Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/deltablast__app_8cpp_source.html below:

NCBI C++ ToolKit: src/app/blast/deltablast_app.cpp Source File

(pssm.

()) {

pssm_bioseq.

().Set().push_back(*it);

query_batch_size = 1;

,

,

,

domain_results = deltablast->GetDomainResults();

pssm = deltablast->GetPssm();

blast::CSearchResultSet::const_iterator domain_it;

domain_it = domain_results->begin();

(domain_it != domain_results->end());

blast::CPsiBlastIterationState::TSeqIds(),

blast::CSearchResults& res = (*results)[0];

res.GetAncillaryData());

*deltablast->GetDomainResults()) {

blast::CPsiBlastIterationState::TSeqIds(),

<<

converged =

;

blast::CSearchResults& results_1st_query = (*results)[0];

( !results_1st_query.HasAlignments() ) {

(*

)[0].GetAncillaryData());

(psiblast.

()) {

blast::CSearchResults& results_1st_query = (*results)[0];

( !results_1st_query.HasAlignments() ) {

aln.

(results_1st_query.GetSeqAlign());

results_1st_query.GetAncillaryData());

(

argc,

* argv[]

)

User-defined methods of the data storage class.

Produce formatted blast output for command line applications.

CRef< blast::CRemoteBlast > InitializeRemoteBlast(CRef< blast::IQueryFactory > queries, CRef< blast::CBlastDatabaseArgs > db_args, CRef< blast::CBlastOptionsHandle > opts_hndl, bool verbose_output, const string &client_id, CRef< objects::CPssmWithParameters > pssm)

Initializes a CRemoteBlast instance for usage by command line BLAST binaries.

blast::SDataLoaderConfig InitializeQueryDataLoaderConfiguration(bool query_is_protein, CRef< blast::CLocalDbAdapter > db_adapter)

Initialize the data loader configuration for the query.

void SaveSearchStrategy(const CArgs &args, blast::CBlastAppArgs *cmdline_args, CRef< blast::IQueryFactory > queries, CRef< blast::CBlastOptionsHandle > opts_hndl, CRef< objects::CPssmWithParameters > pssm, unsigned int num_iters)

Save the search strategy corresponding to the current command line search.

void QueryBatchCleanup()

Clean up formatter scope and release.

string RegisterOMDataLoader(CRef< CSeqDB > db_handle)

Register the BLAST database data loader using the already initialized CSeqDB object.

CRef< CBlastAncillaryData > ExtractPssmAncillaryData(const CPssmWithParameters &pssm)

Auxiliary function to extract the ancillary data from the PSSM.

bool RecoverSearchStrategy(const CArgs &args, blast::CBlastAppArgs *cmdline_args)

Recover search strategy from input file.

void PrintErrorArchive(const CArgs &a, const list< CRef< CBlast4_error > > &msg)

Function to print blast archive with only error messages (search failed) to output stream.

void InitializeSubject(CRef< blast::CBlastDatabaseArgs > db_args, CRef< blast::CBlastOptionsHandle > opts_hndl, bool is_remote_search, CRef< blast::CLocalDbAdapter > &db_adapter, CRef< objects::CScope > &scope)

Initializes the subject/database as well as its scope.

string GetCmdlineArgs(const CNcbiArguments &a)

void BlastFormatter_PreFetchSequenceData(const blast::CSearchResultSet &results, CRef< CScope > scope, blast::CFormattingArgs::EOutputFormat format_type)

This method optimize the retrieval of sequence data to scope.

bool UseXInclude(const CFormattingArgs &f, const string &s)

bool IsIStreamEmpty(CNcbiIstream &in)

void LogQueryInfo(CBlastUsageReport &report, const CBlastInput &q_info)

Utility functions for BLAST command line applications.

#define CATCH_ALL(exit_code)

Standard catch statement for all BLAST command line programs.

#define BLAST_EXIT_SUCCESS

Command line binary exit code: success.

Interface for reading SRA sequences into blast input.

PSIDiagnosticsRequest * PSIDiagnosticsRequestNewEx(Boolean save_ascii_pssm)

Allocates a PSIDiagnosticsRequest structure, setting fields to their default values for their use in ...

