NCBI C++ ToolKit
Public Types | Public Member Functions | Public Attributes | Private Member Functions | Private Attributes | List of all members
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 *, boolUpdateMap
 

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
 
BlockMultipleAlignmentCreateMultipleFromPairwiseWithIBM (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 VectorGetAlignmentColor (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 BlockMultipleAlignmentGetCurrentMultipleAlignment (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

Threaderthreader
 
BLASTerblaster
 
BlockAlignerblockAligner
 

Private Member Functions

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

Private Attributes

const SequenceSetsequenceSet
 
const AlignmentSetalignmentSet
 
std::vector< booldependentsVisible
 
SequenceViewersequenceViewer
 
UpdateViewerupdateViewer
 
BlockMultipleAlignmentoriginalMultiple
 
std::vector< unsigned intoriginalRowOrder
 

Detailed Description

Definition at line 67 of file alignment_manager.hpp.

Member Typedef Documentation

◆ 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

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 
)

◆ ~AlignmentManager()

AlignmentManager::~AlignmentManager ( void  )
virtual

Member Function Documentation

◆ BlockAlignAllUpdates()

void AlignmentManager::BlockAlignAllUpdates ( void  )

◆ BlockAlignUpdate()

void AlignmentManager::BlockAlignUpdate ( BlockMultipleAlignment single)

◆ CalculateRowScoresWithThreader()

void AlignmentManager::CalculateRowScoresWithThreader ( double  weightPSSM)

◆ CreateMultipleFromPairwiseWithIBM()

BlockMultipleAlignment * AlignmentManager::CreateMultipleFromPairwiseWithIBM ( const PairwiseAlignmentList alignments)

◆ ExtendAllUpdates()

void AlignmentManager::ExtendAllUpdates ( void  )

◆ ExtendUpdate()

void AlignmentManager::ExtendUpdate ( BlockMultipleAlignment single)

◆ GetAlignmentColor()

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

◆ 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

◆ GetCurrentMultipleAlignment()

const BlockMultipleAlignment * AlignmentManager::GetCurrentMultipleAlignment ( void  ) const

◆ GetStructureProteins()

bool AlignmentManager::GetStructureProteins ( std::vector< const Sequence * > *  chains) const

◆ GetUpdateSequences()

void AlignmentManager::GetUpdateSequences ( std::list< const Sequence * > *  updateSequences) const

◆ 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

◆ IsInAlignment()

bool AlignmentManager::IsInAlignment ( const Sequence sequence) const

◆ MergeUpdates()

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

◆ NewAlignments()

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

◆ NewMultipleWithRows()

void AlignmentManager::NewMultipleWithRows ( const std::vector< bool > &  visibilities)

◆ 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)

◆ RealignAllDependentStructures()

void AlignmentManager::RealignAllDependentStructures ( bool  highlightedOnly) const

◆ RealignDependentSequences()

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

◆ ReplaceUpdatesInASN()

void AlignmentManager::ReplaceUpdatesInASN ( ncbi::objects::CCdd::TPending &  newUpdates) const

◆ SavePairwiseFromMultiple()

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

◆ ShowHideCallbackFunction()

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

◆ ShowSequenceViewer()

void AlignmentManager::ShowSequenceViewer ( bool  showNow) const

◆ ShowUpdateWindow()

void AlignmentManager::ShowUpdateWindow ( void  ) const

◆ ThreadAllUpdates()

void AlignmentManager::ThreadAllUpdates ( const ThreaderOptions options)

◆ ThreadUpdate()

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

Member Data Documentation

◆ alignmentSet

const AlignmentSet* AlignmentManager::alignmentSet
private

◆ blaster

BLASTer* AlignmentManager::blaster

◆ 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

◆ originalMultiple

BlockMultipleAlignment* AlignmentManager::originalMultiple
private

◆ 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

◆ threader

Threader* AlignmentManager::threader

◆ updateViewer

UpdateViewer* AlignmentManager::updateViewer
private

The documentation for this class was generated from the following files:
Modified on Thu May 30 12:24:05 2024 by modify_doxy.py rev. 669887