Represents ASN.1 type Seq-align defined in file seqalign.asn

#include <objects/seqalign/Seq_align.hpp>

Inheritance diagram for CSeq_align:

Collaboration diagram for CSeq_align:

Classes
struct	SIndel

struct	SSeqIdChooser
	Create a Dense-seg from a Std-seg Used by AlnMgr to handle nucl2prot alignments. More...

Public Types
enum	EScoreType { eScore_Score , eScore_Blast , eScore_BitScore , eScore_EValue , eScore_AlignLength , eScore_IdentityCount , eScore_PositiveCount , eScore_NegativeCount , eScore_MismatchCount , eScore_GapCount , eScore_PercentIdentity_Gapped , eScore_PercentIdentity_Ungapped , eScore_PercentIdentity_GapOpeningOnly , eScore_PercentCoverage , eScore_SumEValue , eScore_CompAdjMethod , eScore_HighQualityPercentCoverage , eScore_Matches , eScore_OverallIdentity , eScore_Splices , eScore_ConsensusSplices , eScore_ProductCoverage , eScore_ExonIdentity , eScore_PercentIdentity = eScore_PercentIdentity_Gapped }
	enum controlling known named scores More...

typedef pair< TSeqPos, TSeqPos >	TLengthRange

typedef map< string, EScoreType >	TScoreNameMap

Public Types inherited from CSeq_align_Base
enum	EType { eType_not_set = 0 , eType_global = 1 , eType_diags = 2 , eType_partial = 3 , eType_disc = 4 , eType_other = 255 }

enum class	E_memberIndex { e__allMandatory = 0 , e_type , e_dim , e_score , e_segs , e_bounds , e_id , e_ext }

typedef EType	TType

typedef int	TDim

typedef vector< CRef< CScore > >	TScore

typedef C_Segs	TSegs

typedef list< CRef< CSeq_loc > >	TBounds

typedef list< CRef< CObject_id > >	TId

typedef list< CRef< CUser_object > >	TExt

typedef Tparent::CMemberIndex< E_memberIndex, 8 >	TmemberIndex

Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...

typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...

typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Public Member Functions
	CSeq_align (void)
	constructor More...

	~CSeq_align (void)
	destructor More...

TDim	CheckNumRows (void) const
	Validatiors. More...

void	Validate (bool full_test=false) const

CRange< TSeqPos >	GetSeqRange (TDim row) const
	GetSeqRange NB: On a Spliced-seg, in case the product-type is protein, these only return the amin part of Prot-pos. More...

TSeqPos	GetSeqStart (TDim row) const

TSeqPos	GetSeqStop (TDim row) const

ENa_strand	GetSeqStrand (TDim row) const
	Get strand (the first one if segments have different strands). More...

const CSeq_id &	GetSeq_id (TDim row) const
	Get seq-id (the first one if segments have different ids). More...

TSeqPos	GetTotalGapCount (TDim row=-1) const
	Retrieves the total number of gaps in the given row an alignment; all gaps by default. More...

TSeqPos	GetTotalGapCountWithinRange (const TSeqRange &range, TDim row=-1) const

TSeqPos	GetTotalGapCountWithinRanges (const CRangeCollection< TSeqPos > &ranges, TDim row=-1) const

TSeqPos	GetNumGapOpenings (TDim row=-1) const
	Retrieves the number of gap openings in a given row in an alignment (ignoring how many gaps are in the gapped region); all gaps by default. More...

TSeqPos	GetNumGapOpeningsWithinRange (const TSeqRange &range, TDim row=-1) const

TSeqPos	GetNumGapOpeningsWithinRanges (const CRangeCollection< TSeqPos > &ranges, TDim row=-1) const

TSeqPos	GetNumFrameshifts (TDim row=-1) const
	Retrieves the number of times a given row shifts frames; i.e. More...

TSeqPos	GetNumFrameshiftsWithinRange (const TSeqRange &range, TDim row=-1) const

TSeqPos	GetNumFrameshiftsWithinRanges (const CRangeCollection< TSeqPos > &ranges, TDim row=-1) const

vector< SIndel >	GetIndels (TDim row=-1) const
	Retrieves descriptions of all indels on a given row. More...

vector< SIndel >	GetIndelsWithinRange (const TSeqRange &range, TDim row=-1) const

vector< SIndel >	GetIndelsWithinRanges (const CRangeCollection< TSeqPos > &ranges, TDim row=-1) const

vector< SIndel >	GetFrameshifts (TDim row=-1) const
	Retrieves descriptions of all frameshifts on a given row; i.e. More...

vector< SIndel >	GetFrameshiftsWithinRange (const TSeqRange &range, TDim row=-1) const

vector< SIndel >	GetFrameshiftsWithinRanges (const CRangeCollection< TSeqPos > &ranges, TDim row=-1) const

vector< SIndel >	GetNonFrameshifts (TDim row=-1) const
	Retrieves descriptions of all non-frameshift indels on a given row; i.e. More...

vector< SIndel >	GetNonFrameshiftsWithinRange (const TSeqRange &range, TDim row=-1) const

vector< SIndel >	GetNonFrameshiftsWithinRanges (const CRangeCollection< TSeqPos > &ranges, TDim row=-1) const

CRangeCollection< TSeqPos >	GetAlignedBases (TDim row) const
	Retrieves the locations of aligned bases in the given row, excluding gaps and incontinuities. More...

TSeqPos	GetAlignLength (bool include_gaps=true) const
	Get the length of this alignment. More...

TSeqPos	GetAlignLengthWithinRange (const TSeqRange &range, bool include_gaps=true) const
	Get the length of this alignment within a specified range By default, this function computes an alignment length including all gap segments. More...

TSeqPos	GetAlignLengthWithinRanges (const CRangeCollection< TSeqPos > &ranges, bool include_gaps=true) const
	Get the length of this alignment within a specified range By default, this function computes an alignment length including all gap segments. More...

double	AlignLengthRatio () const

bool	GetNamedScore (const string &id, int &score) const
	Get score. More...

bool	GetNamedScore (const string &id, double &score) const
	--------------------------------------------------------------------------- PRE : name of score to return POST: whether or not we found that score; score converted to double More...

bool	GetNamedScore (EScoreType type, int &score) const

bool	GetNamedScore (EScoreType type, double &score) const

void	SetNamedScore (const string &id, int score)

void	SetNamedScore (const string &id, double score)

void	SetNamedScore (EScoreType type, int score)

void	SetNamedScore (EScoreType type, double score)

void	ResetNamedScore (const string &name)

void	ResetNamedScore (EScoreType type)

void	Reverse (void)
	Reverse the segments' orientation NOTE: currently only works for dense-seg. More...

void	SwapRows (TDim row1, TDim row2)
	Swap the position of two rows in the alignment NOTE: currently only works for dense-seg & disc. More...

CRef< CSeq_align >	CreateDensegFromStdseg (SSeqIdChooser *SeqIdChooser=0) const
	---------------------------------------------------------------------------- PRE : the Seq-align has StdSeg segs POST: Seq_align of type Dense-seg is created with m_Widths if necessary More...

CRef< CSeq_align >	CreateDensegFromDisc (SSeqIdChooser *SeqIdChooser=0) const

CRef< CSeq_align >	CreateTranslatedDensegFromNADenseg (void) const
	Create a Dense-seg with widths from Dense-seg of nucleotides Used by AlnMgr to handle translated nucl2nucl alignments IMPORTANT NOTE: Do NOT use for alignments containing proteins; the code will not check for this. More...

void	SplitOnLongDiscontinuity (list< CRef< CSeq_align > > &aligns, TSeqPos discontinuity_threshold) const
	Split the alignment at any discontinuity greater than threshold; populate aligns list with new alignments. More...

void	OffsetRow (TDim row, TSignedSeqPos offset)
	Offset row's coords. More...

void	RemapToLoc (TDim row, const CSeq_loc &dst_loc, bool ignore_strand=false)

CRef< CSeq_loc >	CreateRowSeq_loc (TDim row) const

TLengthRange	GapLengthRange () const

TLengthRange	IntronLengthRange () const

TLengthRange	ExonLengthRange () const

CConstRef< CUser_object >	FindExt (const string &ext_type) const
	Find extension by type in ext container. More...