Definition of classes which constitute the results of running a BLAST search.

const CSeq_id * GetFirstId() const

virtual CNcbiIstream & GetInputStream()

Get the input stream.

size_t GetNumThreads() const

Get the number of threads to spawn.

CRef< CBlastOptionsHandle > SetOptions(const CArgs &args)

Extract the command line arguments into a CBlastOptionsHandle object.

CRef< CBlastDatabaseArgs > GetBlastDatabaseArgs() const

Get the BLAST database arguments.

CArgDescriptions * SetCommandLine()

Set the command line arguments.

bool ExecuteRemotely() const

Determine whether the search should be executed remotely or not.

bool ProduceDebugRemoteOutput() const

Return whether debug (verbose) output should be produced on remote searches (only available when comp...

CRef< CQueryOptionsArgs > GetQueryOptionsArgs() const

Get the options for the query sequence(s)

string GetClientId() const

Retrieve the client ID for remote requests.

CRef< CFormattingArgs > GetFormattingArgs() const

Get the formatting options.

bool ProduceDebugOutput() const

Return whether debug (verbose) output should be produced on remote searches (only available when comp...

virtual CNcbiOstream & GetOutputStream()

Get the output stream.

Class to capture message from diag handler.

static const int kSubjectsDataLoaderPriority

The default priority for subjects, should be used for subjects/databases.

Class representing a text file containing sequences in fasta format.

This class formats the BLAST results for command line applications.

void LogBlastSearchInfo(blast::CBlastUsageReport &report)

void PrintOneResultSet(const blast::CSearchResults &results, CConstRef< blast::CBlastQueryVector > queries, unsigned int itr_num=numeric_limits< unsigned int >::max(), blast::CPsiBlastIterationState::TSeqIds prev_seqids=blast::CPsiBlastIterationState::TSeqIds(), bool is_deltablast_domain_result=false)

Print all alignment information for a single query sequence along with any errors or warnings (errors...

void PrintEpilog(const blast::CBlastOptions &options)

Print the footer of the blast report.

void SetBaseFile(string base)

For use by XML2 only.

void ResetScopeHistory()

Resets the scope history for some output formats.

void SetLineLength(size_t len)

Set Alignment Length.

void WriteArchive(blast::IQueryFactory &queries, blast::CBlastOptionsHandle &options_handle, const blast::CSearchResultSet &results, unsigned int num_iters=0, const list< CRef< objects::CBlast4_error > > &msg=list< CRef< objects::CBlast4_error > >())

Writes out the query and results as an "archive" format.

void PrintProlog()

Print the header of the blast report.

void SetQueryRange(const TSeqRange &query_range)

Set query range.

Class that centralizes the configuration data for sequences to be converted.

Generalized converter from an abstract source of biological sequence data to collections of blast inp...

Encapsulates ALL the BLAST algorithm's options.

CRef< CBlastSearchQuery > GetBlastSearchQuery(size_type i) const

Get the CBlastSearchQuery object at index i.

void AddParam(EUsageParams p, int val)

Keeps track of the version of the BLAST engine in the NCBI C++ toolkit.

void DebugDumpText(ostream &out, const string &bundle, unsigned int depth) const

Handle command line arguments for deltablast binary.

size_t GetNumberOfPsiBlastIterations(void) const

Get number of PSI-BLAST iterations.

CNcbiOstream * GetCheckpointStream(void)

Get stream for saving Pssm.

bool GetSaveLastPssm(void) const

Should PSSM after last database search be saved.

virtual int GetQueryBatchSize(void) const

Get query batch size.

bool GetShowDomainHits(void) const

Was printing domain hits requested.

CNcbiOstream * GetAsciiPssmStream(void)

Get stream for saving ascii Pssm.

bool SaveAsciiPssm(void) const

Was saving ascii Pssm requested.

bool SaveCheckpoint(void) const

Was saving Pssm requested.

CRef< CSearchDatabase > GetDomainDatabase(void)

Get conserved domain database.

