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NCBI C++ ToolKit: src/algo/structure/cd_utils/cuSequence.cpp Source File

(ID1.Empty() || ID2.Empty()) {

ID1->Match(*ID2);

(

.

())

;

CBioseq::TId::const_iterator cit = bioseqIds.begin(), cend = bioseqIds.end();

(; cit != cend && !

; ++cit) {

(

.NotEmpty() && id->

()) {

pssmId =

->GetGeneral().GetTag().GetId();

list< CRef< CSeq_annot > >::const_iterator j;

list< CRef< CSeq_id > >::const_iterator k;

((*j)->GetData().IsIds()) {

(k = (*j)->GetData().GetIds().begin(); k != (*j)->GetData().GetIds().end(); k++) {

((*k)->IsGeneral()) {

((*k)->GetGeneral().GetDb() ==

) {

((*k)->GetGeneral().GetTag().IsId()) {

= (*k)->GetGeneral().GetTag().GetId();

isTaxIdFound =

;

list< CRef< CSeqdesc > >::const_iterator j, jend;

(j=bioseq.

().

().begin(); j!=jend; j++)

org = &((*j)->GetOrg());

((*j)->IsSource())

org = &((*j)->GetSource().GetOrg());

vector < CRef< CDbtag > >::const_iterator k, kend = org->

().end();

(k=org->

().begin(); k != kend; ++k) {

((*k)->GetDb() ==

) {

((*k)->GetTag().IsId()) {

(isTaxIdFound && taxid != thisTaxid && taxid != -thisTaxid) {

taxid = (thisTaxid >

) ? thisTaxid : -thisTaxid;

isTaxIdFound =

;

list< CRef< CSeqdesc > >::const_iterator j;

((*j)->IsSource()) {

((*j)->GetSource().GetOrg().IsSetTaxname()) {

((*j)->GetSource().GetOrg().GetTaxname());

((*j)->GetSource().GetOrg().IsSetCommon()) {

((*j)->GetSource().GetOrg().GetCommon());

(Seq.

() || Seq->

())

;

->resize(vec.size());

}

(exception& e) {

(

.size() > 0) {

vec.reserve(

.size());

seqData.assign(vec.begin(), vec.end());

MY_NCBISTDAA_TO_AMINOACID[28] = {

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

s.resize(vec.size());

(

=0;

<vec.size();

++) {

s.at(

) = MY_NCBISTDAA_TO_AMINOACID[(

)vec[

]];

(zeroBased && pos < (

)

.size()) {

}

(!zeroBased && pos <= (

)

.size() && pos != 0) {

residue =

[pos-1];

list< CRef< CSeq_id > >& seqIds = bioseq->

();

cit != seqIds.end(); cit++)

* textId = (*cit)->GetTextseq_Id();

acc.size() != 0;

(seqEntry->

())

list< CRef< CSeqdesc > >& descrList = seqEntry->

().

().

();

list< CRef< CSeqdesc > >::const_iterator cit = descrList.begin();

(; cit != descrList.end(); cit++)

list< CRef< CSeqdesc > >& descrList = seqEntry->

().

().

();

list< CRef< CSeqdesc > >::const_iterator cit = descrList.begin();

(; cit != descrList.end(); cit++)

list< CRef< CSeq_entry > >::const_iterator lsei;

list< CRef< CSeq_entry > >& seqEntryList = seqEntry->

().

();

(lsei = seqEntryList.begin(); lsei != seqEntryList.end(); ++lsei)

ctr = 0;

CBioseq::TId::const_iterator idCit, idEnd;

idEnd = bioseq->

().end();

(idCit = bioseq->

().begin(); idCit != idEnd && ctr < nth; ++idCit) {

((*idCit).NotEmpty() && (*idCit)->IsGi()) {

(ctr != nth)

;

giSeqId->

(**idCit);

gi = giSeqId->

();

ctr = 0;

CBioseq::TId::const_iterator idCit, idEnd;

idEnd = bioseq->

().end();

(idCit = bioseq->

().begin(); idCit != idEnd && ctr < nth; ++idCit) {

((*idCit).NotEmpty() && (*idCit)->IsPdb()) {

(ctr != nth)

;

pdbSeqId->

(**idCit);

CBioseq::TId::const_iterator idCit = bioseq.

