakeReport(), OnSelectAll(), OnSelectStrongModerate(), OnSort(), OnTrimSelected(), OnUnselectAll(), OnUnselectInternal(), and x_TrimSelected().

m_pParentWindow

wxWindow* CVectorTrimPanel::m_pParentWindow

private

Definition at line 285 of file vectortrimpanel.hpp.

Referenced by Create(), OnDismiss(), and OnTrimSelected().

m_radioBoxInternalTrimOptions

wxRadioBox* CVectorTrimPanel::m_radioBoxInternalTrimOptions

private

Definition at line 268 of file vectortrimpanel.hpp.

Referenced by CreateControls(), x_AdjustInternalCutLocations(), and x_TrimSelected().

m_radioBoxSort

wxRadioBox* CVectorTrimPanel::m_radioBoxSort

private

Definition at line 265 of file vectortrimpanel.hpp.

Referenced by CreateControls(), and OnSort().

m_sizerVectorResults

wxBoxSizer* CVectorTrimPanel::m_sizerVectorResults

private

Definition at line 248 of file vectortrimpanel.hpp.

Referenced by CreateControls().

m_textFind

wxTextCtrl* CVectorTrimPanel::m_textFind

private

Definition at line 260 of file vectortrimpanel.hpp.

Referenced by CreateControls(), OnFindForward(), and OnFindReverse().

m_TopSeqEntry

objects::CSeq_entry_Handle CVectorTrimPanel::m_TopSeqEntry

private

Definition at line 239 of file vectortrimpanel.hpp.

Referenced by OnRunVecscreen(), x_DeleteSelected(), x_FindCompleteDeletions(), x_GetSortedCuts(), x_GetTrimCoordinates(), x_TrimAlignments(), x_TrimSelected(), and x_TrimSeqGraphs().

m_vectorscreen

CVectorScreen CVectorTrimPanel::m_vectorscreen

private

Definition at line 241 of file vectortrimpanel.hpp.

Referenced by OnRunVecscreen().

m_viewAlignGraphic

wxHtmlWindow* CVectorTrimPanel::m_viewAlignGraphic

private

Definition at line 252 of file vectortrimpanel.hpp.

Referenced by CreateControls().

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

• include/gui/widgets/edit/vectortrimpanel.hpp
• src/gui/widgets/edit/vectortrimpanel.cpp