SequenceViewer Class Reference

Search Toolkit Book for SequenceViewer

#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
SequenceViewerWindow *	sequenceWindow

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 AlignmentList &	GetCurrentAlignments (void) const
AlignmentList &	GetCurrentAlignments (void)
SequenceDisplay *	GetCurrentDisplay (void)
Protected Attributes inherited from ViewerBase
AlignmentManager *	alignmentManager
ViewerWindowBase **const	viewerWindow

Detailed Description

Definition at line 52 of file sequence_viewer.hpp.

Member Typedef Documentation

SequenceList

typedef std::list< const Sequence * > SequenceViewer::SequenceList

Definition at line 64 of file sequence_viewer.hpp.

Member Enumeration Documentation

eExportType

enum SequenceViewer::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

Definition at line 74 of file sequence_viewer.cpp.

References ViewerBase::GetCurrentDisplay(), SequenceDisplay::GetStartingColumn(), GlobalMessenger(), ViewerWindowBase::NewDisplay(), Messenger::PostRedrawSequenceViewer(), ViewerWindowBase::ScrollToColumn(), SequenceViewerWindow, sequenceWindow, and Messenger::UnPostRedrawSequenceViewer().

Referenced by DisplayAlignment(), DisplaySequences(), AlignmentManager::ShowSequenceViewer(), and TurnOnEditor().

DisplayAlignment()

void SequenceViewer::DisplayAlignment

(

BlockMultipleAlignment *

multipleAlignment

)

Definition at line 116 of file sequence_viewer.cpp.

References SequenceDisplay::AddRowFromAlignment(), CreateSequenceWindow(), BlockMultipleAlignment::GetFirstAlignedBlockPosition(), ViewerBase::InitData(), IsWindowedMode(), BlockMultipleAlignment::NRows(), row, SequenceDisplay, sequenceWindow, SequenceDisplay::SetStartingColumn(), ViewerWindowBase::UpdateDisplay(), and ViewerBase::viewerWindow.

Referenced by AlignmentManager::MergeUpdates(), and AlignmentManager::NewMultipleWithRows().

DisplaySequences()

void SequenceViewer::DisplaySequences

(

const SequenceList *

sequenceList

)

Definition at line 162 of file sequence_viewer.cpp.

References SequenceDisplay::AddRowFromSequence(), SequenceDisplay::AddRowFromString(), CreateSequenceWindow(), ViewerBase::InitData(), IsWindowedMode(), SequenceDisplay::NRows(), NULL, SequenceDisplay, sequenceWindow, ViewerWindowBase::UpdateDisplay(), and ViewerBase::viewerWindow.

Referenced by AlignmentManager::NewAlignments().

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
	)

Definition at line 134 of file sequence_viewer.cpp.

References SequenceDisplay::AddBlockBoundaryRow(), SequenceDisplay::AddRowFromAlignment(), DELETE_ALL_AND_CLEAR, ViewerWindowBase::EditorIsOn(), SequenceDisplay::Empty(), ERRORMSG, ViewerBase::GetCurrentAlignments(), ViewerBase::GetCurrentDisplay(), BlockMultipleAlignment::GetFirstAlignedBlockPosition(), BlockMultipleAlignment::NRows(), row, ViewerBase::Save(), sequenceWindow, SequenceDisplay::SetStartingColumn(), and ViewerWindowBase::UpdateDisplay().

SaveAlignment()

void SequenceViewer::SaveAlignment

(

void

)

Definition at line 101 of file sequence_viewer.cpp.

References ViewerBase::alignmentManager, ViewerBase::GetCurrentAlignments(), ViewerBase::GetCurrentDisplay(), i, ViewerBase::KeepCurrent(), DisplayRowFromAlignment::row, SequenceDisplay::rows, and AlignmentManager::SavePairwiseFromMultiple().

Referenced by SequenceViewerWindow::SaveDialog().

TurnOnEditor()

void SequenceViewer::TurnOnEditor

(

void

)

Definition at line 187 of file sequence_viewer.cpp.

References CreateSequenceWindow(), sequenceWindow, and SequenceViewerWindow::TurnOnEditor().

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

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

Definition at line 89 of file sequence_viewer.hpp.

Referenced by CreateSequenceWindow(), DisplayAlignment(), DisplaySequences(), ReplaceAlignment(), and TurnOnEditor().

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

• src/app/cn3d/sequence_viewer.hpp
• src/app/cn3d/sequence_viewer.cpp