NCBI C++ ToolKit
Public Types | Public Member Functions | Public Attributes | Static Public Attributes | Private Attributes | List of all members
Sequence Class Reference

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#include <algo/structure/struct_util/su_sequence_set.hpp>

+ Inheritance diagram for Sequence:
+ Collaboration diagram for Sequence:

Public Types

typedef list< CRef< objects::CSeq_id > > SeqIdList
 
typedef std::map< const MoleculeIdentifier *, std::vector< bool > > MoleculeHighlightMap
 

Public Member Functions

 Sequence (ncbi::objects::CBioseq &bioseq)
 
 ~Sequence (void)
 
unsigned int Length (void) const
 
const ncbi::objects::CSeq_id & GetPreferredIdentifier (void) const
 
const ncbi::objects::CBioseq::TId & GetAllIdentifiers (void) const
 
bool MatchesSeqId (const ncbi::objects::CSeq_id &seqID) const
 
std::string IdentifierString (void) const
 
 Sequence (const objects::CBioseq &bioseq)
 
unsigned int Length (void) const
 
bool Matches (const objects::CSeq_id &seqID) const
 
bool Matches (const SeqIdList &others) const
 
string GetTitle (void) const
 
string GetLabel (void) const
 
int Status (void) const
 
 Sequence (SequenceSet *parent, ncbi::objects::CBioseq &bioseq)
 
std::string GetDescription (void) const
 
unsigned int Length (void) const
 
int GetOrSetMMDBLink (void) const
 
void AddMMDBAnnotTag (int mmdbID) const
 
ncbi::objects::CSeq_id * CreateSeqId (void) const
 
void FillOutSeqId (ncbi::objects::CSeq_id *sid) const
 
void LaunchWebBrowserWithInfo (void) const
 
bool HighlightPattern (const std::string &pattern, const MoleculeHighlightMap &restrictTo) const
 
- Public Member Functions inherited from StructureBase
 StructureBase (StructureBase *parent)
 
virtual ~StructureBase (void)
 
virtual bool DrawAll (const AtomSet *atomSet=NULL) const
 
virtual bool Draw (const AtomSet *atomSet=NULL) const
 
template<class T >
bool GetParentOfType (const T **ptr, bool warnIfNotFound=true) const
 

Public Attributes

ncbi::CRef< ncbi::objects::CBioseq > m_bioseqASN
 
std::string m_sequenceString
 
std::string m_description
 
bool m_isProtein
 
CConstRef< objects::CBioseq > bioseqASN
 
const SeqIdList seqIDs
 
string sequenceString
 
string description
 
int mmdbLink
 
ncbi::CRef< ncbi::objects::CBioseq > bioseqASN
 
const MoleculeIdentifieridentifier
 
const Moleculemolecule
 
bool isProtein
 
std::string sequenceString
 
std::string title
 
std::string taxonomy
 
- Public Attributes inherited from StructureBase
StructureSetparentSet
 

Static Public Attributes

static const int NOT_SET = -1
 

Private Attributes

int status
 

Detailed Description

Definition at line 51 of file su_sequence_set.hpp.

Member Typedef Documentation

◆ MoleculeHighlightMap

typedef std::map< const MoleculeIdentifier *, std::vector < bool > > Sequence::MoleculeHighlightMap

Definition at line 103 of file sequence_set.hpp.

◆ SeqIdList

typedef list< CRef < objects::CSeq_id > > Sequence::SeqIdList

Definition at line 91 of file cav_seqset.hpp.

Constructor & Destructor Documentation

◆ Sequence() [1/3]

Sequence::Sequence ( ncbi::objects::CBioseq &  bioseq)

◆ ~Sequence()

Sequence::~Sequence ( void  )

Definition at line 269 of file su_sequence_set.cpp.

◆ Sequence() [2/3]

Sequence::Sequence ( const objects::CBioseq &  bioseq)

◆ Sequence() [3/3]

Sequence::Sequence ( SequenceSet parent,
ncbi::objects::CBioseq &  bioseq 
)

Member Function Documentation

◆ AddMMDBAnnotTag()

void Sequence::AddMMDBAnnotTag ( int  mmdbID) const

◆ CreateSeqId()

CSeq_id * Sequence::CreateSeqId ( void  ) const

Definition at line 375 of file sequence_set.cpp.

References FillOutSeqId().

Referenced by CreatePairwiseSeqAlignFromMultipleRow().

◆ FillOutSeqId()

void Sequence::FillOutSeqId ( ncbi::objects::CSeq_id *  sid) const

◆ GetAllIdentifiers()

const ncbi::objects::CBioseq::TId& Sequence::GetAllIdentifiers ( void  ) const
inline

Definition at line 65 of file su_sequence_set.hpp.