CRef< CPssmWithParameters > ComputePssmForNextPsiBlastIteration(const CBioseq &bioseq, CConstRef< CSeq_align_set > sset, CConstRef< CPSIBlastOptionsHandle > opts_handle, CRef< CScope > scope, CRef< CBlastAncillaryData > ancillary_data)

Compute PSSM for next PSI-BLAST iteration.

void SavePssmToFile(CConstRef< CPssmWithParameters > pssm)

Save Pssm to file.

CBlastUsageReport m_UsageReport

virtual void Init()

@inheritDoc

virtual int Run()

@inheritDoc

CDeltaBlastApp()

@inheritDoc

bool DoPsiBlastIterations(CRef< CBlastOptionsHandle > opts_hndl, CRef< CBlastQueryVector > query, CConstRef< CBioseq > query_bioseq, CRef< blast::CSearchResultSet > results, CRef< CBlastDatabaseArgs > db_args, const CArgs &args, CRef< CLocalDbAdapter > db_adapter, CRef< CScope > scope, CBlastFormat &formatter)

Do PSI-BLAST iterations follwing DELTA-BLAST.

CRef< CDeltaBlastAppArgs > m_CmdLineArgs

This application's command line args.

CBlastAppDiagHandler m_bah

CRef< CBlastAncillaryData > m_AncillaryData

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

A simple realization of the DELTA-BLAST algorithm: seacrch domain database, compute PSSM,...

bool HasStructuredOutputFormat() const

Returns true if the desired output format is structured (needed to determine whether to print or not ...

virtual bool ArchiveFormatRequested(const CArgs &args) const

string GetCustomOutputFormatSpec() const

Retrieve for string that specifies the custom output format for tabular and comma-separated value.

EOutputFormat GetFormattedOutputChoice() const

Get the choice of formatted output.

@ eArchiveFormat

BLAST archive format.

TSeqPos GetNumAlignments() const

Number of alignments to show in traditional BLAST output.

bool ShowGis() const

Display the NCBI GIs in formatted output?

TSeqPos GetNumDescriptions() const

Number of one-line descriptions to show in traditional BLAST output.

size_t GetLineLength() const

bool DisplayHtmlOutput() const

Display HTML output?

Interface to create a BlastSeqSrc suitable for use in CORE BLAST from a a variety of BLAST database/s...

NCBI C++ Object Manager dependant implementation of IQueryFactory.

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

Wrapper class for PSIDiagnosticsRequest .

Represents the iteration state in PSI-BLAST.

Runs a single iteration of the PSI-BLAST algorithm on a BLAST database.

const CSeq_entry & GetQuery() const

Retrieve the query sequence.

CSeq_entry & SetQuery()

Retrieve the query sequence.

objects::ENa_strand GetStrand() const

Get strand to search in query sequence(s)

bool GetParseDeflines() const

Should the defline be parsed?

bool QueryIsProtein() const

Is the query sequence protein?

TSeqRange GetRange() const

Get query sequence range restriction.

bool UseLowercaseMasks() const

Use lowercase masking in FASTA input?

const string kArgOutput

Output file name.

void Print(const CCompactSAMApplication::AlignInfo &ai)

Declares CPsiBlast, the C++ API for the PSI-BLAST engine.

static void s_AddSeqDataToPssm(CRef< CPssmWithParameters > pssm, CRef< CBlastQueryVector > query_batch, CRef< CScope > scope)

int main(int argc, const char *argv[])

static void s_AddSeqTitleToPssm(CRef< CPssmWithParameters > pssm, CRef< CBlastQueryVector > query_batch, CRef< CScope > scope)

Main argument class for DELTA-BLAST application.

CRef< CSearchResultSet > Run()

Run the PSI-BLAST engine for one iteration.

CRef< objects::CPssmWithParameters > GetPSSM(void)

Get the PSSM produced by the search.

int GetDbGeneticCode() const

string GetDatabaseName() const

Returns the database name if appropriate, else kEmptyStr for subject sequences.

virtual void SetNumberOfThreads(size_t nthreads)

Mutator for the number of threads.

void ResetMessages(void)

Reset messgae buffer, erase all saved message.

unsigned int GetIterationNumber() const

Return the number of the current iteration.

