AlignmentManager Class Reference

Search Toolkit Book for AlignmentManager

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

Inheritance diagram for AlignmentManager:

Collaboration diagram for AlignmentManager:

Public Types
typedef std::list< ncbi::CRef< ncbi::objects::CUpdate_align > >	UpdateAlignList
typedef std::list< const MasterDependentAlignment * >	PairwiseAlignmentList
typedef std::map< BlockMultipleAlignment *, bool >	UpdateMap

Public Member Functions
	AlignmentManager (const SequenceSet *sSet, const AlignmentSet *aSet)
	AlignmentManager (const SequenceSet *sSet, const AlignmentSet *aSet, const UpdateAlignList &updates)
virtual	~AlignmentManager (void)
void	ReplaceUpdatesInASN (ncbi::objects::CCdd::TPending &newUpdates) const
BlockMultipleAlignment *	CreateMultipleFromPairwiseWithIBM (const PairwiseAlignmentList &alignments)
void	SavePairwiseFromMultiple (const BlockMultipleAlignment *multiple, const std::vector< unsigned int > &rowOrder)
void	RealignAllDependentStructures (bool highlightedOnly) const
void	GetAlignmentSetDependentSequences (std::vector< const Sequence * > *sequences) const
void	GetAlignmentSetDependentVisibilities (std::vector< bool > *visibilities) const
void	ShowHideCallbackFunction (const std::vector< bool > &itemsEnabled)
void	NewMultipleWithRows (const std::vector< bool > &visibilities)
bool	IsAligned (const Sequence *sequence, unsigned int seqIndex) const
bool	IsInAlignment (const Sequence *sequence) const
const Vector *	GetAlignmentColor (const Sequence *sequence, unsigned int seqIndex, StyleSettings::eColorScheme colorScheme) const
void	RealignDependentSequences (BlockMultipleAlignment *multiple, const std::vector< unsigned int > &dependentsToRealign)
void	ThreadUpdate (const ThreaderOptions &options, BlockMultipleAlignment *single)
void	ThreadAllUpdates (const ThreaderOptions &options)
void	BlockAlignAllUpdates (void)
void	BlockAlignUpdate (BlockMultipleAlignment *single)
void	ExtendAllUpdates (void)
void	ExtendUpdate (BlockMultipleAlignment *single)
void	MergeUpdates (const UpdateMap &updates, bool mergeToNeighbor)
void	CalculateRowScoresWithThreader (double weightPSSM)
const BlockMultipleAlignment *	GetCurrentMultipleAlignment (void) const
bool	GetStructureProteins (std::vector< const Sequence * > *chains) const
unsigned int	NUpdates (void) const
void	GetUpdateSequences (std::list< const Sequence * > *updateSequences) const
void	PurgeSequence (const MoleculeIdentifier *identifier)
void	ShowSequenceViewer (bool showNow) const
void	ShowUpdateWindow (void) const
Public Member Functions inherited from ShowHideCallbackObject
virtual	~ShowHideCallbackObject (void)
virtual bool	SelectionChangedCallback (const std::vector< bool > &original, std::vector< bool > &itemsEnabled)

Public Attributes
Threader *	threader
BLASTer *	blaster
BlockAligner *	blockAligner

Private Member Functions
void	Init (void)
void	NewAlignments (const SequenceSet *sSet, const AlignmentSet *aSet)

Private Attributes
const SequenceSet *	sequenceSet
const AlignmentSet *	alignmentSet
std::vector< bool >	dependentsVisible
SequenceViewer *	sequenceViewer
UpdateViewer *	updateViewer
BlockMultipleAlignment *	originalMultiple
std::vector< unsigned int >	originalRowOrder

Detailed Description

Definition at line 67 of file alignment_manager.hpp.

Member Typedef Documentation

PairwiseAlignmentList

typedef std::list< const MasterDependentAlignment * > AlignmentManager::PairwiseAlignmentList

Definition at line 83 of file alignment_manager.hpp.

UpdateAlignList

typedef std::list< ncbi::CRef< ncbi::objects::CUpdate_align > > AlignmentManager::UpdateAlignList

Definition at line 71 of file alignment_manager.hpp.

UpdateMap

typedef std::map< BlockMultipleAlignment *, bool > AlignmentManager::UpdateMap

Definition at line 122 of file alignment_manager.hpp.

