Search Toolkit Book for CAgpRow

A container for both the original string column values (Get*() methods) and the values converted to int, char, bool types (member variables). More...

#include <objtools/readers/agp_util.hpp>

Inheritance diagram for CAgpRow:

Collaboration diagram for CAgpRow:

Public Types
enum	EOrientation { eOrientationPlus = 43 , eOrientationMinus = 45 , eOrientationUnknown = 48 , eOrientationIrrelevant = 110 }

enum	EGap { eGapClone , eGapFragment , eGapRepeat , eGapScaffold , eGapContamination , eGapContig , eGapCentromere , eGapShort_arm , eGapHeterochromatin , eGapTelomere , eGapCount , eGapYes_count =eGapContamination+1 }

enum	ELinkageEvidence { fLinkageEvidence_paired_ends = (1 << 0) , fLinkageEvidence_align_genus = (1 << 1) , fLinkageEvidence_align_xgenus = (1 << 2) , fLinkageEvidence_align_trnscpt = (1 << 3) , fLinkageEvidence_within_clone = (1 << 4) , fLinkageEvidence_clone_contig = (1 << 5) , fLinkageEvidence_map = (1 << 6) , fLinkageEvidence_strobe = (1 << 7) , fLinkageEvidence_pcr = (1 << 8) , fLinkageEvidence_proximity_ligation = (1 << 9) , fLinkageEvidence_HIGHEST_BIT_MASK = fLinkageEvidence_proximity_ligation , fLinkageEvidence_unspecified = 0 , fLinkageEvidence_INVALID = -1 , fLinkageEvidence_na = -2 }

typedef vector< ELinkageEvidence >	TLinkageEvidenceVec
	Might have duplicates, and is empty on error or if there are no actual linkage evidences (e.g. More...

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
virtual	~CAgpRow ()

CRef< CAgpRow >	Clone (void) const

int	FromString (const string &line)

string	GetErrorMessage ()

string	ToString (bool reorder_linkage_evidences=false)

string &	GetObject ()

string &	GetObjectBeg ()

string &	GetObjectEnd ()

string &	GetPartNumber ()

string &	GetComponentType ()

string &	GetComponentId ()

string &	GetComponentBeg ()

string &	GetComponentEnd ()

string &	GetOrientation ()

string &	GetGapLength ()

string &	GetGapType ()

string &	GetLinkage ()

string &	GetLinkageEvidence ()

bool	IsGap () const

bool	IsDraftComponent ()

bool	GapEndsScaffold () const

bool	GapValidAtObjectEnd () const

bool	CheckComponentEnd (TAgpLen comp_len)

string	LinkageEvidencesToString (void)

string	LinkageEvidenceFlagsToString ()

string	SubstOldGap (bool do_subst)
	Returns a string describing suggested replacement, or "" if none is needed. More...

string	OrientationToString (EOrientation orientation)

virtual void	SetVersion (EAgpVersion ver)

CAgpErr *	GetErrorHandler ()

void	SetErrorHandler (CAgpErr *arg)

EAgpVersion	GetVersion ()

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...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. 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 CRef< CAgpRow >	New (CAgpErr arg, EAgpVersion agp_version=eAgpVersion_auto, CAgpReader reader=nullptr)

static CRef< CAgpRow >	New (EAgpVersion agp_version=eAgpVersion_auto, CAgpReader *reader=nullptr)

static bool	IsGap (char c)

static bool	IsDraftComponent (char c)

static bool	GapValidAtObjectEnd (EGap gap_type)

static bool	CheckComponentEnd (const string &comp_id, TAgpPos comp_end, TAgpLen comp_len, CAgpErr &agp_err)

static string	LinkageEvidenceFlagsToString (int le)

static const char *	le_str (ELinkageEvidence le)

static int	str_to_le (const string &str)

static const char *	GapTypeToString (int i)

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)

Public Attributes
SIZE_TYPE	pcomment

vector< string >	cols

TAgpPos	object_beg

TAgpPos	object_end

TAgpPos	part_number

char	component_type

bool	is_gap

TAgpPos	component_beg

TAgpPos	component_end

EOrientation	orientation

TAgpLen	gap_length

EGap	gap_type

bool	linkage

TLinkageEvidenceVec	linkage_evidences

int	linkage_evidence_flags
	a bit map which holds summary of info in linkage_evidences. More...

