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StructureSet Class Reference

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#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 intDisplayLists
 
typedef std::vector< DisplayListsFrameMap
 
typedef std::map< unsigned int, const Matrix *const * > TransformMap
 
typedef std::vector< std::stringTextLines
 
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::stringGetCDDName (void) const
 
bool SetCDDName (const std::string &name)
 
const std::stringGetCDDDescription (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 SequenceFindOrCreateSequence (ncbi::objects::CBioseq &bioseq)
 
void RejectAndPurgeSequence (const Sequence *reject, std::string reason, bool purge)
 
const RejectListGetRejects (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 SequenceSetsequenceSet
 
const AlignmentSetalignmentSet
 
AlignmentManageralignmentManager
 
OpenGLRendererrenderer
 
ShowHideManagershowHideManager
 
StyleManagerstyleManager
 
Vector center
 
double maxDistFromCenter
 
Vector rotationCenter
 
unsigned int lastDisplayList
 
FrameMap frameMap
 
TransformMap transformMap
 
std::map< int, boolusedFeatures
 
- Public Attributes inherited from StructureBase
StructureSetparentSet
 

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 *, intNamePair
 
typedef std::map< unsigned int, NamePairNameMap
 

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

ASNDataManagerdataManager
 
std::map< const ncbi::objects::CBiostruc *, boolusedStructures
 
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

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  )

Member Function Documentation

◆ AddBiostrucToASN()

bool StructureSet::AddBiostrucToASN ( ncbi::objects::CBiostruc *  biostruc)

◆ AddStructureAlignment()

void StructureSet::AddStructureAlignment ( ncbi::objects::CBiostruc_feature *  feature,
int  masterDomainID,
int  dependentDomainID 
)

◆ CenterViewOnAlignedResidues()

bool StructureSet::CenterViewOnAlignedResidues ( void  )

◆ CenterViewOnStructure()

void StructureSet::CenterViewOnStructure ( void  )

◆ ConvertMimeDataToCDD()

bool StructureSet::ConvertMimeDataToCDD ( const std::string cddName)

◆ 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)

◆ 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

◆ 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

◆ InitStructureAlignments()

void StructureSet::InitStructureAlignments ( int  masterMMDBID)

◆ IsCDD()

bool StructureSet::IsCDD ( void  ) const

◆ 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

◆ Load()

void StructureSet::Load ( unsigned int  structureLimit)
private

◆ LoadAlignmentsAndStructures()

void StructureSet::LoadAlignmentsAndStructures ( unsigned int  structureLimit)
private

◆ LoadMaster()

bool StructureSet::LoadMaster ( int  masterMMDBID)
private

◆ LoadSequencesForSingleStructure()

void StructureSet::LoadSequencesForSingleStructure ( void  )
private

◆ MatchSequenceToMoleculeInObject()

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

◆ 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 
)

◆ 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 
)

◆ 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 
)

◆ SetCDDDescription()

bool StructureSet::SetCDDDescription ( const std::string descr)

◆ 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

◆ 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, lastDisplayList, and TRACEMSG.

Referenced by Load().

Member Data Documentation

◆ alignmentManager

AlignmentManager* StructureSet::alignmentManager

◆ alignmentSet

const AlignmentSet* StructureSet::alignmentSet

◆ center

Vector StructureSet::center

◆ dataManager

ASNDataManager* StructureSet::dataManager
private

◆ 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

◆ 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

◆ 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

Definition at line 176 of file structure_set.hpp.

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

◆ eUserAnnotationData

const unsigned int StructureSet::eUserAnnotationData = 0x80
static

◆ frameMap

FrameMap StructureSet::frameMap

◆ 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

◆ 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

◆ 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

◆ prevPickedAtomCoord

Vector StructureSet::prevPickedAtomCoord
private

Definition at line 245 of file structure_set.hpp.

Referenced by SelectedAtom().

◆ renderer

OpenGLRenderer* StructureSet::renderer

◆ rotationCenter

Vector StructureSet::rotationCenter

◆ sequenceSet

const SequenceSet* StructureSet::sequenceSet

◆ showHideManager

ShowHideManager* StructureSet::showHideManager

◆ styleManager

StyleManager* StructureSet::styleManager

◆ transformMap

TransformMap StructureSet::transformMap

◆ 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().


The documentation for this class was generated from the following files:
Modified on Wed Jun 12 11:18:41 2024 by modify_doxy.py rev. 669887