().begin(), idEnd = bioseq.

().end();

(; idCit != idEnd && !

; ++idCit) {

((*idCit)->Which() == choice) {

CBioseq_set::TSeq_set::const_iterator bssCit, bssEnd;

(seqEntry->

()) {

(; bssCit != bssEnd && !

; ++bssCit) {

((*bssCit)->IsSeq()) {

}

((*bssCit)->IsSet()) {

}

(seqEntry->

()) {

CBioseq::TId::const_iterator idCit = bioseq.

().begin(), idEnd = bioseq.

().end();

(; idCit != idEnd; ++idCit) {

((*idCit)->Which() == choice) {

->Assign(**idCit);

idsOfType.push_back(

);

idsOfType.size();

list< CRef< CSeq_id > > tmpList;

CBioseq_set::TSeq_set::const_iterator bssCit, bssEnd;

(seqEntry->

()) {

(; bssCit != bssEnd; ++bssCit) {

((*bssCit)->IsSeq()) {

idsOfType.insert(idsOfType.end(), tmpList.begin(), tmpList.end());

}

((*bssCit)->IsSet()) {

idsOfType.insert(idsOfType.end(), tmpList.begin(), tmpList.end());

}

(seqEntry->

()) {

idsOfType.size();

list< CRef< CSeq_id > > tmpList;

CBioseq_set::TSeq_set::const_iterator bssCit, bssEnd;

(seqEntry->

()) {

(; bssCit != bssEnd && !

; ++bssCit) {

((*bssCit)->IsSeq()) {

seqEntryBioseq->

((*bssCit)->GetSeq());

}

(seqEntry->

()) {

list< CRef< CSeq_id > > tmpList;

CBioseq_set::TSeq_set::iterator bssIt, bssEnd;

(seqEntry->

()) {

(; bssIt != bssEnd && !

; ++bssIt) {

((*bssIt)->IsSeq()) {

seqEntryBioseq = &(*bssIt)->SetSeq();

}

(seqEntry->

()) {

seqEntryBioseq = &(seqEntry->

());

seqDescr.

().push_back(seqdescComment);

hasSource =

;

hasTitle =

;

(seqDescr.

()) {

list< CRef< CSeqdesc > >& descrList = seqDescr.

();

list< CRef< CSeqdesc > >::iterator it = descrList.begin();

(!hasTitle && it != descrList.end()) {

hasTitle = ((*it)->IsTitle());

it = descrList.begin();

(it != descrList.end()) {

((*it)->IsSource() && (!hasSource)) {

}

((*it)->IsTitle()) {

}

((*it)->IsComment() && find(keptComments.begin(), keptComments.end(), (*it)->GetComment()) != keptComments.end()) {

}

((*it)->IsPdb()) {

& pdbBlock = (*it)->GetPdb();

(newTitle.length() > 0) {

descrList.push_back(addedTitle);

it = descrList.erase(it);

it = descrList.erase(it);

(seqEntry.

())

;

(seqEntry->

()) {

}

(seqEntry->

()) {

(; bssIt != bssEnd; ++bssIt) {

acc, dbSource;

acc, dbSource;

accession =

;

(seqID->

()) {

(seqID->

()) {

(pLocal.

()) {

(pLocal.

()) {

accession = pLocal.

();

(pGeneral.

() && !getGenericSource) {

dbSource = dbSource +

+ pGeneral.

();

(seqID->

()) {

(!textseqId)

;

(!getGenericSource && !seqID->

()) {

.acession.erase();

list< CRef< CSeq_id > >& seqIds = bioseq->

();

cit != seqIds.end(); cit++)

* textId = (*cit)->GetTextseq_Id();

(

.acession.size() > 0)

.dbsource = (*cit)->Which();

list< CRef< CSeqdesc > >::const_iterator dit;

((*dit)->IsTitle())

.defline = ((*dit)->GetTitle());

!

