NCBI C++ ToolKit
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SequenceViewer Class Reference

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

+ Inheritance diagram for SequenceViewer:
+ Collaboration diagram for SequenceViewer:

Public Types

enum  eExportType {
  asFASTA , asFASTAa2m , asText , asHTML ,
  asPSSM
}
 
typedef std::list< const Sequence * > SequenceList
 
- Public Types inherited from ViewerBase
typedef std::list< BlockMultipleAlignment * > AlignmentList
 

Public Member Functions

 SequenceViewer (AlignmentManager *alnMgr)
 
 ~SequenceViewer (void)
 
void DisplaySequences (const SequenceList *sequenceList)
 
void DisplayAlignment (BlockMultipleAlignment *multipleAlignment)
 
void TurnOnEditor (void)
 
bool ReplaceAlignment (const BlockMultipleAlignment *origAln, BlockMultipleAlignment *newAln)
 
void SaveAlignment (void)
 
void ExportAlignment (eExportType type)
 
- Public Member Functions inherited from ViewerBase
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)
 

Private Member Functions

void CreateSequenceWindow (bool showNow)
 

Private Attributes

SequenceViewerWindowsequenceWindow
 

Friends

class SequenceViewerWindow
 
class SequenceDisplay
 
class AlignmentManager
 

Additional Inherited Members

- Protected Member Functions inherited from ViewerBase
 ViewerBase (ViewerWindowBase **window, AlignmentManager *alnMgr)
 
virtual ~ViewerBase (void)
 
const AlignmentListGetCurrentAlignments (void) const
 
AlignmentListGetCurrentAlignments (void)
 
SequenceDisplayGetCurrentDisplay (void)
 
- Protected Attributes inherited from ViewerBase
AlignmentManageralignmentManager
 
ViewerWindowBase **const viewerWindow
 

Detailed Description

Definition at line 52 of file sequence_viewer.hpp.

Member Typedef Documentation

◆ SequenceList

Definition at line 64 of file sequence_viewer.hpp.

Member Enumeration Documentation

◆ eExportType

Enumerator
asFASTA 
asFASTAa2m 
asText 
asHTML 
asPSSM 

Definition at line 78 of file sequence_viewer.hpp.

Constructor & Destructor Documentation

◆ SequenceViewer()

SequenceViewer::SequenceViewer ( AlignmentManager alnMgr)

Definition at line 63 of file sequence_viewer.cpp.

◆ ~SequenceViewer()

SequenceViewer::~SequenceViewer ( void  )

Definition at line 70 of file sequence_viewer.cpp.

Member Function Documentation

◆ CreateSequenceWindow()

void SequenceViewer::CreateSequenceWindow ( bool  showNow)
private

◆ DisplayAlignment()

void SequenceViewer::DisplayAlignment ( BlockMultipleAlignment multipleAlignment)

◆ DisplaySequences()

void SequenceViewer::DisplaySequences ( const SequenceList sequenceList)

◆ ExportAlignment()

void SequenceViewer::ExportAlignment ( eExportType  type)

Definition at line 513 of file sequence_viewer.cpp.

Referenced by SequenceViewerWindow::OnExport().

◆ ReplaceAlignment()

bool SequenceViewer::ReplaceAlignment ( const BlockMultipleAlignment origAln,
BlockMultipleAlignment newAln 
)

◆ SaveAlignment()

void SequenceViewer::SaveAlignment ( void  )

◆ TurnOnEditor()

void SequenceViewer::TurnOnEditor ( void  )

Friends And Related Function Documentation

◆ AlignmentManager

friend class AlignmentManager
friend

Definition at line 56 of file sequence_viewer.hpp.

◆ SequenceDisplay

friend class SequenceDisplay
friend

Definition at line 55 of file sequence_viewer.hpp.

Referenced by DisplayAlignment(), and DisplaySequences().

◆ SequenceViewerWindow

friend class SequenceViewerWindow
friend

Definition at line 54 of file sequence_viewer.hpp.

Referenced by CreateSequenceWindow().

Member Data Documentation

◆ sequenceWindow

SequenceViewerWindow* SequenceViewer::sequenceWindow
private

The documentation for this class was generated from the following files:
Modified on Fri Jan 05 07:22:45 2024 by modify_doxy.py rev. 669887