◆ GetDescription()

string Sequence::GetDescription ( void  ) const

◆ GetLabel()

string Sequence::GetLabel ( void  ) const

Definition at line 313 of file cav_seqset.cpp.

References eContent, kEmptyStr, label, and seqIDs.

◆ GetOrSetMMDBLink()

int Sequence::GetOrSetMMDBLink ( void  ) const

◆ GetPreferredIdentifier()

const CSeq_id & Sequence::GetPreferredIdentifier ( void  ) const

◆ GetTitle()

string Sequence::GetTitle ( void  ) const

Definition at line 290 of file cav_seqset.cpp.

References kEmptyStr, NStr::NumericToString(), seqIDs, string, and title.

Referenced by AlignmentSet::AlignmentSet().

◆ HighlightPattern()

bool Sequence::HighlightPattern ( const std::string pattern,
const MoleculeHighlightMap restrictTo 
) const

◆ IdentifierString()

string Sequence::IdentifierString ( void  ) const

◆ LaunchWebBrowserWithInfo()

void Sequence::LaunchWebBrowserWithInfo ( void  ) const

◆ Length() [1/3]

unsigned int Sequence::Length ( void  ) const
inline

◆ Length() [2/3]

unsigned int Sequence::Length ( void  ) const
inline

Definition at line 98 of file cav_seqset.hpp.

References sequenceString.

◆ Length() [3/3]

unsigned int Sequence::Length ( void  ) const
inline

Definition at line 88 of file sequence_set.hpp.

References sequenceString.

◆ Matches() [1/2]

bool Sequence::Matches ( const objects::CSeq_id &  seqID) const

◆ Matches() [2/2]

bool Sequence::Matches ( const SeqIdList others) const

Definition at line 350 of file cav_seqset.cpp.

References Matches().

◆ MatchesSeqId()

bool Sequence::MatchesSeqId ( const ncbi::objects::CSeq_id &  seqID) const

◆ Status()

int Sequence::Status ( void  ) const
inline

Definition at line 104 of file cav_seqset.hpp.

References status.

Referenced by SequenceSet::UnpackSeqEntry(), and SequenceSet::UnpackSeqSet().

Member Data Documentation

◆ bioseqASN [1/2]

CConstRef< objects::CBioseq > Sequence::bioseqASN

◆ bioseqASN [2/2]

ncbi::CRef< ncbi::objects::CBioseq > Sequence::bioseqASN

Definition at line 77 of file sequence_set.hpp.

◆ description

string Sequence::description

Definition at line 93 of file cav_seqset.hpp.

◆ identifier

const MoleculeIdentifier* Sequence::identifier

◆ isProtein

bool Sequence::isProtein

◆ m_bioseqASN

ncbi::CRef< ncbi::objects::CBioseq > Sequence::m_bioseqASN

Definition at line 57 of file su_sequence_set.hpp.

Referenced by GetPreferredIdentifier(), IdentifierString(), and MatchesSeqId().

◆ m_description

std::string Sequence::m_description

Definition at line 59 of file su_sequence_set.hpp.

Referenced by Sequence().

◆ m_isProtein

bool Sequence::m_isProtein

Definition at line 60 of file su_sequence_set.hpp.

Referenced by Sequence().

◆ m_sequenceString

std::string Sequence::m_sequenceString

◆ mmdbLink

int Sequence::mmdbLink

Definition at line 96 of file cav_seqset.hpp.

◆ molecule

const Molecule* Sequence::molecule

◆ NOT_SET

const int Sequence::NOT_SET = -1
static

Definition at line 95 of file cav_seqset.hpp.

◆ seqIDs

const SeqIdList Sequence::seqIDs

Definition at line 92 of file cav_seqset.hpp.

Referenced by GetLabel(), and GetTitle().

◆ sequenceString [1/2]

string Sequence::sequenceString

◆ sequenceString [2/2]

std::string Sequence::sequenceString

Definition at line 85 of file sequence_set.hpp.

◆ status

int Sequence::status
private

Definition at line 85 of file cav_seqset.hpp.

Referenced by Status().

◆ taxonomy

std::string Sequence::taxonomy

Definition at line 85 of file sequence_set.hpp.

Referenced by GetDescription(), and Sequence().

◆ title

std::string Sequence::title

Definition at line 85 of file sequence_set.hpp.

Referenced by GetDescription(), GetTitle(), and Sequence().


The documentation for this class was generated from the following files:
Modified on Thu Sep 28 03:33:52 2023 by modify_doxy.py rev. 669887