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NCBI C++ ToolKit: src/objtools/readers/agp_validate_reader.cpp Source File

;

m_is_chr=for_chr_from_scaf;

m_CheckObjLen=

;

m_CommentLineCount=m_EolComments=0;

m_componentsInLastScaffold=m_componentsInLastObject=0;

m_gapsInLastScaffold=m_gapsInLastObject=0;

m_prev_component_beg = m_prev_component_end = 0;

m_SingleCompScaffolds = 0;

m_SingleCompObjects = 0;

m_SingleCompScaffolds_withGaps=0;

m_SingleCompObjects_withGaps=0;

m_comp_name_matches=0;

memset(m_CompOri, 0,

(m_CompOri));

memset(m_GapTypeCnt, 0,

(m_GapTypeCnt));

m_ln_ev_flags2count.clear();

m_Ngap_ln2count.clear();

m_Ugap_ln2count.clear();

m_max_comp_beg=m_max_obj_beg=0;

m_has_partial_comp=m_has_comp_of_unknown_len=

;

(for_chr_from_scaf) {

(m_explicit_scaf,

);

m_obj_id_pattern.clear();

m_obj_id_digits->clear();

m_prev_id_digits->clear();

m_prev_component_id.clear();

m_TypeCompCnt.clear();

m_objNamePatterns.clear();

m_CompId2Spans.clear();

m_comp2len = &m_scaf2len;

);

(!res.second) res.first->second++;

(!res.second) res.first->second++;

pair<TCompId2Spans::iterator, bool> id_insert_result =

sameComId_otherScaf;

(id_insert_result.second ==

) {

& spans = (id_insert_result.first)->second;

(

)+ check_sp.first->ToString(

)

(

)+ check_sp.first->ToString(

)

prev_comp_file=spans.rbegin()->file_num;

prev_comp_line=spans.rbegin()->line_num;

sameComId_otherScaf=

;

sameComId_otherScaf +=

;

sameComId_otherScaf+=

;

sameComId_otherScaf+=

(prev_comp_line);

sameComId_otherScaf+=

;

sameComId_otherScaf+=

;

sameComId_otherScaf +=

;

sameComId_otherScaf+=

;

+

(it->second)+

row_saved =

;

(!intersection.

()) {

(; it != intersection.

() && masked_spans.size() < 80; ++it) {

(masked_spans.size()) masked_spans +=

;

masked_spans +=

(it->GetFrom()) +

+

(it->GetTo());

(it != intersection.

()) masked_spans +=

;

(sameComId_otherScaf.size()) {

);

details=

;

parsing_error;

parsing_error = e.

();

(

) + (parsing_error.size()?

:

) + parsing_error );

(obj_insert_result.second ==

) {

(

!= p_space) {

,

(xml_tag.size()==0) {

uc = !add_label_as_attribute;

(string::const_iterator it =

.begin(); it !=

.end(); ++it) {

(*it==

)

;

uc = !add_label_as_attribute;

(xml_tag.size() && xml_tag[xml_tag.size()-1]==

) {

xml_tag.resize( xml_tag.size()-1 );

( add_label_as_attribute ) {

xml_tag =

+

+ xml_tag +

;

(pos!=

) xml_tag.resize(pos);

<<

<< xml_tag <<

;

(mf_len_cnt < it->second) {

mf_len_cnt = it->second;

(mf_len_cnt>1 && mf_len_cnt==gap_cnt)

;

(mf_len_cnt>=10 || (mf_len_cnt>2 && mf_len_cnt*10>=gap_cnt && mf_len%10==0) ) {

mf_len, mf_len_cnt;

(pct!=

) eol_text +=

(mf_len_cnt) +

;

eol_text += pct +

+

(mf_len)+

;

attrs =

+

(mf_len)+

;

attrs+=

+

(mf_len_cnt)+

;

attrs+=

+pct+

;

(

) + str_gap_type +

(

).substr(0, 15-str_gap_type.size() ) +

xprint.

+

+ str_gap_type +

+ attrs

not_in_agp_msg = not_in_agp.

();

(not_in_agp_msg.size()) {

singleton_ori_not_plus_count =

e_count += singleton_ori_not_plus_count;

w_count -= singleton_ori_not_plus_count;

<<

;

;

;

(not_in_agp_msg.size() && !use_xml) {

<<

<< not_in_agp_msg <<

;

<<

;

s_comp, s_gap;

(CValuesCount::TValPtrVec::iterator

it = comp_cnt.begin();

it != comp_cnt.end();

( s->size() ) *s+=

;

*s+=

((*it)->second);

(use_xml)

<<

;

( s_comp.size() ) {

comp_by_type =

+ s_comp;

comp_by_type = comp_by_type.substr(8) + comp_by_type.substr(0, 8);

<< comp_by_type;

xprint.

