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

numFilteredByOverlap(0){}

+=

+=

;

+=

;

+=

;

(

= 0;

< gis.size();

++)

+= NStr::NumericToString<TGi>( gis[

] );

(giPairs.size() <= 0)

(

= 0 ;

< giPairs.size();

++)

+= NStr::NumericToString<TGi>(giPairs[

].second);

+= NStr::NumericToString<TGi>(giPairs[

].

);

(

= 0;

< cds.size();

++)

(list<UpdaterInterface*>::iterator lit =

->begin();

((*lit)->hasCd(cds[

]))

(

= 0;

< updaters.size();

++)

(list<UpdaterInterface*>::iterator lit =

->begin();

((*lit) == updaters[

])

list<UpdaterInterface*>::iterator lit =

->begin();

blasted.push_back(updater);

blasted.size();

(

= 0;

< cds.size();

++)

allDone =

;

(

);

allDone =

;

: m_config(

), m_cd(cd), m_guideAlignment(0), m_processPendingThreshold(-1), m_hitsNeeded(-1),

blasted =

;

(blast::CBlastException& be) {

(blasted ? 1 : 0);

updated =

;

(numNoAlignment > 0)

(

<<numNoAlignment

<<

);

cds.push_back(

);

blast::CRemoteBlast* rblast;

blast::CBlastProteinOptionsHandle* blastopt;

blastopt =

blast::CBlastProteinOptionsHandle(blast::CBlastOptions::eRemote);

rblast =

blast::CRemoteBlast(blastopt);

psiopt =

blast::CPSIBlastOptionsHandle(blast::CBlastOptions::eRemote);

rblast =

blast::CRemoteBlast(psiopt);

entrezQuery +=

;

(!entrezQuery.empty())

rblast->SetEntrezQuery(entrezQuery.c_str());

list< CRef< CSeq_entry > >& seqList = bioseqs->SetSeq_set();

seqList.push_back(seqOld);

(masks.size() > 0)

masking_locations.push_back(masks);

rblast->SetQueries(bioseqs,masking_locations);

rblast->SetQueries(bioseqs);

useConsensus =

;

.unalignedSegThreshold = 35;

.requestFrequencyRatios =

;

rblast->SetQueries(pssm);

blasted =

;

rblast-> SubmitSync();

= rblast->GetRID();

blasted = rblast->Submit();

= rblast->GetRID();

blast::CRemoteBlast rblast(

());

= rblast.CheckDone();

hits = rblast.GetAlignments();

blast::CRemoteBlast rblast(

());

= rblast.CheckDone();

(!seqAligns.

())

(numNoAlignment > 0)

(

);

(

<<

->

() <<

);

nIdent = 0;

qLen = queryString.length(), sLen = subjectString.length();

, j, qStart, qStop, sStart, sStop;

(alignment.

() || qLen == 0 || sLen == 0)

;

denom = (denseg.GetSeqStop(0) - denseg.GetSeqStart(0) + 1);

(

= 0;

< lens.size(); ++

) {

(starts[2*

] < 0 || starts[2*

+ 1] < 0)

;

qStart = starts[2*

];

sStart = starts[2*

+ 1];

qStop = qStart + lens[

] - 1;

sStop = sStart + lens[

] - 1;

(qStop >= qLen || sStop >= sLen)

;

(j = 0; j < lens[

]; ++j) {

(queryString[qStart + j] == subjectString[sStart + j]) ++nIdent;

= 100.0*nIdent/denom;

( !cd || (!alignments.

()))

pidScore = 0.0;

list< CRef< CSeq_align > >& seqAligns = alignments.

();

vector< CRef< CBioseq > > bioseqs;

vector< CRef< CBioseq > > bioseqVec;

(

= 0;

< bioseqs.size();

++)

list< CRef< CSeq_align > >::iterator it = seqAligns.begin();

queryString, subjectString;

(it != seqAligns.end()) {

querySeqID = (*it)->SetSegs().SetDenseg().GetIds()[0];

queryBioseq.