Protected Types
typedef const char *	TStr

typedef map< string, EGap >	TMapStrEGap

Protected Member Functions
	CAgpRow (CAgpErr arg, EAgpVersion agp_version=eAgpVersion_auto, CAgpReader reader=nullptr)

	CAgpRow (EAgpVersion agp_version=eAgpVersion_auto, CAgpReader *reader=nullptr)

	CAgpRow (const CAgpRow &)

TAgpPos	ReadSeqPos (const CTempString seq_pos_str, const string &details, int *perror_code, bool log_errors=true)

int	ParseComponentCols (bool log_errors=true)

int	ParseGapCols (bool log_errors=true)

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

Static Protected Member Functions
static TMapStrEGap *	gap_type_codes_creator (void)

Static Protected Attributes
static const TStr	gap_types [eGapCount]

static CSafeStatic< TMapStrEGap >	gap_type_codes

Private Attributes
EAgpVersion	m_agp_version

CAgpReader *	m_reader

CRef< CAgpErr >	m_AgpErr

Additional Inherited Members
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

A container for both the original string column values (Get*() methods) and the values converted to int, char, bool types (member variables).

Detects formatting errors within a single line, checks that object range length equals gap length or component range length.

Definition at line 71 of file agp_util.hpp.

Member Typedef Documentation

◆ TLinkageEvidenceVec

typedef vector<ELinkageEvidence> CAgpRow::TLinkageEvidenceVec

Might have duplicates, and is empty on error or if there are no actual linkage evidences (e.g.

"na" or "unspecified") It does NOT hold unusual values like fLinkageEvidence_INVALID.

Definition at line 215 of file agp_util.hpp.

◆ TMapStrEGap

typedef map<string, EGap> CAgpRow::TMapStrEGap

protected

Definition at line 294 of file agp_util.hpp.

◆ TStr

typedef const char* CAgpRow::TStr

protected

Definition at line 291 of file agp_util.hpp.

Member Enumeration Documentation

◆ EGap

enum CAgpRow::EGap

Enumerator
eGapClone
eGapFragment
eGapRepeat
eGapScaffold
eGapContamination
eGapContig
eGapCentromere
eGapShort_arm
eGapHeterochromatin
eGapTelomere
eGapCount
eGapYes_count

Definition at line 175 of file agp_util.hpp.

◆ ELinkageEvidence

enum CAgpRow::ELinkageEvidence

Enumerator
fLinkageEvidence_paired_ends
fLinkageEvidence_align_genus
fLinkageEvidence_align_xgenus
fLinkageEvidence_align_trnscpt
fLinkageEvidence_within_clone
fLinkageEvidence_clone_contig
fLinkageEvidence_map
fLinkageEvidence_strobe
fLinkageEvidence_pcr
fLinkageEvidence_proximity_ligation
fLinkageEvidence_HIGHEST_BIT_MASK
fLinkageEvidence_unspecified
fLinkageEvidence_INVALID
fLinkageEvidence_na

Definition at line 194 of file agp_util.hpp.

◆ EOrientation

enum CAgpRow::EOrientation

Enumerator
eOrientationPlus
eOrientationMinus
eOrientationUnknown
eOrientationIrrelevant

Definition at line 159 of file agp_util.hpp.

Constructor & Destructor Documentation

◆ CAgpRow() [1/3]

CAgpRow::CAgpRow	(	CAgpErr *	arg,
		EAgpVersion	agp_version = `eAgpVersion_auto`,
		CAgpReader *	reader = `nullptr`
	)

protected

Definition at line 381 of file agp_util.cpp.

Referenced by Clone(), and New().

◆ CAgpRow() [2/3]

CAgpRow::CAgpRow	(	EAgpVersion	agp_version = `eAgpVersion_auto`,
		CAgpReader *	reader = `nullptr`
	)

protected

Definition at line 375 of file agp_util.cpp.

◆ CAgpRow() [3/3]

CAgpRow::CAgpRow ( const CAgpRow & src )

protected

Definition at line 387 of file agp_util.cpp.

