NCBI C++ ToolKit
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ViewerBase Class Reference

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

+ Inheritance diagram for ViewerBase:
+ Collaboration diagram for ViewerBase:

Public Types

typedef std::list< BlockMultipleAlignment * > AlignmentList
 

Public Member Functions

void Refresh (void)
 
void DestroyGUI (void)
 
void GUIDestroyed (void)
 
void SetWindowTitle (void) const
 
bool EditorIsOn (void) const
 
void RemoveBlockBoundaryRows (void)
 
virtual void SaveDialog (bool prompt)
 
void NewFont (void)
 
void MakeResidueVisible (const Molecule *molecule, int seqIndex)
 
void MakeSequenceVisible (const MoleculeIdentifier *identifier)
 
void CalculateSelfHitScores (const BlockMultipleAlignment *multiple)
 
void InitData (const AlignmentList *alignments, SequenceDisplay *display)
 
void EnableStacks (void)
 
void Save (void)
 
void Undo (void)
 
void Redo (void)
 
void Revert (void)
 
void KeepCurrent (void)
 

Protected Member Functions

 ViewerBase (ViewerWindowBase **window, AlignmentManager *alnMgr)
 
virtual ~ViewerBase (void)
 
const AlignmentList & GetCurrentAlignments (void) const
 
AlignmentList & GetCurrentAlignments (void)
 
SequenceDisplay * GetCurrentDisplay (void)
 

Protected Attributes

AlignmentManager * alignmentManager
 
ViewerWindowBase **const viewerWindow
 

Private Types

typedef std::list< AlignmentList > AlignmentStack
 
typedef std::list< SequenceDisplay * > DisplayStack
 

Private Member Functions

void CopyDataFromStack (void)
 
void ClearAllData (void)
 
void SetUndoRedoMenuStates (void)
 

Private Attributes

AlignmentList currentAlignments
 
AlignmentStack alignmentStack
 
SequenceDisplay * currentDisplay
 
DisplayStack displayStack
 
int nRedosStored
 
bool stacksEnabled
 

Static Private Attributes

static const unsigned int MAX_UNDO_STACK_SIZE = 50
 

Friends

class ViewerWindowBase
 
class AlignmentManager
 
class SequenceDisplay
 

Detailed Description

Definition at line 55 of file viewer_base.hpp.

Member Typedef Documentation

◆ AlignmentList

typedef std::list< BlockMultipleAlignment * > ViewerBase::AlignmentList

Definition at line 89 of file viewer_base.hpp.

◆ AlignmentStack

typedef std::list< AlignmentList > ViewerBase::AlignmentStack
private

Definition at line 104 of file viewer_base.hpp.

◆ DisplayStack

typedef std::list< SequenceDisplay * > ViewerBase::DisplayStack
private

Definition at line 108 of file viewer_base.hpp.

Constructor & Destructor Documentation

◆ ViewerBase()

ViewerBase::ViewerBase ( ViewerWindowBase **  window,
AlignmentManager *  alnMgr 
)
protected

Definition at line 57 of file viewer_base.cpp.

References ERRORMSG.

◆ ~ViewerBase()

ViewerBase::~ViewerBase ( void  )
protectedvirtual

Definition at line 63 of file viewer_base.cpp.

References ClearAllData(), and DestroyGUI().

Member Function Documentation

◆ CalculateSelfHitScores()

void ViewerBase::CalculateSelfHitScores ( const BlockMultipleAlignment *  multiple)

Definition at line 299 of file viewer_base.cpp.

References alignmentManager, AlignmentManager::blaster, and BLASTer::CalculateSelfHitScores().

◆ ClearAllData()

void ViewerBase::ClearAllData ( void  )
private

Definition at line 206 of file viewer_base.cpp.

References alignmentStack, currentAlignments, currentDisplay, DELETE_ALL_AND_CLEAR, displayStack, and NULL.

Referenced by InitData(), and ~ViewerBase().

◆ CopyDataFromStack()

void ViewerBase::CopyDataFromStack ( void  )
private

Definition at line 179 of file viewer_base.cpp.

References a, alignmentStack, SequenceDisplay::Clone(), BlockMultipleAlignment::Clone(), currentAlignments, currentDisplay, DELETE_ALL_AND_CLEAR, displayStack, i, and nRedosStored.

Referenced by Redo(), Revert(), and Undo().

◆ DestroyGUI()

void ViewerBase::DestroyGUI ( void  )

Definition at line 69 of file viewer_base.cpp.

References GUIDestroyed(), and viewerWindow.

