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NCBI C++ ToolKit: StructureSet Class Reference

Search Toolkit Book for StructureSet

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

  StructureSet (ncbi::objects::CNcbi_mime_asn1 *mime, unsigned int structureLimit, OpenGLRenderer *r)     StructureSet (ncbi::objects::CCdd *cdd, unsigned int structureLimit, OpenGLRenderer *r)     ~StructureSet (void)   bool  IsMultiStructure (void) const   void  SetCenter (const Vector *setTo=NULL)   void  CenterViewOnStructure (void)   bool  CenterViewOnAlignedResidues (void)   bool  Draw (const AtomSet *atomSet) const   unsigned int  CreateName (const Residue *residue, int atomID)   bool  GetAtomFromName (unsigned int name, const Residue **residue, int *atomID) const   void  SelectedAtom (unsigned int name, bool setCenter)   void  SelectByDistance (double cutoff, unsigned int options) const   void  RemoveUnusedSequences (void)   void  ReplaceAlignmentSet (AlignmentSet *newAlignmentSet)   void  ReplaceUpdates (ncbi::objects::CCdd::TPending &newUpdates)   bool  HasDataChanged (void) const   void  SetDataChanged (unsigned int what) const   bool  IsCDD (void) const   bool  IsCDDInMime (void) const   bool  HasStructuredMaster (void) const   const std::string &  GetCDDName (void) const   bool  SetCDDName (const std::string &name)   const std::string &  GetCDDDescription (void) const   bool  SetCDDDescription (const std::string &descr)   bool  GetCDDNotes (TextLines *lines) const   bool  SetCDDNotes (const TextLines &lines)   ncbi::objects::CCdd_descr_set *  GetCDDDescrSet (void)   ncbi::objects::CAlign_annot_set *  GetCDDAnnotSet (void)   bool  ConvertMimeDataToCDD (const std::string &cddName)   bool  SaveASNData (const char *filename, bool doBinary, unsigned int *changeFlags)   const Sequence *  FindOrCreateSequence (ncbi::objects::CBioseq &bioseq)   void  RejectAndPurgeSequence (const Sequence *reject, std::string reason, bool purge)   const RejectList *  GetRejects (void) const   void  ShowRejects (void) const   bool  AddBiostrucToASN (ncbi::objects::CBiostruc *biostruc)   void  InitStructureAlignments (int masterMMDBID)   void  AddStructureAlignment (ncbi::objects::CBiostruc_feature *feature, int masterDomainID, int dependentDomainID)   void  RemoveStructureAlignments (void)   bool  MonitorAlignments (void) const     StructureBase (StructureBase *parent)   virtual  ~StructureBase (void)   virtual bool  DrawAll (const AtomSet *atomSet=NULL) const   template<class T > bool  GetParentOfType (const T **ptr, bool warnIfNotFound=true) const  

Definition at line 82 of file structure_set.hpp.

◆ DisplayLists ◆ FrameMap ◆ NameMap ◆ NamePair ◆ ObjectList ◆ RejectList ◆ TextLines ◆ TransformMap ◆ StructureSet() [1/2] StructureSet::StructureSet ( ncbi::objects::CNcbi_mime_asn1 *  mime, unsigned int  structureLimit, OpenGLRenderer *  r  ) ◆ StructureSet() [2/2] StructureSet::StructureSet ( ncbi::objects::CCdd *  cdd, unsigned int  structureLimit, OpenGLRenderer *  r  ) ◆ ~StructureSet() StructureSet::~StructureSet ( void  ) ◆ AddBiostrucToASN() bool StructureSet::AddBiostrucToASN ( ncbi::objects::CBiostruc *  biostruc ) ◆ AddStructureAlignment() void StructureSet::AddStructureAlignment ( ncbi::objects::CBiostruc_feature *  feature, int  masterDomainID, int  dependentDomainID  )

Definition at line 644 of file structure_set.cpp.