Constructor & Destructor Documentation

AlignmentManager() [1/2]

AlignmentManager::AlignmentManager	(	const SequenceSet *	sSet,
		const AlignmentSet *	aSet
	)

Definition at line 89 of file alignment_manager.cpp.

References Init(), and NewAlignments().

AlignmentManager() [2/2]

AlignmentManager::AlignmentManager	(	const SequenceSet *	sSet,
		const AlignmentSet *	aSet,
		const UpdateAlignList &	updates
	)

Definition at line 95 of file alignment_manager.cpp.

References UpdateViewer::AddAlignments(), CreateMultipleFromPairwiseWithIBM(), ERRORMSG, Init(), AlignmentSet::master, NewAlignments(), NULL, SequenceSet::sequences, UpdateViewer::SetInitialState(), BlockMultipleAlignment::updateOrigin, and updateViewer.

~AlignmentManager()

AlignmentManager::~AlignmentManager ( void  )

virtual

Definition at line 152 of file alignment_manager.cpp.

References blaster, blockAligner, GlobalMessenger(), originalMultiple, Messenger::RemoveSequenceViewer(), sequenceViewer, threader, and updateViewer.

Member Function Documentation

BlockAlignAllUpdates()

void AlignmentManager::BlockAlignAllUpdates

(

void

)

Definition at line 905 of file alignment_manager.cpp.

References blockAligner, BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment(), ViewerBase::GetCurrentAlignments(), ViewerBase::GetCurrentDisplay(), NULL, UpdateViewer::ReplaceAlignments(), SequenceDisplay::RowsAdded(), sequenceViewer, and updateViewer.

Referenced by UpdateViewerWindow::OnBlockAlign().

BlockAlignUpdate()

void AlignmentManager::BlockAlignUpdate

(

BlockMultipleAlignment *

single

)

Definition at line 932 of file alignment_manager.cpp.

References a, blockAligner, BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment(), ERRORMSG, ViewerBase::GetCurrentAlignments(), ViewerBase::GetCurrentDisplay(), n, ne(), NULL, UpdateViewer::ReplaceAlignments(), SequenceDisplay::RowsAdded(), sequenceViewer, and updateViewer.

Referenced by SequenceDisplay::MouseDown().

CalculateRowScoresWithThreader()

void AlignmentManager::CalculateRowScoresWithThreader

(

double

weightPSSM

)

Definition at line 813 of file alignment_manager.cpp.

References Threader::CalculateScores(), GetCurrentMultipleAlignment(), and threader.

Referenced by SequenceDisplay::CalculateRowScoresWithThreader().

CreateMultipleFromPairwiseWithIBM()

BlockMultipleAlignment * AlignmentManager::CreateMultipleFromPairwiseWithIBM

(

const PairwiseAlignmentList &

alignments

)

Definition at line 310 of file alignment_manager.cpp.

References a, BlockMultipleAlignment::AddAlignedBlockAtEnd(), BlockMultipleAlignment::AddUnalignedBlocks(), AlignedToAllDependents(), ERRORMSG, BlockMultipleAlignment::GetMaster(), if(), int, Sequence::Length(), NoBlockBoundariesBetween(), NoDependentInsertionsBetween(), NULL, row, Block::SetRangeOfRow(), BlockMultipleAlignment::UpdateBlockMapAndColors(), and Block::width.

Referenced by AlignmentManager(), and NewMultipleWithRows().

ExtendAllUpdates()

void AlignmentManager::ExtendAllUpdates

(

void

)

Definition at line 1118 of file alignment_manager.cpp.

References CreateNewPairwiseAlignmentsByBlockExtension(), ViewerBase::GetCurrentAlignments(), NULL, UpdateViewer::ReplaceAlignments(), sequenceViewer, and updateViewer.

Referenced by UpdateViewerWindow::OnExtend().

ExtendUpdate()

void AlignmentManager::ExtendUpdate

(

BlockMultipleAlignment *

single

)

Definition at line 1135 of file alignment_manager.cpp.

References a, CreateNewPairwiseAlignmentsByBlockExtension(), ERRORMSG, ViewerBase::GetCurrentAlignments(), NULL, UpdateViewer::ReplaceAlignments(), sequenceViewer, and updateViewer.

Referenced by SequenceDisplay::MouseDown().