();

vector< CRef< CSeq_id > >& seqIds= denseg->SetIds();

vector< CRef< CSeq_id > > pdbIds;

((pdbIds.size() > 0) &&

(masterSeq, *seqIds[0]) && (!seqIds[0] ->IsPdb()))

(; it != seqAligns.end(); it++)

start = denseg.GetSeqStart(0);

stop = denseg.GetSeqStop(0);

pidScore = 100*pidScore/(stop - start + 1);

(denseg.GetDim() > 1)

seqID = denseg.GetIds()[1];

vector< CRef< CBioseq > > bioseqVec;

(bioseqVec.size() > 1)

index =

(refresher, seqAlignRef, bioseqVec);

seqEntry->

(*bioseqVec[index]);

seqID = denseg.GetIds()[1];

gi = seqID->

();

seqEntry->

(*bioseqVec[0]);

replacedGi = refresher->

(seqAlignRef, seqEntry);

((completed % 500) == 0)

vector< CRef< CSeq_id > > seqIds;

(seqIds.size() == 0)

(SeqID->

())

vector< CRef< CSeq_id > >& seqIdVec = denseg.SetIds();

(denseg.GetDim() > 1);

(

= 0;

< (

) bioseqVec.size();

++)

CBioseq::TId::const_iterator it = ids.begin(), itend = ids.end();

(; it != itend; ++it)

(

= 0;

< (

) bioseqVec.size();

++)

CBioseq::TId::const_iterator it = ids.begin(), itend = ids.end();

foundPDB =

;

(; it != itend; ++it)

((*it)->IsGi())

(

= 0;

< (

) bioseqVec.size();

++)

CBioseq::TId::const_iterator it = ids.begin(), itend = ids.end();

(; it != itend; ++it)

foundOldSeq =

;

(

= 0;

< num;

++)

((oAcc == nAcc) && (giNew != giOld))

(overlap < 0)

;

lastPos =

.getLastAlignedPosition();

firstPos =

.getFirstAlignedPosition();

(lo + overlap <= firstPos)

= (hi - overlap >= firstPos);

= (lo + overlap <lastPos);

(

<<

<<

<< lo <<

<< hi <<

<< firstPos <<

<< lastPos <<

<< overlap);

(

<<

<<

<< lo <<

<< hi <<

<< firstPos <<

<< lastPos <<

);

(lenAligned >= pssmLen)

( ( mGapToN - sGapToN > allowed) ||

(mGapToC - sGapToC > allowed))

(

= 0;

< bioseqs.size();

++)

CBioseq::TId::const_iterator it = ids.begin(), itend = ids.end();

(; it != itend; ++it) {

seqEntry->

(*bioseqs[

]);

loaderName = loader->GetName();

(

<< seqid->GetSeqIdString() <<

);

bioseqs.push_back(bioseq);

vector< CRef<CSeq_id> > seqids;

batchSize = 500;

maxBatchSize = 2000;

list< CRef< CSeq_align > >& seqAligns = alignments.

();

list< CRef< CSeq_align > >::iterator lit = seqAligns.begin();

(; lit != seqAligns.end(); lit++)

seqids.push_back((*lit)->SetSegs().SetDenseg().GetIds()[1]);

list< CRef< CSeq_align > >::iterator

= lit;

(seqids.size() >= batchSize || (

== (seqAligns.end())) )

errors, warnings;

vector< CRef< CBioseq > > bioseqBatch;

(

<< bioseqBatch.size() <<

);

(

<< dbName <<

<< bioseqBatch.size() <<

);

(blast::CBlastException& be)

(seqids.size() > maxBatchSize)

(

<<be.GetErrCodeString());

(

);

(seqids.size()!= bioseqBatch.size())

(

<< seqids.size()<<

<<bioseqBatch.size()<<

);

(

<<errors<<

<<warnings);

(

= 0 ;

< bioseqBatch.size();

++)

bioseqs.push_back(bioseqBatch[

]);

vector< CRef< CSeq_id > > seqIds;

(

= 0;

< seqIds.size();

++)

(seqIds[

]->IsGi())

seqIds[

]->GetGi();

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

();

list< CRef< CSeq_id > >::const_iterator cit = seqIds.begin();

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

(*cit)->GetGi();

vector< CRef< CSeq_id > >& seqIds= denseg->SetIds();

(seqIds.size() <= 1)

vector< CRef< CSeq_id > > slaveIds;

(slaveIds.size() > 0)

seqIds[1].Reset( (slaveIds[0]).GetPointer() );

(seqEntry->

())

seqEntry->

(*bioseq);

hasSource =

;

hasTitle =

;

(seqDescr.