◆ ~CAgpRow()

CAgpRow::~CAgpRow ( )

virtual

Definition at line 394 of file agp_util.cpp.

Member Function Documentation

◆ CheckComponentEnd() [1/2]

bool CAgpRow::CheckComponentEnd	(	const string &	comp_id,
		TAgpPos	comp_end,
		TAgpLen	comp_len,
		CAgpErr &	agp_err
	)

static

Definition at line 846 of file agp_util.cpp.

References CAgpErr::G_CompEndGtLength, i2s, and CAgpErr::Msg().

Referenced by CheckComponentEnd(), CAgpValidateReader::OnGapOrComponent(), CAltValidator::ProcessQueue(), and CAgpValidateApplication::x_ValidateFile().

◆ CheckComponentEnd() [2/2]

bool CAgpRow::CheckComponentEnd ( TAgpLen comp_len )

inline

Definition at line 262 of file agp_util.hpp.

References CheckComponentEnd(), component_end, GetComponentId(), and m_AgpErr.

◆ Clone()

CRef<CAgpRow> CAgpRow::Clone ( void ) const

inline

Definition at line 103 of file agp_util.hpp.

References CAgpRow(), and Ref().

Referenced by CAgpCompSpanSplitter::SaveRow().

◆ FromString()

int CAgpRow::FromString ( const string & line )

Definition at line 423 of file agp_util.cpp.

References cols, component_beg, component_end, component_type, CAgpErr::E_ColumnCount, CAgpErr::E_EmptyColumn, CAgpErr::E_EmptyLine, CAgpErr::E_InvalidValue, CAgpErr::E_MustBePositive, CAgpErr::E_ObjEndLtBeg, CAgpErr::E_ObjRangeNeComp, CAgpErr::E_ObjRangeNeGap, eAgpVersion_1_1, eAgpVersion_2_0, gap_length, GetComponentType(), GetObjectBeg(), GetObjectEnd(), GetPartNumber(), i, i2s, is_gap, m_agp_version, m_AgpErr, CAgpErr::Msg(), NcbiEmptyString, NPOS, object_beg, object_end, ParseComponentCols(), ParseGapCols(), part_number, pcomment, ReadSeqPos(), ncbi::grid::netcache::search::fields::size, NStr::Split(), CAgpErr::W_ExtraTab, CAgpErr::W_GapLineIgnoredCol9, CAgpErr::W_LooksLikeComp, and CAgpErr::W_LooksLikeGap.

Referenced by CAgpReader::ReadStream(), CAgpCompSpanSplitter::SaveRow(), and CAgpValidateApplication::x_ValidateFile().

◆ gap_type_codes_creator()

CAgpRow::TMapStrEGap * CAgpRow::gap_type_codes_creator ( void )

staticprotected

Definition at line 362 of file agp_util.cpp.

◆ GapEndsScaffold()

bool CAgpRow::GapEndsScaffold ( ) const

inline

Definition at line 247 of file agp_util.hpp.

References eGapFragment, gap_type, and linkage.

Referenced by CAgpReader::Finalize(), CAgpValidateReader::OnGapOrComponent(), ParseGapCols(), and CAgpReader::ProcessThisRow().

◆ GapTypeToString()

static const char* CAgpRow::GapTypeToString ( int i )

inlinestatic

Definition at line 311 of file agp_util.hpp.

References eGapCount, gap_types, i, and NcbiEmptyCStr.

Referenced by CAgpValidateReader::x_PrintGapCountsLine().

◆ GapValidAtObjectEnd() [1/2]

bool CAgpRow::GapValidAtObjectEnd ( ) const

inline

Definition at line 253 of file agp_util.hpp.

References gap_type.

◆ GapValidAtObjectEnd() [2/2]

static bool CAgpRow::GapValidAtObjectEnd ( EGap gap_type )

inlinestatic

Definition at line 230 of file agp_util.hpp.

References eGapCentromere, eGapContamination, eGapHeterochromatin, eGapShort_arm, eGapTelomere, and gap_type.

Referenced by CAgpReader::Finalize(), and CAgpReader::ProcessThisRow().

◆ GetComponentBeg()

string& CAgpRow::GetComponentBeg ( )

inline

Definition at line 127 of file agp_util.hpp.

