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NCBI C++ ToolKit: include/algo/structure/cd_utils/cuCdUpdater.hpp Source File

(

detailed=

);

(vector<OldNewGiPair>& giPairs,

);

(vector<CCdCore*>&) = 0;

IsEmpty();

checkAllBlasts(vector< UpdaterInterface* >& blasted);

removeUpdaters(

vector<CCdCore*>& cds);

removeUpdaters(

vector<UpdaterInterface*>& updaters);

submitBlast(

wait =

,

= 0);

processBlastHits();

getCds(vector<CCdCore*>&);

blast(

wait =

,

= 0);

(

& lastError) { m_lastError = lastError;}

checkBlastAndUpdate();

processPendingToNormal(

overlap,

* cd);

mergePending(

* cd,

threshold,

remaster);

BioseqHasSeqId(

& bioseq,

& seqId);

RemoveBlastDefline (

& handle);

ComputePercentIdentity(

& alignment,

& queryString,

& subjectString);

submitBlast(

wait=

,

=0);

processBlastHits();

getCds(vector<CCdCore*>&);

User-defined methods of the data storage class.

Declares the CBlastProteinOptionsHandle class.

AccessionBioseqMap m_accSeqMap

map< string, CRef< CBioseq > > AccessionBioseqMap

CdUpdateParameters & getUpdateParameters()

void requireProcessPending(int threshold)

CRef< CSeq_align_set > getAlignments()

void setHitsNeeded(int num)

cd_utils::BlockModelPair * m_guideAlignment

const string getLastError()

void setLastError(const string &lastError)

CDUpdateStats & getStats()

void SetAlignments(CRef< CSeq_align_set > &hits)

CRef< CSeq_id > m_masterPdb

const CRef< CSeq_align_set > & GetAlignments() const

CdUpdateParameters m_config

int m_processPendingThreshold

CRef< CSeq_align_set > m_hits

vector< CDUpdater * > m_cdUpdaters

static CSafeStatic< list< UpdaterInterface * > > m_updaterList

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

virtual void getCds(vector< CCdCore * > &)=0

virtual bool processBlastHits()=0

virtual bool getBlastHits()=0

virtual bool hasCd(CCdCore *)=0

virtual ~UpdaterInterface()

#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.

#define NCBI_CDUTILS_EXPORT

vector< vector< char > * > TOss

static std::string toString(boost::unit_test::const_string bstr)

Static variables safety - create on demand, destroy on application termination.

Declares the CRemoteBlast class.

static CNamedPipeClient * client

#define row(bind, expected)

pair< TGi, TGi > OldNewGiPair

vector< OldNewGiPair > oldNewPairs

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