GetAlignmentColor()

const Vector * AlignmentManager::GetAlignmentColor	(	const Sequence *	sequence,
		unsigned int	seqIndex,
		StyleSettings::eColorScheme	colorScheme
	)		const

Definition at line 597 of file alignment_manager.cpp.

References BlockMultipleAlignment::GetAlignmentColor(), GetCurrentMultipleAlignment(), and NULL.

GetAlignmentSetDependentSequences()

void AlignmentManager::GetAlignmentSetDependentSequences

(

std::vector< const Sequence * > *

sequences

)

const

Definition at line 498 of file alignment_manager.cpp.

References a, AlignmentSet::alignments, alignmentSet, and i.

Referenced by SequenceViewerWindow::OnShowHideRows().

GetAlignmentSetDependentVisibilities()

void AlignmentManager::GetAlignmentSetDependentVisibilities

(

std::vector< bool > *

visibilities

)

const

Definition at line 509 of file alignment_manager.cpp.

References AlignmentSet::alignments, alignmentSet, and dependentsVisible.

Referenced by SequenceViewerWindow::OnShowHideRows(), and SequenceViewerWindow::QueryShowAllRows().

GetCurrentMultipleAlignment()

const BlockMultipleAlignment * AlignmentManager::GetCurrentMultipleAlignment

(

void

)

const

Definition at line 271 of file alignment_manager.cpp.

References ViewerBase::GetCurrentAlignments(), NULL, and sequenceViewer.

Referenced by UpdateViewer::BlastNeighbor(), UpdateViewer::BlastUpdate(), CalculateRowScoresWithThreader(), StructureSet::CenterViewOnAlignedResidues(), DoHighlightMotif(), GetAlignmentColor(), StyleManager::GetAtomStyle(), BlockMultipleAlignment::GetCharacterTraitsAt(), CDDAnnotateDialog::GetCurrentHighlightedIntervals(), IBISAnnotateDialog::GetIntervalsForSet(), UpdateViewer::GetMasterSequence(), GetStructureProteins(), CDDAnnotateDialog::HighlightInterval(), IBISAnnotateDialog::HighlightInterval(), UpdateViewer::ImportStructure(), IsAligned(), IsInAlignment(), SequenceDisplay::MouseDown(), NewAlignments(), CDDAnnotateDialog::NewOrEditMotif(), StructureWindow::OnAlignStructures(), UpdateViewerWindow::OnRunThreader(), SequenceViewerWindow::OnShowHideRows(), IBISAnnotateDialog::PopulateInteractionData(), RealignAllDependentStructures(), StructureObject::RealignStructure(), UpdateViewer::SavePendingStructures(), and UpdateViewer::SortByPSSM().

GetStructureProteins()

bool AlignmentManager::GetStructureProteins

(

std::vector< const Sequence * > *

chains

)

const

Definition at line 833 of file alignment_manager.cpp.

References ViewerBase::GetCurrentDisplay(), GetCurrentMultipleAlignment(), SequenceDisplay::GetProteinSequences(), NULL, and sequenceViewer.

Referenced by UpdateViewer::GetMasterSequence().

GetUpdateSequences()

void AlignmentManager::GetUpdateSequences

(

std::list< const Sequence * > *

updateSequences

)

const

Definition at line 823 of file alignment_manager.cpp.

References ViewerBase::GetCurrentAlignments(), and updateViewer.

Referenced by StructureSet::RemoveUnusedSequences().

Init()

void AlignmentManager::Init ( void  )

private

Definition at line 74 of file alignment_manager.cpp.

References Messenger::AddSequenceViewer(), GlobalMessenger(), and NULL.

Referenced by AlignmentManager().

IsAligned()

bool AlignmentManager::IsAligned	(	const Sequence *	sequence,
		unsigned int	seqIndex
	)		const

Definition at line 574 of file alignment_manager.cpp.

References GetCurrentMultipleAlignment(), and BlockMultipleAlignment::IsAligned().

Referenced by StyleManager::GetAtomStyle().

IsInAlignment()

bool AlignmentManager::IsInAlignment

(

const Sequence *

sequence

)

const

Definition at line 584 of file alignment_manager.cpp.

References GetCurrentMultipleAlignment(), BlockMultipleAlignment::GetSequences(), i, and ncbi::grid::netcache::search::fields::size.

MergeUpdates()

void AlignmentManager::MergeUpdates	(	const UpdateMap &	updates,
		bool	mergeToNeighbor
	)

Definition at line 700 of file alignment_manager.cpp.