.acession.empty();

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.

static string SeqIdTypeToSource(unsigned int seqIdType, string accession=kEmptyStr)

static string GetSourceName(EDbSource priority)

string GetEffectiveChain_id(EBothUnsetPriority bothUnsetPriority=eBothUnset_ChainId) const

static SIZE_TYPE Convert(const CTempString &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst, TCoding dst_coding)

@Seq_descr.hpp User-defined methods of the data storage class.

bool NcbieaaToNcbistdaaString(const std::string &str, vector< char > &vec)

bool ExtractGi(const CRef< CBioseq > &bioseq, TGi &gi, unsigned int nth)

bool SeqIdHasMatchInBioseq(const CRef< CSeq_id > &id, const CBioseq &bioseq)

void NcbistdaaToNcbieaaString(const std::vector< char > &vec, std::string *str)

TTaxId GetTaxIdInBioseq(const CBioseq &bioseq)

bool GetNcbistdSeq(const CBioseq &bioseq, vector< char > &seqData)

bool CopyBioseqWithType(const CRef< CSeq_entry > &seqEntry, CSeq_id::E_Choice choice, CRef< CBioseq > &seqEntryBioseq)

bool GetNcbieaaString(const CRef< CSeq_entry > &Seq, string &Str)

int GetSeqLength(const CBioseq &bioseq)

bool GetBioseqWithType(CRef< CSeq_entry > &seqEntry, CSeq_id::E_Choice choice, CRef< CBioseq > &seqEntryBioseq)

void SimplifySeqEntryForCD(CRef< CSeq_entry > &seqEntry, const vector< string > &keptComments, bool keepPDBBlock)

bool AddCommentToBioseq(CBioseq &bioseq, const string &comment)

string GetSpeciesFromBioseq(const CBioseq &bioseq)

bool CopyGiSeqId(const CRef< CBioseq > &bioseq, CRef< CSeq_id > &giSeqId, unsigned int nth)

void SimplifyBioseqForCD(CBioseq &bioseq, const vector< string > &keptComments, bool keepPDBBlock)

char GetResidueAtPosition(const CRef< CSeq_entry > &seqEntry, int pos, bool zeroBased)

bool GetPDBBlockFromSeqEntry(CRef< CSeq_entry > seqEntry, CRef< CPDB_block > &pdbBlock)

bool extractBioseqInfo(const CRef< CBioseq > bioseq, BioseqInfo &info)

string GetAccessionForSeqId(const CRef< CSeq_id > &seqID)

string GetDbSourceForSeqId(const CRef< CSeq_id > &seqID)

int GetCDDPssmIdFromSeqId(const CRef< CSeq_id > &id)

bool IsEnvironmentalSeq(const CBioseq &bioseq)

string GetRawSequenceString(const CBioseq &bioseq)

bool CopyPdbSeqId(const CRef< CBioseq > &bioseq, CRef< CSeq_id > &pdbSeqId, unsigned int nth)

bool ExtractPdbMolChain(const CRef< CBioseq > &bioseq, string &pdbMol, string &pdbChain, unsigned int nth)

void GetAccessionAndDatabaseSource(const CRef< CSeq_id > &seqID, string &accession, string &dbSource, bool getGenericSource)

unsigned int CopySeqIdsOfType(const CBioseq &bioseq, CSeq_id::E_Choice choice, list< CRef< CSeq_id > > &idsOfType)

bool HasSeqIdOfType(const CBioseq &bioseq, CSeq_id::E_Choice choice)

int GetMMDBId(const CBioseq &bioseq)

bool SeqIdsMatch(const CRef< CSeq_id > &ID1, const CRef< CSeq_id > &ID2)

bool IsConsensus(const CRef< CSeq_id > &seqId)

bool GetAccAndVersion(const CRef< CBioseq > bioseq, string &acc, int &version, CRef< CSeq_id > &seqId)

const TTaxId ENVIRONMENTAL_SEQUENCE_TAX_ID

bool Empty(const CNcbiOstrstream &src)

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

SStrictId_Tax::TId TTaxId

Taxon id type.

#define TAX_ID_FROM(T, value)

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

Set object to copy of another one.

const TPrim & Get(void) const

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

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

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

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

Convert int to string.

