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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gff3__location__merger_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/readers/gff3_location_merger.cpp Source File

: m_pMessageListener(pListener)

(

) +

+

);

mapIt =

.emplace(

, list<CGffIdTrackRecord>()).first;

mapIt->second.push_back(trackRecord);

(!parentId.empty()) {

& recordList = mapIt->second;

(pendingType ==

) {

recordList.push_back(trackRecord);

(!parentId.empty()) {

(!

.

()) {

expectedType = recordList.front().mSeqType;

(pendingType != expectedType) {

errorDuplicateId;

pendingSeqId = record.

();

expectedSeqId = recordList.front().mSeqId;

(pendingSeqId != expectedSeqId) {

errorDuplicateId;

(!parentId.empty()) {

recordList.push_back(trackRecord);

(

+ parentId +

));

errorBadParentId;

mIdResolver(idResolver),

mIdTracker(pListener),

m_pMessageListener(pListener)

seqSize = seqSizeIt->second;

(record.

() >= seqSize) {

message =

;

message +=

;

message =

;

message +=

;

(

&

: ids) {

& locations = existingEntry->second;

(locations.size() == 1 && locations.front().mType ==

) {

existingEntry->second.push_front(

);

(recordType ==

||

recordType ==

||

recordType ==

) {

(

&

: ids) {

= record.

() +

+ id;

& seqId)

sizeIt = mSequenceSizes.find(seqId);

(sizeIt == mSequenceSizes.end()) {

sizeIt->second;

& seqId = *(locRecord.

);

(sequenceSize == 0) {

pInterval->

().Assign(seqId);

pLocation->

(*pInterval);

(locRecord.

>= sequenceSize || locRecord. mStop < sequenceSize) {

pInterval->

().Assign(seqId);

pInterval->

(locRecord.

% sequenceSize);

pLocation->

(*pInterval);

pTop->

().Assign(seqId);

pTop->

(locRecord.

% sequenceSize);

pBottom->

().Assign(seqId);

pBottom->

(sequenceSize - 1);

(locRecord.

>= sequenceSize || locRecord.

< sequenceSize) {

pInterval->

().Assign(seqId);

pInterval->

(locRecord.

% sequenceSize);

pLocation->

(*pInterval);

pBottom->

().Assign(seqId);

pBottom->

(sequenceSize - 1);

pTop->

().Assign(seqId);

pTop->

(locRecord.

% sequenceSize);

(locations.empty()) {

(locations.size() == 1) {

& onlyOne = locations.front();

frame = onlyOne.mFrame;

& mix = pSeqLoc->

();

(

&

: locations) {

&

= locations.front();

frame =

.mFrame;

(

&

: locations) {

bool GetAttribute(const string &, string &) const

void GetLocation(const string &, CRef< CSeq_loc > &, CCdregion::EFrame &)

map< string, TSeqPos > mSequenceSizes

CReaderListener * m_pMessageListener

void MergeLocation(CRef< CSeq_loc > &, CCdregion::EFrame &, LOCATIONS &)

CGff3ReadRecord::SeqIdResolver mIdResolver

LOCATION_MAP mMapIdToLocations

TSeqPos GetSequenceSize(const string &) const

CRef< CSeq_loc > xGetRecordLocation(const CGff3LocationRecord &)

bool AddRecord(const CGff2Record &)

static bool xGetLocationIds(const CGff2Record &, list< string > &)

list< CGff3LocationRecord > LOCATIONS

CGff3LocationMerger(unsigned int flags=0, CGff3ReadRecord::SeqIdResolver=CReadUtil::AsSeqId, TSeqPos sequenceSize=0, CReaderListener *pListener=nullptr)

void VerifyRecordLocation(const CGff2Record &)

void AddRecordForId(const string &, const CGff2Record &)

static void xSortLocations(LOCATIONS &)

static bool ComparePositions(const CGff3LocationRecord &lhs, const CGff3LocationRecord &rhs)

static bool ComparePartNumbers(const CGff3LocationRecord &lhs, const CGff3LocationRecord &rhs)

CConstRef< CSeq_id > mpGffId

CGff3LocationRecord(const CGff2Record &, unsigned int, CGff3ReadRecord::SeqIdResolver)

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

const string & Type() const

ENa_strand Strand() const

const string & Id() const

const string & NormalizedType() const

CGffIdTracker(CReaderListener *pListener=nullptr)

CReaderListener * m_pMessageListener

map< string, list< CGffIdTrackRecord > > mIds

void CheckAndIndexRecord(string id, const CGff2Record &record)

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.

@ eDiag_Error

Error message.

void SetPacked_int(TPacked_int &v)

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

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

void SetNull(void)

Override all setters to incorporate cache invalidation.

#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.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

@ eFrame_not_set

not set, code uses one

void SetTo(TTo value)

Assign a value to To data member.

void SetId(TId &value)

Assign a value to Id data member.

void SetFrom(TFrom value)

Assign a value to From data member.

virtual void Reset(void)

Reset the whole object.

void SetStrand(TStrand value)

Assign a value to Strand data member.

constexpr auto front(list< Head, As... >, T=T()) noexcept -> Head

constexpr bool empty(list< Ts... >) noexcept

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