StructureSet Class Reference

Search Toolkit Book for StructureSet

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

Inheritance diagram for StructureSet:

Collaboration diagram for StructureSet:

Public Types
typedef std::list< const StructureObject * >	ObjectList
typedef std::list< unsigned int >	DisplayLists
typedef std::vector< DisplayLists >	FrameMap
typedef std::map< unsigned int, const Matrix *const * >	TransformMap
typedef std::vector< std::string >	TextLines
typedef std::list< ncbi::CRef< ncbi::objects::CReject_id > >	RejectList

Public Member Functions
	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
Public Member Functions inherited from StructureBase
	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

Public Attributes
bool	isAlphaOnly
int	nDomains
bool	hasUserStyle
ObjectList	objects
const SequenceSet *	sequenceSet
const AlignmentSet *	alignmentSet
AlignmentManager *	alignmentManager
OpenGLRenderer *	renderer
ShowHideManager *	showHideManager
StyleManager *	styleManager
Vector	center
double	maxDistFromCenter
Vector	rotationCenter
unsigned int	lastDisplayList
FrameMap	frameMap
TransformMap	transformMap
std::map< int, bool >	usedFeatures
Public Attributes inherited from StructureBase
StructureSet *	parentSet

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

Private Types
typedef std::pair< const Residue *, int >	NamePair
typedef std::map< unsigned int, NamePair >	NameMap

Private Member Functions
void	Load (unsigned int structureLimit)
void	LoadSequencesForSingleStructure (void)
void	LoadAlignmentsAndStructures (unsigned int structureLimit)
bool	MatchSequenceToMoleculeInObject (const Sequence *seq, const StructureObject *obj, const Sequence **seqHandle=NULL)
bool	LoadMaster (int masterMMDBID)
void	VerifyFrameMap (void) const

Private Attributes
ASNDataManager *	dataManager
std::map< const ncbi::objects::CBiostruc *, bool >	usedStructures
NameMap	nameMap
unsigned int	lastAtomName
Vector	prevPickedAtomCoord
bool	havePrevPickedAtomCoord

Detailed Description

Definition at line 82 of file structure_set.hpp.

Member Typedef Documentation

DisplayLists

typedef std::list< unsigned int > StructureSet::DisplayLists

Definition at line 114 of file structure_set.hpp.

FrameMap

typedef std::vector< DisplayLists > StructureSet::FrameMap

Definition at line 115 of file structure_set.hpp.

NameMap

typedef std::map< unsigned int, NamePair > StructureSet::NameMap

private

Definition at line 240 of file structure_set.hpp.

NamePair

typedef std::pair< const Residue*, int > StructureSet::NamePair

private

Definition at line 239 of file structure_set.hpp.

ObjectList

typedef std::list< const StructureObject * > StructureSet::ObjectList

Definition at line 95 of file structure_set.hpp.

RejectList

typedef std::list< ncbi::CRef < ncbi::objects::CReject_id > > StructureSet::RejectList

Definition at line 210 of file structure_set.hpp.

TextLines

typedef std::vector< std::string > StructureSet::TextLines

Definition at line 193 of file structure_set.hpp.

TransformMap

typedef std::map< unsigned int, const Matrix * const * > StructureSet::TransformMap

Definition at line 119 of file structure_set.hpp.

Constructor & Destructor Documentation

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

)

Definition at line 593 of file structure_set.cpp.

References alignmentManager, MoleculeIdentifier::ClearIdentifiers(), dataManager, GlobalMessenger(), Messenger::RemoveAllHighlights(), showHideManager, and styleManager.

Member Function Documentation

AddBiostrucToASN()

bool StructureSet::AddBiostrucToASN

(

ncbi::objects::CBiostruc *

biostruc

)

Definition at line 604 of file structure_set.cpp.

References ASNDataManager::AddBiostrucToASN(), dataManager, and InitStructureAlignments().

Referenced by UpdateViewer::SavePendingStructures().

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

)

Definition at line 845 of file structure_set.cpp.

References OpenGLRenderer::CenterView(), i, Residue::NO_ALPHA_ID, r(), renderer, AtomCoord::site, and TRACEMSG.

