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

kNumIterations);

(

->GetQuerySeqLoc(0)->GetId()) {

kNumIterations)

converged =

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psiblast.

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recovered_from_search_strategy =

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argc,

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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.

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.

@ eAaLookupTable

standard protein (blastp) lookup table

Declares class to encapsulate all BLAST options.

Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

PSIDiagnosticsRequest * PSIDiagnosticsRequestNewEx(Boolean save_ascii_pssm)

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

const CSeq_id * GetFirstId() const

CRef< CBlastOptionsHandle > SetOptionsForSavedStrategy(const CArgs &args)

Combine the command line arguments into a CBlastOptions object recovered from saved search strategy.

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.

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.

void PrintPhiResult(const blast::CSearchResultSet &result_set, CConstRef< blast::CBlastQueryVector > queries, unsigned int itr_num=numeric_limits< unsigned int >::max(), blast::CPsiBlastIterationState::TSeqIds prev_seqids=blast::CPsiBlastIterationState::TSeqIds())

Print all alignment information for aa PHI-BLAST run.

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.

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

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?

Class to perform a BLAST search on local BLAST databases Note that PHI-BLAST can be run using this cl...

NCBI C++ Object Manager dependant implementation of IQueryFactory.

Handle to the protein PHI BLAST options.

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

Wrapper class for PSIDiagnosticsRequest .

Handle command line arguments for psiblast binary Programs supported: psiblast, phi-blastn,...

CNcbiOstream * GetCheckpointStream()

Retrieve the stream to write the checkpoint file.

bool GetSaveLastPssm() const

Should the PSSM after the last database search be saved.

size_t GetNumberOfIterations() const

Get the number of iterations to perform.

CRef< objects::CPssmWithParameters > GetInputPssm() const

Get the PSSM specified as input from the command line.

bool SaveAsciiPssm() const

Should a PSSM be saved as ASCII in a file?

CNcbiOstream * GetAsciiPssmStream()

Retrieve the stream to write the ASCII PSSM.

bool SaveCheckpoint() const

Should a PSSM be saved in a checkpoint file?

CRef< CPsiBlastAppArgs > m_CmdLineArgs

This application's command line args.

void SavePssmToFile(CRef< CPssmWithParameters > pssm, const CPsiBlastIterationState *itr=NULL)

Save the PSSM to a check point file and/or as an ASCII PSSM.

CBlastAppDiagHandler m_bah

virtual int Run()

@inheritDoc

CConstRef< CBlastAncillaryData > m_AncillaryData

Ancillary results for the previously executed PSI-BLAST iteration.

virtual void Init()

@inheritDoc

CPsiBlastApp()

@inheritDoc

bool DoIterations(CRef< CBlastOptionsHandle > opts_hndl, CRef< CBlastQueryVector > query, CRef< CPssmWithParameters > pssm, CRef< CBlastDatabaseArgs > db_args, CRef< CLocalDbAdapter > db_adapter, CRef< CScope > scope, CBlastFormat &formatter)

Performs iterations for either multiple queries or input PSSM.

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

Auxiliary function to create the PSSM for the next iteration.

CBlastUsageReport m_UsageReport

bool x_RunLocalPsiBlastIterations(CRef< CBlastQueryVector > query, CRef< CPssmWithParameters > pssm, CRef< CScope > scope, CRef< CLocalDbAdapter > db_adapter, CRef< CBlastOptionsHandle > opts_hndl, CBlastFormat &formatter, const size_t kNumIterations)

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.

bool HasQuery() const

Has this PSSM a query in it?

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?

Search Results for All Queries.

Search Results for One Query.

const string kArgOutput

Output file name.

const string kArgPHIPatternFile

Argument to specify a PHI-BLAST pattern file.

void Print(const CCompactSAMApplication::AlignInfo &ai)

ECompoAdjustModes

An collection of constants that specify all permissible modes of composition adjustment.

void SetPHIPattern(const char *pattern, bool is_dna)

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

void SetCompositionBasedStats(ECompoAdjustModes mode)

virtual void SetNumberOfThreads(size_t nthreads)

Mutator for the number of threads.

void ResetMessages(void)

Reset messgae buffer, erase all saved message.

const char * GetPHIPattern() const

unsigned int GetIterationNumber() const

Return the number of the current iteration.

CConstRef< objects::CSeq_align_set > GetSeqAlign() const

Accessor for the Seq-align results.

TSeqIds GetPreviouslyFoundSeqIds() const

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

CRef< CSearchResultSet > Run()

Executes the search.

CBlastOptions & SetOptions()

Returns a reference to the internal options class which this object is a handle for.

CRef< CBlastAncillaryData > GetAncillaryData() const

Accessor for the query's search ancillary.

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.

EProgram GetProgram() const

Accessors/Mutators for individual options.

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.

string EProgramToTaskName(EProgram p)

Convert a EProgram enumeration value to a task name (as those used in the BLAST command line binaries...

bool GetSumStatisticsMode() const

Sum statistics options.

ECompoAdjustModes GetCompositionBasedStats() const

CRef< CSearchResultSet > GetResultSet()

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

void DoNotSaveMessages(void)

Call to turn off saving diag message, discard all saved message.

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 SetLookupTableType(ELookupTableType type)

bool HasAlignments() const

Return true if there are any alignments for this query.

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.

void Remove(const string &name)

Remove argument of name "name".

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.

void Warning(CExceptionArgs_Base &args)

#define MSerial_AsnText

I/O stream manipulators –.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

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 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.

bool IsEnabled(void)

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

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

double Elapsed(void) const

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

void Start(void)

Start the timer.

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

TSeq & SetSeq(void)

Select the variant.

Main class to perform a BLAST search on the local machine.

const string version

version string

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

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.

static CConstRef< CBioseq > s_GetQueryBioseq(CConstRef< CBlastQueryVector > query, CRef< CScope > scope, CRef< CPssmWithParameters > pssm)

Extract the bioseq which represents the query from either a PSSM or a CBlastQueryVector.

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

static CRef< IQueryFactory > s_MakeQueryFactory(CRef< CPssmWithParameters > pssm, CRef< CBlastQueryVector > query)

Main argument class for PSI-BLAST application.

Defines class which represents the iteration state in PSI-BLAST.

Declares the CRemoteBlast class.

Implementation of the BlastSeqSrc interface using the C++ BLAST databases API.

Configuration structure for the CBlastScopeSource.

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