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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
Vector center
double maxDistFromCenter
Vector rotationCenter
unsigned int lastDisplayList
FrameMap frameMap
TransformMap transformMap
std::map< int, boolusedFeatures
- Public Attributes inherited from StructureBase

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

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

Definition at line 240 of file structure_set.hpp.

◆ NamePair

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

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

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)

◆ LoadAlignmentsAndStructures()

void StructureSet::LoadAlignmentsAndStructures ( unsigned int  structureLimit)

◆ LoadMaster()

bool StructureSet::LoadMaster ( int  masterMMDBID)

◆ LoadSequencesForSingleStructure()

void StructureSet::LoadSequencesForSingleStructure ( void  )

◆ MatchSequenceToMoleculeInObject()

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

◆ 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

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

◆ eAnyAlignmentData

const unsigned int StructureSet::eAnyAlignmentData = 0x04

Definition at line 173 of file structure_set.hpp.

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

◆ eCDDData

const unsigned int StructureSet::eCDDData = 0x100

◆ eOtherData

const unsigned int StructureSet::eOtherData = 0x200

Definition at line 180 of file structure_set.hpp.

Referenced by ASNDataManager::ConvertMimeToGeneral().

◆ ePSSMData

const unsigned int StructureSet::ePSSMData = 0x01

◆ eRowOrderData

const unsigned int StructureSet::eRowOrderData = 0x02

◆ eSelectHeterogen

const unsigned int StructureSet::eSelectHeterogen = 0x04

◆ eSelectNucleotide

const unsigned int StructureSet::eSelectNucleotide = 0x02

◆ eSelectOtherMoleculesOnly

const unsigned int StructureSet::eSelectOtherMoleculesOnly = 0x10

◆ eSelectProtein

const unsigned int StructureSet::eSelectProtein = 0x01

◆ eSelectSolvent

const unsigned int StructureSet::eSelectSolvent = 0x08

◆ eSequenceData

const unsigned int StructureSet::eSequenceData = 0x10

◆ eStructureAlignmentData

const unsigned int StructureSet::eStructureAlignmentData = 0x08

◆ eStyleData

const unsigned int StructureSet::eStyleData = 0x40

◆ eUpdateData

const unsigned int StructureSet::eUpdateData = 0x20

Definition at line 176 of file structure_set.hpp.

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

◆ eUserAnnotationData

const unsigned int StructureSet::eUserAnnotationData = 0x80

◆ frameMap

FrameMap StructureSet::frameMap

◆ hasUserStyle

bool StructureSet::hasUserStyle

Definition at line 93 of file structure_set.hpp.

Referenced by Load().

◆ havePrevPickedAtomCoord

bool StructureSet::havePrevPickedAtomCoord

Definition at line 246 of file structure_set.hpp.

Referenced by Load(), and SelectedAtom().

◆ isAlphaOnly

bool StructureSet::isAlphaOnly

◆ lastAtomName

unsigned int StructureSet::lastAtomName

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

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

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

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 rev. 669887