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NCBI C++ ToolKit: src/algo/sequence/compare_feats.cpp Source File

(!c1->IsMatch() && c2->IsMatch())

;

(c1->IsMatch() && !c2->IsMatch())

;

(!c1->IsMatch() && !c2->IsMatch())

c1->GetFeatQ().

();

c1_sameType = c1->IsSameType();

c2_sameType = c2->IsSameType();

(c1_sameType && !c2_sameType)

;

(!c1_sameType && c2_sameType)

;

c1_same_product = !c1->GetFeatQ().

() && c1->GetFeatQ()->CanGetProduct()

&& !c1->GetFeatT().

() && c1->GetFeatT()->CanGetProduct()

c2_same_product = !c2->GetFeatQ().

() && c2->GetFeatQ()->CanGetProduct()

&& !c2->GetFeatT().

() && c2->GetFeatT()->CanGetProduct()

(c1_same_product && !c2_same_product)

;

(!c1_same_product && c2_same_product)

;

k = 0.8f;

c1->GetComparison()->GetSplicingSimilarity(score1);

c2->GetComparison()->GetSplicingSimilarity(score2);

score1 = k * score1 + (1.0 - k) * c1->GetComparison()->GetSymmetricalOverlap();

score2 = k * score2 + (1.0 - k) * c2->GetComparison()->GetSymmetricalOverlap();

(score1 < score2)

;

(score2 < score1)

;

c1_sameSubtype = c1->IsSameSubtype();

c2_sameSubtype = c2->IsSameSubtype();

(c1_sameSubtype && !c2_sameSubtype)

;

(!c1_sameSubtype && c2_sameSubtype)

;

.setf(ios::fixed);

.setf(ios::showpoint);

<< sResult <<

;

strm << s_pos1 <<

;

strm <<

<< s_pos2 <<

;

(!grp.

(comp)) {

strm << sep << grp.

() <<

<< ii <<

;

it1_exon_ordinal = 1;

++it1, ++it1_exon_ordinal)

it2_exon_ordinal = 1;

loc1_found_Overlap =

;

++it2, ++it2_exon_ordinal)

it1_cmp_it2 = adjust_for_strand *

&& loc2_reported_set.

(it2_exon_ordinal) == loc2_reported_set.

()

loc2_reported_set.

(it2_exon_ordinal);

, cmp_res, it1_cmp_it2);

loc2_reported_set.

(it2_exon_ordinal);

loc1_found_Overlap =

;

(!loc1_found_Overlap) {

it2_exon_ordinal = 1;

(

it2(*loc2); it2; ++it2, ++it2_exon_ordinal) {

(loc2_reported_set.

(it2_exon_ordinal) == loc2_reported_set.

()) {

(vector<SIntervalComparisonResult>::iterator it =

.begin();

(vector<SIntervalComparisonResult>::reverse_iterator it =

.rbegin();

(it->missing_first()) {

}

(it->missing_second()) {

terminal_jitter_thr = 20.0f;

splice_jitter_thr = 5.0f;

best_match_start = 0.0f;

best_match_stop = 0.0f;

same_strand = strand1 == strand2

= (seg1_start == terminal_start

|| seg1_stop == terminal_stop

|| seg2_start == terminal_start

|| seg2_stop == terminal_stop ) ? terminal_jitter_thr : splice_jitter_thr;

match_stop =

(0.0f, 1.0f -

((

)seg1_stop - (

)seg2_stop) /

);

best_match_stop =

(match_stop, best_match_stop);

(str_result) *str_result =

;

(str_result) *str_result =

;

strm <<

;

strm <<

;

strm <<

;

strm <<

;

strm <<

;

strm <<

;

strm <<

;

strm <<

;

strm <<

;

strm <<

;

((*dbxref)->GetDb() ==

|| (*dbxref)->GetDb() ==

) {

(*dbxref)->GetTag().GetId();

((*dbxref)->GetDb() ==

|| (*dbxref)->GetDb() ==

) {

(*dbxref)->GetTag().GetId();

std::vector<string> tokens;

(tokens.size() == 4 && (tokens[3] ==

|| tokens[3] ==

)) {

vComparisons.clear();

(

);

(; m_loc_q_ci; ++m_loc_q_ci) {

vector<CRef<CCompareFeats> > feat_matches;

x_GetPutativeMatches(feat_matches, feat1);

aggregate_match_loc_t.