References cols.

Referenced by ParseComponentCols().

◆ GetComponentEnd()

string& CAgpRow::GetComponentEnd ( )

inline

Definition at line 128 of file agp_util.hpp.

References cols.

Referenced by ParseComponentCols().

◆ GetComponentId()

string& CAgpRow::GetComponentId ( )

inline

Definition at line 126 of file agp_util.hpp.

References cols.

Referenced by CheckComponentEnd(), CAgpValidateReader::OnGapOrComponent(), CAgpToSeqEntry::OnGapOrComponent(), CAgpValidateReader::OnScaffoldEnd(), ToString(), and CAgpValidateApplication::x_ValidateFile().

◆ GetComponentType()

string& CAgpRow::GetComponentType ( void )

inline

Definition at line 124 of file agp_util.hpp.

References cols.

Referenced by FromString(), and CAgpValidateReader::OnGapOrComponent().

◆ GetErrorHandler()

CAgpErr* CAgpRow::GetErrorHandler ( void )

inline

Definition at line 308 of file agp_util.hpp.

References m_AgpErr.

Referenced by CCompVal::init().

◆ GetErrorMessage()

string CAgpRow::GetErrorMessage ( )

Definition at line 836 of file agp_util.cpp.

References CAgpErr::GetErrorMessage(), and m_AgpErr.

◆ GetGapLength()

string& CAgpRow::GetGapLength ( )

inline

Definition at line 139 of file agp_util.hpp.

References cols.

Referenced by ParseGapCols().

◆ GetGapType()

string& CAgpRow::GetGapType ( void )

inline

Definition at line 140 of file agp_util.hpp.

References cols.

Referenced by ParseGapCols().

◆ GetLinkage()

string& CAgpRow::GetLinkage ( void )

inline

Definition at line 141 of file agp_util.hpp.

References cols.

Referenced by ParseGapCols().

◆ GetLinkageEvidence()

string& CAgpRow::GetLinkageEvidence ( )

inline

Definition at line 142 of file agp_util.hpp.

References cols, and NcbiEmptyString.

Referenced by ParseGapCols().

◆ GetObject()

string& CAgpRow::GetObject ( void )

inline

Definition at line 120 of file agp_util.hpp.

References cols.

Referenced by CAgpReader::Finalize(), CAgpValidateReader::OnGapOrComponent(), CAgpRenumber::OnGapOrComponent(), CAgpToSeqEntry::OnGapOrComponent(), CAgpValidateReader::OnObjectChange(), CAgpRenumber::OnObjectChange(), CAgpValidateReader::OnScaffoldEnd(), CAgpReader::ProcessThisRow(), CAgpCompSpanSplitter::SaveRow(), and ToString().

◆ GetObjectBeg()

string& CAgpRow::GetObjectBeg ( )

inline

Definition at line 121 of file agp_util.hpp.

References cols.

Referenced by FromString().

◆ GetObjectEnd()

string& CAgpRow::GetObjectEnd ( )

inline

Definition at line 122 of file agp_util.hpp.

References cols.

Referenced by FromString().

◆ GetOrientation()

string& CAgpRow::GetOrientation ( void )

inline

Definition at line 129 of file agp_util.hpp.

References cols, and NcbiEmptyString.

Referenced by ParseComponentCols().

◆ GetPartNumber()

string& CAgpRow::GetPartNumber ( void )

inline

Definition at line 123 of file agp_util.hpp.

References cols.

Referenced by FromString().

◆ GetVersion()

EAgpVersion CAgpRow::GetVersion ( void )

inline

Definition at line 317 of file agp_util.hpp.

References m_agp_version.

Referenced by CAgpCompSpanSplitter::SaveRow().

◆ IsDraftComponent() [1/2]

bool CAgpRow::IsDraftComponent ( )

inline

Definition at line 242 of file agp_util.hpp.

References component_type.

◆ IsDraftComponent() [2/2]

static bool CAgpRow::IsDraftComponent ( char c )

inlinestatic

Definition at line 225 of file agp_util.hpp.

Referenced by CAgpValidateReader::OnGapOrComponent().

◆ IsGap() [1/2]

bool CAgpRow::IsGap ( void ) const

inline

Definition at line 238 of file agp_util.hpp.