References b, blocks, BlockMultipleAlignment::Clone(), SequenceViewer::DisplayAlignment(), StyleSettings::eAlignedShortcut, ViewerBase::EditorIsOn(), ERRORMSG, StyleSettings::eTubeShortcut, GetBLOSUM62Score(), ViewerBase::GetCurrentAlignments(), ViewerBase::GetCurrentDisplay(), BlockMultipleAlignment::GetMaster(), BlockMultipleAlignment::GetSequenceOfRow(), BlockMultipleAlignment::GetUngappedAlignedBlocks(), GlobalMessenger(), i, Sequence::identifier, INFOMSG, BlockMultipleAlignment::MergeAlignment(), BlockMultipleAlignment::NRows(), NULL, StructureBase::parentSet, Messenger::PostRedrawAllStructures(), UpdateViewer::ReplaceAlignments(), row, SequenceDisplay::RowsAdded(), SavePairwiseFromMultiple(), UpdateViewer::SavePendingStructures(), Sequence::sequenceString, sequenceViewer, StructureSet::styleManager, MoleculeIdentifier::ToString(), TRACEMSG, SequenceViewer::TurnOnEditor(), and updateViewer.

Referenced by SequenceDisplay::MouseDown(), and UpdateViewerWindow::OnMerge().

NewAlignments()

void AlignmentManager::NewAlignments ( const SequenceSet *  sSet, const AlignmentSet *  aSet  )

private

Definition at line 164 of file alignment_manager.cpp.

References AlignmentSet::alignments, alignmentSet, BlockMultipleAlignment::Clone(), dependentsVisible, SequenceViewer::DisplaySequences(), GetCurrentMultipleAlignment(), i, NewMultipleWithRows(), BlockMultipleAlignment::NRows(), originalMultiple, originalRowOrder, r(), SequenceSet::sequences, sequenceSet, and sequenceViewer.

Referenced by AlignmentManager().

NewMultipleWithRows()

void AlignmentManager::NewMultipleWithRows

(

const std::vector< bool > &

visibilities

)

Definition at line 554 of file alignment_manager.cpp.

References a, AlignmentSet::alignments, alignmentSet, CreateMultipleFromPairwiseWithIBM(), SequenceViewer::DisplayAlignment(), ERRORMSG, i, and sequenceViewer.

Referenced by NewAlignments(), and ShowHideCallbackFunction().

NUpdates()

unsigned int AlignmentManager::NUpdates

(

void

)

const

Definition at line 818 of file alignment_manager.cpp.

References ViewerBase::GetCurrentAlignments(), and updateViewer.

Referenced by Cn3DApp::OnInit().

PurgeSequence()

void AlignmentManager::PurgeSequence

(

const MoleculeIdentifier *

identifier

)

Definition at line 850 of file alignment_manager.cpp.

References BlockMultipleAlignment::Clone(), ViewerBase::EditorIsOn(), ERRORMSG, BlockMultipleAlignment::ExtractRows(), ViewerBase::GetCurrentAlignments(), ViewerBase::GetCurrentDisplay(), BlockMultipleAlignment::GetSequenceOfRow(), i, Sequence::identifier, BlockMultipleAlignment::NRows(), NULL, UpdateViewer::ReplaceAlignments(), SequenceDisplay::RowsRemoved(), sequenceViewer, SequenceViewer::TurnOnEditor(), and updateViewer.

Referenced by StructureSet::RejectAndPurgeSequence().

RealignAllDependentStructures()

void AlignmentManager::RealignAllDependentStructures

(

bool

highlightedOnly

)

const

Definition at line 406 of file alignment_manager.cpp.

References b, blocks, ERRORMSG, GetAlignedResidueIndexes(), Molecule::GetAlphaCoords(), GetCurrentMultipleAlignment(), Sequence::GetOrSetMMDBLink(), StructureBase::GetParentOfType(), BlockMultipleAlignment::GetSequenceOfRow(), BlockMultipleAlignment::GetUngappedAlignedBlocks(), i, Sequence::identifier, INFOMSG, StructureSet::InitStructureAlignments(), MoleculeIdentifier::mmdbID, Sequence::molecule, BlockMultipleAlignment::NRows(), StructureBase::parentSet, MoleculeIdentifier::pdbID, StructureSet::RemoveStructureAlignments(), MoleculeIdentifier::VALUE_NOT_SET, and WARNINGMSG.