())

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

();

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

(cit != descrList.end())

((*cit)->IsSource() && (!hasSource))

( (*cit)->IsTitle())

((*cit)->IsUser() && (!hasSource))

((*cit)->SetUser().SetType().SetStr() ==

)

vector< CRef< CUser_field > >& fields = (*cit)->SetUser().SetData();

( fields.size() > 0)

descrList.push_back(

);

cit = descrList.erase(cit);

cit = descrList.erase(cit);

(seqEntry->

())

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

().

().

();

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

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

((*cit)->IsSource())

seqDescr.

().push_back(*cit);

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

();

list< CRef< CSeq_id > >::const_iterator cit = seqIds.begin();

isPdb =

;

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

((*cit)->IsPdb())

vector<TIntId> uids;

pdb = (*cit)->GetPdb().GetMol().Get();

.Query(pdb,

, uids);

(

<<pdb<<

<<e.

());

(uids.size() > 0)

generalId.

(

);

generalId.

().SetId(mmdbId);

seqAnnot->

().SetIds().push_back(mmdbTag);

bioseq->

().push_back(seqAnnot);

(pdbBlock->CanGetCompound())

list< string >& compounds = pdbBlock->GetCompound();

(compounds.size() != 0)

seqDesc->

(*(compounds.begin()));

seqDescr.

().push_back(seqDesc);

(seqEntry->

())

list< CRef< CSeq_id > >& seqIdList = seqEntry->

().

();

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

(lsii = seqIdList.begin(); lsii != seqIdList.end(); ++lsii)

((*lsii)->IsPdb())

slaveIds.push_back(*lsii);

slaveIds.push_back(*lsii);

slaveIds.size();

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

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

().

();

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

slaveIds.size();

(seqEntry->

())

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

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

().

();

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

vector< CRef< CSeq_id > > seqIds;

(

= 0;

< seqIds.size();

++)

(seqIds[

]->Match(seqId))

CBioseq::TId::const_iterator it = ids.begin(), itend = ids.end();

(; it != itend; ++it)

((*it)->Match(seqId))

list< CRef< CBlast_def_line > >& deflines = blastDefLine->

();

(deflines.size() <= 1)

bioseqs.push_back(

);

iter != deflines.end(); iter++)

bioseqs.push_back(splitBioseq);

deflines.size();

sourceOrder = 0;

(seqDescr.

())

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

();

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

(cit != descrList.end())

((*cit)->IsSource())

(sourceOrder == order)

cit = descrList.erase(cit);

( (*cit)->IsTitle())

cit = descrList.erase(cit);

title->

(blastDefline->GetTitle());

descrList.push_back(title);

bioseq->

().assign(blastDefline->GetSeqid().begin(), blastDefline->GetSeqid().end());

(oss.size() == 1) {

vector<char> & v = *oss.front();

+= (**iter1).size();

temp.reserve(

);

temp.append(& (**iter3)[0], (*iter3)->size());

* asnDeflineObjLabel =

;

list< CRef< CSeqdesc > >& descList = desc.

();

(list<

>::const_iterator iter = descList.begin(); iter != descList.end(); iter++){

((*iter)->IsUser()){

(uobjid.

()){

(

== asnDeflineObjLabel){

vector< CRef< CUser_field > >& usf = uobj.

();

(usf.front()->GetData().IsOss()){

TOss& oss = usf.front()->GetData().GetOss();

* asnDeflineObjLabel =

;

list< CRef< CSeqdesc > >& descList = desc.

