NCBI C++ ToolKit
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AlignmentSet Class Reference

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#include <objtools/cddalignview/cav_alignset.hpp>

+ Inheritance diagram for AlignmentSet:
+ Collaboration diagram for AlignmentSet:

Public Types

typedef vector< const MasterSlaveAlignment * > AlignmentList
 
typedef std::list< ncbi::CRef< ncbi::objects::CSeq_annot > > SeqAnnotList
 
typedef std::list< ncbi::CRef< MasterSlaveAlignment > > AlignmentList
 
typedef std::list< ncbi::CRef< ncbi::objects::CSeq_annot > > SeqAnnotList
 
typedef std::list< const MasterDependentAlignment * > AlignmentList
 

Public Member Functions

 AlignmentSet (SequenceSet *seqSet, const SeqAnnotList &seqAnnots, bool ignoreBadPairwiseAlignments=false)
 
 ~AlignmentSet (void)
 
int Status (void) const
 
 AlignmentSet (const SeqAnnotList &seqAnnots, const SequenceSet &sequenceSet)
 
 AlignmentSet (StructureBase *parent, const Sequence *masterSequence, const SeqAnnotList &seqAnnots)
 
 ~AlignmentSet (void)
 
bool Draw (const AtomSet *atomSet=NULL) 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
 

Static Public Member Functions

static AlignmentSetCreateFromMultiple (const BlockMultipleAlignment *multiple, SeqAnnotList *newAsnAlignmentData, const SequenceSet &sequenceSet, const std::vector< unsigned int > *rowOrder=NULL)
 
static AlignmentSetCreateFromMultiple (StructureBase *parent, const BlockMultipleAlignment *multiple, const std::vector< unsigned int > &rowOrder)
 

Public Attributes

AlignmentList alignments
 
const Sequencemaster
 
AlignmentList m_alignments
 
const Sequencem_master
 
SeqAnnotListnewAsnAlignmentData
 
- Public Attributes inherited from StructureBase
StructureSetparentSet
 

Private Attributes

int status
 

Detailed Description

Definition at line 57 of file cav_alignset.hpp.

Member Typedef Documentation

◆ AlignmentList [1/3]

Definition at line 66 of file cav_alignset.hpp.

◆ AlignmentList [2/3]

typedef std::list< ncbi::CRef < MasterSlaveAlignment > > AlignmentSet::AlignmentList

Definition at line 87 of file su_alignment_set.hpp.

◆ AlignmentList [3/3]

Definition at line 66 of file alignment_set.hpp.

◆ SeqAnnotList [1/2]

typedef std::list< ncbi::CRef< ncbi::objects::CSeq_annot > > AlignmentSet::SeqAnnotList

Definition at line 84 of file su_alignment_set.hpp.

◆ SeqAnnotList [2/2]

typedef std::list< ncbi::CRef< ncbi::objects::CSeq_annot > > AlignmentSet::SeqAnnotList

Definition at line 58 of file alignment_set.hpp.

Constructor & Destructor Documentation

◆ AlignmentSet() [1/3]

AlignmentSet::AlignmentSet ( SequenceSet seqSet,
const SeqAnnotList seqAnnots,
bool  ignoreBadPairwiseAlignments = false 
)

◆ ~AlignmentSet() [1/2]

AlignmentSet::~AlignmentSet ( void  )

Definition at line 76 of file alignment_set.cpp.

References newAsnAlignmentData.

◆ AlignmentSet() [2/3]

AlignmentSet::AlignmentSet ( const SeqAnnotList seqAnnots,
const SequenceSet sequenceSet 
)

◆ AlignmentSet() [3/3]

AlignmentSet::AlignmentSet ( StructureBase parent,
const Sequence masterSequence,
const SeqAnnotList seqAnnots 
)

Definition at line 59 of file alignment_set.cpp.

References a, ERRORMSG, and TRACEMSG.

◆ ~AlignmentSet() [2/2]

AlignmentSet::~AlignmentSet ( void  )

Member Function Documentation

◆ CreateFromMultiple() [1/2]

AlignmentSet * AlignmentSet::CreateFromMultiple ( const BlockMultipleAlignment multiple,
SeqAnnotList newAsnAlignmentData,
const SequenceSet sequenceSet,
const std::vector< unsigned int > *  rowOrder = NULL 
)
static

◆ CreateFromMultiple() [2/2]

AlignmentSet * AlignmentSet::CreateFromMultiple ( StructureBase parent,
const BlockMultipleAlignment multiple,
const std::vector< unsigned int > &  rowOrder 
)
static

◆ Draw()

bool AlignmentSet::Draw ( const AtomSet atomSet = NULL) const
inlinevirtual

Reimplemented from StructureBase.

Definition at line 72 of file alignment_set.hpp.

◆ Status()

int AlignmentSet::Status ( void  ) const
inline

Definition at line 69 of file cav_alignset.hpp.

Member Data Documentation

◆ alignments

AlignmentList AlignmentSet::alignments

◆ m_alignments

AlignmentList AlignmentSet::m_alignments

Definition at line 88 of file su_alignment_set.hpp.

Referenced by AlignmentUtility::DoIBM().

◆ m_master

const Sequence* AlignmentSet::m_master

Definition at line 91 of file su_alignment_set.hpp.

◆ master

const Sequence * AlignmentSet::master

◆ newAsnAlignmentData

SeqAnnotList* AlignmentSet::newAsnAlignmentData

◆ status

int AlignmentSet::status
private

Definition at line 60 of file cav_alignset.hpp.

Referenced by AlignmentSet().


The documentation for this class was generated from the following files:
Modified on Wed May 22 11:29:40 2024 by modify_doxy.py rev. 669887