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NCBI C++ ToolKit: AlignmentManager Class Reference

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

  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   virtual  ~ShowHideCallbackObject (void)   virtual bool  SelectionChangedCallback (const std::vector< bool > &original, std::vector< bool > &itemsEnabled)  

Definition at line 67 of file alignment_manager.hpp.

◆ PairwiseAlignmentList ◆ UpdateAlignList ◆ UpdateMap ◆ AlignmentManager() [1/2] ◆ AlignmentManager() [2/2]

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 ◆ BlockAlignAllUpdates() void AlignmentManager::BlockAlignAllUpdates ( void  ) ◆ BlockAlignUpdate()

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 ) ◆ CreateMultipleFromPairwiseWithIBM()

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  ) ◆ ExtendUpdate() ◆ GetAlignmentColor() ◆ GetAlignmentSetDependentSequences() void AlignmentManager::GetAlignmentSetDependentSequences ( std::vector< const Sequence * > *  sequences ) const ◆ GetAlignmentSetDependentVisibilities() void AlignmentManager::GetAlignmentSetDependentVisibilities ( std::vector< bool > *  visibilities ) const ◆ GetCurrentMultipleAlignment()

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 ◆ GetUpdateSequences() void AlignmentManager::GetUpdateSequences ( std::list< const Sequence * > *  updateSequences ) const ◆ Init() void AlignmentManager::Init ( void  ) private ◆ IsAligned() ◆ IsInAlignment() ◆ MergeUpdates()

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()

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 ) ◆ NUpdates() unsigned int AlignmentManager::NUpdates ( void  ) const ◆ PurgeSequence()

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()

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 ◆ SavePairwiseFromMultiple()

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 ◆ ShowUpdateWindow() void AlignmentManager::ShowUpdateWindow ( void  ) const ◆ ThreadAllUpdates() ◆ ThreadUpdate()

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().

◆ alignmentSet ◆ blaster ◆ blockAligner ◆ dependentsVisible std::vector< bool > AlignmentManager::dependentsVisible mutableprivate ◆ originalMultiple ◆ originalRowOrder std::vector< unsigned int > AlignmentManager::originalRowOrder private ◆ sequenceSet ◆ sequenceViewer

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 ◆ updateViewer

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().

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

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