();

(!(*it)->GetFeatT().IsNull() && !(*it)->GetSelfLocT().IsNull()) {

aggregate_match_loc_t.

();

aggregate_match_loc_t.

(*(*it)->GetSelfLocT());

(!group_loc_q->

()

vComparisons.insert(vComparisons.end(), feat_matches.begin(), feat_matches.end());

(!vComparisons.empty()) {

(m_already_processed_unmatched_targets) {

(

);

(m_seen_targets.find(loc_label) != m_seen_targets.end()) {

|| feat_self_loc->

()

mapped = feat_len == 0 ? 0.0f : 1.0 - (len_subtr / feat_len);

vComparisons.push_back(cf);

m_already_processed_unmatched_targets =

;

(

);

!vComparisons.empty();

mapped_identity(0);

feat1_gene_id = s_GetGeneId(*feat1);

(feat1_gene_id == 0) {

had_some_matches =

;

&& feat1_gene_id == s_GetGeneId(*feat_t))

loc_label =

;

this->m_seen_targets.insert(loc_label);

, usingRangeComparison ? *feat1_mapped_range_loc : *feat1_mapped_loc

, usingRangeComparison ? *feat1_self_range_loc : *feat1_self_loc

vComparisons.push_back(cf);

had_some_matches =

;

(!had_some_matches) {

vComparisons.push_back(cf);

merge_single_range)

& mapper = (scope == m_scope_q ? *m_self_mapper_q : *m_self_mapper_t);

new_loc = mapper.

(loc);

(merge_single_range){

(new_loc.

() ? loc : *new_loc),

}

(!obj_id1.

() && !obj_id2.

()) {

*obj_id1 < *obj_id2;

priority_queue<CRef<CCompareFeats>,

vector<CRef<CCompareFeats> >,

(!cf->GetFeatQ().

()) {

q_map[cf->GetFeatQ()].push(cf);

(!cf->GetFeatT().

()) {

t_map[cf->GetFeatT()].push(cf);

(TMatchesMap, it, q_map) {

(!best_match.

() && best_match->IsMatch()) {

(

<<

<< s0 <<

<< s1 <<

<< it->second.size());

(TMatchesMap, it, t_map) {

(!best_match.

() && best_match->IsMatch()) {

(

<<

<< s0 <<

<< s1 <<

<< it->second.size());

(q_map[cf->GetFeatQ()].top() == cf && t_map[cf->GetFeatT()].top() == cf) {

cf->SetIrrelevance(0);

(compset.

(cf) == compset.

() &&

(q_map[cf->GetFeatQ()].top() == cf || cf->GetFeatQ().

()))

cf->SetIrrelevance(1);

(compset.

(cf) == compset.

() &&

(t_map[cf->GetFeatT()].top() == cf || cf->GetFeatT().

()))

cf->SetIrrelevance(2);

vComparisons.clear();

vComparisons.push_back(*it);

User-defined methods of the data storage class.

bool IsReverse(ENa_strand s)

@ eExtreme_Biological

5' and 3'

bool SameOrientation(ENa_strand a, ENa_strand b)

CCompareFeats represens a result of comparison of two features.