Referenced by ~ViewerBase().

◆ EditorIsOn()

bool ViewerBase::EditorIsOn ( void  ) const

Definition at line 264 of file viewer_base.cpp.

References ViewerWindowBase::EditorIsOn(), and viewerWindow.

Referenced by BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment(), AlignmentManager::MergeUpdates(), AlignmentManager::PurgeSequence(), and Threader::Realign().

◆ EnableStacks()

void ViewerBase::EnableStacks ( void  )

Definition at line 92 of file viewer_base.cpp.

References ERRORMSG, nRedosStored, Save(), and stacksEnabled.

Referenced by ViewerWindowBase::OnEditMenu(), UpdateViewerWindow::SaveDialog(), and UpdateViewer::SetInitialState().

◆ GetCurrentAlignments() [1/2]

AlignmentList& ViewerBase::GetCurrentAlignments ( void  )
inlineprotected

Definition at line 138 of file viewer_base.hpp.

References currentAlignments.

◆ GetCurrentAlignments() [2/2]

const AlignmentList& ViewerBase::GetCurrentAlignments ( void  ) const
inlineprotected

Definition at line 137 of file viewer_base.hpp.

References currentAlignments.

Referenced by UpdateViewer::AddAlignments(), UpdateViewer::BlastNeighbor(), UpdateViewer::BlastUpdate(), AlignmentManager::BlockAlignAllUpdates(), AlignmentManager::BlockAlignUpdate(), UpdateViewer::DeleteAlignment(), AlignmentManager::ExtendAllUpdates(), AlignmentManager::ExtendUpdate(), AlignmentManager::GetCurrentMultipleAlignment(), UpdateViewer::GetMasterSequence(), AlignmentManager::GetUpdateSequences(), AlignmentManager::MergeUpdates(), AlignmentManager::NUpdates(), UpdateViewerWindow::OnDelete(), SequenceViewerWindow::OnHighlight(), SequenceViewerWindow::OnMarkBlock(), UpdateViewerWindow::OnMerge(), SequenceViewerWindow::OnRealign(), UpdateViewerWindow::OnRunThreader(), SequenceViewerWindow::OnSelfHit(), UpdateViewerWindow::OnSetRegion(), SequenceViewerWindow::OnTaxonomy(), AlignmentManager::PurgeSequence(), AlignmentManager::RealignDependentSequences(), SequenceViewer::ReplaceAlignment(), UpdateViewer::ReplaceAlignments(), SequenceViewer::SaveAlignment(), UpdateViewer::SaveAlignments(), UpdateViewer::SortByPSSM(), UpdateViewer::SortUpdates(), AlignmentManager::ThreadAllUpdates(), AlignmentManager::ThreadUpdate(), and ViewerWindowBase::UpdateGeometryViolations().

◆ GetCurrentDisplay()

SequenceDisplay* ViewerBase::GetCurrentDisplay ( void  )
inlineprotected

Definition at line 139 of file viewer_base.hpp.

References currentDisplay.

Referenced by UpdateViewer::AddAlignments(), UpdateViewer::BlastNeighbor(), UpdateViewer::BlastUpdate(), AlignmentManager::BlockAlignAllUpdates(), AlignmentManager::BlockAlignUpdate(), SequenceViewer::CreateSequenceWindow(), UpdateViewer::CreateUpdateWindow(), ViewerWindowBase::EnableBaseEditorMenuItems(), SequenceViewerWindow::EnableDerivedEditorMenuItems(), AlignmentManager::GetStructureProteins(), ViewerWindowBase::MakeSequenceVisible(), AlignmentManager::MergeUpdates(), ViewerWindowBase::OnEditMenu(), ViewerWindowBase::OnFindPattern(), SequenceViewerWindow::OnRealign(), SequenceViewerWindow::OnScoreThreader(), SequenceViewerWindow::OnSort(), AlignmentManager::PurgeSequence(), AlignmentManager::RealignDependentSequences(), SequenceViewer::ReplaceAlignment(), UpdateViewer::ReplaceAlignments(), SequenceViewer::SaveAlignment(), SequenceViewerWindow::SaveDialog(), UpdateViewer::SortUpdates(), AlignmentManager::ThreadAllUpdates(), and AlignmentManager::ThreadUpdate().

◆ GUIDestroyed()

void ViewerBase::GUIDestroyed ( void  )
inline

Definition at line 67 of file viewer_base.hpp.

References NULL, and viewerWindow.

