NCBI C++ ToolKit
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CDDAnnotateDialog Class Reference

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#include "cdd_annot_dialog.hpp"
(Private to src/app/cn3d.)

+ Inheritance diagram for CDDAnnotateDialog:
+ Collaboration diagram for CDDAnnotateDialog:

Public Member Functions

 CDDAnnotateDialog (wxWindow *parent, CDDAnnotateDialog **handle, StructureSet *set)
 
 ~CDDAnnotateDialog (void)
 

Private Types

typedef std::list< ncbi::CRef< ncbi::objects::CSeq_interval > > IntervalList
 

Private Member Functions

void GetCurrentHighlightedIntervals (IntervalList *intervals)
 
void NewAnnotation (void)
 
void DeleteAnnotation (void)
 
void EditAnnotation (void)
 
void NewOrEditMotif (void)
 
void DeleteMotif (void)
 
void HighlightAnnotation (void)
 
void HighlightMotif (void)
 
void MoveAnnotation (bool moveUp)
 
void NewEvidence (void)
 
void DeleteEvidence (void)
 
void EditEvidence (void)
 
void ShowEvidence (void)
 
void MoveEvidence (bool moveUp)
 
void OnButton (wxCommandEvent &event)
 
void OnSelection (wxCommandEvent &event)
 
void OnCloseWindow (wxCloseEvent &event)
 
void SetupGUIControls (int selectAnnot, int selectEvidence)
 
bool HighlightInterval (const ncbi::objects::CSeq_interval &interval)
 

Private Attributes

CDDAnnotateDialog ** dialogHandle
 
StructureSet * structureSet
 
ncbi::CRef< ncbi::objects::CAlign_annot_set > annotSet
 

Detailed Description

Definition at line 61 of file cdd_annot_dialog.hpp.

Member Typedef Documentation

◆ IntervalList

typedef std::list< ncbi::CRef < ncbi::objects::CSeq_interval > > CDDAnnotateDialog::IntervalList
private

Definition at line 75 of file cdd_annot_dialog.hpp.

Constructor & Destructor Documentation

◆ CDDAnnotateDialog()

CDDAnnotateDialog::CDDAnnotateDialog ( wxWindow *  parent,
CDDAnnotateDialog **  handle,
StructureSet *  set 
)

Definition at line 188 of file cdd_annot_dialog.cpp.

References GetDataDir(), SetupCDDAnnotDialog(), and STD_ANNOT_TYPES_FILE.

◆ ~CDDAnnotateDialog()

CDDAnnotateDialog::~CDDAnnotateDialog ( void  )

Definition at line 220 of file cdd_annot_dialog.cpp.

References dialogHandle, NULL, and TRACEMSG.

Member Function Documentation

◆ DeleteAnnotation()

void CDDAnnotateDialog::DeleteAnnotation ( void  )
private

Definition at line 487 of file cdd_annot_dialog.cpp.

References a, annotSet, DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR, ERRORMSG, StructureSet::eUserAnnotationData, ID_L_ANNOT, StructureSet::SetDataChanged(), SetupGUIControls(), and structureSet.

Referenced by OnButton().

◆ DeleteEvidence()

void CDDAnnotateDialog::DeleteEvidence ( void  )
private

Definition at line 979 of file cdd_annot_dialog.cpp.

References DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR, ERRORMSG, StructureSet::eUserAnnotationData, ID_L_ANNOT, ID_L_EVID, StructureSet::SetDataChanged(), CAlign_annot_Base::SetEvidence(), SetupGUIControls(), and structureSet.

Referenced by OnButton().

◆ DeleteMotif()

void CDDAnnotateDialog::DeleteMotif ( void  )
private

Definition at line 785 of file cdd_annot_dialog.cpp.

References DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR, ERRORMSG, StructureSet::eUserAnnotationData, ID_L_ANNOT, ID_L_EVID, CAlign_annot_Base::IsSetMotif(), CAlign_annot_Base::ResetMotif(), CAlign_annot_Base::ResetMotifuse(), StructureSet::SetDataChanged(), SetupGUIControls(), and structureSet.

Referenced by OnButton().

◆ EditAnnotation()

void CDDAnnotateDialog::EditAnnotation ( void  )
private

Definition at line 518 of file cdd_annot_dialog.cpp.

References DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR, ERRORMSG, StructureSet::eUserAnnotationData, GetCurrentHighlightedIntervals(), CDDTypedAnnotDialog::GetData(), CAlign_annot_Base::GetDescription(), CAlign_annot_Base::GetType(), ID_L_ANNOT, ID_L_EVID, CAlign_annot_Base::IsSetDescription(), CAlign_annot_Base::IsSetType(), kEmptyStr, CAlign_annot_Base::ResetType(), result, CPacked_seqint_Base::Set(), StructureSet::SetDataChanged(), CAlign_annot_Base::SetDescription(), CAlign_annot_Base::SetLocation(), CAlign_annot_Base::SetType(), SetupGUIControls(), and structureSet.

Referenced by OnButton().

◆ EditEvidence()

void CDDAnnotateDialog::EditEvidence ( void  )
private

Definition at line 1024 of file cdd_annot_dialog.cpp.

References DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR, ERRORMSG, StructureSet::eUserAnnotationData, CDDEvidenceDialog::GetData(), CDDEvidenceDialog::HasDataChanged(), ID_L_ANNOT, ID_L_EVID, result, StructureSet::SetDataChanged(), SetupGUIControls(), and structureSet.

Referenced by OnButton().

◆ GetCurrentHighlightedIntervals()

void CDDAnnotateDialog::GetCurrentHighlightedIntervals ( IntervalList *  intervals)
private

Definition at line 245 of file cdd_annot_dialog.cpp.

References StructureSet::alignmentManager, blocks, Sequence::FillOutSeqId(), first(), BlockMultipleAlignment::GetBlocks(), AlignmentManager::GetCurrentMultipleAlignment(), BlockMultipleAlignment::GetMaster(), GlobalMessenger(), BlockMultipleAlignment::IsAligned(), IsFirstResidueOfABlock(), last(), Sequence::Length(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), CSeq_interval_Base::SetTo(), structureSet, and U.

Referenced by EditAnnotation(), and NewAnnotation().

◆ HighlightAnnotation()

void CDDAnnotateDialog::HighlightAnnotation ( void  )
private

Definition at line 822 of file cdd_annot_dialog.cpp.

References DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR, ERRORMSG, CSeq_loc_Base::GetInt(), CAlign_annot_Base::GetLocation(), GlobalMessenger(), HighlightInterval(), ID_L_ANNOT, CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsPacked_int(), Messenger::RemoveAllHighlights(), and CAlign_annot_Base::SetLocation().

Referenced by HighlightMotif(), NewOrEditMotif(), and OnButton().

◆ HighlightInterval()

bool CDDAnnotateDialog::HighlightInterval ( const ncbi::objects::CSeq_interval &  interval)
private

Definition at line 807 of file cdd_annot_dialog.cpp.

References StructureSet::alignmentManager, ERRORMSG, AlignmentManager::GetCurrentMultipleAlignment(), BlockMultipleAlignment::GetMaster(), BlockMultipleAlignment::HighlightAlignedColumnsOfMasterRange(), Sequence::identifier, MoleculeIdentifier::MatchesSeqId(), and structureSet.

Referenced by HighlightAnnotation().

◆ HighlightMotif()

void CDDAnnotateDialog::HighlightMotif ( void  )
private

Definition at line 854 of file cdd_annot_dialog.cpp.

References DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR, DoHighlightMotif(), ERRORMSG, Messenger::GetHighlights(), CAlign_annot_Base::GetMotif(), GlobalMessenger(), HighlightAnnotation(), ID_L_ANNOT, CAlign_annot_Base::IsSetMotif(), msg(), Prosite2Regex(), PrositePatternLength(), Messenger::RemoveAllHighlights(), and structureSet.

Referenced by OnButton().

◆ MoveAnnotation()

void CDDAnnotateDialog::MoveAnnotation ( bool  moveUp)
private

Definition at line 906 of file cdd_annot_dialog.cpp.

References a, annotSet, DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR, ERRORMSG, StructureSet::eUserAnnotationData, ID_L_ANNOT, ID_L_EVID, StructureSet::SetDataChanged(), SetupGUIControls(), structureSet, and tmp.

Referenced by OnButton().

