AlignmentSet Class Reference

Search Toolkit Book for AlignmentSet

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

Public Attributes
AlignmentList	alignments
const Sequence *	master
AlignmentList	m_alignments
const Sequence *	m_master
SeqAnnotList *	newAsnAlignmentData
Public Attributes inherited from StructureBase
StructureSet *	parentSet

Private Attributes
int	status

Detailed Description

Definition at line 57 of file cav_alignset.hpp.

Member Typedef Documentation

AlignmentList [1/3]

typedef vector< const MasterSlaveAlignment * > AlignmentSet::AlignmentList

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]

typedef std::list< const MasterDependentAlignment * > AlignmentSet::AlignmentList

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
	)

Definition at line 63 of file cav_alignset.cpp.

References a, alignments, CAV_ERROR_ALIGNMENTS, CAV_SUCCESS, ERR_POST_X, Error(), CSeq_align_Base::eType_diags, CSeq_align_Base::eType_partial, Sequence::GetTitle(), i, Info(), master, SequenceSet::master, Sequence::Matches(), n, ne(), SequenceSet::sequences, status, and Warning().

Referenced by CreateFromMultiple().

~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
	)

Definition at line 54 of file su_alignment_set.cpp.

References a, CSeq_align_Base::eType_diags, CSeq_align_Base::eType_partial, Sequence::IdentifierString(), le(), Sequence::MatchesSeqId(), n, ne(), NULL, THROW_MESSAGE, TRACE_MESSAGE, and WARNING_MESSAGE.

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

Definition at line 146 of file su_alignment_set.cpp.

References AlignmentSet(), blocks, CreatePairwiseSeqAlignFromMultipleRow(), ERROR_MESSAGE, CException::GetMsg(), BlockMultipleAlignment::GetUngappedAlignedBlocks(), i, newAsnAlignmentData, BlockMultipleAlignment::NRows(), NULL, row, CSeq_annot_Base::SetData(), and map_checker< Container >::size().

Referenced by AlignmentUtility::GetSeqAnnots(), and AlignmentManager::SavePairwiseFromMultiple().

CreateFromMultiple() [2/2]

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

static

Definition at line 81 of file alignment_set.cpp.

References AlignmentSet(), blocks, CreatePairwiseSeqAlignFromMultipleRow(), ERRORMSG, BlockMultipleAlignment::GetMaster(), BlockMultipleAlignment::GetUngappedAlignedBlocks(), i, newAsnAlignmentData, BlockMultipleAlignment::NRows(), NULL, row, CSeq_annot_Base::SetData(), and map_checker< Container >::size().

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

Definition at line 67 of file cav_alignset.hpp.

Referenced by AlignmentDisplay::AlignmentDisplay(), AlignmentSet(), AlignmentManager::GetAlignmentSetDependentSequences(), AlignmentManager::GetAlignmentSetDependentVisibilities(), StructureSet::LoadAlignmentsAndStructures(), AlignmentManager::NewAlignments(), AlignmentManager::NewMultipleWithRows(), ASNDataManager::RemoveUnusedSequences(), SetStructureRowFlags(), AlignmentManager::ShowHideCallbackFunction(), and VerifyAlignmentData().

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

Definition at line 72 of file cav_alignset.hpp.

Referenced by AlignmentManager::AlignmentManager(), AlignmentSet(), StructureSet::HasStructuredMaster(), and ASNDataManager::RemoveUnusedSequences().

newAsnAlignmentData

SeqAnnotList* AlignmentSet::newAsnAlignmentData

Definition at line 75 of file alignment_set.hpp.

Referenced by CreateFromMultiple(), StructureSet::ReplaceAlignmentSet(), and ~AlignmentSet().

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:

• include/objtools/cddalignview/cav_alignset.hpp
• src/algo/structure/struct_util/su_alignment_set.hpp
• src/app/cn3d/alignment_set.hpp
• src/algo/structure/struct_util/su_alignment_set.cpp
• src/app/cn3d/alignment_set.cpp
• src/objtools/cddalignview/cav_alignset.cpp