CRef< CUser_object >	FindExt (const string &ext_type)
	Non-const version of FindExt(). More...

Public Member Functions inherited from CSeq_align_Base
	CSeq_align_Base (void)

virtual	~CSeq_align_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSetType (void) const
	Check if a value has been assigned to Type data member. More...

bool	CanGetType (void) const
	Check if it is safe to call GetType method. More...

void	ResetType (void)
	Reset Type data member. More...

TType	GetType (void) const
	Get the Type member data. More...

void	SetType (TType value)
	Assign a value to Type data member. More...

TType &	SetType (void)
	Assign a value to Type data member. More...

bool	IsSetDim (void) const
	dimensionality Check if a value has been assigned to Dim data member. More...

bool	CanGetDim (void) const
	Check if it is safe to call GetDim method. More...

void	ResetDim (void)
	Reset Dim data member. More...

TDim	GetDim (void) const
	Get the Dim member data. More...

void	SetDim (TDim value)
	Assign a value to Dim data member. More...

TDim &	SetDim (void)
	Assign a value to Dim data member. More...

bool	IsSetScore (void) const
	for whole alignment Check if a value has been assigned to Score data member. More...

bool	CanGetScore (void) const
	Check if it is safe to call GetScore method. More...

void	ResetScore (void)
	Reset Score data member. More...

const TScore &	GetScore (void) const
	Get the Score member data. More...

TScore &	SetScore (void)
	Assign a value to Score data member. More...

bool	IsSetSegs (void) const
	Check if a value has been assigned to Segs data member. More...

bool	CanGetSegs (void) const
	Check if it is safe to call GetSegs method. More...

void	ResetSegs (void)
	Reset Segs data member. More...

const TSegs &	GetSegs (void) const
	Get the Segs member data. More...

void	SetSegs (TSegs &value)
	Assign a value to Segs data member. More...

TSegs &	SetSegs (void)
	Assign a value to Segs data member. More...

bool	IsSetBounds (void) const
	regions of sequence over which align was computed Check if a value has been assigned to Bounds data member. More...

bool	CanGetBounds (void) const
	Check if it is safe to call GetBounds method. More...

void	ResetBounds (void)
	Reset Bounds data member. More...

const TBounds &	GetBounds (void) const
	Get the Bounds member data. More...

TBounds &	SetBounds (void)
	Assign a value to Bounds data member. More...

bool	IsSetId (void) const
	alignment id Check if a value has been assigned to Id data member. More...

bool	CanGetId (void) const
	Check if it is safe to call GetId method. More...

void	ResetId (void)
	Reset Id data member. More...

const TId &	GetId (void) const
	Get the Id member data. More...

TId &	SetId (void)
	Assign a value to Id data member. More...

bool	IsSetExt (void) const
	extra info Check if a value has been assigned to Ext data member. More...

bool	CanGetExt (void) const
	Check if it is safe to call GetExt method. More...

void	ResetExt (void)
	Reset Ext data member. More...

const TExt &	GetExt (void) const
	Get the Ext member data. More...

TExt &	SetExt (void)
	Assign a value to Ext data member. More...

virtual void	Reset (void)
	Reset the whole object. More...

Public Member Functions inherited from CSerialObject
	CSerialObject (void)

virtual	~CSerialObject (void)

virtual const CTypeInfo *	GetThisTypeInfo (void) const =0

virtual void	Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive)
	Set object to copy of another one. More...

virtual bool	Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const
	Check if both objects contain the same values. More...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...

void	ThrowUnassigned (TMemberIndex index) const

void	ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const

bool	HasNamespaceName (void) const
	Check if object data type has namespace name. More...

const string &	GetNamespaceName (void) const
	Get namespace name. More...

bool	HasNamespacePrefix (void) const
	Check if data type has namespace prefix. More...

const string &	GetNamespacePrefix (void) const
	Get namespace prefix. More...

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...

bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...

bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...

bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...

bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...

void	AddReference (void) const
	Add reference to object. More...

void	RemoveReference (void) const
	Remove reference to object. More...

void	ReleaseReference (void) const
	Remove reference without deleting object. More...

virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...

virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...

void *	operator new (size_t size)
	Define new operator for memory allocation. More...

void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...

void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...

void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...

void *	operator new (size_t size, void *place)
	Define new operator. More...

void	operator delete (void ptr, void place)
	Define delete operator. More...

void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...

void	operator delete (void ptr, CObjectMemoryPool place)
	Define delete operator. More...

Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)

virtual	~CDebugDumpable (void)

void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const

void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const

void	DumpToConsole (void) const

Static Public Member Functions
static const TScoreNameMap &	ScoreNameMap ()

static string	ScoreName (EScoreType score)

static string	HelpText (EScoreType score)

static bool	IsIntegerScore (EScoreType score)

Static Public Member Functions inherited from CSeq_align_Base
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	EType (void)
	Access to EType's attributes (values, names) as defined in spec. More...

Static Public Member Functions inherited from CSerialObject
static void	SetVerifyDataThread (ESerialVerifyData verify)

static void	SetVerifyDataGlobal (ESerialVerifyData verify)

static string	UnassignedString (void)

static CStringUTF8	UnassignedStringUTF8 (void)

static char	UnassignedByte (void)

Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...

static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)

static EAllocFillMode	GetAllocFillMode (void)

static void	SetAllocFillMode (EAllocFillMode mode)

static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...

Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Protected Member Functions
CConstRef< CScore >	x_GetNamedScore (const string &name) const
	retrieve a named score object More...

CRef< CScore >	x_SetNamedScore (const string &name)

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Private Types
typedef CSeq_align_Base	Tparent

Private Member Functions
	CSeq_align (const CSeq_align &value)
	Prohibit copy constructor and assignment operator. More...

CSeq_align &	operator= (const CSeq_align &value)

CRef< CSeq_align >	x_CreateSubsegAlignment (int from, int to) const
	Create a partial alignment containing the specified range of segments. More...

Additional Inherited Members
Static Public Attributes inherited from CSerialObject
static const char *	ms_UnassignedStr = "<unassigned>"

static const char	ms_UnassignedByte = char(0xcd)

Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...

static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...

static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...

static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...

static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...

static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Detailed Description

Definition at line 54 of file Seq_align.hpp.

Member Typedef Documentation

◆ TLengthRange

typedef pair<TSeqPos, TSeqPos> CSeq_align::TLengthRange

Definition at line 192 of file Seq_align.hpp.

◆ Tparent

typedef CSeq_align_Base CSeq_align::Tparent

private

Definition at line 56 of file Seq_align.hpp.

◆ TScoreNameMap

typedef map<string, EScoreType> CSeq_align::TScoreNameMap

Definition at line 194 of file Seq_align.hpp.

Member Enumeration Documentation

◆ EScoreType

enum CSeq_align::EScoreType

enum controlling known named scores

A word on scores, since definitions are quite important: Scores here are to be represented as a standard set of computations, comparable across alignment generation algorithms. The class CScoreBuilder holds reference implementations for most of the scores below (modulo interpretation difficulties with a score named 'score'). The intended meanings of scores are as follows:

'score' generic score, definable by any algorithm; not comparable across algorithms.

'bit_score' BLAST-specific bit score; reference implementation in the BLAST code, which is also exposed in CScoreBuilder.

'e_value' BLAST-specific e-value; reference implementation in the BLAST code, which is also exposed in CScoreBuilder.

alignment length not a score per se, but a useful metric nonetheless. This is the sum of all aligned segments and all gaps; this excludes introns and discontinuities

percent identity percent identity, computed as *UNGAPPED* percent identity. That is, the computation is strictly (matches) / (matches + mismatches) NOTE: there are, historically, at least four separate methods of computation for this: 1. C++ toolkit (CScoreBuilder): ungapped percent identity: (matches) / (matches + mismatches) 2. BLAST: gapped percent identity: (matches) / (alignment length) 3. gbDNA and contig processes: modified alignment length to count each gap as 1 base long always (matches) / (matches + mismatches + gap count) 4. Spidey: compute identity per coverage: (matches) / (stop - start + 1) Several of these are provided directly, as: pct_identity_gap pct_identity_ungap pct_identity_gapopen_only

alignable bases More a concept than a score. The alignable region of a sequence, as defined by the underlying sequencing technology or biology - that is, the region of a sequence noted as high quality minus a poly-A tail in the case of a cDNA. This quantity can be used in computing more appropriate coverage scores.

