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NCBI C++ ToolKit: src/app/blastvdb/blast_formatter_vdb.cpp Source File

arg_desc->SetUsageContext(

().GetProgramBasename(),

arg_desc->SetCurrentGroup(

);

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->SetCurrentGroup(

);

arg_desc->AddDefaultKey(

,

,

,

arg_desc->SetCurrentGroup(

);

,

);

arg_desc->SetCurrentGroup(

);

first_time =

;

(seqloc, scope);

runtime_error(

);

( !seq_entry.

() ) {

runtime_error(

);

(b4_queries->

()) {

( !(*seqloc)->GetId()->IsLocal() );

(CBlastFormatUtil::SDbInfo & dbInfo,

& dbNames,

isProtein)

dbInfo.is_protein =

;

dbInfo.name =dbNames;

dbInfo.definition = dbInfo.name;

dbInfo.total_length = (

)length;

dbInfo.number_seqs = (

) seqs;

vector<string> paths;

);

vector< CBlastFormatUtil::SDbInfo > vecDbInfo(1);

isPsiBlast = (

==

);

);

);

kRid = args[

].AsString();

cerr <<

<< kRid <<

<< endl;

cerr <<

<< kRid <<

<< endl;

cerr <<

<< kRid <<

<< endl;

(args[

].

()) {

(

argc,

* argv[]

)

Declares singleton objects to store the version and reference for the BLAST engine.

Produce formatted blast output for command line applications.

string GetCmdlineArgs(const CNcbiArguments &a)

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

#define CATCH_ALL(exit_code)

Standard catch statement for all BLAST command line programs.

#define EXIT_CODE__UNKNOWN_RID

static void s_FillDBInfo(CBlastFormatUtil::SDbInfo &dbInfo, const string &dbNames, bool isProtein)

#define EXIT_CODE__SEARCH_PENDING

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

#define EXIT_CODE__SEARCH_FAILED

Auxiliary classes/functions for BLAST input library.

bool HasRawSequenceData(const objects::CBioseq &bioseq)

Returns true if the Bioseq passed as argument has the full, raw sequence data in its Seq-inst field.

Boolean Blast_QueryIsProtein(EBlastProgramType p)

Returns true if the query is protein.

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

CRef< CScope > GetVDBScope(string dbAllNames)

Utility functions for BLAST VDB command line applications.

const CSeq_id * GetFirstId() const

size_t GetNumQueries() const

Retrieve the number of queries in this object.

Defines BLAST error codes (user errors included)

This class formats the BLAST results for command line applications.

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 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.

virtual void Init()

@inheritDoc

CRef< CBlastScopeSource > m_QueryScopeSource

The source of CScope objects for queries.

CRef< CBlastSearchQuery > x_BuildQueryFromPssm(const CPssmWithParameters &pssm)

Build the query from a PSSM.

int PrintFormattedOutput(void)

Prints the BLAST formatted output.

virtual int Run()

@inheritDoc

SSeqLoc x_QueryBioseqToSSeqLoc(const CBioseq &bioseq, CRef< CScope > scope)

Package a scope and Seq-loc into a SSeqLoc from a Bioseq.

CBlastFormatterVdbApp()

@inheritDoc

bool m_LoadFromArchive

Tracks whether results come from an archive file.

CRef< CRemoteBlast > m_RmtBlast

Our link to the NCBI BLAST service.

CBlastUsageReport m_UsageReport

CRef< CBlastQueryVector > x_ExtractQueries(bool query_is_protein)

Extracts the queries to be formatted.

Encapsulates ALL the BLAST algorithm's options.

void AddQuery(CRef< CBlastSearchQuery > q)

Add a query to the set.

CRef< objects::CScope > GetScope(size_type i) const

Get the scope containing a query by index.

size_type size() const

Identical to Size, provided to facilitate STL-style iteration.

Class whose purpose is to create CScope objects which have data loaders added with different prioriti...

void AddDataLoaders(CRef< objects::CScope > scope)

Add the data loader configured in the object to the provided scope.

CRef< objects::CScope > NewScope()

Create a new, properly configured CScope.

void AddParam(EUsageParams p, int val)

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

Argument class to collect debugging options.

bool ProduceDebugRemoteOutput() const

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

virtual void ExtractAlgorithmOptions(const CArgs &cmd_line_args, CBlastOptions &options)

Interface method,.

bool ProduceDebugOutput() const

Return whether debug (verbose) output should be produced (only available when compiled with _DEBUG)

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

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

Argument class to collect formatting options, use this to create a CBlastFormat object.

virtual bool ArchiveFormatRequested(const CArgs &args) const

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

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.

virtual void ExtractAlgorithmOptions(const CArgs &args, CBlastOptions &opts)

Interface method,.