(

,

,

(

)+s_comp+

);

xprint.

(

);

( s_gap.size() ) {

gap_u_n =

+ s_gap;

gap_u_n = gap_u_n.substr(7) + gap_u_n.substr(0, 7);

xprint.

(

,

,

(

)+s_gap+

);

linkageNoCnt =

- linkageYesCnt;

xprint.

(

, doNotBreakCnt,

);

(doNotBreakCnt) {

xprint.

=

;

xprint.

=

;

xprint.

=

;

xprint.

(

, breakCnt,

);

xprint.

=

;

mf_len, mf_len_cnt;

=

+ pct +

+

(mf_len_cnt) +

;

=

+ pct +

+

(mf_len_cnt) +

;

xprint.

(

);

xprint.

=

;

multimap<int,int> TMultiMapIntInt;

TMultiMapIntInt cnt2ln_ev;

label_width=0;

(

.size() > label_width) label_width =

.size();

(label_width>40) label_width=40;

(TMultiMapIntInt::reverse_iterator it = cnt2ln_ev.rbegin(); it != cnt2ln_ev.rend(); ++it) {

(

).substr(0, label_width-

.size());

xprint.

(

(

) +

+

, it->first );

compNamePatterns.

(it->first);

hasSuspicious =

(compNamePatterns,

,

xprint.

(

);

MAX_objname_eq_comp=3;

cnt_objname_eq_comp=0;

str_objname_eq_comp;

cnt_objname_eq_comp++;

(cnt_objname_eq_comp<=MAX_objname_eq_comp) {

(cnt_objname_eq_comp>1) str_objname_eq_comp+=

;

str_objname_eq_comp+=*it;

(cnt_objname_eq_comp && !use_xml) {

<<

<< cnt_objname_eq_comp <<

<< (cnt_objname_eq_comp==1?

:

)

<<

;

<<

<< str_objname_eq_comp;

(cnt_objname_eq_comp>MAX_objname_eq_comp)

<<

;

(use_xml)

<<

;

(not_in_agp_msg.size()) {

(use_xml) not_in_agp.

(

, not_in_agp_msg);

not_in_agp.

(

, not_in_agp_msg);

openBracket=

;

( s[pos]==

) {

( pos<(

)s.size() ) {

(openBracket) {

(pos==p1)

;

(ch==

|| ch==

) {

( pos >= (

)s.size()-1 || len1 )

( pos >= (

)s.size() || s[pos] !=

)

;

(ch==

) {

( !p2 || p2==pos )

;

openBracket=

;

(openBracket || pos==p1)

;

sd1=s.substr(p1, pos-p1);

sd1=s.substr(p1, len1);

sd2=s.substr(p2, pos-1-p2);

( !

(s[numLetters]) && s[numLetters]!=

)

;

(sd2.size()==0 && s[pos]==

) {

(pos<(

)s.size()) {

(ver1.size()) ver1=

(

)+ver1;

(ver2.size()) ver2=

(

)+ver2;

(sd2.size()==0) {

ltr=s.substr(0, numLetters);

|(c1>c2?c1:c2);

& namePatterns,

& strHeader,

fasta_count,

* count_label,

MaxPatterns=10;

SPACES=

;

cnt_pat.rbegin()->first

wPattern=strHeader.size()-2;

patternsPrinted=0;

mixedPattern=

;

CAccPatternCounter::TMapCountToString::reverse_iterator

it = cnt_pat.rbegin(); it != cnt_pat.rend(); it++

( ++patternsPrinted<=MaxPatterns ||

cnt_pat_size<=2*MaxPatterns

= it->second.size();

(

> wPattern ) wPattern =

;

(w+15>wPattern) wPattern = w+15;

totalCount+=it->first;

(

&

) mixedPattern=

;

mixedCategories=(nucCount && otherCount);

(mixedCategories && wPattern<20) wPattern=20;

xml_outer_tag;

(strHeader.size()) {

xml_outer_tag = strHeader.substr(0, strHeader.find(

)) +

;

<<

<< xml_outer_tag <<

;

(fasta_count && fasta_count!=totalCount) {

(count_label ? count_label :

)+

;

strHeader+SPACES.substr(

0, wPattern+2>(

)strHeader.size() ? wPattern+2-strHeader.size() : 0

printNuc=(nucCount>0);

(mixedCategories) {

xprint.

(

(

).substr(0, wPattern-20)+

);

(printNuc) xprint.

(

, nucCount);

xprint.