'pct_coverage' Percent of a sequence (query) aligned to another (subject), minus poly-A tail: (matches + mismatches) / (query length - polyA tail)

alignable percent coverage (NB: no named score yet) Percent of the alignable region actually aligned to a subject (matches + mismatches in alignable region) / (length of alignable region)

exonic coverage (NB: no named score yet) Measure of the percent of the query represented in a set of exons (sum of lengths of exon on query) / (query length - polyA)

Warning: The order of this enumeration and the sc_ScoreNames, sc_ScoreHelpText, and sc_IsInteger arrays must correspond!

Enumerator
eScore_Score
eScore_Blast
eScore_BitScore
eScore_EValue
eScore_AlignLength
eScore_IdentityCount
eScore_PositiveCount
eScore_NegativeCount
eScore_MismatchCount
eScore_GapCount
eScore_PercentIdentity_Gapped
eScore_PercentIdentity_Ungapped
eScore_PercentIdentity_GapOpeningOnly
eScore_PercentCoverage
eScore_SumEValue
eScore_CompAdjMethod
eScore_HighQualityPercentCoverage
eScore_Matches
eScore_OverallIdentity
eScore_Splices
eScore_ConsensusSplices
eScore_ProductCoverage
eScore_ExonIdentity
eScore_PercentIdentity

Definition at line 128 of file Seq_align.hpp.

Constructor & Destructor Documentation

◆ CSeq_align() [1/2]

CSeq_align::CSeq_align ( void )

inline

constructor

Definition at line 445 of file Seq_align.hpp.

◆ ~CSeq_align()

CSeq_align::~CSeq_align ( void )

destructor

Definition at line 68 of file Seq_align.cpp.

◆ CSeq_align() [2/2]

CSeq_align::CSeq_align ( const CSeq_align & value )

private

Prohibit copy constructor and assignment operator.

Member Function Documentation

◆ AlignLengthRatio()

double CSeq_align::AlignLengthRatio ( ) const

Definition at line 2017 of file Seq_align.cpp.

References COpenRange< Position >::GetLength(), GetSeqRange(), and r().

Referenced by CScore_AlignLengthRatio::Get().

◆ CheckNumRows()

CSeq_align::TDim CSeq_align::CheckNumRows ( void ) const

Validatiors.

Definition at line 73 of file Seq_align.cpp.

References CDense_seg::CheckNumRows(), CSparse_seg::CheckNumRows(), CSeq_align_Base::C_Segs::e_Dendiag, CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_Sparse, CSeq_align_Base::C_Segs::e_Spliced, CSeq_align_Base::C_Segs::e_Std, Get(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::GetSparse(), ITERATE, and NCBI_THROW.

Referenced by CRemoveSeqFromAlignDlg::ApplyToCSeq_entry(), BuildAlignDataSource(), IProjectViewFactory::CombineInputObjects(), IProjectViewFactory::CombineObjects(), CTableViewWithTextViewNav::CombineObjects(), ConvertSeqAlignToPairwiseAln(), CreatePairwiseAlnFromSeqAlign(), CMAViewManager::DoTransition(), CEditSeqEndsWithAlign::FindPosition(), CEditSeqEndsWithAlign::FindRow(), CSequenceUpdater::FindRowInAlignment(), GapLengthRange(), CSGAlignmentJob::GetAlignType(), CDataTrackUtils::GetAlignType(), GetAnchors(), CScoreBuilder::GetBlastScore(), CSeqUtils::GetLocPlacements(), CAlignGroup::GroupByStrand(), CAlignFilter::Match(), CMAViewManager::NeedAnchorPanel(), PatchTargetSequence(), CTabularFormatter_Defline::Print(), CTabularFormatter_ProtRef::Print(), CTabularFormatter_TaxId::Print(), CTabularFormatter_Comment::Print(), CTabularFormatter_OrgName::Print(), CRevCompSequencesDlg::RevCompBioSeq(), CFeatCompareJob_Align::Run(), s_ComputeTraceback(), s_ExtendEntriesFromAlignments(), s_GetAlignmentTooltip(), s_GetAlnMapplingLocs(), s_GetRnaMappingLocs(), s_Seq_align_Seq_loc(), CConversionResultPanel::SetObjects(), sFindAnchorRow(), sGenerateFields(), CFeatureGenerator::SImplementation::SMapper::SMapper(), UpdateDensegAlignment(), Validate(), CCleanupAlignmentsToolManager::x_AreSelfAlignmentsOnly(), CTableViewWithTextViewNav::x_EditObject(), CSequenceEditingEventHandler::x_FindRelevantAlignRow(), CValidatePanel::x_LaunchEditor(), CBatchFeatJob::x_LoadFeatProducts(), CSplitDataLoader::x_SplitAligns(), and CEditObjectFeaturePropagate::xInit().

◆ CreateDensegFromDisc()

CRef< CSeq_align > CSeq_align::CreateDensegFromDisc ( SSeqIdChooser * SeqIdChooser = 0 ) const

Definition at line 1015 of file Seq_align.cpp.

Referenced by CFeaturePropagator::CFeaturePropagator(), and s_GetIndels().

◆ CreateDensegFromStdseg()

CRef< CSeq_align > CSeq_align::CreateDensegFromStdseg ( SSeqIdChooser * SeqIdChooser = 0 ) const

---------------------------------------------------------------------------- PRE : the Seq-align has StdSeg segs POST: Seq_align of type Dense-seg is created with m_Widths if necessary

Definition at line 728 of file Seq_align.cpp.

References CSeq_id::AsFastaString(), CSeq_interval_Base::CanGetStrand(), CSeq_align::SSeqIdChooser::ChooseSeqId(), eNa_strand_unknown, CSeq_align_Base::eType_not_set, CStd_seg_Base::GetDim(), CSeq_interval_Base::GetFrom(), CStd_seg_Base::GetLoc(), CDense_seg_Base::GetNumseg(), CSeq_align_Base::GetScore(), CSeq_align_Base::GetSegs(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), i, CSeq_align_Base::IsSetScore(), ITERATE, NCBI_THROW, CDense_seg::ResetWidths(), row, SerialAssign(), SerialEquals(), CDense_seg_Base::SetDim(), CDense_seg_Base::SetIds(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CSeq_align_Base::SetScore(), CSeq_align_Base::SetSegs(), CDense_seg_Base::SetStarts(), CDense_seg_Base::SetStrands(), CSeq_align_Base::SetType(), CDense_seg::SetWidths(), and string.

Referenced by CAlnMix::Add(), CFeaturePropagator::CFeaturePropagator(), CDisplaySeqalign::DisplaySeqalign(), CAlignFormatUtil::GetAlignmentLength(), SCigarAlignment::operator()(), s_SeqAlignSetToXMLHsps(), CBlastTabularInfo::SetFields(), CCIGAR_Formatter::x_FormatAlignmentRows(), and CDisplaySeqalign::x_GetAlnVecForSeqalign().

◆ CreateRowSeq_loc()

CRef< CSeq_loc > CSeq_align::CreateRowSeq_loc ( TDim row ) const

◆ CreateTranslatedDensegFromNADenseg()

CRef< CSeq_align > CSeq_align::CreateTranslatedDensegFromNADenseg ( void ) const

Create a Dense-seg with widths from Dense-seg of nucleotides Used by AlnMgr to handle translated nucl2nucl alignments IMPORTANT NOTE: Do *NOT* use for alignments containing proteins; the code will not check for this.

---------------------------------------------------------------------------- PRE : the Seq-align is a Dense-seg of aligned nucleotide sequences POST: Seq_align of type Dense-seg is created with each of the m_Widths equal to 3 and m_Lengths devided by 3.

Definition at line 953 of file Seq_align.cpp.