◆ MoveEvidence()

void CDDAnnotateDialog::MoveEvidence ( bool  moveUp)
private

Definition at line 1249 of file cdd_annot_dialog.cpp.

References DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR, ERRORMSG, StructureSet::eUserAnnotationData, ID_L_ANNOT, ID_L_EVID, StructureSet::SetDataChanged(), CAlign_annot_Base::SetEvidence(), SetupGUIControls(), structureSet, and tmp.

Referenced by OnButton().

◆ NewAnnotation()

void CDDAnnotateDialog::NewAnnotation ( void  )
private

Definition at line 450 of file cdd_annot_dialog.cpp.

References annotSet, ERRORMSG, StructureSet::eUserAnnotationData, GetCurrentHighlightedIntervals(), CDDTypedAnnotDialog::GetData(), CRef< C, Locker >::GetPointer(), kEmptyStr, result, CPacked_seqint_Base::Set(), StructureSet::SetDataChanged(), SetupGUIControls(), and structureSet.

Referenced by OnButton().

◆ NewEvidence()

void CDDAnnotateDialog::NewEvidence ( void  )
private

Definition at line 947 of file cdd_annot_dialog.cpp.

References DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR, ERRORMSG, StructureSet::eUserAnnotationData, CDDEvidenceDialog::GetData(), CAlign_annot_Base::GetEvidence(), CRef< C, Locker >::GetPointer(), ID_L_ANNOT, result, StructureSet::SetDataChanged(), CAlign_annot_Base::SetEvidence(), SetupGUIControls(), and structureSet.

Referenced by OnButton().

◆ NewOrEditMotif()

void CDDAnnotateDialog::NewOrEditMotif ( void  )
private

Definition at line 648 of file cdd_annot_dialog.cpp.

References StructureSet::alignmentManager, DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR, DoHighlightMotif(), ERRORMSG, StructureSet::eUserAnnotationData, AlignmentManager::GetCurrentMultipleAlignment(), CSeq_interval_Base::GetFrom(), Messenger::GetHighlights(), CSeq_loc_Base::GetInt(), CSeq_interval::GetLength(), CAlign_annot_Base::GetLocation(), BlockMultipleAlignment::GetMaster(), CAlign_annot_Base::GetMotif(), CSeq_interval_Base::GetTo(), GlobalMessenger(), HighlightAnnotation(), ID_L_ANNOT, ID_L_EVID, CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsPacked_int(), CAlign_annot_Base::IsSetMotif(), kEmptyStr, PatternDialog::m_Mode, PatternDialog::m_Pattern, PatternDialog::m_Text, msg(), Prosite2Regex(), PrositePatternLength(), Messenger::RemoveAllHighlights(), Sequence::sequenceString, StructureSet::SetDataChanged(), CAlign_annot_Base::SetLocation(), CAlign_annot_Base::SetMotif(), CAlign_annot_Base::SetMotifuse(), SetupGUIControls(), structureSet, and WX_TO_STD.

Referenced by OnButton().

◆ OnButton()

void CDDAnnotateDialog::OnButton ( wxCommandEvent &  event)
private

Definition at line 280 of file cdd_annot_dialog.cpp.

References DeleteAnnotation(), DeleteEvidence(), DeleteMotif(), EditAnnotation(), EditEvidence(), HighlightAnnotation(), HighlightMotif(), ID_B_ANNOT_DOWN, ID_B_ANNOT_UP, ID_B_DEFINE_MOTIF, ID_B_DEL_ANNOT, ID_B_DEL_EVID, ID_B_DEL_MOTIF, ID_B_EDIT_ANNOT, ID_B_EDIT_EVID, ID_B_EVID_DOWN, ID_B_EVID_UP, ID_B_HIGHLIGHT, ID_B_HIGHLIGHT_MOTIF, ID_B_NEW_ANNOT, ID_B_NEW_EVID, ID_B_SHOW, MoveAnnotation(), MoveEvidence(), NewAnnotation(), NewEvidence(), NewOrEditMotif(), and ShowEvidence().

◆ OnCloseWindow()

void CDDAnnotateDialog::OnCloseWindow ( wxCloseEvent &  event)
private

Definition at line 227 of file cdd_annot_dialog.cpp.

