NCBI C++ ToolKit
Classes | Typedefs | Functions | Variables
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>
+ Include dependency graph for validerror_align.cpp:

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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().

Referenced by CValidError_align::ValidateSeqAlign().

◆ s_AmbiguousMatch()

static bool s_AmbiguousMatch ( char  a,
char  b 
)
static

◆ s_CalculateMatchingColumns()

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

◆ s_DensegHasAccessionWithZeroVersion()

bool s_DensegHasAccessionWithZeroVersion ( const CDense_seg denseg)

◆ s_DescribeSegment()

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

◆ s_FixZeroVersions()

void s_FixZeroVersions ( CDense_seg denseg)

◆ s_GetNumIdsToUse()

static unsigned s_GetNumIdsToUse ( const CDense_seg denseg)
static

◆ s_PercentBioseqMatch()

static size_t s_PercentBioseqMatch ( CBioseq_Handle  b1,
CBioseq_Handle  b2 
)
static

◆ 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

◆ 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().

Modified on Wed Feb 21 09:56:35 2024 by modify_doxy.py rev. 669887