References CSerialObject::Assign(), CSeq_align_Base::eType_not_set, CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CSeq_align_Base::GetSegs(), NStr::IntToString(), NCBI_THROW, CDense_seg_Base::SetLens(), CSeq_align_Base::SetSegs(), CSeq_align_Base::SetType(), CDense_seg::SetWidths(), string, and CDense_seg::Validate().

Referenced by CAlignFormatUtil::GetAlignmentLength(), s_SeqAlignSetToXMLHsps(), CBlastTabularInfo::SetFields(), and CDisplaySeqalign::x_GetAlnVecForSeqalign().

◆ ExonLengthRange()

CSeq_align::TLengthRange CSeq_align::ExonLengthRange ( ) const

Definition at line 2214 of file Seq_align.cpp.

References SLengthRange::AddLength(), CSpliced_exon_Base::GetGenomic_end(), CSpliced_exon_Base::GetGenomic_start(), CSeq_align_Base::GetSegs(), ITERATE, NCBI_THROW, and SLengthRange::range.

Referenced by CScore_MinExonLength::Get().

◆ FindExt() [1/2]

CRef< CUser_object > CSeq_align::FindExt ( const string & ext_type )

Non-const version of FindExt().

Definition at line 2289 of file Seq_align.cpp.

References CObject_id_Base::GetStr(), CSeq_align_Base::IsSetExt(), CObject_id_Base::IsStr(), NON_CONST_ITERATE, CRef< C, Locker >::Reset(), and CSeq_align_Base::SetExt().

◆ FindExt() [2/2]

CConstRef< CUser_object > CSeq_align::FindExt ( const string & ext_type ) const

Find extension by type in ext container.

Parameters

ext_type String id of the extension to find.

Returns: User-object of the requested type or NULL.

Definition at line 2274 of file Seq_align.cpp.

References CSeq_align_Base::GetExt(), CObject_id_Base::GetStr(), CSeq_align_Base::IsSetExt(), CObject_id_Base::IsStr(), ITERATE, and CConstRef< C, Locker >::Reset().

Referenced by PrintSAM(), and PrintTabular().

◆ GapLengthRange()

CSeq_align::TLengthRange CSeq_align::GapLengthRange ( ) const

◆ GetAlignedBases()

CRangeCollection< TSeqPos > CSeq_align::GetAlignedBases ( TDim row ) const

Retrieves the locations of aligned bases in the given row, excluding gaps and incontinuities.

Exceptions

CSeqalignException if alignment type is not supported

Definition at line 1796 of file Seq_align.cpp.

References CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_Spliced, Get(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CSeq_align_Base::GetSegs(), CDense_seg_Base::GetStarts(), i, ITERATE, NCBI_THROW, and row.

Referenced by CScore_Overlap::Get(), CScore_OverlapBoth::Get(), CTabularFormatter_GapRanges::Print(), and CAlignFilter::x_FuncCall().

◆ GetAlignLength()

TSeqPos CSeq_align::GetAlignLength ( bool include_gaps = true ) const

Get the length of this alignment.

This length corresponds to the score 'align_length'. By default, this function computes an alignment length including all gap segments.

Definition at line 1993 of file Seq_align.cpp.

References COpenRange< TSeqPos >::GetWhole(), and s_GetAlignmentLength().

Referenced by CSAM_CIGAR_Formatter::AddRow(), sequpd::CompareAlignments(), CScore_AlignLength::Get(), CScore_SymmetricOverlap::Get(), CScore_Coverage::Get(), CScoreBuilderBase::GetAlignLength(), SAlignmentScoringModel::GetIdentOdds(), SAlignmentScoringModel::GetScore(), CAlignModel::MakeSeqAlign(), SSeqAlignsBySize::operator()(), SSeqAlignsByPctIdent::operator()(), CTabularFormatter_AlignLengthRatio::Print(), s_CompareSeqAlignByEvalue(), s_CompareSeqAlignByScore(), s_CompareSeqAlignByScoreAndName(), ScorePositionSort::s_CompareSeqAlignByScoreAndPosition(), s_GetCountIdentityMismatch(), SAlignmentScoringModel::s_GetIdentOdds_protSS(), s_IsSeqAlignAsGood(), s_SeqAlignSetToXMLHsps(), s_SortSeqAlignByLength(), and CWeightedIdentityScorer::ScoreAlignments().

◆ GetAlignLengthWithinRange()

TSeqPos CSeq_align::GetAlignLengthWithinRange	(	const TSeqRange &	range,
		bool	include_gaps = `true`
	)		const

Get the length of this alignment within a specified range By default, this function computes an alignment length including all gap segments.

Definition at line 2001 of file Seq_align.cpp.

References compile_time_bits::range(), and s_GetAlignmentLength().

Referenced by CScoreBuilderBase::GetAlignLength().

◆ GetAlignLengthWithinRanges()

TSeqPos CSeq_align::GetAlignLengthWithinRanges	(	const CRangeCollection< TSeqPos > &	ranges,
		bool	include_gaps = `true`
	)		const

Get the length of this alignment within a specified range By default, this function computes an alignment length including all gap segments.

Definition at line 2010 of file Seq_align.cpp.

References s_GetAlignmentLength().

Referenced by CScoreBuilderBase::ComputeScore(), CScoreBuilderBase::GetAlignLength(), s_GetPercentCoverage(), and s_GetPercentIdentity().

◆ GetFrameshifts()

vector< CSeq_align::SIndel > CSeq_align::GetFrameshifts ( TDim row = -1 ) const

Retrieves descriptions of all frameshifts on a given row; i.e.

all gaps with a length that is not a multiple of 3.

Exceptions

CSeqalignException if alignment type is not supported

Definition at line 1741 of file Seq_align.cpp.

References COpenRange< TSeqPos >::GetWhole(), row, and s_GetIndels().

◆ GetFrameshiftsWithinRange()

vector< CSeq_align::SIndel > CSeq_align::GetFrameshiftsWithinRange	(	const TSeqRange &	range,
		TDim	row = `-1`
	)		const

Definition at line 1747 of file Seq_align.cpp.

References compile_time_bits::range(), row, and s_GetIndels().

Referenced by CTabularFormatter_Indels::Print().

◆ GetFrameshiftsWithinRanges()

vector< CSeq_align::SIndel > CSeq_align::GetFrameshiftsWithinRanges	(	const CRangeCollection< TSeqPos > &	ranges,
		TDim	row = `-1`
	)		const

Definition at line 1753 of file Seq_align.cpp.

References row, and s_GetIndels().

◆ GetIndels()

vector< CSeq_align::SIndel > CSeq_align::GetIndels ( TDim row = -1 ) const

Retrieves descriptions of all indels on a given row.

Exceptions

CSeqalignException if alignment type is not supported

Definition at line 1777 of file Seq_align.cpp.

References COpenRange< TSeqPos >::GetWhole(), row, and s_GetIndels().

◆ GetIndelsWithinRange()

vector< CSeq_align::SIndel > CSeq_align::GetIndelsWithinRange	(	const TSeqRange &	range,
		TDim	row = `-1`
	)		const

Definition at line 1783 of file Seq_align.cpp.

References compile_time_bits::range(), row, and s_GetIndels().

Referenced by CTabularFormatter_Indels::Print().

◆ GetIndelsWithinRanges()

vector< CSeq_align::SIndel > CSeq_align::GetIndelsWithinRanges	(	const CRangeCollection< TSeqPos > &	ranges,
		TDim	row = `-1`
	)		const

Definition at line 1789 of file Seq_align.cpp.

References row, and s_GetIndels().

◆ GetNamedScore() [1/4]

bool CSeq_align::GetNamedScore	(	const string &	id,
		double &	score
	)		const

--------------------------------------------------------------------------- PRE : name of score to return POST: whether or not we found that score; score converted to double

Definition at line 580 of file Seq_align.cpp.

References x_GetNamedScore().

◆ GetNamedScore() [2/4]

bool CSeq_align::GetNamedScore	(	const string &	id,
		int &	score
	)		const

Get score.

--------------------------------------------------------------------------- PRE : name of score to return POST: whether or not we found that score; score converted to int

Definition at line 563 of file Seq_align.cpp.