CConstRef< CSeq_feat > m_feat1

CConstRef< CSeq_loc > m_feat1_mapped_loc

static string s_GetLocLabel(const CSeq_loc &loc, bool merged=false)

CRef< CCompareSeq_locs > m_compare

static string s_GetFeatLabel(const CSeq_feat &gene_feat, feature::TFeatLabelFlags type=feature::fFGL_Both)

CConstRef< CSeq_feat > m_feat2

double GetMappedIdentity() const

static int s_GetGeneId(const CSeq_feat &feat)

CConstRef< CSeq_loc > x_GetSelfLoc(const CSeq_loc &loc, CScope *scope, bool merge_single_range)

bool NextComparisonGroup(vector< CRef< CCompareFeats > > &v)

Return the next group of comparisons on the region (return true iff found any) A group is a set of fe...

void SelectMatches(vector< CRef< CCompareFeats > > &v)

void x_GetPutativeMatches(vector< CRef< CCompareFeats > > &v, CConstRef< CSeq_feat > q_feat)

double GetRelativeOverlap() const

Relative overlap is defined as ratio of the length of the overlap to the length of the shorter featur...

vector< SIntervalComparisonResult > m_IntComparisons

string GetEvidenceString() const

The evidence string is a whitespace-separated list of exon comparisons Each exon comparison is a pair...

TSeqPos m_len_seqloc_overlap

void x_ComputeOverlapValues() const

Recompute m_len_seqloc_overlap, m_len_seqloc1, and m_len_seqloc2.

TCompareLocsFlags GetResult(string *str_out=NULL) const

str_out will contain human-readable summary of the internal comparison

int m_loc1_interval_count

float m_shared_sites_score

FCompareLocs x_CompareInts(const CSeq_loc &loc1, const CSeq_loc &loc2) const

Compare two exons.

int m_loc2_interval_count

bool m_cachedOverlapValues

double GetSymmetricalOverlap() const

Symmetrical overlap is defined as length(intersection(loc1, loc2) / (length(loc1) + length(loc2)) int...

@ fCmp_Subset

comparison loc is a subset of the reference loc; some interval boundaries do not match

@ fCmp_5pExtension

5' terminal interval extended (other splice junction matches)

@ fCmp_intsExtra_internal

comparinos loc has extra interval(s) internally

@ fCmp_5pTruncation

5' terminal interval truncated (other splice junction matches)

@ fCmp_Superset

comparison loc is a superset of the reference loc; some interval boundaries do not match

@ fCmp_intsExtra_5p

comparinos loc has extra interval(s) at 5' end

@ fCmp_RegionOverlap

overlap of the extremes

@ fCmp_intsMissing_3p

comparison loc is missing interval(s) at 3' end

@ fCmp_3pExtension

3' terminal interval extended (other splice junction matches)

@ fCmp_3pTruncation

3' terminal interval truncated (other splice junction matches)

@ fCmp_NoOverlap

seq_locs do not overlap at all

@ fCmp_StrandDifferent

different strand

@ fCmp_Unknown

failed to compare

@ fCmp_Overlap

at least one interval overlaps

@ fCmp_intsMissing_internal

comparison loc is missing interval(s) internally

@ fCmp_intsMissing_5p

comparison loc is missing interval(s) at 5' end

@ fCmp_Match

all junctions match (fuzz-agnostic)

@ fCmp_intsExtra_3p

comparinos loc has extra interval(s) at 3' end

void x_Compare()

Process the seq_locs and generate the m_IntComparisons vector; Recompute the counts.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

ESubtype GetSubtype(void) const

namespace ncbi::objects::

int Compare(const CSeq_feat &f2) const

Compare relative order of this feature and feature f2, ordering first by features' coordinates,...

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

CNcbiOstream & operator<<(CNcbiOstream &out, const CCompareFeats &cf)

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

main entry point for tests

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void Info(CExceptionArgs_Base &args)

#define MSerial_AsnText

I/O stream manipulators –.

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

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

string GetLabel(const CSeq_id &id)

@ eContent

Untagged human-readable accession or the like.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Override Assign() to incorporate cache invalidation.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

void Add(const CSeq_loc &other)

Simple adding of seq-locs.

void GetLabel(string *label) const

Appends a label suitable for display (e.g., error messages) label must point to an existing string ob...

void SetNull(void)

Override all setters to incorporate cache invalidation.

TSeqPos GetStop(ESeqLocExtremes ext) const

@ eEmpty_Allow

ignore empty locations

TSeqPos GetStop(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the stop of the location.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

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...

