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UpdateViewer Class Reference

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

+ Inheritance diagram for UpdateViewer:
+ Collaboration diagram for UpdateViewer:


struct  StructureAlignmentInfo

Public Types

typedef std::list< BlockMultipleAlignment * > AlignmentList
- Public Types inherited from ViewerBase
typedef std::list< BlockMultipleAlignment * > AlignmentList

Public Member Functions

 UpdateViewer (AlignmentManager *alnMgr)
 ~UpdateViewer (void)
void CreateUpdateWindow (void)
void AddAlignments (const AlignmentList &alignmentList)
void ReplaceAlignments (const AlignmentList &alignmentList)
void DeleteAlignment (BlockMultipleAlignment *toDelete)
void ImportSequences (void)
void ImportStructure (void)
void SetInitialState (void)
void SaveDialog (bool prompt)
void SaveAlignments (void)
void BlastUpdate (BlockMultipleAlignment *alignment, bool usePSSMFromMultiple)
void BlastNeighbor (BlockMultipleAlignment *update)
void SavePendingStructures (void)
void SortByIdentifier (void)
void SortByPSSM (void)
- 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)
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 Types

typedef std::list< const Sequence * > SequenceList
typedef std::list< ncbi::CRef< ncbi::objects::CBiostruc > > BiostrucList
typedef std::list< StructureAlignmentInfoPendingStructureAlignments

Private Member Functions

const SequenceGetMasterSequence (void) const
void FetchSequencesViaHTTP (SequenceList *newSequences, StructureSet *sSet) const
void ReadSequencesFromFile (SequenceList *newSequences, StructureSet *sSet) const
void FetchSequences (StructureSet *sSet, SequenceList *newSequences) const
void SortUpdates (void)
void MakeEmptyAlignments (const SequenceList &newSequences, const Sequence *master, AlignmentList *newAlignments) const
void GetVASTAlignments (const SequenceList &newSequences, const Sequence *master, AlignmentList *newAlignments, PendingStructureAlignments *structureAlignments, unsigned int masterFrom=kMax_UInt, unsigned int masterTo=kMax_UInt) const

Private Attributes

BiostrucList pendingStructures
PendingStructureAlignments pendingStructureAlignments


class UpdateViewerWindow
class SequenceDisplay

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
ViewerWindowBase **const viewerWindow

Detailed Description

Definition at line 56 of file update_viewer.hpp.

Member Typedef Documentation

◆ AlignmentList

Definition at line 69 of file update_viewer.hpp.

◆ BiostrucList

typedef std::list< ncbi::CRef < ncbi::objects::CBiostruc > > UpdateViewer::BiostrucList

Definition at line 117 of file update_viewer.hpp.

◆ PendingStructureAlignments

Definition at line 123 of file update_viewer.hpp.

◆ SequenceList

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

Definition at line 108 of file update_viewer.hpp.

Constructor & Destructor Documentation

◆ UpdateViewer()

UpdateViewer::UpdateViewer ( AlignmentManager alnMgr)

Definition at line 99 of file update_viewer.cpp.

◆ ~UpdateViewer()

UpdateViewer::~UpdateViewer ( void  )

Definition at line 111 of file update_viewer.cpp.

Member Function Documentation

◆ AddAlignments()

void UpdateViewer::AddAlignments ( const AlignmentList alignmentList)

◆ BlastNeighbor()

void UpdateViewer::BlastNeighbor ( BlockMultipleAlignment update)

◆ BlastUpdate()

void UpdateViewer::BlastUpdate ( BlockMultipleAlignment alignment,
bool  usePSSMFromMultiple 

◆ CreateUpdateWindow()

void UpdateViewer::CreateUpdateWindow ( void  )

◆ DeleteAlignment()

void UpdateViewer::DeleteAlignment ( BlockMultipleAlignment toDelete)

Definition at line 184 of file update_viewer.cpp.

References a, ViewerBase::GetCurrentAlignments(), and ReplaceAlignments().

Referenced by SequenceDisplay::MouseDown().

◆ FetchSequences()

void UpdateViewer::FetchSequences ( StructureSet sSet,
SequenceList newSequences 
) const

◆ FetchSequencesViaHTTP()

void UpdateViewer::FetchSequencesViaHTTP ( SequenceList newSequences,
StructureSet sSet 
) const

◆ GetMasterSequence()

const Sequence * UpdateViewer::GetMasterSequence ( void  ) const

◆ GetVASTAlignments()

void UpdateViewer::GetVASTAlignments ( const SequenceList newSequences,
const Sequence master,
AlignmentList newAlignments,
PendingStructureAlignments structureAlignments,
unsigned int  masterFrom = kMax_UInt,
unsigned int  masterTo = kMax_UInt 
) const

◆ ImportSequences()

void UpdateViewer::ImportSequences ( void  )

◆ ImportStructure()

void UpdateViewer::ImportStructure ( void  )

◆ MakeEmptyAlignments()

void UpdateViewer::MakeEmptyAlignments ( const SequenceList newSequences,
const Sequence master,
AlignmentList newAlignments 
) const

Definition at line 391 of file update_viewer.cpp.

References MakeEmptyAlignment().

Referenced by ImportSequences().

◆ ReadSequencesFromFile()

void UpdateViewer::ReadSequencesFromFile ( SequenceList newSequences,
StructureSet sSet 
) const

◆ ReplaceAlignments()

void UpdateViewer::ReplaceAlignments ( const AlignmentList alignmentList)

◆ SaveAlignments()

void UpdateViewer::SaveAlignments ( void  )

◆ SaveDialog()

void UpdateViewer::SaveDialog ( bool  prompt)

Reimplemented from ViewerBase.

Definition at line 121 of file update_viewer.cpp.

References UpdateViewerWindow::SaveDialog(), and updateWindow.

◆ SavePendingStructures()

void UpdateViewer::SavePendingStructures ( void  )

◆ SetInitialState()

void UpdateViewer::SetInitialState ( void  )

◆ SortByIdentifier()

void UpdateViewer::SortByIdentifier ( void  )

◆ SortByPSSM()

void UpdateViewer::SortByPSSM ( void  )

◆ SortUpdates()

void UpdateViewer::SortUpdates ( void  )

Friends And Related Function Documentation

◆ SequenceDisplay

friend class SequenceDisplay

Definition at line 59 of file update_viewer.hpp.

◆ UpdateViewerWindow

friend class UpdateViewerWindow

Definition at line 58 of file update_viewer.hpp.

Referenced by CreateUpdateWindow().

Member Data Documentation

◆ pendingStructureAlignments

PendingStructureAlignments UpdateViewer::pendingStructureAlignments

Definition at line 124 of file update_viewer.hpp.

Referenced by ImportStructure(), and SavePendingStructures().

◆ pendingStructures

BiostrucList UpdateViewer::pendingStructures

Definition at line 118 of file update_viewer.hpp.

Referenced by ImportStructure(), and SavePendingStructures().

◆ updateWindow

UpdateViewerWindow* UpdateViewer::updateWindow

Definition at line 105 of file update_viewer.hpp.

Referenced by AddAlignments(), CreateUpdateWindow(), and SaveDialog().

The documentation for this class was generated from the following files:
Modified on Wed Apr 17 13:08:47 2024 by rev. 669887