Referenced by DestroyGUI(), SequenceViewerWindow::OnCloseWindow(), UpdateViewerWindow::OnCloseWindow(), and ViewerWindowBase::~ViewerWindowBase().

◆ InitData()

void ViewerBase::InitData ( const AlignmentList *  alignments,
SequenceDisplay *  display 
)

Definition at line 83 of file viewer_base.cpp.

References ClearAllData(), currentAlignments, currentDisplay, SetUndoRedoMenuStates(), and stacksEnabled.

Referenced by SequenceViewer::DisplayAlignment(), and SequenceViewer::DisplaySequences().

◆ KeepCurrent()

void ViewerBase::KeepCurrent ( void  )

Definition at line 246 of file viewer_base.cpp.

References alignmentStack, DELETE_ALL_AND_CLEAR, displayStack, nRedosStored, SetUndoRedoMenuStates(), and stacksEnabled.

Referenced by SequenceViewer::SaveAlignment(), SequenceViewerWindow::SaveDialog(), and UpdateViewer::SetInitialState().

◆ MakeResidueVisible()

void ViewerBase::MakeResidueVisible ( const Molecule *  molecule,
int  seqIndex 
)

Definition at line 274 of file viewer_base.cpp.

References column, currentDisplay, SequenceDisplay::GetDisplayCoordinates(), row, and viewerWindow.

◆ MakeSequenceVisible()

void ViewerBase::MakeSequenceVisible ( const MoleculeIdentifier *  identifier)

Definition at line 284 of file viewer_base.cpp.

References viewerWindow.

◆ NewFont()

void ViewerBase::NewFont ( void  )

Definition at line 269 of file viewer_base.cpp.

References viewerWindow.

◆ Redo()

void ViewerBase::Redo ( void  )

Definition at line 159 of file viewer_base.cpp.

References CopyDataFromStack(), ERRORMSG, nRedosStored, SetUndoRedoMenuStates(), and stacksEnabled.

Referenced by ViewerWindowBase::OnEditMenu().

◆ Refresh()

void ViewerBase::Refresh ( void  )

Definition at line 294 of file viewer_base.cpp.

References viewerWindow.

Referenced by AlignmentManager::ShowHideCallbackFunction().

◆ RemoveBlockBoundaryRows()

void ViewerBase::RemoveBlockBoundaryRows ( void  )

Definition at line 304 of file viewer_base.cpp.

References currentDisplay, and SequenceDisplay::RemoveBlockBoundaryRows().

Referenced by SequenceViewerWindow::OnCloseWindow().

◆ Revert()

void ViewerBase::Revert ( void  )

Definition at line 222 of file viewer_base.cpp.

References alignmentStack, CopyDataFromStack(), DELETE_ALL_AND_CLEAR, displayStack, ERRORMSG, nRedosStored, SetUndoRedoMenuStates(), and stacksEnabled.

Referenced by SequenceViewerWindow::SaveDialog(), and UpdateViewerWindow::SaveDialog().

◆ Save()

void ViewerBase::Save ( void  )

Definition at line 104 of file viewer_base.cpp.

References a, alignmentStack, SequenceDisplay::Clone(), BlockMultipleAlignment::Clone(), currentAlignments, currentDisplay, DELETE_ALL_AND_CLEAR, displayStack, ERRORMSG, MAX_UNDO_STACK_SIZE, nRedosStored, SetUndoRedoMenuStates(), stacksEnabled, TRACEMSG, and WARNINGMSG.

Referenced by UpdateViewer::AddAlignments(), EnableStacks(), and SequenceViewer::ReplaceAlignment().

◆ SaveDialog()

void ViewerBase::SaveDialog ( bool  prompt)
virtual

Reimplemented in UpdateViewer.

Definition at line 289 of file viewer_base.cpp.

References viewerWindow.

◆ SetUndoRedoMenuStates()

void ViewerBase::SetUndoRedoMenuStates ( void  )
private

Definition at line 171 of file viewer_base.cpp.

References alignmentStack, nRedosStored, stacksEnabled, and viewerWindow.

Referenced by InitData(), KeepCurrent(), ViewerWindowBase::NewDisplay(), Redo(), Revert(), Save(), Undo(), and ViewerWindowBase::UpdateDisplay().

◆ SetWindowTitle()

void ViewerBase::SetWindowTitle ( void  ) const

Definition at line 77 of file viewer_base.cpp.

References viewerWindow.

◆ Undo()

void ViewerBase::Undo ( void  )

Definition at line 147 of file viewer_base.cpp.