TSeqIds GetPreviouslyFoundSeqIds() const

Retrieve the set of Seq-id's found in the previous iteration.

int GetFilteringAlgorithm()

Retrieve the database filtering algorithm.

void SetPssm(CConstRef< objects::CPssmWithParameters > pssm)

This method allows the same object to be reused when performing multiple iterations.

bool HasConverged()

Determines if the PSI-BLAST search has converged (i.e.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

int GetQueryGeneticCode() const

CRef< objects::CPssmWithParameters > PsiBlastComputePssmFromAlignment(const objects::CBioseq &query, CConstRef< objects::CSeq_align_set > alignment, CRef< objects::CScope > database_scope, const CPSIBlastOptionsHandle &opts_handle, CConstRef< CBlastAncillaryData > ancillary_data, PSIDiagnosticsRequest *diagnostics_req=0)

Computes a PSSM from the result of a PSI-BLAST iteration.

bool GetSumStatisticsMode() const

Sum statistics options.

CRef< CSearchResultSet > GetResultSet()

Submit the search (if necessary) and return the results.

void Advance(const TSeqIds &list)

Advance the iterator by passing it the list of Seq-ids which passed the inclusion criteria for the cu...

static void GetSeqIds(CConstRef< objects::CSeq_align_set > seqalign, CConstRef< CPSIBlastOptionsHandle > opts, TSeqIds &retval)

Extract the sequence ids from the sequence alignment which identify those sequences that will be used...

const char * GetMatrixName() const

list< CRef< objects::CBlast4_error > > & GetMessages(void)

Return list of saved diag messages.

void SetFullVersion(CRef< CVersionAPI > version)

Set version data for the program.

void HideStdArgs(THideStdArgs hide_mask)

Set the hide mask for the Hide Std Flags.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

CVersionInfo GetVersion(void) const

Get the program version information.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

@ fHideXmlHelp

Hide XML help description.

@ fHideLogfile

Hide log file description.

@ fHideFullVersion

Hide full version description.

@ fHideDryRun

Hide dryrun description.

@ fHideConffile

Hide configuration file description.

static void PrintAsciiPssm(const objects::CPssmWithParameters &pssm, CConstRef< blast::CBlastAncillaryData > ancillary_data, CNcbiOstream &out)

Prints the PSSM in ASCII format (as in blastpgp's -Q option)

void SetDiagPostPrefix(const char *prefix)

Specify a string to prefix all subsequent error postings with.

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

#define ERR_POST(message)

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

void SetDiagHandler(CDiagHandler *handler, bool can_delete=true)

Set the diagnostic handler using the specified diagnostic handler class.

@ eDiag_Warning

Warning message.

#define NCBI_THROW(exception_class, err_code, message)

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

void Warning(CExceptionArgs_Base &args)

#define MSerial_AsnText

I/O stream manipulators –.

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

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

Add data loader by name.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

TObjectType * GetNonNullPointer(void)

Get pointer value and throw a null pointer exception if pointer is null.

bool Empty(void) const THROWS_NONE

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

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CConstRef 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.

bool IsEnabled(void)

Indicates whether application usage statistics collection is enabled for a current reporter instance.

double Elapsed(void) const

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

void Start(void)

Start the timer.

const TQuery & GetQuery(void) const

Get the Query member data.

const TPssm & GetPssm(void) const

Get the Pssm member data.

const TSeq & GetSeq(void) const

Get the variant data.

TSeq & SetSeq(void)

Select the variant.

list< CRef< CSeqdesc > > Tdata

bool IsSetSeq_data(void) const

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

const TInst & GetInst(void) const

Get the Inst member data.

const Tdata & Get(void) const

Get the member data.

void SetInst(TInst &value)

Assign a value to Inst data member.

bool IsSetDescr(void) const

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

void SetDescr(TDescr &value)

Assign a value to Descr 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.

const string version

version string

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

The NCBI C++/STL use hints.

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

Declares CPsiBlast, the C++ API for the PSI-BLAST engine.

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

Declares the CRemoteBlast class.

Configuration structure for the CBlastScopeSource.

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4