References dataManager, eStructureAlignmentData, f, CBiostruc_annot_set_Base::GetFeatures(), ASNDataManager::GetStructureAlignments(), InitStructureAlignments(), NO_DOMAIN, SetDataChanged(), CBiostruc_annot_set_Base::SetFeatures(), CBiostruc_feature_Base::SetId(), and WARNINGMSG.

Referenced by StructureObject::RealignStructure(), and UpdateViewer::SavePendingStructures().

◆ CenterViewOnAlignedResidues() bool StructureSet::CenterViewOnAlignedResidues ( void  )

Definition at line 893 of file structure_set.cpp.

References alignmentManager, OpenGLRenderer::CenterView(), StructureObject::coordSets, AlignmentManager::GetCurrentMultipleAlignment(), StructureBase::GetParentOfType(), BlockMultipleAlignment::GetSequenceOfRow(), i, Molecule::id, BlockMultipleAlignment::IsAligned(), Sequence::molecule, Residue::NO_ALPHA_ID, r(), renderer, Molecule::residues, AtomCoord::site, Vector< T >::size(), TRACEMSG, and U.

Referenced by OpenGLRenderer::ComputeBestView().

◆ CenterViewOnStructure() void StructureSet::CenterViewOnStructure ( void  ) ◆ ConvertMimeDataToCDD() ◆ CreateName() ◆ Draw() ◆ FindOrCreateSequence() const Sequence * StructureSet::FindOrCreateSequence ( ncbi::objects::CBioseq &  bioseq )

Definition at line 1032 of file structure_set.cpp.

References dataManager, ERRORMSG, eSequenceData, SequenceSet::FindMatchingSequence(), ASNDataManager::GetSequences(), Sequence::identifier, NULL, SequenceSet::sequences, sequenceSet, SetDataChanged(), and CSeq_entry_Base::SetSeq().

Referenced by UpdateViewer::FetchSequencesViaHTTP(), UpdateViewer::ImportStructure(), and UpdateViewer::ReadSequencesFromFile().

◆ GetAtomFromName() ◆ GetCDDAnnotSet() ncbi::objects::CAlign_annot_set * StructureSet::GetCDDAnnotSet ( void  ) ◆ GetCDDDescription() const string & StructureSet::GetCDDDescription ( void  ) const ◆ GetCDDDescrSet() ncbi::objects::CCdd_descr_set * StructureSet::GetCDDDescrSet ( void  ) ◆ GetCDDName() ◆ GetCDDNotes() ◆ GetRejects() ◆ HasDataChanged() bool StructureSet::HasDataChanged ( void  ) const ◆ HasStructuredMaster() bool StructureSet::HasStructuredMaster ( void  ) const ◆ InitStructureAlignments() void StructureSet::InitStructureAlignments ( int  masterMMDBID )

Definition at line 614 of file structure_set.cpp.

References dataManager, eStructureAlignmentData, ASNDataManager::GetStructureAlignments(), NO_DOMAIN, SetDataChanged(), CBiostruc_annot_set_Base::SetDescr(), CBiostruc_annot_set_Base::SetFeatures(), CBiostruc_annot_set_Base::SetId(), and ASNDataManager::SetStructureAlignments().

Referenced by AddBiostrucToASN(), AddStructureAlignment(), and AlignmentManager::RealignAllDependentStructures().

◆ IsCDD() bool StructureSet::IsCDD ( void  ) const ◆ IsCDDInMime() bool StructureSet::IsCDDInMime ( void  ) const ◆ IsMultiStructure() bool StructureSet::IsMultiStructure ( void  ) const ◆ Load() void StructureSet::Load ( unsigned int  structureLimit ) private

Definition at line 513 of file structure_set.cpp.