Referenced by OpenGLRenderer::ComputeBestView().

ConvertMimeDataToCDD()

bool StructureSet::ConvertMimeDataToCDD

(

const std::string &

cddName

)

Definition at line 1104 of file structure_set.cpp.

References ASNDataManager::ConvertMimeDataToCDD(), dataManager, ERRORMSG, SequenceSet::sequences, sequenceSet, and MoleculeIdentifier::VALUE_NOT_SET.

Referenced by StructureWindow::OnSave().

CreateName()

unsigned int StructureSet::CreateName	(	const Residue *	residue,
		int	atomID
	)

Definition at line 942 of file structure_set.cpp.

References lastAtomName, and nameMap.

Referenced by Residue::Residue().

Draw()

bool StructureSet::Draw ( const AtomSet *  atomSet ) const

virtual

Reimplemented from StructureBase.

Definition at line 935 of file structure_set.cpp.

References StyleManager::CheckGlobalStyleSettings(), styleManager, and TRACEMSG.

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()

bool StructureSet::GetAtomFromName	(	unsigned int	name,
		const Residue **	residue,
		int *	atomID
	)		const

Definition at line 949 of file structure_set.cpp.

References i, and nameMap.

Referenced by SelectedAtom().

GetCDDAnnotSet()

ncbi::objects::CAlign_annot_set * StructureSet::GetCDDAnnotSet

(

void

)

Definition at line 1138 of file structure_set.cpp.

References dataManager, and ASNDataManager::GetCDDAnnotSet().

GetCDDDescription()

const string & StructureSet::GetCDDDescription

(

void

)

const

Definition at line 1133 of file structure_set.cpp.

References dataManager, and ASNDataManager::GetCDDDescription().

Referenced by StructureWindow::OnCDD().

GetCDDDescrSet()

ncbi::objects::CCdd_descr_set * StructureSet::GetCDDDescrSet

(

void

)

Definition at line 1137 of file structure_set.cpp.

References dataManager, and ASNDataManager::GetCDDDescrSet().

GetCDDName()

const string & StructureSet::GetCDDName

(

void

)

const

Definition at line 1131 of file structure_set.cpp.

References dataManager, and ASNDataManager::GetCDDName().

Referenced by StructureWindow::OnCDD(), StructureWindow::OnSave(), and SetWorkingTitle().

GetCDDNotes()

bool StructureSet::GetCDDNotes

(

StructureSet::TextLines *

lines

)

const

Definition at line 1135 of file structure_set.cpp.

References dataManager, and ASNDataManager::GetCDDNotes().

Referenced by StructureWindow::OnCDD().

GetRejects()

const StructureSet::RejectList * StructureSet::GetRejects

(

void

)

const

Definition at line 1078 of file structure_set.cpp.

References dataManager, and ASNDataManager::GetRejects().

Referenced by StructureWindow::OnCDD(), and ShowRejects().

HasDataChanged()

bool StructureSet::HasDataChanged

(

void

)

const

Definition at line 1127 of file structure_set.cpp.

References dataManager, and ASNDataManager::HasDataChanged().

Referenced by StructureWindow::SaveDialog().

HasStructuredMaster()

bool StructureSet::HasStructuredMaster

(

void

)

const

Definition at line 1140 of file structure_set.cpp.

References alignmentSet, MoleculeIdentifier::HasStructure(), Sequence::identifier, and AlignmentSet::master.

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

Definition at line 1129 of file structure_set.cpp.

References dataManager, and ASNDataManager::IsCDD().

Referenced by StructureWindow::LoadData(), StructureWindow::OnCDD(), StructureWindow::OnSave(), and SetWorkingTitle().

IsCDDInMime()

bool StructureSet::IsCDDInMime

(

void

)

const

Definition at line 1130 of file structure_set.cpp.

References dataManager, and ASNDataManager::IsCDDInMime().

Referenced by StructureWindow::OnSave(), and SetWorkingTitle().

IsMultiStructure()

bool StructureSet::IsMultiStructure

(

void

)

const

Definition at line 1126 of file structure_set.cpp.

References dataManager, and ASNDataManager::IsSingleStructure().

