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

{

, TYPE_start_codon},

{

, TYPE_stop_codon},

{

, TYPE_5utr},

{

, TYPE_initial},

{

, TYPE_exon},

{

, TYPE_exon},

{

, TYPE_exon},

{

, TYPE_terminal},

{

, TYPE_3utr},

(recordPart.empty()) {

typeIt->second;

(mStrand != other.mStrand) {

((mStart <= other.mStart) && (mStop >= other.mStop));

pLocation->

(*pInterval);

mIdResolver(idResolver)

& prefixOverride)

list<string> cdsTypes{

,

,

};

list<string> transcriptTypes = {

,

,

,

,

,

,

};

prefix = prefixOverride;

(prefixOverride.empty()) {

(std::find(cdsTypes.begin(), cdsTypes.end(), prefix) != cdsTypes.end()) {

(std::find(transcriptTypes.begin(), transcriptTypes.end(), prefix)

!= transcriptTypes.end()) {

prefix =

;

(prefix ==

) {

(prefix +

+ record.

());

(prefix +

+ record.

());

(

& existingRecord: existingEntry->second) {

(existingRecord.Contains(

)) {

existingRecord.mType =

.mType;

existingRecord.mPartNum =

.mPartNum;

(

.Contains(existingRecord)) {

.mPartNum = existingRecord.mPartNum;

existingEntry->second.push_back(

);

(locations.empty()) {

);

(locations.size() == 1) {

& onlyOne = locations.front();

pSeqloc = onlyOne.GetLocation();

& mix = pSeqloc->

();

(

&

: locations) {

mix.AddSeqLoc(*

.GetLocation());

);

& mix = pSeqloc->

();

(

&

: locations) {

mix.AddSeqLoc(*

.GetLocation());

);

(pSeqloc->

()) {

(rangeStart >= rangeStop) {

(*pRangeId, rangeStop, rangeStart, rangeStrand));

pSeqloc->

(*pOverlap);

it = seqlocIntervals.begin();

oldFrom = (*it)->GetFrom();

oldTo = (*it)->GetTo();

(it++; it != seqlocIntervals.end(); it++) {

newFrom = (*it)->GetFrom();

newTo = (*it)->GetTo();

(newTo >= oldFrom) {

pMix->AddInterval(*pRangeId, 0, oldTo, rangeStrand);

oldFrom = newFrom, oldTo = newTo;

(oldFrom > oldTo) {

pMix->AddInterval(*pRangeId, oldFrom, oldTo, rangeStrand);

(rangeStart <= rangeStop) {

(*pRangeId, rangeStart, rangeStop, rangeStrand));

pSeqloc->

(*pOverlap);

it = seqlocIntervals.begin();

oldFrom = (*it)->GetFrom();

oldTo = (*it)->GetTo();

(it++; it != seqlocIntervals.end(); it++) {

newFrom = (*it)->GetFrom();

newTo = (*it)->GetTo();

(newFrom >= oldTo) {

pMix->AddInterval(*pRangeId, oldFrom, oldTo, rangeStrand);

oldFrom = 0, oldTo = newTo;

(oldFrom > oldTo) {

pMix->AddInterval(*pRangeId, oldFrom, oldTo, rangeStrand);

@ eExtreme_Biological

5' and 3'

CRef< CSeq_id > GetSeqId(TReaderFlags, SeqIdResolver=nullptr) const

ENa_strand Strand() const

const string & NormalizedType() const

string ValueOf(const string &key) const

CRef< CSeq_loc > MergeLocationForCds(LOCATIONS &)

void AddRecordForId(const string &, const CGtfReadRecord &)

void AddRecord(const CGtfReadRecord &)

CRef< CSeq_loc > MergeLocation(CSeqFeatData::ESubtype, LOCATIONS &)

void AddStubForId(const string &)

CGtfLocationMerger(unsigned int flags=0, CGff3ReadRecord::SeqIdResolver=nullptr)

CRef< CSeq_loc > MergeLocationDefault(LOCATIONS &)

CRef< CSeq_loc > MergeLocationForTranscript(LOCATIONS &)

CRef< CSeq_loc > MergeLocationForGene(LOCATIONS &)

CGff3ReadRecord::SeqIdResolver mIdResolver

list< CGtfLocationRecord > LOCATIONS

LOCATION_MAP mMapIdToLocations

string GetFeatureIdFor(const CGtfReadRecord &, const string &="")

CGtfLocationRecord & operator=(const CGtfLocationRecord &)

RecordType GetRecordType(const CGtfReadRecord &)

bool Contains(const CGtfLocationRecord &) const

static TYPEORDER_MAP msTypeOrder

static bool CompareTypeAndPartNumbers(const CGtfLocationRecord &lhs, const CGtfLocationRecord &rhs)

CGtfLocationRecord(const CGtfReadRecord &, unsigned int, CGff3ReadRecord::SeqIdResolver)

CRef< CSeq_loc > GetLocation()

const CGtfAttributes & GtfAttributes() const

string FeatureKey() const

const_iterator end() const

const_iterator find(const key_type &key) const

The NCBI C++ standard methods for dealing with std::string.

static const char location[]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define NCBI_ASSERT(expr, mess)

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

ENa_strand GetStrand(void) const

Get the location's strand.

void ChangeToPackedInt(void)

Works only if location is currently an interval, point, packed-int (handled trivially),...

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

CRef< CSeq_loc > Merge(TOpFlags flags, ISynonymMapper *syn_mapper) const

All functions create and return a new seq-loc object.

bool IsSetStrand(EIsSetStrand flag=eIsSetStrand_Any) const

Check if strand is set for any/all part(s) of the seq-loc depending on the flag.

const CSeq_id * GetId(void) const

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

void SetNull(void)

Override all setters to incorporate cache invalidation.

TSeqPos GetStop(ESeqLocExtremes ext) 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 int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

void SetTo(TTo value)

Assign a value to To data member.

const Tdata & Get(void) const

Get the member data.

void SetId(TId &value)

Assign a value to Id data member.

void SetFrom(TFrom value)

Assign a value to From data member.

bool IsInt(void) const

Check if variant Int is selected.

void SetStrand(TStrand value)

Assign a value to Strand data member.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

static bool s_IsTranscriptType(int recType)

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