References alignmentManager, alignmentSet, StyleManager::CheckGlobalStyleSettings(), ShowHideManager::ConstructShowHideArray(), dataManager, ERRORMSG, ASNDataManager::GetMasterStructure(), ASNDataManager::GetSequenceAlignments(), ASNDataManager::GetSequences(), ASNDataManager::GetStructureList(), ASNDataManager::GetStyleDictionary(), ASNDataManager::GetUpdates(), ASNDataManager::GetUserAnnotations(), hasUserStyle, havePrevPickedAtomCoord, isAlphaOnly, ASNDataManager::IsSingleStructure(), lastAtomName, lastDisplayList, LoadAlignmentsAndStructures(), StyleManager::LoadFromASNStyleDictionary(), StyleManager::LoadFromASNUserAnnotations(), OpenGLRenderer::LoadFromASNViewSettings(), LoadSequencesForSingleStructure(), nDomains, OpenGLRenderer::NO_LIST, OpenGLRenderer::NO_NAME, NULL, StructureBase::parentSet, ASNDataManager::RemoveStyleDictionary(), ASNDataManager::RemoveUserAnnotations(), renderer, sequenceSet, SetCenter(), ASNDataManager::SetDataUnchanged(), ShowHideManager::ShowAlignedOrAnnotatedDomains(), showHideManager, styleManager, and VerifyFrameMap().

◆ LoadAlignmentsAndStructures() void StructureSet::LoadAlignmentsAndStructures ( unsigned int  structureLimit ) private

Definition at line 291 of file structure_set.cpp.

References a, AlignmentSet::alignments, alignmentSet, b, dataManager, CRef< C, Locker >::Empty(), ERRORMSG, ASNDataManager::GetBiostrucModelType(), ASNDataManager::GetCDDMaster3d(), ASNDataManager::GetMasterStructure(), StructureObject::GetPDBID(), ASNDataManager::GetSequenceAlignments(), ASNDataManager::GetStructureAlignments(), ASNDataManager::GetStructureList(), Sequence::identifier, NStr::IntToString(), ASNDataManager::IsCDD(), ASNDataManager::IsGeneralMime(), l(), le(), LoadMaster(), LoadStructureViaCache(), MoleculeIdentifier::MatchesSeqId(), MatchSequenceToMoleculeInObject(), MoleculeIdentifier::mmdbID, NULL, row, SequenceSet::sequences, sequenceSet, SetStructureRowFlags(), MoleculeIdentifier::ToString(), TRACEMSG, usedStructures, MoleculeIdentifier::VALUE_NOT_SET, and WARNINGMSG.

Referenced by Load().

◆ LoadMaster() bool StructureSet::LoadMaster ( int  masterMMDBID ) private

Definition at line 174 of file structure_set.cpp.

References b, dataManager, ERRORMSG, ASNDataManager::GetBiostrucModelType(), ASNDataManager::GetMasterStructure(), ASNDataManager::GetStructureList(), NStr::IntToString(), LoadStructureViaCache(), NULL, TRACEMSG, usedStructures, and MoleculeIdentifier::VALUE_NOT_SET.

Referenced by LoadAlignmentsAndStructures().

◆ LoadSequencesForSingleStructure() void StructureSet::LoadSequencesForSingleStructure ( void  ) private ◆ MatchSequenceToMoleculeInObject()

Definition at line 202 of file structure_set.cpp.

References Sequence::bioseqASN, ERRORMSG, CConstRef< C, Locker >::GetObject(), StructureObject::GetPDBID(), MoleculeIdentifier::gi, StructureObject::graph, Sequence::identifier, Sequence::Length(), Sequence::molecule, ChemicalGraph::molecules, SequenceSet::sequences, sequenceSet, MoleculeIdentifier::ToString(), and TRACEMSG.

Referenced by LoadAlignmentsAndStructures().

◆ MonitorAlignments() bool StructureSet::MonitorAlignments ( void  ) const ◆ RejectAndPurgeSequence() ◆ RemoveStructureAlignments() void StructureSet::RemoveStructureAlignments ( void  ) ◆ RemoveUnusedSequences() void StructureSet::RemoveUnusedSequences ( void  ) ◆ ReplaceAlignmentSet() void StructureSet::ReplaceAlignmentSet ( AlignmentSet *  newAlignmentSet ) ◆ ReplaceUpdates() void StructureSet::ReplaceUpdates ( ncbi::objects::CCdd::TPending &  newUpdates ) ◆ SaveASNData() bool StructureSet::SaveASNData ( const char *  filename, bool  doBinary, unsigned int *  changeFlags  )

Definition at line 728 of file structure_set.cpp.