References int, and x_GetNamedScore().

Referenced by BOOST_AUTO_TEST_CASE(), CMatePairGlyph::CMatePairGlyph(), CVecscreenRun::CFormatter::FormatResults(), CBlastAligner::GenerateAlignments(), CRemoteBlastAligner::GenerateAlignments(), GetNamedScore(), CdBlaster::getPsiBlastEValue(), CdBlaster::getPsiBlastScore(), SSeqAlignsByScore::operator()(), SSeqAlignsByPctIdent::operator()(), CTabularFormatter_EValue_Mantissa::Print(), CTabularFormatter_EValue_Exponent::Print(), PrintSAM(), PrintTabular(), CdBlaster::processBlastHits(), CSimpleB2SWrapper::processBlastHits(), CFeatureGenerator::SImplementation::RecalculateScores(), CTestBlastp_All::RunTest(), s_AddReciprocityScore(), s_CheckTraceMateAlign(), s_CompareSeqAlignByEvalue(), s_CompareSeqAlignByScore(), s_CompareSeqAlignByScoreAndName(), ScorePositionSort::s_CompareSeqAlignByScoreAndPosition(), s_GetAlignmentTooltip(), s_GetCountIdentityMismatch(), s_GetPercentCoverage(), s_IsSecondPassAlignment(), s_IsSeqAlignAsGood(), s_ScoreAlignments(), CInversionMergeAligner::s_SortByPctCoverage(), CWeightedIdentityScorer::ScoreAlignments(), CClippedScorer::ScoreAlignments(), CIgBlastTabularInfo::SetAirrFormatData(), sGenerateFields(), CDUpdater::update(), CTableDataAlnSummary::x_GetAlnSummary(), CBlastTabularInfo::x_SetQueryCovSeqalign(), CBlastTabularInfo::x_SetQueryCovSubject(), and CBlastTabularInfo::x_SetQueryCovUniqSubject().

◆ GetNamedScore() [3/4]

bool CSeq_align::GetNamedScore	(	EScoreType	type,
		double &	score
	)		const

Definition at line 600 of file Seq_align.cpp.

References GetNamedScore(), and sc_ScoreNames.

◆ GetNamedScore() [4/4]

bool CSeq_align::GetNamedScore	(	EScoreType	type,
		int &	score
	)		const

Definition at line 595 of file Seq_align.cpp.

References GetNamedScore(), and sc_ScoreNames.

◆ GetNonFrameshifts()

vector< CSeq_align::SIndel > CSeq_align::GetNonFrameshifts ( TDim row = -1 ) const

Retrieves descriptions of all non-frameshift indels on a given row; i.e.

all gaps with a length that is a multiple of 3.

Exceptions

CSeqalignException if alignment type is not supported

Definition at line 1759 of file Seq_align.cpp.

References COpenRange< TSeqPos >::GetWhole(), row, and s_GetIndels().

◆ GetNonFrameshiftsWithinRange()

vector< CSeq_align::SIndel > CSeq_align::GetNonFrameshiftsWithinRange	(	const TSeqRange &	range,
		TDim	row = `-1`
	)		const

Definition at line 1765 of file Seq_align.cpp.

References compile_time_bits::range(), row, and s_GetIndels().

Referenced by CTabularFormatter_Indels::Print().

◆ GetNonFrameshiftsWithinRanges()

vector< CSeq_align::SIndel > CSeq_align::GetNonFrameshiftsWithinRanges	(	const CRangeCollection< TSeqPos > &	ranges,
		TDim	row = `-1`
	)		const

Definition at line 1771 of file Seq_align.cpp.

References row, and s_GetIndels().

◆ GetNumFrameshifts()

TSeqPos CSeq_align::GetNumFrameshifts ( TDim row = -1 ) const

Retrieves the number of times a given row shifts frames; i.e.

the number of gaps with a length that is not a multiple of 3.

Exceptions

CSeqalignException if alignment type is not supported

Definition at line 1716 of file Seq_align.cpp.

References COpenRange< TSeqPos >::GetWhole(), row, and s_GetIndels().

Referenced by CScore_FrameShifts::Get(), and SAlignmentScoringModel::GetScore().

◆ GetNumFrameshiftsWithinRange()

TSeqPos CSeq_align::GetNumFrameshiftsWithinRange	(	const TSeqRange &	range,
		TDim	row = `-1`
	)		const

Definition at line 1725 of file Seq_align.cpp.

References compile_time_bits::range(), row, and s_GetIndels().

Referenced by CScore_FrameShifts::Get().

◆ GetNumFrameshiftsWithinRanges()

TSeqPos CSeq_align::GetNumFrameshiftsWithinRanges	(	const CRangeCollection< TSeqPos > &	ranges,
		TDim	row = `-1`
	)		const

Definition at line 1733 of file Seq_align.cpp.

References row, and s_GetIndels().

◆ GetNumGapOpenings()

TSeqPos CSeq_align::GetNumGapOpenings ( TDim row = -1 ) const

Retrieves the number of gap openings in a given row in an alignment (ignoring how many gaps are in the gapped region); all gaps by default.

Exceptions

CSeqalignException if alignment type is not supported

Definition at line 1557 of file Seq_align.cpp.

References COpenRange< TSeqPos >::GetWhole(), row, and s_GetGapCount().

Referenced by CScore_GapCount::Get(), CScore_FrameShifts::Get(), CScoreBuilderBase::GetGapCount(), SAlignmentScoringModel::GetScore(), and CTabularFormatter_GapCount::Print().

◆ GetNumGapOpeningsWithinRange()

TSeqPos CSeq_align::GetNumGapOpeningsWithinRange	(	const TSeqRange &	range,
		TDim	row = `-1`
	)		const

Definition at line 1570 of file Seq_align.cpp.

References compile_time_bits::range(), row, and s_GetGapCount().

Referenced by CScore_FrameShifts::Get(), and CScoreBuilderBase::GetGapCount().

◆ GetNumGapOpeningsWithinRanges()

TSeqPos CSeq_align::GetNumGapOpeningsWithinRanges	(	const CRangeCollection< TSeqPos > &	ranges,
		TDim	row = `-1`
	)		const

Definition at line 1582 of file Seq_align.cpp.

References row, and s_GetGapCount().

Referenced by CScoreBuilderBase::GetGapCount(), and s_GetPercentIdentity().

◆ GetSeq_id()

const CSeq_id & CSeq_align::GetSeq_id ( TDim row ) const

Get seq-id (the first one if segments have different ids).

Throw exception if row is invalid.

Definition at line 317 of file Seq_align.cpp.

◆ GetSeqRange()

CRange< TSeqPos > CSeq_align::GetSeqRange ( TDim row ) const

GetSeqRange NB: On a Spliced-seg, in case the product-type is protein, these only return the amin part of Prot-pos.

The frame is ignored.

Definition at line 153 of file Seq_align.cpp.

Referenced by AlignLengthRatio(), AlnFromRangeAscendingSort(), BuildAlignDataSource(), CScore_Overlap::Get(), CScore_OverlapBoth::Get(), CScore_SegPct::Get(), CScore_Entropy::Get(), CSGAlignmentJob::GetAlignType(), GetSeqStart(), GetSeqStop(), CAlignFilter::Match(), SSeqAlignsBySize::operator()(), CAlignSort::SAlignExtractor::operator()(), PatchTargetSequence(), CTabularFormatter_AlignStart::Print(), CTabularFormatter_AlignEnd::Print(), CTabularFormatter_MismatchPositions::Print(), CTabularFormatter_GapRanges::Print(), CTabularFormatter_ExonIntrons::Print(), CTabularFormatter_AlignLengthRatio::Print(), CTabularFormatter_NearestGap::Print(), PrintSAM(), PrintTabular(), CFeatCompareJob_Align::Run(), CTestCompartApplication::Run(), CTestSingleAln_All::RunTest(), s_AlignDist(), s_GetAlignmentSpans_Exon(), s_GetAlignmentSpans_Span(), s_GetAlignmentTooltip(), s_GetCigarString(), s_Seq_align_Seq_loc(), CAlignCompare::SAlignment::SAlignment(), SCompartmentData::SCompartmentData(), CExpansionScorer::ScoreAlignments(), CHangScorer::ScoreAlignments(), CClippedScorer::ScoreAlignments(), sGenerateFields(), CLDS2_AnnotType_Hook::SkipObject(), CAlignCompare::SAlignment::Slice(), CFeatureGenerator::SImplementation::x_CheckMatch(), CQuerySet::x_ContainsAlignment(), CVecscreen::x_GetMatchType(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), COligoSpecificityCheck::x_IsPcrLengthInRange(), CUnorderedSplitter::x_MakeAlignmentPairUnique(), CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile(), CSGAlnQualityScore::x_RetrieveQualityMap(), COligoSpecificityCheck::x_SavePrimerInfo(), COligoSpecificityCheck::x_SequencesMappedToSameTarget(), and COligoSpecificityTemplate::x_SortHit().