();

(list<

>::iterator iter = descList.begin(); iter != descList.end(); iter++)

((*iter)->IsUser())

(uobjid.

())

(

== asnDeflineObjLabel)

descList.erase(iter);

vector< CRef< CSeq_align > > seqAlignVec;

(

= 0;

< num;

++)

cd_utils::BlockFormater bf(seqAlignVec, seqlen);

list< CRef< CSeq_align > >& seqAlignList = cd->

();

(seqAlignList.size() > 0)

(

.getMaster() ==

.getSlave())

seqAlignList.erase(seqAlignList.begin());

(seqAlignList.size() > 0)

bf.setReferenceSeqAlign(*seqAlignList.begin());

numGood = bf.findIntersectingBlocks(overlap);

bf.formatBlocksForQualifiedRows(seqAlignList);

bf.getQualifiedRows(rows);

(

= 0;

< rows.size();

++)

num - numGood;

(seqEntry.

())

list< CRef< CSeq_entry > >::iterator it = seqSet.begin();

(; it != seqSet.end(); it++)

newgi != oldgi;

newStr, oldStr;

(newStr.size() != oldStr.size())

vector< CRef< CSeq_id > > newIds;

(

= 0;

< newIds.size();

++)

(newIds[

]->IsGi())

(newIds[

]->IsPdb())

pdbId = newIds[

];

replaced =

;

(list<

>::iterator lit = seqAlignList.begin(); lit != seqAlignList.end(); lit++)

(seqAlign, idInAlign,

);

.getSlave().setSeqId(pdbId);

seqAlign =

.toSeqAlign();

.getSlave().setSeqId(giId);

seqAlign =

.toSeqAlign();

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Declares the BLAST exception class.

Declares the CBlastServices class.

CRef< CSeq_align > getSeqAlign(int row) const

int getGapToNTerminal(int bn) const

int getGapToCTerminal(int bn, int len=-1) const

vector< Block > & getBlocks()

int GetUpperBound(int Row) const

string GetSequenceStringByRow(int rowId)

bool AddSequence(CRef< CSeq_entry > seqAntry)

bool GetSeqIDFromAlignment(int RowIndex, CRef< CSeq_id > &SeqID) const

bool AddPendingSeqAlign(CRef< CSeq_align > seqAlign)

bool GetSeqEntryForRow(int rowId, CRef< CSeq_entry > &seqEntry) const

bool CopyBioseqForSeqId(const CRef< CSeq_id > &seqId, CRef< CBioseq > &bioseq) const

void ErasePendingRows(set< int > &rows)

int GetLowerBound(int Row) const

const list< CRef< CSeq_align > > & GetSeqAligns() const

bool GetBioseqForRow(int rowId, CRef< CBioseq > &bioseq)

string GetAccession(int &Version) const

bool GetSeqIDForRow(int Pair, int DenDiagRow, CRef< CSeq_id > &SeqID) const

AccessionBioseqMap m_accSeqMap

bool hasOlderVersion(CRef< CBioseq > bioseq)

void addSequence(CRef< CBioseq > bioseq)

TGi refresh(CRef< CSeq_align > seqAlign, CRef< CSeq_entry > seqEntry)

void addSequences(CSeq_entry &seqEntry)

int submitBlast(bool wait=false, int row=0)

bool findSeq(CRef< CSeq_id > seqID, vector< CRef< CBioseq > > &bioseqs, CRef< CSeq_entry > &seqEntry)

static int mergePending(CCdCore *cd, int threshold, bool remaster)

bool isFragmentedSeq(CCdCore *cd, CRef< CSeq_align > seqAlign, CRef< CSeq_entry > seqEntry)

double ComputePercentIdentity(const CRef< CSeq_align > &alignment, const string &queryString, const string &subjectString)

static void reformatBioseqByBlastDefline(CRef< CBioseq > bioseq, CRef< CBlast_def_line > blastDefline, int order)

static CRef< CBlast_def_line_set > GetBlastDefline(const CBioseq &handle)

bool overlapWithCDRow(CCdCore *cd, CRef< CSeq_align > seqAlign)