TSeqPos GetStart(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the start of the location.

sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

Returns the sequence::ECompare containment relationship between CSeq_locs.

CRef< CSeq_loc > Seq_loc_Subtract(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)

Subtract the second seq-loc from the first one.

CRef< CSeq_loc > Seq_loc_Merge(const CSeq_loc &loc, CSeq_loc::TOpFlags flags, CScope *scope)

Merge ranges in the seq-loc.

bool IsOneBioseq(const CSeq_loc &loc, CScope *scope)

Returns true if all embedded CSeq_ids represent the same CBioseq, else false.

CRef< CSeq_loc > Seq_loc_Add(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)

Add two seq-locs.

int TestForOverlap(const CSeq_loc &loc1, const CSeq_loc &loc2, EOverlapType type, TSeqPos circular_len=kInvalidSeqPos, CScope *scope=0)

Calls TestForOverlap64() and if the result is greater than kMax_Int truncates it to kMax_Int.

bool IsSameBioseq(const CSeq_id &id1, const CSeq_id &id2, CScope *scope, CScope::EGetBioseqFlag get_flag=CScope::eGetBioseq_All)

Determines if two CSeq_ids represent the same CBioseq.

@ fCompareOverlapping

Check if seq-locs are overlapping.

@ eOverlap_Simple

any overlap of extremes

@ eContains

First CSeq_loc contains second.

@ eOverlap

CSeq_locs overlap.

@ eSame

CSeq_locs contain each other.

@ eContained

First CSeq_loc contained by second.

@ eNoOverlap

CSeq_locs do not overlap or abut.

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

SAnnotSelector & SetOverlapIntervals(void)

Check overlapping of individual intervals.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

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

Convert int to string.

static const char label[]

const TDb & GetDb(void) const

Get the Db member data.

const TLocus & GetLocus(void) const

Get the Locus member data.

vector< CRef< CDbtag > > TDbxref

E_Choice Which(void) const

Which variant is currently selected.

const TId & GetId(void) const

Get the Id member data.

const TLocal & GetLocal(void) const

Get the variant data.

const TLocation & GetLocation(void) const

Get the Location member data.

bool IsLocal(void) const

Check if variant Local is selected.

bool IsGene(void) const

Check if variant Gene is selected.

const TData & GetData(void) const

Get the Data member data.

bool CanGetData(void) const

Check if it is safe to call GetData method.

const TDbxref & GetDbxref(void) const

Get the Dbxref member data.

bool CanGetId(void) const

Check if it is safe to call GetId method.

const TProduct & GetProduct(void) const

Get the Product member data.

const TGene & GetGene(void) const

Get the variant data.

bool CanGetProduct(void) const

Check if it is safe to call GetProduct method.

bool IsSetDbxref(void) const

support for xref to other databases Check if a value has been assigned to Dbxref data member.

bool IsRna(void) const

Check if variant Rna is selected.

bool IsEmpty(void) const

Check if variant Empty is selected.

ENa_strand

strand of nucleic acid

const TWhole & GetWhole(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsNull(void) const

Check if variant Null is selected.

@ eNa_strand_both

in forward orientation

@ e_not_set

No variant selected.

unsigned missing_internal() const

unsigned extra_internal() const

unsigned partially_matched

This helper struct is used to accumulate the neighboring comparisons of the same class,...

bool Add(const SIntervalComparisonResult &r)

if the comparison is neighboring and of the same class, set the terminal compariosn to it and return ...

void Reset(const SIntervalComparisonResult &r)

SIntervalComparisonResult m_last

SIntervalComparisonResult m_first

int m_position_comparison

Comparison functor for pqueue storing related comparisons.

bool operator()(const CRef< CCompareFeats > &c1, const CRef< CCompareFeats > &c2) const

bool operator()(CConstRef< CSeq_feat > f1, CConstRef< CSeq_feat > f2) const

CRef< CTestThread > thr[k_NumThreadsMax]

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