References is_gap.

Referenced by CAgpValidateReader::x_PrintTotals().

◆ IsGap() [2/2]

static bool CAgpRow::IsGap ( char c )

inlinestatic

Definition at line 221 of file agp_util.hpp.

Referenced by CAgpValidateReader::OnGapOrComponent(), CAgpRenumber::OnGapOrComponent(), and CAgpValidateApplication::x_ValidateFile().

◆ le_str()

const char * CAgpRow::le_str ( CAgpRow::ELinkageEvidence le )

static

◆ LinkageEvidenceFlagsToString() [1/2]

string CAgpRow::LinkageEvidenceFlagsToString ( )

inline

Definition at line 270 of file agp_util.hpp.

References linkage_evidence_flags.

Referenced by ToString(), and CAgpValidateReader::x_PrintTotals().

◆ LinkageEvidenceFlagsToString() [2/2]

string CAgpRow::LinkageEvidenceFlagsToString ( int le )

static

Definition at line 886 of file agp_util.cpp.

References fLinkageEvidence_HIGHEST_BIT_MASK, le(), le_str(), and mask.

◆ LinkageEvidencesToString()

string CAgpRow::LinkageEvidencesToString ( void )

Definition at line 899 of file agp_util.cpp.

References i2s, ITERATE, le(), le_str(), linkage, linkage_evidences, and result.

Referenced by ToString().

◆ New() [1/2]

static CRef<CAgpRow> CAgpRow::New	(	CAgpErr *	arg,
		EAgpVersion	agp_version = `eAgpVersion_auto`,
		CAgpReader *	reader = `nullptr`
	)

inlinestatic

Definition at line 90 of file agp_util.hpp.

References CAgpRow(), and Ref().

Referenced by CAgpReader::Init(), CAgpCompSpanSplitter::SaveRow(), and CAgpValidateApplication::x_ValidateFile().

◆ New() [2/2]

static CRef<CAgpRow> CAgpRow::New	(	EAgpVersion	agp_version = `eAgpVersion_auto`,
		CAgpReader *	reader = `nullptr`
	)

inlinestatic

Definition at line 97 of file agp_util.hpp.

References CAgpRow(), and Ref().

◆ OrientationToString()

string CAgpRow::OrientationToString ( EOrientation orientation )

Definition at line 916 of file agp_util.cpp.

References eAgpVersion_1_1, eOrientationIrrelevant, eOrientationMinus, eOrientationPlus, eOrientationUnknown, i2s, m_agp_version, and orientation.

Referenced by ToString().

◆ ParseComponentCols()

int CAgpRow::ParseComponentCols ( bool log_errors = true )

protected

Definition at line 602 of file agp_util.cpp.

References component_beg, component_end, CAgpErr::E_CompEndLtBeg, CAgpErr::E_InvalidValue, eAgpVersion_1_1, eAgpVersion_2_0, eOrientationIrrelevant, eOrientationMinus, eOrientationPlus, eOrientationUnknown, GetComponentBeg(), GetComponentEnd(), GetOrientation(), m_agp_version, m_AgpErr, CAgpErr::Msg(), orientation, ReadSeqPos(), ncbi::grid::netcache::search::fields::size, and CAgpErr::W_OrientationZeroDeprecated.

Referenced by FromString().

◆ ParseGapCols()

int CAgpRow::ParseGapCols ( bool log_errors = true )

protected

Definition at line 670 of file agp_util.cpp.

References component_type, CAgpErr::E_InvalidLinkage, CAgpErr::E_InvalidValue, eAgpVersion_1_1, eAgpVersion_2_0, eAgpVersion_auto, eGapClone, eGapContamination, eGapFragment, eGapRepeat, eGapScaffold, fLinkageEvidence_INVALID, fLinkageEvidence_na, fLinkageEvidence_unspecified, gap_length, gap_type, gap_type_codes, GapEndsScaffold(), GetGapLength(), GetGapType(), GetLinkage(), GetLinkageEvidence(), ITERATE, linkage, linkage_evidence_flags, linkage_evidences, m_agp_version, m_AgpErr, m_reader, CAgpErr::Msg(), ReadSeqPos(), CAgpReader::SetVersion(), ncbi::grid::netcache::search::fields::size, NStr::Split(), str_to_le(), SubstOldGap(), CAgpErr::W_AssumingVersion, CAgpErr::W_DuplicateEvidence, CAgpErr::W_GapSizeNot100, CAgpErr::W_MissingLinkage, CAgpErr::W_NaLinkageExpected, and CAgpErr::W_OldGapType.

