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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__node_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/api/blast_node.cpp Source File

->GetRegisteredNames(loader_names);

(

->RevokeDataLoader(*loader_name)){

(

+ *loader_name);

(

+ *loader_name);

(

+ *loader_name);

m_NodeNum(node_num), m_NcbiArgs(ncbi_args), m_Args(args),

m_Bah(bah), m_QueryIndex(query_index), m_NumOfQueries(num_queries),

m_QueriesLength(0), m_DataLoaderPrefix(

)

(mailbox !=

) {

m_OutputStream(out_stream), m_MaxNumThreads(num_threads), m_MaxNumNodes(num_threads + 2),

m_NumErrStatus(0), m_NumQueries(0), m_QueriesLength(0)

(mailbox ==

) {

(itr->second->GetNumMsgs() > 0) {

chunk_num = itr->first;

(

.NotEmpty()) {

(

->GetMsgType()) {

pair< int, double > p(chunk_num,

);

pair<int,CRef<CBlastNodeMsg> > m(chunk_num, empty_msg);

(

<< chunk_num <<

<<

->GetNodeIdStr());

itr->second->UnreadMsg(

);

err_msg =

+

(itr->first);

node_num =

->GetNodeNum();

(

<< node_num <<

<<

->GetStatus() <<

);

in_buffer = rr->first - ra->first;

kMainAccSize = 32;

digit_pos = line.find_last_of(

, kMainAccSize);

(digit_pos !=

) {

( !

()) {

(c ==

|| c ==

|| c ==

) {

( isId || ( c ==

)) {

static const string kPrefixThread

Interface for reading SRA sequences into blast input.

static void s_UnregisterDataLoader(const string &dbloader_prefix)

bool s_IsSeqID(string &line)

Class to capture message from diag handler.

Defines BLAST error codes (user errors included)

TActiveNodes m_ActiveNodes

CConditionVariable m_NewEvent

CBlastMasterNode(CNcbiOstream &out_stream, int num_threads)

void RegisterNode(CBlastNode *node, CBlastNodeMailbox *mailbox)

TRegisteredNodes m_RegisteredNodes

TFormatQueue m_FormatQueue

CNcbiOstream & m_OutputStream

const int m_QueryBatchSize

const int m_EstAvgQueryLength

int GetQueryBatch(string &queries, int &query_no)

list< CRef< CBlastNodeMsg > > m_MsgQueue

void SendMsg(CRef< CBlastNodeMsg > msg)

CConditionVariable & m_Notify

string m_DataLoaderPrefix

void SendMsg(CBlastNodeMsg::EMsgType msg_type, void *ptr=NULL)

CRef< CBlastNodeMailbox > m_Mailbox

void SetDataLoaderPrefix()

virtual ~CBlastNode(void)

CBlastNode(int node_num, const CNcbiArguments &ncbi_args, const CArgs &args, CBlastAppDiagHandler &bah, int query_index, int num_queries, CBlastNodeMailbox *mailbox)

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define INFO_POST(message)

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

void UngetLine(void)

Unget current line, which must be valid.

bool AtEOF(void) const

Indicates (negatively) whether there is any more input.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

vector< string > TRegisteredNames

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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static CTempString TruncateSpaces_Unsafe(const CTempString str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

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

Convert int to string.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

@ eTrunc_Begin

Truncate leading whitespace only.

void SignalSome(void)

Wake at least one of the threads that are currently waiting on this condition variable (if any thread...

bool WaitForSignal(CMutex &mutex, const CDeadline &deadline=CDeadline::eInfinite)

Release mutex and lock the calling thread until the condition variable is signalled.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

string AsSmartString(ESmartStringPrecision precision, ERound rounding, ESmartStringZeroMode zero_mode=eSSZ_SkipZero) const

Transform time span to "smart" string.

void Start(void)

Start the timer.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Declares the CRemoteBlast class.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

CRef< objects::CObjectManager > om

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