(

, otherCount);

accessionsSkipped=0;

patternsSkipped=0;

CAccPatternCounter::TMapCountToString::reverse_iterator

it = cnt_pat.rbegin(); it != cnt_pat.rend(); it++

( ++patternsPrinted<=MaxPatterns ||

cnt_pat_size<=2*MaxPatterns

acc_warning =

;

;

acc_warning =

;

;

:

(!(mixedCategories || mixedPattern))

;

: acc_warning =

;

;

: acc_warning =

;

;

( acc_warning.size() ) {

( acc_warning.size() ?

(

)+acc_warning+

:

)+

(

) + it->second +

SPACES.substr(0, wPattern - it->second.size()) +

,

accessionsSkipped += it->first;

(accessionsSkipped) {

s =

;

s+=

(patternsSkipped);

xprint.

(

+ s + SPACES.substr(0, wPattern - s.size()) +

,

(!mixedCategories || !printNuc)

;

(use_xml && xml_outer_tag.size()) {

<<

<< xml_outer_tag <<

;

mixedCategories||mixedPattern;

(

.

() &&

.find(

) ==

(

>0)

;

<<

<< (m_reader.m_AgpErr->m_strict?

:

)

<<

<< m_cnt <<

<<

<<

;

<< *(m_ids.begin()) <<

;

(m_cnt<m_reader.m_AgpErr->m_MaxRepeat||m_reader.m_AgpErr->m_MaxRepeat==0) {

<<

<< *it <<

;

<<

+

+

;

<<

;

(

it = begin(); it != end(); ++it) {

.push_back(&*it);

(

->second !=

->second ){

->second >

->second;

->first <

->first;

(iterator it = begin(); it != end(); ++it) {

( (it->beg <= span_beg && span_beg <= it->end) ||

(it->beg <= span_end && span_end <= it->end) )

( ( isPlus && span_beg < it->beg) ||

(!isPlus && span_end > it->end)

(insert_result.second ==

) {

(insert_result.first->second !=

)

insert_result.first->second;

(increment_count) m_count++;

@ eAgpVersion_auto

auto-detect using the first gap line

@ eAgpVersion_2_0

AGP spec 2.0 or later.

static int GetNameCategory(const string &s)

string MostFrequentGapSize(CAgpValidateReader::TMapIntInt &ln2count, int &mf_len, int &mf_len_cnt)

static bool ReadNumberOrRange(const string &s, int &pos, string &sd1, string &sd2)

Accession naming patterns; find ranges for consequtive digits.

vector< double > TDoubleVec

iterator AddName(const string &name, TDoubleVec *runsOfDigits=nullptr)

void GetSortedPatterns(TMapCountToString &dst)

Correctly print multiple errors and warnings on consequitive lines; suppress undesired or higly repet...

virtual void Msg(int code, const string &details, int appliesTo=fAtThisLine)

void PrintMessageCounts(CNcbiOstream &ostr, int from, int to=E_First, bool report_lines_skipped=false, TMapCcodeToString *hints=nullptr)

void UpgradeToError(EErrCode code)

@ CODE_First

The number of the first CAgpErr error enum.

@ CODE_Last

This is one past the last code allowed, after built-in and user errors.

string GetPrintableCode(int code, bool strict=false) const

virtual void LineDone(const string &s, int line_num, bool invalid_line=false)

static void PrintTotalsXml(CNcbiOstream &ostr, int e_count, int w_count, int note_count, int skipped_count)

static void PrintTotals(CNcbiOstream &ostr, int e_count, int w_count, int note_count, int skipped_count)

int GetCount(EErrCode code) const

const string & GetFile(int num)

int CountTotals(int from, int to=E_First)

@ W_BreakingGapSameCompId

@ W_UnSingleCompNotInFull

Detects scaffolds, object boundaries, errors that involve 2 consecutive lines, and is intended as a s...

CAgpErr * GetErrorHandler()

CRef< CAgpRow > m_prev_row

CRef< CAgpRow > m_this_row

EAgpVersion m_agp_version

string & GetComponentId()

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

string LinkageEvidenceFlagsToString()

int linkage_evidence_flags

a bit map which holds summary of info in linkage_evidences.

static bool IsGap(char c)

bool GapEndsScaffold() const

static bool IsDraftComponent(char c)

string & GetComponentType()

static const char * GapTypeToString(int i)

CAgpValidateReader & m_reader

void PrintXml(CNcbiOstream &out, const string &msg)

void Print(CNcbiOstream &out, const string &msg)

CAccPatternCounter m_patterns

static bool x_PrintPatterns(CAccPatternCounter &namePatterns, const string &strHeader, int fasta_count, const char *count_label=nullptr, CNcbiOstream &out=cout, bool use_xml=false)

bool m_last_scaf_start_is_obj

TAgpPos m_prev_component_beg

TMapIntInt m_NgapByType_ln2count[CAgpRow::eGapCount+CAgpRow::eGapYes_count]

void x_GetMostFreqGapsText(int gap_type, string &eol_text, string &attrs)