Referenced by FromString().

◆ ReadSeqPos()

TAgpPos CAgpRow::ReadSeqPos	(	const CTempString	seq_pos_str,
		const string &	details,
		int *	perror_code,
		bool	log_errors = `true`
	)

protected

Definition at line 398 of file agp_util.cpp.

References CAgpErr::E_MustBePositive, CAgpErr::E_MustFitSeqPosType, NStr::fConvErr_NoThrow, m_AgpErr, max(), CAgpErr::Msg(), and NStr::StringToInt8().

Referenced by FromString(), ParseComponentCols(), and ParseGapCols().

◆ SetErrorHandler()

void CAgpRow::SetErrorHandler ( CAgpErr * arg )

Definition at line 841 of file agp_util.cpp.

References m_AgpErr.

Referenced by CAgpReader::SetErrorHandler().

◆ SetVersion()

void CAgpRow::SetVersion ( EAgpVersion ver )

virtual

Definition at line 962 of file agp_util.cpp.

References m_agp_version.

Referenced by CAgpReader::SetVersion(), and CAgpReader::x_CheckPragmaComment().

◆ str_to_le()

int CAgpRow::str_to_le ( const string & str )

static

Definition at line 653 of file agp_util.cpp.

References fLinkageEvidence_align_genus, fLinkageEvidence_align_trnscpt, fLinkageEvidence_align_xgenus, fLinkageEvidence_clone_contig, fLinkageEvidence_INVALID, fLinkageEvidence_map, fLinkageEvidence_paired_ends, fLinkageEvidence_pcr, fLinkageEvidence_proximity_ligation, fLinkageEvidence_strobe, fLinkageEvidence_unspecified, fLinkageEvidence_within_clone, and str().

Referenced by ParseGapCols().

◆ SubstOldGap()

string CAgpRow::SubstOldGap ( bool do_subst )

Returns a string describing suggested replacement, or "" if none is needed.

Use do_subst=true to do the actial substitution in this object.

Definition at line 933 of file agp_util.cpp.

References eGapClone, eGapContig, eGapFragment, eGapScaffold, fLinkageEvidence_clone_contig, fLinkageEvidence_paired_ends, fLinkageEvidence_unspecified, fLinkageEvidence_within_clone, gap_type, le(), le_str(), linkage, linkage_evidence_flags, linkage_evidences, NcbiEmptyString, and string.

Referenced by ParseGapCols().

◆ ToString()

string CAgpRow::ToString ( bool reorder_linkage_evidences = false )

Definition at line 805 of file agp_util.cpp.

References component_beg, component_end, component_type, eAgpVersion_1_1, gap_length, gap_type, gap_types, GetComponentId(), GetObject(), i2s, is_gap, linkage, LinkageEvidenceFlagsToString(), LinkageEvidencesToString(), m_agp_version, object_beg, object_end, orientation, OrientationToString(), and part_number.

Referenced by CAgpReader::GetErrorMessage(), CAgpRenumber::OnGapOrComponent(), and CAgpCompSpanSplitter::SaveRow().

Member Data Documentation

◆ cols

vector<string> CAgpRow::cols

Definition at line 118 of file agp_util.hpp.

Referenced by FromString(), GetComponentBeg(), GetComponentEnd(), GetComponentId(), GetComponentType(), GetGapLength(), GetGapType(), GetLinkage(), GetLinkageEvidence(), GetObject(), GetObjectBeg(), GetObjectEnd(), GetOrientation(), GetPartNumber(), and CAgpReader::ReadStream().

◆ component_beg

TAgpPos CAgpRow::component_beg

Definition at line 158 of file agp_util.hpp.

