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NCBI C++ ToolKit: src/objtools/validator/validerror_graph.cpp Source File

74 if

( min < 0 || min > 100 ) {

85 if

( max <= 0 || max > 100 ) {

121 ") length mismatch"

, seq, graph);

146 "Bioseq not found for Graph location "

label

, graph);

155 "SeqGraph location ("

label

") is invalid"

, graph);

177 if

(start1 < start2) {

179

}

else if

(start1 == start2 && stop1 < stop2) {

193

vector <CRef <CSeq_graph> > graph_list;

196 if

((*it)->IsGraph()) {

200

graph_list.push_back(

);

206 if

(graph_list.size() == 0) {

211 bool

overlaps =

false

;

213 size_t

num_graphs = 0;

214 size_t

graphs_len = 0;

223 size_t

Ns_with_score = 0,

225

ACGTs_without_score = 0,

233 for

(vector<

CRef <CSeq_graph>

>::iterator grp = graph_list.begin(); grp != graph_list.end(); ++grp) {

237 x_ValidateGraphValues

(graph, seq, first_N, first_ACGT, num_bases, Ns_with_score, gaps_with_score, ACGTs_without_score, vals_below_min, vals_above_max);

244

overlap_graph = &graph;

253 if

( ACGTs_without_score > 0 ) {

254 if

(ACGTs_without_score * 10 > num_bases) {

255 double

pct = (double) (ACGTs_without_score) * 100.0 / (double) num_bases;

264 " ACGT bases have zero score value - first one at position "

268 if

( Ns_with_score > 0 ) {

269 if

(Ns_with_score * 10 > num_bases) {

270 double

pct = (double) (Ns_with_score) * 100.0 / (double) num_bases;

279 " N bases have positive score value - first one at position "

283 if

( gaps_with_score > 0 ) {

286 " gap bases have positive score value"

289 if

( vals_below_min > 0 ) {

292 " quality scores have values below the reported minimum or 0"

295 if

( vals_above_max > 0 ) {

298 " quality scores have values above the reported maximum or 100"

304 "Graph components overlap, with multiple scores for " 305 "a single base"

, seq, *overlap_graph);

309 if

( (seq_len != graphs_len) && (inst.

GetLength

() != graphs_len) ) {

325 if

(graph_list.size() < 2) {

332 for

(

size_t i

= 1;

< graph_list.size();

++) {

337

|| (left == last_left && right < last_right)) {

339 "Graph components are out of order - may be a software bug"

355 size_t

& Ns_with_score,

356 size_t

& gaps_with_score,

357 size_t

& ACGTs_without_score,

358 size_t

& vals_below_min,

359 size_t

& vals_above_max)

388

CByte_graph::TValues::const_iterator val_iter = values.begin();

389

CByte_graph::TValues::const_iterator val_end = values.end();

391 size_t

score_pos = 0;

393 while

(seq_iter != seq_end && score_pos < graph.

GetNumval

()) {

397 if

(val_iter == val_end) {

400 val

= (short)(*val_iter);

425

ACGTs_without_score++;

426 if

(first_ACGT == -1) {

447 string

(

"Exception while validating graph values. EXCEPTION: "

) +

457

CDelta_ext::Tdata::const_iterator curr =

delta

.Get().begin(),

459

end =

delta

.Get().end();

461 size_t

num_delta_seq = 0;

469 while

( curr != end && grp ) {

472 switch

( (*curr)->Which() ) {

474 const CSeq_loc

& loc = (*curr)->GetLoc();

481 ") length mismatch"

, graph);

505 ") length mismatch"

, graph);

508 if

( graph_loc.

IsInt

() ) {

515 ") start do not coincide"

519 if

( to !=

offset

+ litlen - 1 ) {

524 ") stop do not coincide"

544 while

( curr != end) {

546 switch

( (*curr)->Which() ) {

548 const CSeq_loc

& loc = (*curr)->GetLoc();

573 size_t

num_graphs = 0;

582 if

( num_delta_seq != num_graphs ) {

584 "Different number of SeqGraph ("

621 switch

( (*dseq)->Which() ) {

626 if

( (*dseq)->GetLiteral().IsSetSeq_data() && !(*dseq)->GetLiteral().GetSeq_data().IsGap() ) {

627

seq_len += (*dseq)->GetLiteral().GetLength();

642 if

(

delta

.IsLiteral() ) {

@ eExtreme_Positional

numerical value

User-defined methods of the data storage class.

@ eErr_SEQ_GRAPH_GraphACGTScoreMany

@ eErr_SEQ_GRAPH_GraphDiffNumber

@ eErr_SEQ_GRAPH_GraphNScore

@ eErr_SEQ_GRAPH_GraphBioseqId

@ eErr_SEQ_GRAPH_GraphOverlap

@ eErr_SEQ_GRAPH_GraphByteLen

@ eErr_SEQ_GRAPH_GraphSeqLocLen

@ eErr_SEQ_GRAPH_GraphGapScore

@ eErr_SEQ_GRAPH_GraphNScoreMany

@ eErr_SEQ_GRAPH_GraphSeqLitLen

@ eErr_SEQ_GRAPH_GraphMax

@ eErr_SEQ_GRAPH_GraphLocInvalid

@ eErr_SEQ_GRAPH_GraphAbove

@ eErr_SEQ_GRAPH_GraphBioseqLen

@ eErr_SEQ_GRAPH_GraphStopPhase

@ eErr_SEQ_GRAPH_GraphStartPhase

@ eErr_SEQ_GRAPH_GraphACGTScore

@ eErr_SEQ_GRAPH_GraphOutOfOrder

@ eErr_INTERNAL_Exception

@ eErr_SEQ_GRAPH_GraphMin

@ eErr_SEQ_GRAPH_GraphBelow

const CSeq_id * GetFirstId() const

void PostErr(EDiagSev sv, EErrType et, const string &msg, const CSerialObject &obj)

static bool IsSupportedGraphType(const CSeq_graph &graph)

