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

sLocalID = sLocalID.

(sPrefixToRemove.

());

( id_as_num > 0 ) {

seq_inst->

().SetDelta().Set().push_back(delta_seq);

delta_seq->SetLiteral().SetFuzz().SetLim();

delta_seq->SetLiteral().SetSeq_data().SetGap();

& loc = delta_seq->SetLoc();

loc.

().SetId(*comp_id);

TGapTrans sc_GapTrans[] = {

TGapMap::const_iterator find_iter =

( find_iter == sc_GapMap.end() ) {

out_gap_info.

( find_iter->second );

TEvidTrans sc_EvidTrans[] = {

TEvidMap::const_iterator find_iter =

sc_EvidMap.find(eLinkageEvidence);

( find_iter == sc_EvidMap.end() ) {

<<

(eLinkageEvidence) );

pEvid->SetType( find_iter->second );

link_evid.push_back( pEvid );

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

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

virtual int Finalize()

This is called at the end of the file, usually automatically but can be called manually if the automa...

CRef< CAgpRow > m_prev_row

CRef< CAgpRow > m_this_row

@ fLinkageEvidence_strobe

@ fLinkageEvidence_align_genus

@ fLinkageEvidence_paired_ends

@ fLinkageEvidence_align_xgenus

@ fLinkageEvidence_align_trnscpt

@ fLinkageEvidence_within_clone

@ fLinkageEvidence_clone_contig

@ fLinkageEvidence_proximity_ligation

@ fLinkageEvidence_unspecified

string & GetComponentId()

int linkage_evidence_flags

a bit map which holds summary of info in linkage_evidences.

TLinkageEvidenceVec linkage_evidences

vector< ELinkageEvidence > TLinkageEvidenceVec

Might have duplicates, and is empty on error or if there are no actual linkage evidences (e....

virtual void OnGapOrComponent(void)

Builds new part of delta-seq in current bioseq, or adds bioseq and starts building a new one.

void x_FinishedBioseq(void)

Our own finalization after parent's finalization.

static CRef< objects::CSeq_id > s_DefaultSeqIdFromStr(const std::string &str)

This is the default method used to turn strings into Seq-ids in AGP contexts.

vector< CRef< objects::CSeq_entry > > m_entries

Holds the results.

@ fSetSeqGap

Found gaps will not be given Seq-data such as Type and Linkage.

@ fForceLocalId

All IDs will be treated as local IDs.

virtual CRef< objects::CSeq_id > x_GetSeqIdFromStr(const std::string &str)

If you must change exactly how strings are turned into Seq-ids, you can override this in a subclass.

CAgpToSeqEntry(TFlags fFlags=0, EAgpVersion agp_version=eAgpVersion_auto, CAgpErr *arg=nullptr)

After construction, you probably want to do something like call ReadStream and then GetResult.

virtual int Finalize(void)

Parent finalize plus making sure last m_bioseq is added.

static CRef< objects::CSeq_id > s_LocalSeqIdFromStr(const std::string &str)

Turn a string into a local Seq-id (removing "lcl|" from the beginning if needed)

void x_SetSeqGap(objects::CSeq_gap &out_gap_info)

Fills in out_gap_info based on current CAgpRow.

CRef< objects::CBioseq > m_bioseq

This is the bioseq currently being built.

class CStaticArrayMap<> is an array adaptor that provides an STLish interface to statically-defined a...

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

static const char * str(char *buf, int n)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_USER_THROW_FMT(message)

Throw a "user exception" with message processed as output to ostream.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Convert string to int.

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

Convert int to string.

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

Check if a string starts with a specified prefix value.

size_type length(void) const

Return the length of the represented array.

CTempString substr(size_type pos) const

Obtain a substring from this string, beginning at a given offset.

@ fAllowTrailingSpaces

Ignore trailing whitespace characters.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fAllowLeadingSpaces

Ignore leading whitespace characters in converted string.

@ eNocase

Case insensitive compare.

TStr & SetStr(void)

Select the variant.

TId & SetId(void)

Select the variant.

TLocal & SetLocal(void)

Select the variant.

TSeq & SetSeq(void)

Select the variant.

void SetExt(TExt &value)

Assign a value to Ext data member.

void SetType(TType value)

Assign a value to Type data member.

void SetRepr(TRepr value)

Assign a value to Repr data member.

void SetLength(TLength value)

Assign a value to Length data member.

TLinkage_evidence & SetLinkage_evidence(void)

Assign a value to Linkage_evidence data member.

void SetLinkage(TLinkage value)

Assign a value to Linkage data member.

void SetMol(TMol value)

Assign a value to Mol data member.

list< CRef< CLinkage_evidence > > TLinkage_evidence

@ eRepr_delta

sequence made by changes (delta) to others

@ eType_clone

Deprecated. Used only for AGP 1.1.

@ eType_fragment

Deprecated. Used only for AGP 1.1.

@ eType_proximity_ligation

#define DEFINE_STATIC_ARRAY_MAP(Type, Var, Array)

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

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