CAccPatternCounter::TDoubleVec * m_prev_id_digits

TMapIntInt m_ln_ev_flags2count

pair< TObjSet::iterator, bool > TObjSetResult

pair< string, CCompSpans > TCompIdSpansPair

void PrintTotals(CNcbiOstream &out=cout, bool use_xml=false)

int m_last_scaf_start_line

void x_PrintTotals(CNcbiOstream &out=cout, bool use_xml=false)

void Reset(bool for_chr_from_scaf=false)

int m_GapTypeCnt[CAgpRow::eGapCount+CAgpRow::eGapYes_count]

pair< TAgpPos, int > TPairIntInt

IAgpRowOutput * m_row_output

pair< TMapIntInt::iterator, bool > TMapIntIntResult

CAgpValidateReader(CAgpErrEx &agpErr, CMapCompLen &comp2len, TMapStrRangeColl &comp2range_coll)

string m_prev_component_id

int m_SingleCompObjects_withGaps

TAgpLen m_expected_obj_len

int m_componentsInLastObject

int m_SingleCompScaffolds

int m_SingleCompScaffolds_withGaps

CAccPatternCounter m_objNamePatterns

void x_PrintGapCountsLine(XPrintTotalsItem &xprint, int gap_type, const string &label=NcbiEmptyString)

int m_componentsInLastScaffold

virtual void OnScaffoldEnd()

bool m_has_comp_of_unknown_len

TMapIntInt m_Ngap_ln2count

virtual ~CAgpValidateReader()

TCompId2Spans m_CompId2Spans

virtual void OnObjectChange()

void SetRowOutput(IAgpRowOutput *row_output)

CValuesCount m_TypeCompCnt

TMapStrRangeColl * m_comp2range_coll

CAccPatternCounter::TDoubleVec * m_obj_id_digits

int m_last_scaf_start_file

TMapIntInt m_Ugap_ln2count

TAgpPos m_prev_component_end

virtual void OnGapOrComponent()

pair< iterator, TAgpPos > TCheckSpan

TCheckSpan CheckSpan(TAgpPos span_beg, TAgpPos span_end, bool isPlus)

void AddSpan(const CCompVal &span)

void init(CAgpRow &row, int line_num_arg)

pair< TMapStrInt::iterator, bool > TMapStrIntResult

TAgpLen AddCompLen(const string &acc, TAgpLen len, bool increment_count=true)

TRangeVector::const_iterator const_iterator

const_iterator end() const

TThisType & IntersectWith(const TRange &r)

const_iterator begin() const

vector< value_type * > TValPtrVec

static int x_byCount(value_type *a, value_type *b)

void add(const string &c)

void GetSortedValues(TValPtrVec &out)

virtual void SaveRow(const string &s, CRef< CAgpRow > row, TRangeColl *runs_of_Ns)=0

Output the count as text or as xml.

void line(const string &s=NcbiEmptyString)

void line(const string &label, int value, const string &xml_tag=NcbiEmptyString)

void line(const string &label, const string &value, string xml_tag=NcbiEmptyString)

XPrintTotalsItem(CNcbiOstream &out, bool use_xml, int w)

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator begin() const

parent_type::iterator iterator

const_iterator find(const key_type &key) const

const_iterator end() const

std::ofstream out("events_result.xml")

main entry point for tests

#define NCBI_ASSERT(expr, mess)

const string & GetMsg(void) const

Get message string.

static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...

EAccessionInfo

For IdentifyAccession (below)

static SIZE_TYPE ParseFastaIds(CBioseq::TId &ids, const CTempString &s, bool allow_partial_failure=false)

Parse an entire set of |-delimited FASTA-style IDs, appending the results to IDS.

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

NCBI_NS_STD::string::size_type SIZE_TYPE

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

Convert double to string.

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static string & Replace(const string &src, const string &search, const string &replace, string &dst, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static string XmlEncode(const CTempString str, TXmlEncode flags=eXmlEnc_Contents)

Encode a string for XML.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

@ fDoubleFixed

DoubleToString*(): Use n.nnnn format for double conversions.

@ eNocase

Case insensitive compare.

static const char label[]

list< CRef< CSeq_id > > TId

constexpr auto sort(_Init &&init)

double value_type

The numeric datatype used by the parser.

const struct ncbi::grid::netcache::search::fields::SIZE size

Magic spell ;-) needed for some weird compilers... very empiric.

const GenericPointer< typename T::ValueType > T2 value

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

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