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.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetDb(void) const

name of database or system Check if a value has been assigned to Db data member.

const TTag & GetTag(void) const

Get the Tag member data.

bool IsId(void) const

Check if variant Id is selected.

bool IsSetTag(void) const

appropriate tag Check if a value has been assigned to Tag data member.

const TDb & GetDb(void) const

Get the Db member data.

const TStr & GetStr(void) const

Get the variant data.

TId GetId(void) const

Get the variant data.

const TDb & GetDb(void) const

Get the Db member data.

bool IsPatent(void) const

Check if variant Patent is selected.

const TPdb & GetPdb(void) const

Get the variant data.

TGibbsq GetGibbsq(void) const

Get the variant data.

TId GetId(void) const

Get the Id member data.

const TName & GetName(void) const

Get the Name member data.

bool IsGibbmt(void) const

Check if variant Gibbmt is selected.

bool IsGeneral(void) const

Check if variant General is selected.

bool CanGetName(void) const

Check if it is safe to call GetName method.

E_Choice Which(void) const

Which variant is currently selected.

bool IsPdb(void) const

Check if variant Pdb is selected.

TGi GetGi(void) const

Get the variant data.

bool CanGetDb(void) const

Check if it is safe to call GetDb method.

TVersion GetVersion(void) const

Get the Version member data.

bool CanGetVersion(void) const

Check if it is safe to call GetVersion method.

const TMol & GetMol(void) const

Get the Mol member data.

TSeqid GetSeqid(void) const

Get the Seqid member data.

E_Choice

Choice variants.

const TGiim & GetGiim(void) const

Get the variant data.

const TLocal & GetLocal(void) const

Get the variant data.

bool IsGiim(void) const

Check if variant Giim is selected.

bool IsLocal(void) const

Check if variant Local is selected.

bool CanGetAccession(void) const

Check if it is safe to call GetAccession method.

const TGeneral & GetGeneral(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

const TPatent & GetPatent(void) const

Get the variant data.

TGibbmt GetGibbmt(void) const

Get the variant data.

bool IsGibbsq(void) const

Check if variant Gibbsq is selected.

const TDb & GetDb(void) const

Get the Db member data.

const TAccession & GetAccession(void) const

Get the Accession member data.

const TSeq & GetSeq(void) const

Get the variant data.

const TDescr & GetDescr(void) const

Get the Descr member data.

TSet & SetSet(void)

Select the variant.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

const TIupacaa & GetIupacaa(void) const

Get the variant data.

void ResetDescr(void)

Reset Descr data member.

bool IsSetSeq_data(void) const

the sequence Check if a value has been assigned to Seq_data data member.

bool IsNcbieaa(void) const

Check if variant Ncbieaa is selected.

const TInst & GetInst(void) const

Get the Inst member data.

TTitle & SetTitle(void)

Select the variant.

bool IsIupacaa(void) const

Check if variant Iupacaa is selected.

bool IsNcbistdaa(void) const

Check if variant Ncbistdaa is selected.

bool IsSetAnnot(void) const

Check if a value has been assigned to Annot data member.

TPdb & SetPdb(void)

Select the variant.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

const TId & GetId(void) const

Get the Id member data.

void ResetAnnot(void)

Reset Annot data member.

const Tdata & Get(void) const

Get the member data.

TLength GetLength(void) const

Get the Length member data.

list< CRef< CSeq_id > > TId

const TNcbieaa & GetNcbieaa(void) const

Get the variant data.

TComment & SetComment(void)

Select the variant.

const TNcbistdaa & GetNcbistdaa(void) const

Get the variant data.

bool IsSetLength(void) const

length of sequence in residues Check if a value has been assigned to Length data member.

bool IsSetDescr(void) const

descriptors Check if a value has been assigned to Descr data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

Tdata & Set(void)

Assign a value to data member.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

const TDescr & GetDescr(void) const

Get the Descr member data.

bool CanGetCompound(void) const

Check if it is safe to call GetCompound method.

const TCompound & GetCompound(void) const

Get the Compound member data.

unsigned int

A callback function used to compare two keys in a database.

use only n Cassandra database for the lookups</td > n</tr > n< tr > n< td > yes</td > n< td > do not use tables BIOSEQ_INFO and BLOB_PROP in the Cassandra database

const string version

version string

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