References StyleManager::CreateASNStyleDictionary(), dataManager, eFNP_Replace, ERRORMSG, ASNDataManager::GetDataChanged(), CRef< C, Locker >::GetPointer(), GlobalMessenger(), CCn3d_user_annotations_Base::IsSetAnnotations(), CCn3d_user_annotations_Base::IsSetView(), MonitorAlignments(), ASNDataManager::RemoveStyleDictionary(), RemoveUnusedSequences(), ASNDataManager::RemoveUserAnnotations(), renderer, StyleManager::SaveToASNUserAnnotations(), OpenGLRenderer::SaveToASNViewSettings(), Messenger::SequenceWindowsSave(), ASNDataManager::SetDataUnchanged(), ASNDataManager::SetStyleDictionary(), ASNDataManager::SetUserAnnotations(), styleManager, and ASNDataManager::WriteDataToFile().

Referenced by StructureWindow::OnSave().

◆ SelectByDistance() void StructureSet::SelectByDistance ( double  cutoff, unsigned int  options  ) const ◆ SelectedAtom() void StructureSet::SelectedAtom ( unsigned int  name, bool  setCenter  )

Definition at line 958 of file structure_set.cpp.

References ApplyTransformation(), StructureObject::coordSets, GetAtomFromName(), Residue::GetAtomInfo(), StructureBase::GetParentOfType(), StructureObject::GetPDBID(), GlobalMessenger(), havePrevPickedAtomCoord, Molecule::id, Residue::id, Molecule::identifier, INFOMSG, StructureObject::IsDependent(), Molecule::IsHeterogen(), Molecule::IsSolvent(), Residue::AtomInfo::name, Residue::nameGraph, Residue::namePDB, OpenGLRenderer::NO_NAME, NULL, prevPickedAtomCoord, rotationCenter, AtomCoord::site, Messenger::ToggleHighlight(), MoleculeIdentifier::ToString(), StructureObject::transformToMaster, and WARNINGMSG.

Referenced by Cn3DGLCanvas::OnMouseEvent().

◆ SetCDDDescription() ◆ SetCDDName() ◆ SetCDDNotes() ◆ SetCenter() ◆ SetDataChanged() void StructureSet::SetDataChanged ( unsigned int  what ) const

Definition at line 1128 of file structure_set.cpp.

References dataManager, and ASNDataManager::SetDataChanged().

Referenced by AddStructureAlignment(), StyleManager::AddUserAnnotation(), StyleManager::AddUserStyle(), CDDAnnotateDialog::DeleteAnnotation(), IBISAnnotateDialog::DeleteAnnotation(), CDDAnnotateDialog::DeleteEvidence(), CDDAnnotateDialog::DeleteMotif(), StyleManager::DisplayUserAnnotation(), AnnotateDialog::EditAnnotation(), CDDAnnotateDialog::EditAnnotation(), CDDAnnotateDialog::EditEvidence(), FindOrCreateSequence(), InitStructureAlignments(), IBISAnnotateDialog::MakeAnnotationFromInteraction(), CDDAnnotateDialog::MoveAnnotation(), AnnotateDialog::MoveAnnotation(), CDDAnnotateDialog::MoveEvidence(), StyleManager::MoveUserAnnotation(), CDDAnnotateDialog::NewAnnotation(), CDDAnnotateDialog::NewEvidence(), CDDAnnotateDialog::NewOrEditMotif(), CDDRefDialog::OnButton(), CDDBookRefDialog::OnClick(), RemoveStructureAlignments(), StyleManager::RemoveUserAnnotation(), StyleManager::RemoveUserStyle(), ReplaceAlignmentSet(), and AlignmentManager::SavePairwiseFromMultiple().