Referenced by StructureWindow::OnAlignStructures().

RealignDependentSequences()

void AlignmentManager::RealignDependentSequences	(	BlockMultipleAlignment *	multiple,
		const std::vector< unsigned int > &	dependentsToRealign
	)

Definition at line 617 of file alignment_manager.cpp.

References UpdateViewer::AddAlignments(), UpdateViewer::CreateUpdateWindow(), eDiag_Info, eDiag_Warning, ERRORMSG, BlockMultipleAlignment::ExtractRows(), ViewerBase::GetCurrentAlignments(), ViewerBase::GetCurrentDisplay(), SequenceDisplay::RowsRemoved(), sequenceViewer, SetDiagPostLevel(), TRACEMSG, and updateViewer.

Referenced by SequenceDisplay::MouseDown(), and SequenceViewerWindow::OnRealign().

ReplaceUpdatesInASN()

void AlignmentManager::ReplaceUpdatesInASN

(

ncbi::objects::CCdd::TPending &

newUpdates

)

const

Definition at line 842 of file alignment_manager.cpp.

References ERRORMSG, StructureBase::parentSet, StructureSet::ReplaceUpdates(), and sequenceSet.

Referenced by UpdateViewer::SaveAlignments().

SavePairwiseFromMultiple()

void AlignmentManager::SavePairwiseFromMultiple	(	const BlockMultipleAlignment *	multiple,
		const std::vector< unsigned int > &	rowOrder
	)

Definition at line 186 of file alignment_manager.cpp.

References alignmentSet, BlockMultipleAlignment::Clone(), AlignmentSet::CreateFromMultiple(), StructureSet::ePSSMData, StructureSet::eRowOrderData, ERRORMSG, CPssm_Base::GetByRow(), CPssm_Base::GetFinalData(), CPssmFinalData_Base::GetH(), CPssmFinalData_Base::GetKappa(), CPssmFinalData_Base::GetLambda(), BlockMultipleAlignment::GetMaster(), CPssm_Base::GetNumColumns(), CPssm_Base::GetNumRows(), BlockMultipleAlignment::GetPSSM(), CPssmWithParameters_Base::GetPssm(), CPssmFinalData_Base::GetScalingFactor(), CPssmFinalData_Base::GetScores(), BlockMultipleAlignment::GetSequenceOfRow(), BlockMultipleAlignment::HasNoAlignedBlocks(), CPssm_Base::IsSetFinalData(), BlockMultipleAlignment::NRows(), originalMultiple, originalRowOrder, StructureBase::parentSet, BlockMultipleAlignment::RemovePSSM(), StructureSet::ReplaceAlignmentSet(), row, StructureSet::SetDataChanged(), and TRACEMSG.

Referenced by MergeUpdates(), and SequenceViewer::SaveAlignment().

ShowHideCallbackFunction()

void AlignmentManager::ShowHideCallbackFunction ( const std::vector< bool > &  itemsEnabled )

virtual

Implements ShowHideCallbackObject.

Definition at line 518 of file alignment_manager.cpp.

References a, AlignmentSet::alignments, alignmentSet, dependentsVisible, ERRORMSG, GlobalMessenger(), i, NewMultipleWithRows(), StructureBase::parentSet, Messenger::PostRedrawAllSequenceViewers(), Messenger::PostRedrawMolecule(), ViewerBase::Refresh(), sequenceViewer, ShowHideManager::Show(), StructureSet::showHideManager, and Messenger::UnPostRedrawSequenceViewer().

Referenced by SequenceViewerWindow::QueryShowAllRows().

ShowSequenceViewer()

void AlignmentManager::ShowSequenceViewer

(

bool

showNow

)

const

Definition at line 607 of file alignment_manager.cpp.

References SequenceViewer::CreateSequenceWindow(), and sequenceViewer.

Referenced by StructureWindow::LoadData(), and StructureWindow::OnShowWindow().

ShowUpdateWindow()

void AlignmentManager::ShowUpdateWindow

(

void

)

const

Definition at line 612 of file alignment_manager.cpp.

References UpdateViewer::CreateUpdateWindow(), and updateViewer.

Referenced by Cn3DApp::OnInit(), and SequenceViewerWindow::OnShowUpdates().