◆ GetSeqStart()

TSeqPos CSeq_align::GetSeqStart ( TDim row ) const

Definition at line 252 of file Seq_align.cpp.

Referenced by CGBProjectHelper::AddProjectItemsFromRID(), BOOST_AUTO_TEST_CASE(), Compare(), CVecscreenRun::CFormatter::FormatResults(), CInstance::GapDistance(), CScore_AlignStartStop::Get(), GetUnalignedLength_3p(), GetUnalignedLength_5p(), CInstance::IsAlignmentContained(), CInstance::MergeIn(), compare_alignments_fwrev_first::operator()(), compare_alignments_revfw_first::operator()(), SAlignSortByQueryId::operator()(), CAlignSort::SAlignExtractor::operator()(), SCompareAlignments::operator()(), SFlybaseCompareAlignments::operator()(), CTabularFormatter_AlignStart::Print(), CTabularFormatter_AlignEnd::Print(), PrintSAM(), PrintTabular(), variation::CVariationUtil::Remap(), CTestSingleAln_All::RunTest(), ScorePositionSort::s_CompareSeqAlignByScoreAndPosition(), s_DJNotCompatible(), s_GetAlignmentMismatches(), s_GetIndels(), s_GetPolyA_genomic_priming(), s_SeqAlignInSet(), s_SeqAlignSetToXMLHsps(), CUnorderedSplitter::s_SortByQueryStart(), s_SortSeqAlignByQuery_Subjt(), s_SortSeqAlignByQueryMinus_Subjt(), COverlapScorer::ScoreAlignments(), CCommonComponentScorer::ScoreAlignments(), CIgBlastTabularInfo::SetAirrFormatData(), CAlignFormatUtil::SortHspByMasterStartAscending(), CAlignFormatUtil::SortHspBySubjectStartAscending(), CQuerySet::x_AlreadyContains(), CIgBlast::x_AnnotateC(), CIgBlast::x_AnnotateD(), CIgBlast::x_AnnotateDJ(), CIgBlast::x_AnnotateDomain(), CIgBlast::x_AnnotateJ(), CIgBlast::x_AnnotateV(), CInversionMergeAligner::x_CreateDiscAlignment(), CIgBlast::x_FillJDomain(), CTableDataAlnSummary::x_GetAlnSummary(), CPrimaryItem::x_GetStrForPrimary(), COligoSpecificityCheck::x_IsPcrLengthInRange(), CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile(), CSGAlnQualityScore::x_RetrieveQualityMap(), CMagicBlastResults::x_SetInfo(), CBlastTabularInfo::x_SetQueryCovSeqalign(), and CUpdateSeqPanel::x_SetUpdateTypes().

◆ GetSeqStop()

TSeqPos CSeq_align::GetSeqStop ( TDim row ) const

Definition at line 273 of file Seq_align.cpp.

References CSeq_align_Base::C_Segs::e_Dendiag, CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_Sparse, CSeq_align_Base::C_Segs::e_Spliced, CSeq_align_Base::C_Segs::e_Std, CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::GetSegs(), GetSeqRange(), CDense_seg::GetSeqStop(), CSparse_seg::GetSeqStop(), CSpliced_seg::GetSeqStop(), CSeq_align_Base::C_Segs::GetSparse(), CSeq_align_Base::C_Segs::GetSpliced(), CRange_Base::GetTo(), NCBI_THROW, and row.

Referenced by CGBProjectHelper::AddProjectItemsFromRID(), CVecscreenRun::CFormatter::FormatResults(), CInstance::GapDistance(), CScore_AlignStartStop::Get(), CScore_3PrimeUnaligned::Get(), GetUnalignedLength_3p(), GetUnalignedLength_5p(), CInstance::IsAlignmentContained(), CInstance::MergeIn(), SAlignSortByQueryId::operator()(), CAlignSort::SAlignExtractor::operator()(), SCompareAlignments::operator()(), SFlybaseCompareAlignments::operator()(), CTabularFormatter_AlignStart::Print(), CTabularFormatter_AlignEnd::Print(), variation::CVariationUtil::Remap(), CTestSingleAln_All::RunTest(), s_DJNotCompatible(), s_GetAlignmentMismatches(), s_GetIndels(), s_GetPolyA_genomic_priming(), s_SeqAlignInSet(), s_SeqAlignSetToXMLHsps(), s_SortSeqAlignByQuery_Subjt(), s_SortSeqAlignByQueryMinus_Subjt(), COverlapScorer::ScoreAlignments(), CCommonComponentScorer::ScoreAlignments(), CIgBlastTabularInfo::SetAirrFormatData(), CAlignFormatUtil::SortHspByMasterStartAscending(), CAlignFormatUtil::SortHspBySubjectStartAscending(), CQuerySet::x_AlreadyContains(), CIgBlast::x_AnnotateC(), CIgBlast::x_AnnotateD(), CIgBlast::x_AnnotateDJ(), CIgBlast::x_AnnotateDomain(), CIgBlast::x_AnnotateJ(), CIgBlast::x_AnnotateV(), CInversionMergeAligner::x_CreateDiscAlignment(), CIgBlast::x_FillJDomain(), CTableDataAlnSummary::x_GetAlnSummary(), CPrimaryItem::x_GetStrForPrimary(), COligoSpecificityCheck::x_IsPcrLengthInRange(), CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile(), CSGAlnQualityScore::x_RetrieveQualityMap(), CBlastTabularInfo::x_SetQueryCovSeqalign(), and CUpdateSeqPanel::x_SetUpdateTypes().

◆ GetSeqStrand()

ENa_strand CSeq_align::GetSeqStrand ( TDim row ) const

Get strand (the first one if segments have different strands).

Definition at line 294 of file Seq_align.cpp.

Referenced by CVecscreenRun::CFormatter::FormatResults(), CScoreBuilder::GetBlastScoreProtToNucl(), SAlignmentScoringModel::GetPolyA_length(), CProductStringBuilder::GetProductString(), GetTerminalPartialness(), GetUnalignedLength_3p(), GetUnalignedLength_5p(), CAlignGroup::GroupByStrand(), IntronLengthRange(), CInstance::IsAlignmentContained(), CMergeTreeThread::Main(), CTreeAlignMerger::Merge_AllAtOnce(), CTreeAlignMerger::Merge_Pairwise(), compare_alignments_fwrev_first::operator()(), compare_alignments_revfw_first::operator()(), CAlignSort::SAlignExtractor::operator()(), SCompareAlignments::operator()(), SFlybaseCompareAlignments::operator()(), PatchTargetSequence(), CTabularFormatter_AlignStart::Print(), CTabularFormatter_AlignEnd::Print(), CTabularFormatter_AlignStrand::Print(), CTabularFormatter_MismatchPositions::Print(), CTabularFormatter_ExonIntrons::Print(), PrintSAM(), PrintTabular(), ProjectExons(), CMergeyApp::Run(), CFeatCompareJob_Align::Run(), ScorePositionSort::s_CompareSeqAlignByScoreAndPosition(), s_ComputeTraceback(), s_GetAlignmentMismatches(), s_GetAlignmentTooltip(), s_GetCigarString(), s_GetSeqStrand(), s_SeqAlignSetToXMLHsps(), s_SortSeqAlignByQuery_Subjt(), s_SortSeqAlignByQueryMinus_Subjt(), CAlignCompare::SAlignment::SAlignment(), COverlapScorer::ScoreAlignments(), CIgBlastTabularInfo::SetAirrFormatData(), sGenerateFields(), CAlignmentAssistant::TranslateLocations(), CIgBlast::x_AnnotateC(), CIgBlast::x_AnnotateDomain(), CFeatureGenerator::SImplementation::x_CheckMatch(), CInversionMergeAligner::x_CreateDiscAlignment(), CIgBlast::x_FillJDomain(), CTableDataAlnSummary::x_GetAlnSummary(), CPrimaryItem::x_GetStrForPrimary(), CTreeAlignMerger::x_MakeMergeableGroups(), CVecscreen::x_MergeSeqalign(), CAlignFilter::x_Query_Op(), CTabularFormatter_DiscStrand::x_RecurseStrands(), CSGAlnQualityScore::x_RetrieveQualityMap(), and CMagicBlastResults::x_SetInfo().