◆ ShowRejects() void StructureSet::ShowRejects ( void  ) const ◆ VerifyFrameMap() void StructureSet::VerifyFrameMap ( void  ) const private ◆ alignmentManager

Definition at line 101 of file structure_set.hpp.

Referenced by UpdateViewer::BlastNeighbor(), BLASTer::CalculateSelfHitScores(), CenterViewOnAlignedResidues(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), DoHighlightMotif(), GetAlignmentByBestNeighbor(), StyleManager::GetAtomStyle(), CDDAnnotateDialog::GetCurrentHighlightedIntervals(), IBISAnnotateDialog::GetIntervalsForSet(), UpdateViewer::GetVASTAlignments(), CDDAnnotateDialog::HighlightInterval(), IBISAnnotateDialog::HighlightInterval(), UpdateViewer::ImportStructure(), Load(), StructureWindow::LoadData(), MakeEmptyAlignment(), CDDAnnotateDialog::NewOrEditMotif(), StructureWindow::OnAlignStructures(), StructureWindow::OnCDD(), Cn3DApp::OnInit(), StructureWindow::OnShowWindow(), IBISAnnotateDialog::PopulateInteractionData(), StructureObject::RealignStructure(), RejectAndPurgeSequence(), RemoveUnusedSequences(), UnpackDPResult(), and ~StructureSet().

◆ alignmentSet ◆ center ◆ dataManager

Definition at line 226 of file structure_set.hpp.

Referenced by AddBiostrucToASN(), AddStructureAlignment(), ConvertMimeDataToCDD(), FindOrCreateSequence(), GetCDDAnnotSet(), GetCDDDescription(), GetCDDDescrSet(), GetCDDName(), GetCDDNotes(), GetRejects(), HasDataChanged(), InitStructureAlignments(), IsCDD(), IsCDDInMime(), IsMultiStructure(), Load(), LoadAlignmentsAndStructures(), LoadMaster(), LoadSequencesForSingleStructure(), MonitorAlignments(), RejectAndPurgeSequence(), RemoveStructureAlignments(), RemoveUnusedSequences(), ReplaceAlignmentSet(), ReplaceUpdates(), SaveASNData(), SetCDDDescription(), SetCDDName(), SetCDDNotes(), SetDataChanged(), and ~StructureSet().

◆ eAnyAlignmentData const unsigned int StructureSet::eAnyAlignmentData = 0x04 static ◆ eCDDData const unsigned int StructureSet::eCDDData = 0x100 static ◆ eOtherData const unsigned int StructureSet::eOtherData = 0x200 static ◆ ePSSMData const unsigned int StructureSet::ePSSMData = 0x01 static ◆ eRowOrderData const unsigned int StructureSet::eRowOrderData = 0x02 static ◆ eSelectHeterogen const unsigned int StructureSet::eSelectHeterogen = 0x04 static ◆ eSelectNucleotide const unsigned int StructureSet::eSelectNucleotide = 0x02 static ◆ eSelectOtherMoleculesOnly const unsigned int StructureSet::eSelectOtherMoleculesOnly = 0x10 static ◆ eSelectProtein const unsigned int StructureSet::eSelectProtein = 0x01 static ◆ eSelectSolvent const unsigned int StructureSet::eSelectSolvent = 0x08 static ◆ eSequenceData const unsigned int StructureSet::eSequenceData = 0x10 static ◆ eStructureAlignmentData const unsigned int StructureSet::eStructureAlignmentData = 0x08 static ◆ eStyleData const unsigned int StructureSet::eStyleData = 0x40 static ◆ eUpdateData const unsigned int StructureSet::eUpdateData = 0x20 static ◆ eUserAnnotationData const unsigned int StructureSet::eUserAnnotationData = 0x80 static

Definition at line 178 of file structure_set.hpp.