◆ OnSelection()

void CDDAnnotateDialog::OnSelection ( wxCommandEvent &  event)
private

Definition at line 331 of file cdd_annot_dialog.cpp.

References DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR, ID_L_ANNOT, ID_L_EVID, and SetupGUIControls().

◆ SetupGUIControls()

void CDDAnnotateDialog::SetupGUIControls ( int  selectAnnot,
int  selectEvidence 
)
private

Definition at line 342 of file cdd_annot_dialog.cpp.

References a, annotSet, DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR, CFeature_evidence_Base::GetReference(), QueryValueType::GetTypeAsString(), ID_B_ANNOT_DOWN, ID_B_ANNOT_UP, ID_B_DEFINE_MOTIF, ID_B_DEL_ANNOT, ID_B_DEL_EVID, ID_B_DEL_MOTIF, ID_B_EDIT_ANNOT, ID_B_EDIT_EVID, ID_B_EVID_DOWN, ID_B_EVID_UP, ID_B_HIGHLIGHT, ID_B_HIGHLIGHT_MOTIF, ID_B_NEW_ANNOT, ID_B_NEW_EVID, ID_B_SHOW, ID_L_ANNOT, ID_L_EVID, int, IS_STRUCTURE_EVIDENCE_BSANNOT, CFeature_evidence_Base::IsComment(), CPub_Base::IsPmid(), CFeature_evidence_Base::IsReference(), CAlign_annot_Base::IsSetEvidence(), CAlign_annot_Base::IsSetMotif(), NULL, REG_ADVANCED_SECTION, REG_CDD_ANNOT_READONLY, RegistryGetBoolean(), and CAlign_annot_Base::SetEvidence().

Referenced by DeleteAnnotation(), DeleteEvidence(), DeleteMotif(), EditAnnotation(), EditEvidence(), MoveAnnotation(), MoveEvidence(), NewAnnotation(), NewEvidence(), NewOrEditMotif(), and OnSelection().

◆ ShowEvidence()

void CDDAnnotateDialog::ShowEvidence ( void  )
private

Definition at line 1176 of file cdd_annot_dialog.cpp.

References DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR, ERRORMSG, StructureSet::frameMap, CAliasBase< TPrim >::Get(), CFeature_evidence_Base::GetBsannot(), CFeature_evidence_Base::GetComment(), CBiostruc_annot_set_Base::GetFeatures(), CPub_Base::GetPmid(), CFeature_evidence_Base::GetReference(), GlobalMessenger(), StructureObject::graph, HighlightResidues(), ID_L_EVID, IS_STRUCTURE_EVIDENCE_BSANNOT, CFeature_evidence_Base::IsComment(), CPub_Base::IsPmid(), CFeature_evidence_Base::IsReference(), LaunchWebPage(), ShowHideManager::MakeAllVisible(), StructureObject::mmdbID, ChemicalGraph::molecules, StructureSet::objects, Messenger::ProcessRedraws(), StructureSet::renderer, ShowHideManager::Show(), OpenGLRenderer::ShowFrameNumber(), StructureSet::showHideManager, and structureSet.

Referenced by OnButton().

Member Data Documentation

◆ annotSet

ncbi::CRef< ncbi::objects::CAlign_annot_set > CDDAnnotateDialog::annotSet
private

Definition at line 72 of file cdd_annot_dialog.hpp.

Referenced by DeleteAnnotation(), MoveAnnotation(), NewAnnotation(), and SetupGUIControls().

◆ dialogHandle

CDDAnnotateDialog** CDDAnnotateDialog::dialogHandle
private

Definition at line 70 of file cdd_annot_dialog.hpp.

Referenced by ~CDDAnnotateDialog().

◆ structureSet

StructureSet* CDDAnnotateDialog::structureSet
private

Definition at line 71 of file cdd_annot_dialog.hpp.

Referenced by DeleteAnnotation(), DeleteEvidence(), DeleteMotif(), EditAnnotation(), EditEvidence(), GetCurrentHighlightedIntervals(), HighlightInterval(), HighlightMotif(), MoveAnnotation(), MoveEvidence(), NewAnnotation(), NewEvidence(), NewOrEditMotif(), and ShowEvidence().

The documentation for this class was generated from the following files:
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Modified on Fri Sep 20 14:58:09 2024 by modify_doxy.py rev. 669887