SequenceSet Class Reference

Search Toolkit Book for SequenceSet

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

Inheritance diagram for SequenceSet:

Collaboration diagram for SequenceSet:

Public Types
typedef std::list< ncbi::CRef< ncbi::objects::CSeq_entry > >	SeqEntryList
typedef std::list< ncbi::CRef< Sequence > >	SequenceList
typedef vector< const Sequence * >	SequenceList
typedef std::list< ncbi::CRef< ncbi::objects::CSeq_entry > >	SeqEntryList
typedef std::list< const Sequence * >	SequenceList

Public Member Functions
	SequenceSet (SeqEntryList &seqEntries)
	SequenceSet (const objects::CSeq_entry &seqEntry)
	SequenceSet (const SeqEntryList &seqEntries)
	~SequenceSet ()
int	Status (void) const
	SequenceSet (StructureBase *parent, SeqEntryList &seqEntries)
bool	Draw (const AtomSet *atomSet=NULL) const
const Sequence *	FindMatchingSequence (const ncbi::objects::CBioseq::TId &ids) 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
SequenceList	m_sequences
SequenceList	sequences
const Sequence *	master
Public Attributes inherited from StructureBase
StructureSet *	parentSet

Private Member Functions
void	UnpackSeqSet (const objects::CBioseq_set &bss)
void	UnpackSeqEntry (const objects::CSeq_entry &seqEntry)

Private Attributes
int	status

Detailed Description

Definition at line 70 of file su_sequence_set.hpp.

Member Typedef Documentation

SeqEntryList [1/2]

typedef std::list< ncbi::CRef < ncbi::objects::CSeq_entry > > SequenceSet::SeqEntryList

Definition at line 73 of file su_sequence_set.hpp.

SeqEntryList [2/2]

typedef std::list< ncbi::CRef < ncbi::objects::CSeq_entry > > SequenceSet::SeqEntryList

Definition at line 60 of file sequence_set.hpp.

SequenceList [1/3]

typedef std::list< ncbi::CRef < Sequence > > SequenceSet::SequenceList

Definition at line 76 of file su_sequence_set.hpp.

SequenceList [2/3]

typedef vector< const Sequence * > SequenceSet::SequenceList

Definition at line 72 of file cav_seqset.hpp.

SequenceList [3/3]

typedef std::list< const Sequence * > SequenceSet::SequenceList

Definition at line 63 of file sequence_set.hpp.

Constructor & Destructor Documentation

SequenceSet() [1/4]

SequenceSet::SequenceSet

(

SeqEntryList &

seqEntries

)

Definition at line 106 of file su_sequence_set.cpp.

References m_sequences, TRACE_MESSAGE, and UnpackSeqEntry().

SequenceSet() [2/4]

SequenceSet::SequenceSet

(

const objects::CSeq_entry &

seqEntry

)

SequenceSet() [3/4]

SequenceSet::SequenceSet

(

const SeqEntryList &

seqEntries

)

Definition at line 120 of file cav_seqset.cpp.

References ERR_POST_X, Info(), sequences, and UnpackSeqEntry().

~SequenceSet()

SequenceSet::~SequenceSet

(

void

)

Definition at line 129 of file cav_seqset.cpp.

References sequences.

SequenceSet() [4/4]

SequenceSet::SequenceSet	(	StructureBase *	parent,
		SeqEntryList &	seqEntries
	)

Definition at line 115 of file sequence_set.cpp.

References sequences, TRACEMSG, and UnpackSeqEntry().

Member Function Documentation

Draw()

bool SequenceSet::Draw ( const AtomSet *  atomSet = NULL ) const

inlinevirtual

Reimplemented from StructureBase.

Definition at line 66 of file sequence_set.hpp.

FindMatchingSequence()

const Sequence * SequenceSet::FindMatchingSequence

(

const ncbi::objects::CBioseq::TId &

ids

)

const

Definition at line 124 of file sequence_set.cpp.

References i, NULL, and sequences.

Referenced by StructureSet::FindOrCreateSequence().

Status()

int SequenceSet::Status ( void  ) const

inline

Definition at line 75 of file cav_seqset.hpp.

UnpackSeqEntry()

void SequenceSet::UnpackSeqEntry ( const objects::CSeq_entry &  seqEntry )

private

Definition at line 99 of file cav_seqset.cpp.

References CAV_SUCCESS, CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), sequences, status, Sequence::Status(), and UnpackSeqSet().

Referenced by SequenceSet().

UnpackSeqSet()

void SequenceSet::UnpackSeqSet ( const objects::CBioseq_set &  bss )

private

Definition at line 73 of file cav_seqset.cpp.

References CAV_SUCCESS, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, CBioseq_set_Base::GetSeq_set(), sequences, status, and Sequence::Status().

Referenced by UnpackSeqEntry().

Member Data Documentation

m_sequences

SequenceList SequenceSet::m_sequences

Definition at line 77 of file su_sequence_set.hpp.

Referenced by MasterSlaveAlignment::MasterSlaveAlignment(), and SequenceSet().

master

const Sequence* SequenceSet::master

Definition at line 79 of file cav_seqset.hpp.

Referenced by AlignmentDisplay::AlignmentDisplay(), and AlignmentSet::AlignmentSet().

sequences

SequenceList SequenceSet::sequences

Definition at line 73 of file cav_seqset.hpp.

Referenced by AlignmentManager::AlignmentManager(), AlignmentSet::AlignmentSet(), StructureSet::ConvertMimeDataToCDD(), FindMatchingSequence(), StructureSet::FindOrCreateSequence(), UpdateViewer::ImportStructure(), StructureSet::LoadAlignmentsAndStructures(), StructureSet::LoadSequencesForSingleStructure(), MasterDependentAlignment::MasterDependentAlignment(), StructureSet::MatchSequenceToMoleculeInObject(), AlignmentManager::NewAlignments(), StructureWindow::OnCDD(), SequenceSet(), UnpackSeqEntry(), UnpackSeqSet(), and ~SequenceSet().

status

int SequenceSet::status

private

Definition at line 63 of file cav_seqset.hpp.

Referenced by UnpackSeqEntry(), and UnpackSeqSet().

---

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

• include/algo/structure/struct_util/su_sequence_set.hpp
• include/objtools/cddalignview/cav_seqset.hpp
• src/app/cn3d/sequence_set.hpp
• src/algo/structure/struct_util/su_sequence_set.cpp
• src/app/cn3d/sequence_set.cpp
• src/objtools/cddalignview/cav_seqset.cpp