Referenced by CDDAnnotateDialog::DeleteAnnotation(), IBISAnnotateDialog::DeleteAnnotation(), CDDAnnotateDialog::DeleteEvidence(), CDDAnnotateDialog::DeleteMotif(), CDDAnnotateDialog::EditAnnotation(), CDDAnnotateDialog::EditEvidence(), IBISAnnotateDialog::MakeAnnotationFromInteraction(), CDDAnnotateDialog::MoveAnnotation(), CDDAnnotateDialog::MoveEvidence(), CDDAnnotateDialog::NewAnnotation(), CDDAnnotateDialog::NewEvidence(), and CDDAnnotateDialog::NewOrEditMotif().

◆ frameMap

Definition at line 116 of file structure_set.hpp.

Referenced by ChemicalGraph::ChemicalGraph(), OpenGLRenderer::Display(), UpdateViewer::ImportStructure(), OpenGLRenderer::IsFrameEmpty(), StructureWindow::OnAnimate(), CDDAnnotateDialog::ShowEvidence(), OpenGLRenderer::ShowFirstFrame(), OpenGLRenderer::ShowFrameNumber(), OpenGLRenderer::ShowLastFrame(), OpenGLRenderer::ShowNextFrame(), OpenGLRenderer::ShowPreviousFrame(), and VerifyFrameMap().

◆ hasUserStyle bool StructureSet::hasUserStyle ◆ havePrevPickedAtomCoord bool StructureSet::havePrevPickedAtomCoord private ◆ isAlphaOnly bool StructureSet::isAlphaOnly ◆ lastAtomName unsigned int StructureSet::lastAtomName private ◆ lastDisplayList unsigned int StructureSet::lastDisplayList ◆ maxDistFromCenter double StructureSet::maxDistFromCenter ◆ nameMap ◆ nDomains int StructureSet::nDomains ◆ objects ◆ prevPickedAtomCoord Vector StructureSet::prevPickedAtomCoord private ◆ renderer

Definition at line 103 of file structure_set.hpp.

Referenced by CenterViewOnAlignedResidues(), CenterViewOnStructure(), Residue::Draw(), Bond::Draw(), Helix3D::Draw(), Strand3D::Draw(), ChemicalGraph::DrawAll(), StructureBase::DrawAll(), Molecule::DrawAllWithTerminiLabels(), Load(), SaveASNData(), ShowHideManager::Show(), CDDAnnotateDialog::ShowEvidence(), and ShowHideManager::UnHideEntityAndChildren().

◆ rotationCenter Vector StructureSet::rotationCenter ◆ sequenceSet ◆ showHideManager

Definition at line 104 of file structure_set.hpp.

Referenced by Residue::Draw(), Bond::Draw(), Molecule::DrawAllWithTerminiLabels(), StyleManager::GetAtomStyle(), StyleManager::GetBondStyle(), StyleManager::GetObjectStyle(), Molecule::GetResidueColor(), Load(), AnnotateDialog::OnButton(), StructureWindow::OnShowHide(), CDDAnnotateDialog::ShowEvidence(), AlignmentManager::ShowHideCallbackFunction(), and ~StructureSet().

◆ styleManager

Definition at line 105 of file structure_set.hpp.

Referenced by OpenGLRenderer::Display(), Residue::Draw(), Draw(), Bond::Draw(), Helix3D::Draw(), Strand3D::Draw(), Molecule::DrawAllWithTerminiLabels(), BlockMultipleAlignment::GetCharacterTraitsAt(), Molecule::GetResidueColor(), SequenceDisplay::GetRowTitle(), Load(), AlignmentManager::MergeUpdates(), StyleDialog::OnChange(), StructureWindow::OnEditFavorite(), StructureWindow::OnSelectFavorite(), StructureWindow::OnSetStyle(), SaveASNData(), and ~StructureSet().

◆ transformMap ◆ usedFeatures std::map< int, bool > StructureSet::usedFeatures ◆ usedStructures std::map< const ncbi::objects::CBiostruc * , bool > StructureSet::usedStructures private

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

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