static int GetAllIdsFromSeqEntry(CRef< CSeq_entry > seqEntry, vector< CRef< CSeq_id > > &slaveIds, bool pdbOnly=false)

bool blast(bool wait=false, int row=0)

cd_utils::BlockModelPair * m_guideAlignment

CDUpdater(CCdCore *cd, CdUpdateParameters &config)

const string getLastError()

void retrieveAllSequences(CSeq_align_set &alignments, vector< CRef< CBioseq > > &bioseqs)

static bool reformatBioseq(CRef< CBioseq > bioseq, CRef< CSeq_entry > seqEntry, CEntrez2Client &client)

static void RemoveBlastDefline(CBioseq &handle)

void getCds(vector< CCdCore * > &)

static int SplitBioseqByBlastDefline(CRef< CBioseq > handle, vector< CRef< CBioseq > > &bioseqs)

CDUpdateStats & getStats()

static bool SeqEntryHasSeqId(CRef< CSeq_entry > seqEntry, const CSeq_id &seqId)

CRef< CSeq_id > m_masterPdb

static int pickBioseq(CDRefresher *refresher, CRef< CSeq_align > seqAlignRef, vector< CRef< CBioseq > > &bioseqVec)

bool getHits(CRef< CSeq_align_set > &hits)

void getSequencesFromGB(vector< CRef< CSeq_id > > seqids, vector< CRef< CBioseq > > &bioseqs)

CdUpdateParameters m_config

static bool GetOneBioseqFromSeqEntry(CRef< CSeq_entry > seqEntry, CRef< CBioseq > &bioseq, const CSeq_id *seqId=0)

int m_processPendingThreshold

bool modifySeqAlignSeqEntry(CCdCore *cd, CRef< CSeq_align > &seqAlign, CRef< CSeq_entry > seqEntry)

static void OssToDefline(const CUser_field::TData::TOss &oss, CBlast_def_line_set &bdls)

Efficiently decode a Blast-def-line-set from binary ASN.1.

bool passedFilters(CCdCore *cd, CRef< CSeq_align > seqAlign, CRef< CSeq_entry > seqEntry)

bool checkBlastAndUpdate()

static int processPendingToNormal(int overlap, CCdCore *cd)

bool findRowsWithOldSeq(CCdCore *cd, CBioseq &bioseq)

static bool BioseqHasSeqId(const CBioseq &bioseq, const CSeq_id &seqId)

CRef< CSeq_align_set > m_hits

static TGi getGi(CRef< CSeq_entry > seqEntry)

bool update(CCdCore *cd, CSeq_align_set &alignments)

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

CObjectIStreamAsnBinary –.

TTaxId SetTaxId(TTaxId tax_id)

Handle to the protein-protein options to the BLAST algorithm.

Exception class for the CRemoteBlast class.

structure for seqloc info

bool GetNamedScore(const string &id, int &score) const

Get score.

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

static string getOrganismName(Organism org)

string getBlastDatabaseName()

int allowedOverlapWithCDRow

int missingResidueThreshold

void getCds(vector< CCdCore * > &)

GroupUpdater(vector< CCdCore * > &cds, CdUpdateParameters &config)

int submitBlast(bool wait=false, int row=0)

vector< CDUpdater * > m_cdUpdaters

void addBatch(CRef< CSeq_align_set > seqAlignSet)

const string & getConsensus()

void setOptions(const PssmMakerOptions &option)

CRef< CPssmWithParameters > make()

const BlockModelPair & getGuideAlignment()

unsigned findSequencesInTheGroup(CRef< CSeq_id > seqId, vector< CRef< CBioseq > > &bioseqVec) const

void addSequences(vector< CRef< CBioseq > > &bioseqVec, bool grouped=false)

Collection of masked regions for a single query sequence.