~CValidError_graph() override

void x_ValidateMinValues(const CByte_graph &bg, const CSeq_graph &graph)

void x_ValidateGraphValues(const CSeq_graph &graph, const CBioseq &seq, int &first_N, int &first_ACGT, size_t &num_bases, size_t &Ns_with_score, size_t &gaps_with_score, size_t &ACGTs_without_score, size_t &vals_below_min, size_t &vals_above_max)

void x_ValidateMaxValues(const CByte_graph &bg, const CSeq_graph &graph)

size_t GetUngappedSeqLen(const CBioseq &seq)

void ValidateSeqGraph(const CSeq_graph &graph)

bool x_GetLitLength(const CDelta_seq &delta, TSeqPos &len)

void ValidateGraphsOnBioseq(const CBioseq &seq)

void x_ValidateGraphOrderOnBioseq(const CBioseq &seq, vector< CRef< CSeq_graph > > graph_list)

bool x_ValidateGraphLocation(const CSeq_graph &graph)

void ValidateSeqGraphContext(const CSeq_graph &graph, const CBioseq_set &set)

void x_ValidateGraphOnDeltaBioseq(const CBioseq &seq)

const CTSE_Handle & GetTSE_Handle()

void IncrementMisplacedGraphCount()

CBioseq_Handle GetBioseqHandleFromLocation(CScope *scope, const CSeq_loc &loc, const CTSE_Handle &tse)

Include a standard set of the NCBI C++ Toolkit most basic headers.

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

EDiagSev

Severity level for the posted diagnostics.

@ eDiag_Error

Error message.

@ eDiag_Warning

Warning message.

@ eDiag_Fatal

Fatal error â guarantees exit(or abort)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

@ eContent

Untagged human-readable accession or the like.

ENa_strand GetStrand(void) const

Get the location's strand.

TRange GetTotalRange(void) const

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

TSeqPos GetStop(ESeqLocExtremes ext) const

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TSeqPos GetBioseqLength(void) const

@ eCoding_Ncbi

Set coding to binary coding (Ncbi4na or Ncbistdaa)

TSeqPos GetPos(void) const

const CSeq_graph & GetOriginalGraph(void) const

Get original graph with unmapped location/product.

void SetCoding(TCoding coding)

const_iterator begin(void) const

const_iterator end(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static string SizetToString(size_t value, TNumToStringFlags flags=0, int base=10)

Convert size_t to string.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static const char label[]

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsInt(void) const

Check if variant Int is selected.

bool IsNull(void) const

Check if variant Null is selected.

@ e_not_set

No variant selected.

bool IsSetLoc(void) const

region this applies to Check if a value has been assigned to Loc data member.

const TGraph & GetGraph(void) const

Get the Graph member data.

const TTitle & GetTitle(void) const

Get the Title member data.

TMax GetMax(void) const

Get the Max member data.

const TByte & GetByte(void) const

Get the variant data.

TMin GetMin(void) const

Get the Min member data.

const TValues & GetValues(void) const

Get the Values member data.

bool IsByte(void) const

Check if variant Byte is selected.

const TLoc & GetLoc(void) const

Get the Loc member data.

TNumval GetNumval(void) const

Get the Numval member data.

bool IsSetTitle(void) const

Check if a value has been assigned to Title data member.

TRepr GetRepr(void) const

Get the Repr member data.

const TInst & GetInst(void) const

Get the Inst member data.

bool IsSetAnnot(void) const

Check if a value has been assigned to Annot data member.

TLength GetLength(void) const

Get the Length member data.

TLength GetLength(void) const

Get the Length member data.

const TExt & GetExt(void) const

Get the Ext member data.

const TDelta & GetDelta(void) const

Get the variant data.

bool IsSetSeq_data(void) const

may have the data Check if a value has been assigned to Seq_data data member.

list< CRef< CDelta_seq > > Tdata

bool IsGap(void) const

Check if variant Gap is selected.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

@ eRepr_delta

sequence made by changes (delta) to others

@ eRepr_raw

continuous sequence

@ e_Ncbi4na

4 bit nucleic acid code

@ e_Literal

a piece of sequence

@ e_Loc

point to a sequence

constexpr auto sort(_Init &&init)

Int4 delta(size_t dimension_, const Int4 *score_)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

#define FOR_EACH_ANNOT_ON_BIOSEQ

#define FOR_EACH_GRAPH_ON_ANNOT

bool s_CompareTwoSeqGraphs(const CRef< CSeq_graph > g1, const CRef< CSeq_graph > g2)

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