◆ GetTotalGapCount()

TSeqPos CSeq_align::GetTotalGapCount ( TDim row = -1 ) const

Retrieves the total number of gaps in the given row an alignment; all gaps by default.

Exceptions

CSeqalignException if alignment type is not supported

Definition at line 1550 of file Seq_align.cpp.

References COpenRange< TSeqPos >::GetWhole(), row, and s_GetGapCount().

Referenced by CScore_GapCount::Get(), CScoreBuilderBase::GetGapBaseCount(), CTabularFormatter_GapBaseCount::Print(), and s_SeqAlignSetToXMLHsps().

◆ GetTotalGapCountWithinRange()

TSeqPos CSeq_align::GetTotalGapCountWithinRange	(	const TSeqRange &	range,
		TDim	row = `-1`
	)		const

Definition at line 1564 of file Seq_align.cpp.

References compile_time_bits::range(), row, and s_GetGapCount().

Referenced by CScoreBuilderBase::GetGapBaseCount().

◆ GetTotalGapCountWithinRanges()

TSeqPos CSeq_align::GetTotalGapCountWithinRanges	(	const CRangeCollection< TSeqPos > &	ranges,
		TDim	row = `-1`
	)		const

Definition at line 1576 of file Seq_align.cpp.

References row, and s_GetGapCount().

Referenced by CScoreBuilderBase::GetGapBaseCount().

◆ HelpText()

string CSeq_align::HelpText ( EScoreType score )

static

Definition at line 508 of file Seq_align.cpp.

References sc_ScoreHelpText.

Referenced by CScoreLookup::HelpText().

◆ IntronLengthRange()

CSeq_align::TLengthRange CSeq_align::IntronLengthRange ( ) const

Definition at line 2186 of file Seq_align.cpp.

References SLengthRange::AddLength(), eNa_strand_minus, CSpliced_exon_Base::GetGenomic_end(), CSpliced_exon_Base::GetGenomic_start(), COpenRange< Position >::GetLength(), CSeq_align_Base::GetSegs(), GetSeqStrand(), ITERATE, NCBI_THROW, NULL, and SLengthRange::range.

Referenced by CScore_MaxIntronLength::Get().

◆ IsIntegerScore()

bool CSeq_align::IsIntegerScore ( EScoreType score )

static

Definition at line 513 of file Seq_align.cpp.

References sc_IsInteger.

Referenced by CScoreBuilderBase::AddScore(), and CScoreLookup::IsIntegerScore().

◆ OffsetRow()

void CSeq_align::OffsetRow	(	TDim	row,
		TSignedSeqPos	offset
	)

Offset row's coords.

Definition at line 1332 of file Seq_align.cpp.

References CSeq_align_Base::C_Segs::e_Dendiag, CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_Std, NCBI_THROW, NON_CONST_ITERATE, offset, CDense_seg::OffsetRow(), row, CSeq_align_Base::C_Segs::SetDenseg(), and CSeq_align_Base::SetSegs().

Referenced by CFarPointerSeq::GetCommand(), and RemapToQueryLoc().

◆ operator=()

CSeq_align& CSeq_align::operator= ( const CSeq_align & value )

private

◆ RemapToLoc()

void CSeq_align::RemapToLoc	(	TDim	row,
		const CSeq_loc &	dst_loc,
		bool	ignore_strand = `false`
	)

Deprecated:: (use sequence::RemapAlignToLoc())

See also: RemapAlignToLoc

Deprecated:

Definition at line 1365 of file Seq_align.cpp.

References CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, CSeq_loc_Base::e_Int, CSeq_align_Base::C_Segs::e_Std, CSeq_loc_Base::e_Whole, NCBI_THROW, NON_CONST_ITERATE, CDense_seg::RemapToLoc(), row, CSeq_align_Base::C_Segs::SetDenseg(), CSeq_align_Base::SetSegs(), and CSeq_loc_Base::Which().

◆ ResetNamedScore() [1/2]

void CSeq_align::ResetNamedScore ( const string & name )

Definition at line 606 of file Seq_align.cpp.

References CSeq_align_Base::IsSetScore(), NON_CONST_ITERATE, and CSeq_align_Base::SetScore().

Referenced by CScoreBuilderBase::AddScore(), CFeatureGenerator::SImplementation::ClearScores(), CFeatureGenerator::SImplementation::RecalculateScores(), and ResetNamedScore().

◆ ResetNamedScore() [2/2]

void CSeq_align::ResetNamedScore ( EScoreType type )

Definition at line 619 of file Seq_align.cpp.

References ResetNamedScore(), and sc_ScoreNames.

◆ Reverse()

void CSeq_align::Reverse ( void )

Reverse the segments' orientation NOTE: currently *only* works for dense-seg.

--------------------------------------------------------------------------- PRE : currently only implemented for dense-seg segments POST: same alignment, opposite orientation

Definition at line 685 of file Seq_align.cpp.

References CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::GetSegs(), NCBI_THROW, CDense_seg::Reverse(), CSeq_align_Base::C_Segs::SetDenseg(), and CSeq_align_Base::SetSegs().

Referenced by CIgBlastTabularInfo::SetAirrFormatData(), COligoSpecificityCheck::x_AnalyzeOnePrimer(), and CVecscreen::x_MergeSeqalign().

◆ ScoreName()

string CSeq_align::ScoreName ( EScoreType score )

static

Definition at line 503 of file Seq_align.cpp.

References sc_ScoreNames, and SStaticPair< FirstType, SecondType >::second.

Referenced by CScoreBuilderBase::AddSplignScores(), and CScoreBuilderBase::ComputeScore().

◆ ScoreNameMap()

const CSeq_align::TScoreNameMap & CSeq_align::ScoreNameMap ( )

static

Definition at line 483 of file Seq_align.cpp.

References DEFINE_STATIC_FAST_MUTEX, map_checker< Container >::empty(), eScore_Blast, eScore_ExonIdentity, SStaticPair< FirstType, SecondType >::first, sc_ScoreNames, and SStaticPair< FirstType, SecondType >::second.

Referenced by CScoreBuilderBase::AddSplignScores(), CScoreLookup::Complexity(), CScoreLookup::GetScore(), CScoreLookup::HelpText(), CScoreLookup::IsIntegerScore(), and CScoreLookup::PrintDictionary().

◆ SetNamedScore() [1/4]

void CSeq_align::SetNamedScore	(	const string &	id,
		double	score
	)

Definition at line 642 of file Seq_align.cpp.

References x_SetNamedScore().

◆ SetNamedScore() [2/4]

void CSeq_align::SetNamedScore	(	const string &	id,
		int	score
	)

Definition at line 636 of file Seq_align.cpp.

References x_SetNamedScore().