ThreadAllUpdates()

void AlignmentManager::ThreadAllUpdates

(

const ThreaderOptions &

options

)

Definition at line 678 of file alignment_manager.cpp.

References ViewerBase::GetCurrentAlignments(), ViewerBase::GetCurrentDisplay(), Threader::Realign(), UpdateViewer::ReplaceAlignments(), sequenceViewer, threader, and updateViewer.

Referenced by UpdateViewerWindow::OnRunThreader().

ThreadUpdate()

void AlignmentManager::ThreadUpdate	(	const ThreaderOptions &	options,
		BlockMultipleAlignment *	single
	)

Definition at line 642 of file alignment_manager.cpp.

References a, ERRORMSG, ViewerBase::GetCurrentAlignments(), ViewerBase::GetCurrentDisplay(), n, ne(), Threader::Realign(), UpdateViewer::ReplaceAlignments(), SequenceDisplay::RowsAdded(), sequenceViewer, threader, and updateViewer.

Referenced by SequenceDisplay::MouseDown().

Member Data Documentation

alignmentSet

const AlignmentSet* AlignmentManager::alignmentSet

private

Definition at line 150 of file alignment_manager.hpp.

Referenced by GetAlignmentSetDependentSequences(), GetAlignmentSetDependentVisibilities(), NewAlignments(), NewMultipleWithRows(), SavePairwiseFromMultiple(), and ShowHideCallbackFunction().

blaster

BLASTer* AlignmentManager::blaster

Definition at line 76 of file alignment_manager.hpp.

Referenced by UpdateViewer::BlastNeighbor(), UpdateViewer::BlastUpdate(), ViewerBase::CalculateSelfHitScores(), SequenceViewerWindow::OnSelfHit(), and ~AlignmentManager().

blockAligner

BlockAligner* AlignmentManager::blockAligner

Definition at line 77 of file alignment_manager.hpp.

Referenced by BlockAlignAllUpdates(), BlockAlignUpdate(), and ~AlignmentManager().

dependentsVisible

std::vector< bool > AlignmentManager::dependentsVisible

mutableprivate

Definition at line 152 of file alignment_manager.hpp.

Referenced by GetAlignmentSetDependentVisibilities(), NewAlignments(), and ShowHideCallbackFunction().

originalMultiple

BlockMultipleAlignment* AlignmentManager::originalMultiple

private

Definition at line 161 of file alignment_manager.hpp.

Referenced by NewAlignments(), SavePairwiseFromMultiple(), and ~AlignmentManager().

originalRowOrder

std::vector< unsigned int > AlignmentManager::originalRowOrder

private

Definition at line 162 of file alignment_manager.hpp.

Referenced by NewAlignments(), and SavePairwiseFromMultiple().

sequenceSet

const SequenceSet* AlignmentManager::sequenceSet

private

Definition at line 149 of file alignment_manager.hpp.

Referenced by NewAlignments(), and ReplaceUpdatesInASN().

sequenceViewer

SequenceViewer* AlignmentManager::sequenceViewer

private

Definition at line 155 of file alignment_manager.hpp.

Referenced by BlockAlignAllUpdates(), BlockAlignUpdate(), ExtendAllUpdates(), ExtendUpdate(), GetCurrentMultipleAlignment(), GetStructureProteins(), MergeUpdates(), NewAlignments(), NewMultipleWithRows(), PurgeSequence(), RealignDependentSequences(), ShowHideCallbackFunction(), ShowSequenceViewer(), ThreadAllUpdates(), ThreadUpdate(), and ~AlignmentManager().

threader

Threader* AlignmentManager::threader

Definition at line 75 of file alignment_manager.hpp.

Referenced by CalculateRowScoresWithThreader(), BlockMultipleAlignment::ShowGeometryViolations(), ThreadAllUpdates(), ThreadUpdate(), and ~AlignmentManager().

updateViewer

UpdateViewer* AlignmentManager::updateViewer

private

Definition at line 158 of file alignment_manager.hpp.

Referenced by AlignmentManager(), BlockAlignAllUpdates(), BlockAlignUpdate(), ExtendAllUpdates(), ExtendUpdate(), GetUpdateSequences(), MergeUpdates(), NUpdates(), PurgeSequence(), RealignDependentSequences(), ShowUpdateWindow(), ThreadAllUpdates(), ThreadUpdate(), and ~AlignmentManager().

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

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