Referenced by ChemicalGraph::ChemicalGraph(), and OpenGLRenderer::ComputeBestView().

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

Definition at line 133 of file structure_set.cpp.

References dataManager, ERRORMSG, ASNDataManager::GetSequences(), NULL, SequenceSet::sequences, sequenceSet, and TRACEMSG.

Referenced by Load().

MatchSequenceToMoleculeInObject()

bool StructureSet::MatchSequenceToMoleculeInObject ( const Sequence *  seq, const StructureObject *  obj, const Sequence **  seqHandle = NULL  )

private

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

Definition at line 723 of file structure_set.cpp.

References dataManager, and ASNDataManager::MonitorAlignments().

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

RejectAndPurgeSequence()

void StructureSet::RejectAndPurgeSequence	(	const Sequence *	reject,
		std::string	reason,
		bool	purge
	)

Definition at line 1061 of file structure_set.cpp.

References ASNDataManager::AddReject(), alignmentManager, dataManager, ASNDataManager::IsCDD(), AlignmentManager::PurgeSequence(), CUpdate_comment_Base::SetComment(), CReject_id_Base::SetDescription(), and CReject_id_Base::SetIds().

RemoveStructureAlignments()

void StructureSet::RemoveStructureAlignments

(

void

)

Definition at line 679 of file structure_set.cpp.

References dataManager, eStructureAlignmentData, NULL, SetDataChanged(), and ASNDataManager::SetStructureAlignments().

Referenced by AlignmentManager::RealignAllDependentStructures().

RemoveUnusedSequences()

void StructureSet::RemoveUnusedSequences

(

void

)

Definition at line 716 of file structure_set.cpp.

References alignmentManager, alignmentSet, dataManager, AlignmentManager::GetUpdateSequences(), and ASNDataManager::RemoveUnusedSequences().

Referenced by SaveASNData().

ReplaceAlignmentSet()

void StructureSet::ReplaceAlignmentSet

(

AlignmentSet *

newAlignmentSet

)

Definition at line 686 of file structure_set.cpp.

References alignmentSet, dataManager, eAnyAlignmentData, ERRORMSG, ASNDataManager::GetOrCreateSequenceAlignments(), n, ne(), AlignmentSet::newAsnAlignmentData, and SetDataChanged().

Referenced by AlignmentManager::SavePairwiseFromMultiple().

ReplaceUpdates()

void StructureSet::ReplaceUpdates

(

ncbi::objects::CCdd::TPending &

newUpdates

)

Definition at line 711 of file structure_set.cpp.

References dataManager, and ASNDataManager::ReplaceUpdates().

Referenced by AlignmentManager::ReplaceUpdatesInASN().

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

Definition at line 1016 of file structure_set.cpp.

References GlobalMessenger(), r(), and Messenger::ToggleHighlight().

Referenced by StructureWindow::OnSelect().

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()

bool StructureSet::SetCDDDescription

(

const std::string &

descr

)

Definition at line 1134 of file structure_set.cpp.

References dataManager, and ASNDataManager::SetCDDDescription().

Referenced by StructureWindow::DialogTextChanged().

SetCDDName()

bool StructureSet::SetCDDName

(

const std::string &

name

)

Definition at line 1132 of file structure_set.cpp.

References dataManager, and ASNDataManager::SetCDDName().

Referenced by StructureWindow::OnCDD().

SetCDDNotes()

bool StructureSet::SetCDDNotes

(

const TextLines &

lines

)

Definition at line 1136 of file structure_set.cpp.

References dataManager, and ASNDataManager::SetCDDNotes().

Referenced by StructureWindow::DialogTextChanged().

SetCenter()

void StructureSet::SetCenter

(

const Vector *

setTo = NULL

)

Definition at line 799 of file structure_set.cpp.

References a, ApplyTransformation(), center, i, maxDistFromCenter, rotationCenter, Vector< T >::Set(), site, and TRACEMSG.

Referenced by Load().

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

Definition at line 1083 of file structure_set.cpp.

References GetRejects(), i, INFOMSG, and r().

Referenced by StructureWindow::OnCDD().

VerifyFrameMap()

void StructureSet::VerifyFrameMap ( void  ) const

private

Definition at line 770 of file structure_set.cpp.