References alignmentStack, CopyDataFromStack(), ERRORMSG, nRedosStored, SetUndoRedoMenuStates(), and stacksEnabled.

Referenced by ViewerWindowBase::OnEditMenu().

Friends And Related Function Documentation

◆ AlignmentManager

friend class AlignmentManager
friend

Definition at line 58 of file viewer_base.hpp.

◆ SequenceDisplay

friend class SequenceDisplay
friend

Definition at line 59 of file viewer_base.hpp.

◆ ViewerWindowBase

friend class ViewerWindowBase
friend

Definition at line 57 of file viewer_base.hpp.

Member Data Documentation

◆ alignmentManager

AlignmentManager* ViewerBase::alignmentManager
protected

Definition at line 96 of file viewer_base.hpp.

Referenced by UpdateViewer::BlastNeighbor(), UpdateViewer::BlastUpdate(), SequenceDisplay::CalculateRowScoresWithThreader(), CalculateSelfHitScores(), UpdateViewer::GetMasterSequence(), UpdateViewer::ImportStructure(), SequenceDisplay::MouseDown(), UpdateViewerWindow::OnBlockAlign(), UpdateViewerWindow::OnExtend(), UpdateViewerWindow::OnMerge(), SequenceViewerWindow::OnRealign(), UpdateViewerWindow::OnRunThreader(), SequenceViewerWindow::OnSelfHit(), SequenceViewerWindow::OnShowHideRows(), SequenceViewerWindow::OnShowUpdates(), SequenceViewerWindow::QueryShowAllRows(), SequenceViewer::SaveAlignment(), UpdateViewer::SaveAlignments(), UpdateViewer::SavePendingStructures(), and UpdateViewer::SortByPSSM().

◆ alignmentStack

AlignmentStack ViewerBase::alignmentStack
private

Definition at line 105 of file viewer_base.hpp.

Referenced by ClearAllData(), CopyDataFromStack(), KeepCurrent(), Revert(), Save(), SetUndoRedoMenuStates(), and Undo().

◆ currentAlignments

AlignmentList ViewerBase::currentAlignments
private

Definition at line 103 of file viewer_base.hpp.

Referenced by ClearAllData(), CopyDataFromStack(), GetCurrentAlignments(), InitData(), Save(), UpdateViewer::SortByPSSM(), and UpdateViewer::SortUpdates().

◆ currentDisplay

SequenceDisplay* ViewerBase::currentDisplay
private

Definition at line 107 of file viewer_base.hpp.

Referenced by ClearAllData(), CopyDataFromStack(), GetCurrentDisplay(), InitData(), MakeResidueVisible(), RemoveBlockBoundaryRows(), and Save().

◆ displayStack

DisplayStack ViewerBase::displayStack
private

Definition at line 109 of file viewer_base.hpp.

Referenced by ClearAllData(), CopyDataFromStack(), KeepCurrent(), Revert(), and Save().

◆ MAX_UNDO_STACK_SIZE

const unsigned int ViewerBase::MAX_UNDO_STACK_SIZE = 50
staticprivate

Definition at line 112 of file viewer_base.hpp.

Referenced by Save().

◆ nRedosStored

int ViewerBase::nRedosStored
private

Definition at line 114 of file viewer_base.hpp.

Referenced by CopyDataFromStack(), EnableStacks(), KeepCurrent(), Redo(), Revert(), Save(), SetUndoRedoMenuStates(), and Undo().

◆ stacksEnabled

bool ViewerBase::stacksEnabled
private

Definition at line 115 of file viewer_base.hpp.

Referenced by EnableStacks(), InitData(), KeepCurrent(), Redo(), Revert(), Save(), SetUndoRedoMenuStates(), and Undo().

◆ viewerWindow

ViewerWindowBase* * const ViewerBase::viewerWindow
protected

Definition at line 99 of file viewer_base.hpp.

Referenced by DestroyGUI(), SequenceViewer::DisplayAlignment(), SequenceViewer::DisplaySequences(), EditorIsOn(), UpdateViewer::FetchSequences(), UpdateViewer::FetchSequencesViaHTTP(), GUIDestroyed(), UpdateViewer::ImportStructure(), MakeResidueVisible(), MakeSequenceVisible(), NewFont(), UpdateViewer::ReadSequencesFromFile(), Refresh(), SaveDialog(), SetUndoRedoMenuStates(), and SetWindowTitle().

The documentation for this class was generated from the following files:
Generated by doxygen 1.9.0
Modified on Wed Sep 04 15:02:29 2024 by modify_doxy.py rev. 669887