Referenced by CScoreBuilderBase::AddScore(), AddStandardAlignmentScores(), CScoreBuilder::AddTieBreaker(), BOOST_AUTO_TEST_CASE(), CBlastAligner::GenerateAlignments(), CRemoteBlastAligner::GenerateAlignments(), CAlignModel::MakeSeqAlign(), MakeSubjectScores(), CDemoSeqQaApp::Run(), s_CreateSeqAlign(), CExpansionScorer::ScoreAlignments(), CWeightedIdentityScorer::ScoreAlignments(), CHangScorer::ScoreAlignments(), COverlapScorer::ScoreAlignments(), CClippedScorer::ScoreAlignments(), CCommonComponentScorer::ScoreAlignments(), CAdvancedAlignCleanup::x_AddStandardAlignmentScores(), CPssmCddInputTest::x_CreateAlignment(), CInversionMergeAligner::x_CreateDiscAlignment(), CVecscreen::x_MergeSeqalign(), CMergeAligner::x_MergeSeqAlignSet(), CInstancedAligner::x_RunAligner(), and CGff2Reader::xAlignmentSetScore().

◆ SetNamedScore() [3/4]

void CSeq_align::SetNamedScore	(	EScoreType	type,
		double	score
	)

Definition at line 630 of file Seq_align.cpp.

References sc_ScoreNames, and x_SetNamedScore().

◆ SetNamedScore() [4/4]

void CSeq_align::SetNamedScore	(	EScoreType	type,
		int	score
	)

Definition at line 624 of file Seq_align.cpp.

References sc_ScoreNames, and x_SetNamedScore().

◆ SplitOnLongDiscontinuity()

void CSeq_align::SplitOnLongDiscontinuity	(	list< CRef< CSeq_align > > &	aligns,
		TSeqPos	discontinuity_threshold
	)		const

Split the alignment at any discontinuity greater than threshold; populate aligns list with new alignments.

If alignment contains no long discontinuities, populate aligns list with a singleton reference to self. Splitting works only for Denseg and Disc; for all other segment types, this function simply populates aligns with a singleton reference to self. This function is only implemented for pairwise alignments; it throws an exception if Dim is more than 2.

Definition at line 1217 of file Seq_align.cpp.

References CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, COpenRange< Position >::Empty(), eUnknown, CSeq_align_set_Base::Get(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::GetDim(), CSeq_align_Base::C_Segs::GetDisc(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CSeq_align_Base::GetSegs(), CDense_seg_Base::GetStarts(), CSeq_align_Base::IsSetDim(), ITERATE, NCBI_THROW, COpenRange< Position >::NotEmpty(), s_Distance(), s_GetJoinedAlignment(), CSeq_align_set_Base::Set(), and x_CreateSubsegAlignment().

◆ SwapRows()

void CSeq_align::SwapRows	(	TDim	row1,
		TDim	row2
	)

Swap the position of two rows in the alignment NOTE: currently *only* works for dense-seg & disc.

--------------------------------------------------------------------------- PRE : currently only implemented for dense-seg segments; two row numbers POST: same alignment, position of the two rows has been swapped

Definition at line 701 of file Seq_align.cpp.

References CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_Std, CSeq_align_Base::GetSegs(), NCBI_THROW, NON_CONST_ITERATE, CSeq_align_Base::C_Segs::SetDenseg(), CSeq_align_Base::C_Segs::SetDisc(), CSeq_align_Base::SetSegs(), CDense_seg::SwapRows(), and CSeq_align_set::SwapRows().

◆ Validate()

void CSeq_align::Validate ( bool full_test = false ) const

Definition at line 649 of file Seq_align.cpp.

References CheckNumRows(), CSeq_align_Base::C_Segs::e_Dendiag, CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_Sparse, CSeq_align_Base::C_Segs::e_Spliced, CSeq_align_Base::C_Segs::e_Std, Get(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::GetSparse(), CSeq_align_Base::C_Segs::GetSpliced(), ITERATE, NCBI_THROW, CDense_seg::Validate(), CSparse_seg::Validate(), and CSpliced_seg::Validate().

Referenced by BOOST_AUTO_TEST_CASE(), CreateDensegFromDisc(), CAlignCleanup::CreatePairwiseFromMultiple(), CAlnContainer::insert(), CAlnBuildApp::InsertAln(), CAlnTestApp::InsertAln(), CPairwiseAlnApp::InsertAln(), LoadAligns(), CAnnotationASN1::CImplementationData::model2spliced_seq_align(), CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()(), CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::push_back(), s_GetJoinedAlignment(), CGff3Writer::WriteAlign(), CAlignCleanup::x_Cleanup_AnchoredAln(), CMergeAlignmentsJob::x_CreateProjectItems(), x_CreateSubsegAlignment(), and CTreeAlignMerger::x_MakeSeqAlign().

◆ x_CreateSubsegAlignment()

CRef< CSeq_align > CSeq_align::x_CreateSubsegAlignment	(	int	from,
		int	to
	)		const

private

Create a partial alignment containing the specified range of segments.

Can only be called for Denseg alignments.

Definition at line 2230 of file Seq_align.cpp.

Referenced by SplitOnLongDiscontinuity().

◆ x_GetNamedScore()

CConstRef< CScore > CSeq_align::x_GetNamedScore ( const string & name ) const

protected

retrieve a named score object

Definition at line 520 of file Seq_align.cpp.

References CSeq_align_Base::GetScore(), CSeq_align_Base::IsSetScore(), and ITERATE.

Referenced by GetNamedScore().

◆ x_SetNamedScore()

CRef< CScore > CSeq_align::x_SetNamedScore ( const string & name )

protected

Definition at line 537 of file Seq_align.cpp.

References CSeq_align_Base::IsSetScore(), NON_CONST_ITERATE, CRef< C, Locker >::Reset(), and CSeq_align_Base::SetScore().

Referenced by SetNamedScore().

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

include/objects/seqalign/Seq_align.hpp
src/objects/seqalign/Seq_align.cpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Types

Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TLengthRange

◆ Tparent

◆ TScoreNameMap

Member Enumeration Documentation

◆ EScoreType

Constructor & Destructor Documentation

◆ CSeq_align() [1/2]

◆ ~CSeq_align()

◆ CSeq_align() [2/2]

Member Function Documentation

◆ AlignLengthRatio()

◆ CheckNumRows()

◆ CreateDensegFromDisc()

◆ CreateDensegFromStdseg()

◆ CreateRowSeq_loc()

◆ CreateTranslatedDensegFromNADenseg()

◆ ExonLengthRange()

◆ FindExt() [1/2]

◆ FindExt() [2/2]

◆ GapLengthRange()

◆ GetAlignedBases()

◆ GetAlignLength()

◆ GetAlignLengthWithinRange()

◆ GetAlignLengthWithinRanges()

◆ GetFrameshifts()

◆ GetFrameshiftsWithinRange()

◆ GetFrameshiftsWithinRanges()

◆ GetIndels()

◆ GetIndelsWithinRange()

◆ GetIndelsWithinRanges()

◆ GetNamedScore() [1/4]

◆ GetNamedScore() [2/4]

◆ GetNamedScore() [3/4]

◆ GetNamedScore() [4/4]

◆ GetNonFrameshifts()

◆ GetNonFrameshiftsWithinRange()

◆ GetNonFrameshiftsWithinRanges()

◆ GetNumFrameshifts()

◆ GetNumFrameshiftsWithinRange()

◆ GetNumFrameshiftsWithinRanges()

◆ GetNumGapOpenings()

◆ GetNumGapOpeningsWithinRange()

◆ GetNumGapOpeningsWithinRanges()

◆ GetSeq_id()

◆ GetSeqRange()

◆ GetSeqStart()

◆ GetSeqStop()

◆ GetSeqStrand()

◆ GetTotalGapCount()

◆ GetTotalGapCountWithinRange()

◆ GetTotalGapCountWithinRanges()

◆ HelpText()

◆ IntronLengthRange()

◆ IsIntegerScore()

◆ OffsetRow()

◆ operator=()

◆ RemapToLoc()

◆ ResetNamedScore() [1/2]

◆ ResetNamedScore() [2/2]

◆ Reverse()

◆ ScoreName()

◆ ScoreNameMap()

◆ SetNamedScore() [1/4]

◆ SetNamedScore() [2/4]

◆ SetNamedScore() [3/4]

◆ SetNamedScore() [4/4]

◆ SplitOnLongDiscontinuity()

◆ SwapRows()

◆ Validate()

◆ x_CreateSubsegAlignment()