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CVectorTrimPanel Class Reference

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#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< SRangeMatchTCuts
 

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< TSeqPosx_GetRetainedRange (const TCuts &sorted_cuts, TSeqPos seqLength)
 

Private Attributes

objects::CSeq_entry_Handle m_TopSeqEntry
 
ICommandProccessorm_CmdProcessor
 
CVectorScreen m_vectorscreen
 
wxBoxSizer * m_sizerVectorResults
 
CMatchesListCtrlm_listMatches
 
wxHtmlWindow * m_viewAlignGraphic
 
CLocationsListCtrlm_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

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 
)

◆ CreateControls()

void CVectorTrimPanel::CreateControls ( )

◆ 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)

◆ OnRunVecscreen()

void CVectorTrimPanel::OnRunVecscreen ( wxCommandEvent &  event)

◆ 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)

◆ OnTrimSelected()

void CVectorTrimPanel::OnTrimSelected ( wxCommandEvent &  event)

◆ 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

◆ x_AdjustInternalCutLocations()

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

◆ x_CutDensegSegment()

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

◆ x_DeleteSelected()

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

◆ x_FindCompleteDeletions()

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

◆ 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

◆ 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

◆ x_GetTrimCoordinates()

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

◆ x_IsCompleteCut()

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

◆ x_MergeCuts()

void CVectorTrimPanel::x_MergeCuts ( TCuts sorted_cuts)
private

◆ x_RetranslateCDS()

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

◆ 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

◆ x_SeqLocDelete()

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

◆ x_SetSeqData()

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

◆ x_TrimAlignments()

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

◆ 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

◆ x_TrimSelected() [1/2]

bool CVectorTrimPanel::x_TrimSelected ( )
private

◆ x_TrimSelected() [2/2]

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

◆ x_TrimSeqGraphData()

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

◆ x_TrimSeqGraphs()

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

◆ x_UpdateSeqGraphLoc()

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

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

◆ 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

◆ 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

◆ 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().


The documentation for this class was generated from the following files:
Modified on Mon Mar 04 05:15:06 2024 by modify_doxy.py rev. 669887