Referenced by FromString(), CCompVal::init(), CAgpValidateReader::OnGapOrComponent(), CAgpRenumber::OnGapOrComponent(), CAgpToSeqEntry::OnGapOrComponent(), ParseComponentCols(), CAgpCompSpanSplitter::SaveRow(), and ToString().

◆ component_end

TAgpPos CAgpRow::component_end

Definition at line 158 of file agp_util.hpp.

Referenced by CheckComponentEnd(), FromString(), CCompVal::init(), CAgpValidateReader::OnGapOrComponent(), CAgpRenumber::OnGapOrComponent(), CAgpToSeqEntry::OnGapOrComponent(), ParseComponentCols(), CAgpCompSpanSplitter::SaveRow(), ToString(), and CAgpValidateApplication::x_ValidateFile().

◆ component_type

char CAgpRow::component_type

Definition at line 154 of file agp_util.hpp.

Referenced by FromString(), IsDraftComponent(), CAgpValidateReader::OnGapOrComponent(), CAgpToSeqEntry::OnGapOrComponent(), ParseGapCols(), and ToString().

◆ gap_length

TAgpLen CAgpRow::gap_length

Definition at line 173 of file agp_util.hpp.

Referenced by FromString(), CAgpValidateReader::OnGapOrComponent(), CAgpRenumber::OnGapOrComponent(), CAgpToSeqEntry::OnGapOrComponent(), ParseGapCols(), CAgpCompSpanSplitter::SaveRow(), and ToString().

◆ gap_type

EGap CAgpRow::gap_type

Definition at line 191 of file agp_util.hpp.

Referenced by GapEndsScaffold(), GapValidAtObjectEnd(), CAgpValidateReader::OnGapOrComponent(), ParseGapCols(), CAgpReader::ProcessThisRow(), CAgpReader::ReadStream(), SubstOldGap(), ToString(), and CAgpToSeqEntry::x_SetSeqGap().

◆ gap_type_codes

CSafeStatic<TMapStrEGap> CAgpRow::gap_type_codes

staticprotected

Definition at line 295 of file agp_util.hpp.

Referenced by ParseGapCols().

◆ gap_types

const CAgpRow::TStr CAgpRow::gap_types

staticprotected

Initial value:

= {
    "clone",
    "fragment",
    "repeat",
    "scaffold",
    "contamination",
 
    "contig",
    "centromere",
    "short_arm",
    "heterochromatin",
    "telomere"
}

Definition at line 292 of file agp_util.hpp.

Referenced by GapTypeToString(), and ToString().

◆ is_gap

bool CAgpRow::is_gap

Definition at line 156 of file agp_util.hpp.

Referenced by CAgpReader::Finalize(), FromString(), IsGap(), CAgpToSeqEntry::OnGapOrComponent(), CAgpReader::ProcessThisRow(), CAgpReader::ReadStream(), and ToString().

◆ linkage

bool CAgpRow::linkage

Definition at line 192 of file agp_util.hpp.

Referenced by GapEndsScaffold(), LinkageEvidencesToString(), CAgpValidateReader::OnGapOrComponent(), ParseGapCols(), CAgpReader::ProcessThisRow(), CAgpReader::ReadStream(), SubstOldGap(), ToString(), and CAgpToSeqEntry::x_SetSeqGap().

◆ linkage_evidence_flags

int CAgpRow::linkage_evidence_flags

a bit map which holds summary of info in linkage_evidences.

In particular, this is useful for weeding out duplicates

Definition at line 219 of file agp_util.hpp.

Referenced by LinkageEvidenceFlagsToString(), CAgpValidateReader::OnGapOrComponent(), ParseGapCols(), SubstOldGap(), and CAgpToSeqEntry::x_SetSeqGap().

◆ linkage_evidences

TLinkageEvidenceVec CAgpRow::linkage_evidences

Definition at line 216 of file agp_util.hpp.

Referenced by LinkageEvidencesToString(), ParseGapCols(), SubstOldGap(), and CAgpToSeqEntry::x_SetSeqGap().

◆ m_agp_version

EAgpVersion CAgpRow::m_agp_version

private

Definition at line 300 of file agp_util.hpp.

Referenced by FromString(), GetVersion(), OrientationToString(), ParseComponentCols(), ParseGapCols(), SetVersion(), and ToString().