References ERRORMSG, f, OpenGLRenderer::FIRST_LIST, frameMap, l(), lastDisplayList, and TRACEMSG.

Referenced by Load().

Member Data Documentation

alignmentManager

AlignmentManager* StructureSet::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

const AlignmentSet* StructureSet::alignmentSet

Definition at line 100 of file structure_set.hpp.

Referenced by HasStructuredMaster(), Load(), LoadAlignmentsAndStructures(), RemoveUnusedSequences(), and ReplaceAlignmentSet().

center

Vector StructureSet::center

Definition at line 107 of file structure_set.hpp.

Referenced by OpenGLRenderer::CenterView(), OpenGLRenderer::ChangeView(), OpenGLRenderer::ResetCamera(), and SetCenter().

dataManager

ASNDataManager* StructureSet::dataManager

private

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

Definition at line 173 of file structure_set.hpp.

Referenced by StructureWindow::OnSave(), and ReplaceAlignmentSet().

eCDDData

const unsigned int StructureSet::eCDDData = 0x100

static

Definition at line 179 of file structure_set.hpp.

Referenced by ASNDataManager::AddReject(), CDDRefDialog::OnButton(), CDDBookRefDialog::OnClick(), StructureWindow::OnSave(), ASNDataManager::SetCDDDescription(), ASNDataManager::SetCDDName(), and ASNDataManager::SetCDDNotes().

eOtherData

const unsigned int StructureSet::eOtherData = 0x200

static

Definition at line 180 of file structure_set.hpp.

Referenced by ASNDataManager::ConvertMimeToGeneral().

ePSSMData

const unsigned int StructureSet::ePSSMData = 0x01

static

Definition at line 171 of file structure_set.hpp.

Referenced by StructureWindow::OnSave(), and AlignmentManager::SavePairwiseFromMultiple().

eRowOrderData

const unsigned int StructureSet::eRowOrderData = 0x02

static

Definition at line 172 of file structure_set.hpp.

Referenced by StructureWindow::OnSave(), and AlignmentManager::SavePairwiseFromMultiple().

eSelectHeterogen

const unsigned int StructureSet::eSelectHeterogen = 0x04

static

Definition at line 154 of file structure_set.hpp.

Referenced by StructureWindow::OnSelect(), and StructureObject::SelectByDistance().

eSelectNucleotide

const unsigned int StructureSet::eSelectNucleotide = 0x02

static

Definition at line 153 of file structure_set.hpp.

Referenced by StructureWindow::OnSelect(), and StructureObject::SelectByDistance().

eSelectOtherMoleculesOnly

const unsigned int StructureSet::eSelectOtherMoleculesOnly = 0x10

static

Definition at line 156 of file structure_set.hpp.

Referenced by StructureWindow::OnSelect(), and StructureObject::SelectByDistance().

eSelectProtein

const unsigned int StructureSet::eSelectProtein = 0x01

static

Definition at line 152 of file structure_set.hpp.

Referenced by StructureWindow::OnSelect(), and StructureObject::SelectByDistance().

eSelectSolvent

const unsigned int StructureSet::eSelectSolvent = 0x08

static

Definition at line 155 of file structure_set.hpp.

Referenced by StructureWindow::OnSelect(), and StructureObject::SelectByDistance().

eSequenceData

const unsigned int StructureSet::eSequenceData = 0x10

static

Definition at line 175 of file structure_set.hpp.

Referenced by FindOrCreateSequence(), and ASNDataManager::RemoveUnusedSequences().

eStructureAlignmentData

const unsigned int StructureSet::eStructureAlignmentData = 0x08

static

Definition at line 174 of file structure_set.hpp.

Referenced by AddStructureAlignment(), InitStructureAlignments(), and RemoveStructureAlignments().

eStyleData

const unsigned int StructureSet::eStyleData = 0x40

static

Definition at line 177 of file structure_set.hpp.