static CSafeStatic< list< UpdaterInterface * > > m_updaterList

static void addUpdater(UpdaterInterface *updater)

static int checkAllBlasts(vector< UpdaterInterface * > &blasted)

virtual bool getBlastHits()=0

static void removeUpdaters(const vector< CCdCore * > &cds)

container_type::iterator iterator

const_iterator end() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

CRef< CSeq_align > Denseg2DenseDiagList(const CRef< CSeq_align > &denseSegSeqAlign)

bool GetSeqID(const CRef< CSeq_align > &seqAlign, CRef< CSeq_id > &SeqID, bool getSlave=true)

int GetNumAlignedResidues(const CRef< CSeq_align > &align)

bool ReMasterCdWithoutUnifiedBlocks(CCdCore *cd, int Row, bool resetFields=true)

bool SetUpdateDate(CCdCore *cd)

bool SeqIdsMatch(const CRef< CSeq_id > &id1, const CRef< CSeq_id > &id2)

int GetSeqLength(const CBioseq &bioseq)

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

string GetRawSequenceString(const CBioseq &bioseq)

bool GetNcbieaaString(const CBioseq &bioseq, string &str)

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

Declares auxiliary class to calculate the effective search space.

thread_local unique_ptr< FtaMsgPost > bmp

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

static void GetSequences(TSeqIdVector &seqids, const string &database, char seqtype, TBioseqVector &bioseqs, string &errors, string &warnings, bool verbose=false, bool target_only=false)

Get a set of Bioseqs given an input set of Seq-ids.

void SetPseudoCount(int p)

Sets PseudoCount.

void SetSegFiltering(bool val)

Enable SEG filtering.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

SStrictId_Tax::TId TTaxId

Taxon id type.

#define TAX_ID_FROM(T, value)

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

string ReportAll(TDiagPostFlags flags=eDPF_Exception) const

Report all exceptions.

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

Set object to copy of another one.

TLoader * GetLoader(void) const

Get pointer to the loader.

void AddDataLoader(const string &loader_name, TPriority pri=kPriority_Default)

Add data loader by name.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

bool NotNull(void) const THROWS_NONE

Check if pointer is not null – same effect as NotEmpty().

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

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 string UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

static const char label[]

Tdata & Set(void)

Assign a value to data member.

void SetSequences(TSequences &value)

Assign a value to Sequences data member.

bool IsStr(void) const

Check if variant Str is selected.

void SetTag(TTag &value)

Assign a value to Tag data member.

const TStrs & GetStrs(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

vector< vector< char > * > TOss

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TLabel & GetLabel(void) const

Get the Label member data.

const TType & GetType(void) const

Get the Type member data.

void SetDb(const TDb &value)

Assign a value to Db data member.

TId GetId(void) const

Get the variant data.

void SetTaxname(const TTaxname &value)

Assign a value to Taxname data member.

const TDenseg & GetDenseg(void) const

Get the variant data.

Tdata & Set(void)

Assign a value to data member.

TDenseg & SetDenseg(void)

Select the variant.

const TStarts & GetStarts(void) const

Get the Starts member data.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

vector< TSignedSeqPos > TStarts

bool IsSet(void) const

Check if a value has been assigned to data member.

list< CRef< CDense_diag > > TDendiag

const TSegs & GetSegs(void) const

Get the Segs member data.

TGeneral & SetGeneral(void)

Select the variant.

bool IsPdb(void) const

Check if variant Pdb is selected.

TGi GetGi(void) const

Get the variant 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.

void SetData(TData &value)

Assign a value to Data data member.

TId & SetId(void)

Assign a value to Id data member.

TTitle & SetTitle(void)

Select the variant.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

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.

list< CRef< CSeq_id > > TId

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 TDescr & GetDescr(void) const

Get the Descr member data.

unsigned int

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

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

const struct ncbi::grid::netcache::search::fields::SIZE size

const CharType(& source)[N]

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

Declares the CPSIBlastOptionsHandle class.

vector< TMaskedQueryRegions > TSeqLocInfoVector

Collection of masked regions for all queries in a BLAST search.

static CNamedPipeClient * client

#define row(bind, expected)

string toString(bool detailed=true)

pair< TGi, TGi > OldNewGiPair

vector< OldNewGiPair > oldNewPairs

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