validerror_align.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Dense_diag.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqalign/Packed_seg.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Std_seg.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/alnmgr/aln_user_options.hpp>
#include <objtools/alnmgr/aln_stats.hpp>
#include <objtools/alnmgr/alnvec.hpp>
#include <objtools/alnmgr/sparse_aln.hpp>
#include <objtools/alnmgr/aln_converters.hpp>
#include <objtools/alnmgr/aln_builders.hpp>
#include <map>
#include <vector>
#include <algorithm>
#include <objtools/validator/validerror_align.hpp>
#include <objtools/validator/utilities.hpp>

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Classes
struct	ambchar

Typedefs
typedef struct ambchar	AmbCharData

Functions
	USING_SCOPE (sequence)
static void	GetInvalidSeqAlignTypeStr (CSeq_align::C_Segs::E_Choice segtype, int order, string &msg)
static bool	s_AmbiguousMatch (char a, char b)
static unsigned	s_GetNumIdsToUse (const CDense_seg &denseg)
void	s_CalculateMatchingColumns (const CDense_seg &denseg, TSeqPos &col, size_t &num_match, bool &ids_missing, bool internal_gaps, CScope &scope)
bool	s_DensegHasAccessionWithZeroVersion (const CDense_seg &denseg)
void	s_FixZeroVersions (CDense_seg &denseg)
static size_t	s_PercentBioseqMatch (CBioseq_Handle b1, CBioseq_Handle b2)
string	s_DescribeSegment (const CSeq_id &id, const CSeq_id &id_context, size_t segment, size_t pos, bool use_in=false)

Variables
static const AmbCharData	ambiguity_list []
static const int	num_ambiguities = sizeof (ambiguity_list) / sizeof (AmbCharData)
static const string	kAlignmentTooLong = "the alignment claims to contain residue coordinates that are past the end of the sequence. Either the sequence is too short, or there are extra characters or formatting errors in the alignment"

Typedef Documentation

AmbCharData

typedef struct ambchar AmbCharData

Function Documentation

GetInvalidSeqAlignTypeStr()

static void GetInvalidSeqAlignTypeStr ( CSeq_align::C_Segs::E_Choice  segtype, int  order, string &  msg  )

static

Definition at line 80 of file validerror_align.cpp.

References NStr::IntToString(), and msg().

Referenced by CValidError_align::ValidateSeqAlign().

s_AmbiguousMatch()

static bool s_AmbiguousMatch ( char  a, char  b  )

static

Definition at line 200 of file validerror_align.cpp.

References a, ambiguity_list, b, NStr::Find(), i, and num_ambiguities.

Referenced by s_CalculateMatchingColumns(), and CValidError_align::x_ValidateAlignPercentIdentity().

s_CalculateMatchingColumns()

void s_CalculateMatchingColumns	(	const CDense_seg &	denseg,
		TSeqPos &	col,
		size_t &	num_match,
		bool &	ids_missing,
		bool	internal_gaps,
		CScope &	scope
	)

Definition at line 307 of file validerror_align.cpp.

References column, NStr::Find(), CAlnMap::GetAlnStop(), CAlnVec::GetColumnVector(), CDense_seg_Base::GetDim(), CException::GetMsg(), CDense_seg_Base::GetNumseg(), CDense_seg_Base::GetStarts(), NStr::IsBlank(), match(), NStr::ReplaceInPlace(), s_AmbiguousMatch(), s_GetNumIdsToUse(), CAlnVec::SetEndChar(), CAlnVec::SetGapChar(), and NStr::StartsWith().

Referenced by CValidError_align::x_ValidateAlignPercentIdentity().

s_DensegHasAccessionWithZeroVersion()

bool s_DensegHasAccessionWithZeroVersion

(

const CDense_seg &

denseg

)

Definition at line 386 of file validerror_align.cpp.

References CDense_seg_Base::GetIds(), CDense_seg_Base::IsSetIds(), and ITERATE.

Referenced by CValidError_align::x_ValidateAlignPercentIdentity().

s_DescribeSegment()

string s_DescribeSegment	(	const CSeq_id &	id,
		const CSeq_id &	id_context,
		size_t	segment,
		size_t	pos,
		bool	use_in = false
	)

Definition at line 1334 of file validerror_align.cpp.

References context, CSeq_id::eContent, CSeq_id::GetLabel(), label, and NStr::NumericToString().

Referenced by CValidError_align::x_ReportAlignErr(), and CValidError_align::x_ValidateSeqLength().

s_FixZeroVersions()

void s_FixZeroVersions

(

CDense_seg &

denseg

)

Definition at line 400 of file validerror_align.cpp.

References CDense_seg_Base::IsSetIds(), NON_CONST_ITERATE, and CDense_seg_Base::SetIds().

Referenced by CValidError_align::x_ValidateAlignPercentIdentity().

s_GetNumIdsToUse()

static unsigned s_GetNumIdsToUse ( const CDense_seg &  denseg )

static

Definition at line 226 of file validerror_align.cpp.

References CDense_seg_Base::GetDim(), CDense_seg_Base::GetIds(), and CDense_seg_Base::IsSetIds().

Referenced by CValidError_align::IsTpaAlignment(), s_CalculateMatchingColumns(), CValidError_align::x_ValidateAlignPercentIdentity(), and CValidError_align::x_ValidateFastaLike().

s_PercentBioseqMatch()

static size_t s_PercentBioseqMatch ( CBioseq_Handle  b1, CBioseq_Handle  b2  )

static

Definition at line 947 of file validerror_align.cpp.

References CBioseq_Handle::eCoding_Iupac, CBioseq_Handle::GetInst(), CSeq_inst_Base::GetLength(), CBioseq_Handle::GetSeqVector(), CBioseq_Handle::IsAa(), and match().

Referenced by CValidError_align::x_ValidateFastaLike().

USING_SCOPE()

USING_SCOPE

(

sequence

)

Variable Documentation

ambiguity_list

const AmbCharData ambiguity_list[]

static

Initial value:

= {
    { 'R', "AG" },
    { 'Y', "CT" },
    { 'M', "AC" },
    { 'K', "GT" },
    { 'S', "CG" },
    { 'W', "AT" },
    { 'H', "ACT" },
    { 'B', "CGT" },
    { 'V', "ACG" },
    { 'D', "AGT" },
}

Definition at line 185 of file validerror_align.cpp.

Referenced by s_AmbiguousMatch().

kAlignmentTooLong

const string kAlignmentTooLong = "the alignment claims to contain residue coordinates that are past the end of the sequence. Either the sequence is too short, or there are extra characters or formatting errors in the alignment"

static

Definition at line 1363 of file validerror_align.cpp.

Referenced by CValidError_align::x_ReportStartMoreThanBiolen(), CValidError_align::x_ReportSumLenStart(), and CValidError_align::x_ValidateSeqLength().

num_ambiguities

const int num_ambiguities = sizeof (ambiguity_list) / sizeof (AmbCharData)

static

Definition at line 198 of file validerror_align.cpp.

Referenced by s_AmbiguousMatch().