Referenced by StyleManager::AddUserAnnotation(), StyleManager::AddUserStyle(), StyleManager::DisplayUserAnnotation(), AnnotateDialog::EditAnnotation(), AnnotateDialog::MoveAnnotation(), StyleManager::MoveUserAnnotation(), StyleManager::RemoveUserAnnotation(), and StyleManager::RemoveUserStyle().

eUpdateData

const unsigned int StructureSet::eUpdateData = 0x20

static

Definition at line 176 of file structure_set.hpp.

Referenced by StructureWindow::OnSave(), and ASNDataManager::ReplaceUpdates().

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

FrameMap StructureSet::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

Definition at line 93 of file structure_set.hpp.

Referenced by Load().

havePrevPickedAtomCoord

bool StructureSet::havePrevPickedAtomCoord

private

Definition at line 246 of file structure_set.hpp.

Referenced by Load(), and SelectedAtom().

isAlphaOnly

bool StructureSet::isAlphaOnly

Definition at line 91 of file structure_set.hpp.

Referenced by Threader::CalculateScores(), StyleManager::CheckStyleSettings(), Threader::CreateFldMtf(), Threader::GetGeometryViolations(), UpdateViewer::ImportStructure(), Load(), Threader::Realign(), BlockMultipleAlignment::ShowGeometryViolations(), and StructureObject::StructureObject().

lastAtomName

unsigned int StructureSet::lastAtomName

private

Definition at line 242 of file structure_set.hpp.

Referenced by CreateName(), and Load().

lastDisplayList

unsigned int StructureSet::lastDisplayList

Definition at line 112 of file structure_set.hpp.

Referenced by ChemicalGraph::ChemicalGraph(), OpenGLRenderer::Display(), Load(), and VerifyFrameMap().

maxDistFromCenter

double StructureSet::maxDistFromCenter

Definition at line 108 of file structure_set.hpp.

Referenced by OpenGLRenderer::ResetCamera(), and SetCenter().

nameMap

NameMap StructureSet::nameMap

private

Definition at line 241 of file structure_set.hpp.

Referenced by CreateName(), and GetAtomFromName().

nDomains

int StructureSet::nDomains

Definition at line 92 of file structure_set.hpp.

Referenced by Load().

objects

ObjectList StructureSet::objects

Definition at line 96 of file structure_set.hpp.

Referenced by ShowHideManager::ConstructShowHideArray(), UpdateViewer::ImportStructure(), StructureWindow::OnSelect(), StructureObject::RealignStructure(), SetWorkingTitle(), CDDAnnotateDialog::ShowEvidence(), and StructureObject::StructureObject().

prevPickedAtomCoord

Vector StructureSet::prevPickedAtomCoord

private

Definition at line 245 of file structure_set.hpp.

Referenced by SelectedAtom().

renderer

OpenGLRenderer* StructureSet::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

Definition at line 109 of file structure_set.hpp.

Referenced by OpenGLRenderer::CenterView(), OpenGLRenderer::ChangeView(), OpenGLRenderer::ResetCamera(), OpenGLRenderer::RestoreSavedView(), OpenGLRenderer::SaveToASNViewSettings(), SelectedAtom(), and SetCenter().

sequenceSet

const SequenceSet* StructureSet::sequenceSet

Definition at line 99 of file structure_set.hpp.

Referenced by ConvertMimeDataToCDD(), FindOrCreateSequence(), UpdateViewer::ImportStructure(), Load(), LoadAlignmentsAndStructures(), LoadSequencesForSingleStructure(), MasterDependentAlignment::MasterDependentAlignment(), MatchSequenceToMoleculeInObject(), and StructureWindow::OnCDD().

showHideManager

ShowHideManager* StructureSet::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

StyleManager* 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

TransformMap StructureSet::transformMap

Definition at line 120 of file structure_set.hpp.

Referenced by OpenGLRenderer::AddTransparentSpheresForList(), ChemicalGraph::ChemicalGraph(), and OpenGLRenderer::Display().

usedFeatures

std::map< int, bool > StructureSet::usedFeatures

Definition at line 123 of file structure_set.hpp.

Referenced by StructureObject::SetTransformToMaster().

usedStructures

std::map< const ncbi::objects::CBiostruc * , bool > StructureSet::usedStructures

private

Definition at line 232 of file structure_set.hpp.

Referenced by LoadAlignmentsAndStructures(), and LoadMaster().

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

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