◆ m_AgpErr

CRef<CAgpErr> CAgpRow::m_AgpErr

private

Definition at line 305 of file agp_util.hpp.

Referenced by CheckComponentEnd(), FromString(), GetErrorHandler(), GetErrorMessage(), ParseComponentCols(), ParseGapCols(), ReadSeqPos(), and SetErrorHandler().

◆ m_reader

CAgpReader* CAgpRow::m_reader

private

Definition at line 303 of file agp_util.hpp.

Referenced by ParseGapCols().

◆ object_beg

TAgpPos CAgpRow::object_beg

Definition at line 153 of file agp_util.hpp.

Referenced by FromString(), CAgpValidateReader::OnGapOrComponent(), CAgpReader::ProcessThisRow(), CAgpCompSpanSplitter::SaveRow(), and ToString().

◆ object_end

TAgpPos CAgpRow::object_end

Definition at line 153 of file agp_util.hpp.

Referenced by FromString(), CAgpValidateReader::OnObjectChange(), CAgpReader::ProcessThisRow(), CAgpCompSpanSplitter::SaveRow(), and ToString().

◆ orientation

EOrientation CAgpRow::orientation

Definition at line 171 of file agp_util.hpp.

Referenced by CCompVal::init(), CAgpValidateReader::OnGapOrComponent(), CAgpToSeqEntry::OnGapOrComponent(), OrientationToString(), ParseComponentCols(), and ToString().

◆ part_number

TAgpPos CAgpRow::part_number

Definition at line 153 of file agp_util.hpp.

Referenced by FromString(), CAgpReader::ProcessThisRow(), CAgpCompSpanSplitter::SaveRow(), and ToString().

◆ pcomment

SIZE_TYPE CAgpRow::pcomment

Definition at line 117 of file agp_util.hpp.

Referenced by FromString(), CAgpValidateReader::OnError(), CAgpValidateReader::OnGapOrComponent(), and CAgpRenumber::OnGapOrComponent().

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

include/objtools/readers/agp_util.hpp
src/objtools/readers/agp_util.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Types

Protected Member Functions

Static Protected Member Functions

Static Protected Attributes

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TLinkageEvidenceVec

◆ TMapStrEGap

◆ TStr

Member Enumeration Documentation

◆ EGap

◆ ELinkageEvidence

◆ EOrientation

Constructor & Destructor Documentation

◆ CAgpRow() [1/3]

◆ CAgpRow() [2/3]

◆ CAgpRow() [3/3]

◆ ~CAgpRow()

Member Function Documentation

◆ CheckComponentEnd() [1/2]

◆ CheckComponentEnd() [2/2]

◆ Clone()

◆ FromString()

◆ gap_type_codes_creator()

◆ GapEndsScaffold()

◆ GapTypeToString()

◆ GapValidAtObjectEnd() [1/2]

◆ GapValidAtObjectEnd() [2/2]

◆ GetComponentBeg()

◆ GetComponentEnd()

◆ GetComponentId()

◆ GetComponentType()

◆ GetErrorHandler()

◆ GetErrorMessage()

◆ GetGapLength()

◆ GetGapType()

◆ GetLinkage()

◆ GetLinkageEvidence()

◆ GetObject()

◆ GetObjectBeg()

◆ GetObjectEnd()

◆ GetOrientation()

◆ GetPartNumber()

◆ GetVersion()

◆ IsDraftComponent() [1/2]

◆ IsDraftComponent() [2/2]

◆ IsGap() [1/2]

◆ IsGap() [2/2]

◆ le_str()

◆ LinkageEvidenceFlagsToString() [1/2]

◆ LinkageEvidenceFlagsToString() [2/2]

◆ LinkageEvidencesToString()

◆ New() [1/2]

◆ New() [2/2]

◆ OrientationToString()

◆ ParseComponentCols()

◆ ParseGapCols()

◆ ReadSeqPos()

◆ SetErrorHandler()

◆ SetVersion()

◆ str_to_le()

◆ SubstOldGap()

◆ ToString()

Member Data Documentation

◆ cols

◆ component_beg

◆ component_end

◆ component_type

◆ gap_length

◆ gap_type

◆ gap_type_codes

◆ gap_types

◆ is_gap

◆ linkage