@ eXml2_S

XML2 single file.

@ eJson_S

JSON2 single file.

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?

Defines user input exceptions.

NCBI C++ Object Manager dependant implementation of IQueryFactory.

const CSeq_entry & GetQuery() const

Retrieve the query sequence.

bool HasQuery() const

Has this PSSM a query in it?

API for Remote Blast Requests.

Search Results for All Queries.

Root class for all serialization exceptions.

Template class for iteration on objects of class C (non-medifiable version)

static void FindVDBPaths(const string &dbname, bool isProtein, vector< string > &paths, vector< string > *db_alias_list=NULL, vector< string > *vdb_alias_list=NULL, bool recursive=true, bool expand_links=true, bool verify_dbs=true)

Get the list of vdb names.

static void GetVDBStats(const string &strAllRuns, Uint8 &num_seqs, Uint8 &length, bool getRefStats=false)

Fucntion to get around the OID (blastseqsrc) limit So num of seqs > int4 can be returned.

const string kArgOutput

Output file name.

const string kArgArchive

Argument to blast_formatter to request BLAST archive file name.

const string kTask

Task to perform.

const string kArgParseDeflines

Argument to specify if the query and subject sequences defline should be parsed.

const string kArgRid

Argument to blast_formatter to request RID.

void Print(const CCompactSAMApplication::AlignInfo &ai)

std::ofstream out("events_result.xml")

main entry point for tests

bool LoadFromArchive()

Loads next chunk of archive from file.

CRef< CBlastOptionsHandle > GetSearchOptions()

Get the search options used for this search.

string GetErrors(void)

This returns a string containing any errors that were produced by the search.

ESearchStatus CheckStatus()

Returns the status of a previously submitted search/RID.

void SetVerbose(EDebugMode verb=eDebug)

Adjust the debugging level.

CBlastOptions & SetOptions()

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

CRef< objects::CBlast4_queries > GetQueries()

Get the queries used for this search.

EBlastProgramType GetProgramType() const

Returns the CORE BLAST notion of program type.

CRef< objects::CBlast4_database > GetDatabases()

Get the database used by the search.

CRef< CSearchResultSet > GetResultSet()

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

unsigned int GetPsiNumberOfIterations(void)

@ eInvalidArgument

Invalid argument to some function/method (could be programmer error - prefer assertions in those case...

@ eStatus_Failed

Completed but failed, call GetErrors/GetErrorVector()

@ eStatus_Pending

Not completed yet.

@ eStatus_Unknown

Never submitted or purged from the system.

@ eStatus_Done

Completed successfully.

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.

@ eExcludes

One argument excludes another.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eDS_Default

Try standard log file (app.name + ".log") in /log/, use stderr on failure.

TErrCode GetErrCode(void) const

Get error code.

#define NCBI_THROW(exception_class, err_code, message)

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

#define NCBI_RETHROW(prev_exception, exception_class, err_code, message)

Generic macro to re-throw an exception.

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void AddScope(CScope &scope, TPriority pri=kPriority_Default)

Add the scope's datasources as a single group with the given priority All data sources (data loaders ...

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

int64_t Int8

8-byte (64-bit) signed integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

bool IsEnabled(void)

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

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

double Elapsed(void) const

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

void Start(void)

Start the timer.

bool IsSeq_loc_list(void) const

Check if variant Seq_loc_list is selected.

bool IsPssm(void) const

Check if variant Pssm is selected.

list< CRef< CSeq_loc > > TSeq_loc_list

const TBioseq_set & GetBioseq_set(void) const

Get the variant data.

bool IsBioseq_set(void) const

Check if variant Bioseq_set is selected.

const TSeq_loc_list & GetSeq_loc_list(void) const

Get the variant data.

const TPssm & GetPssm(void) const

Get the variant data.

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

unsigned int

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

const string version

version string

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

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.

void OptimizeForWholeLargeSequenceRetrieval(bool value=true)

Configures the BLAST database data loader to optimize the retrieval of *entire* large sequences.

Structure to represent a single sequence to be fed to BLAST.

CConstRef< objects::CSeq_loc > seqloc

Seq-loc describing the sequence to use as query/subject to BLAST The types of Seq-loc currently suppo...

CRef< objects::CScope > scope

Scope where the sequence referenced can be found by the toolkit's object manager.

Defines database alias file access classes.

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